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Li X, Chen X, Fang J, Feng X, Zhang X, Lin H, Chen W, Zhang N, He H, Huang Z, Xue X, Li Y, Fan L, Lai R, Huo Z, Cui M, Deng G, Zaid C, Su Y, Zhang J, Cai W, Qi Y. Whole-genome sequencing of a worldwide collection of sugarcane cultivars (Saccharum spp.) reveals the genetic basis of cultivar improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2151-2167. [PMID: 38852163 DOI: 10.1111/tpj.16861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/12/2024] [Accepted: 05/20/2024] [Indexed: 06/11/2024]
Abstract
Sugarcane is the main source of sugar worldwide, and 80% of the sucrose production comes from sugarcane. However, the genetic differentiation and basis of agronomic traits remain obscure. Here, we sequenced the whole-genome of 219 elite worldwide sugarcane cultivar accessions. A total of approximately 6 million high-quality genome-wide single nucleotide polymorphisms (SNPs) were detected. A genome-wide association study identified a total of 2198 SNPs that were significantly associated with sucrose content, stalk number, plant height, stalk diameter, cane yield, and sugar yield. We observed homozygous tendency of favor alleles of these loci, and over 80% of cultivar accessions carried the favor alleles of the SNPs or haplotypes associated with sucrose content. Gene introgression analysis showed that the number of chromosome segments from Saccharum spontaneum decreased with the breeding time of cultivars, while those from S. officinarum increased in recent cultivars. A series of selection signatures were identified in sugarcane improvement procession, of which 104 were simultaneously associated with agronomic traits and 45 of them were mainly associated with sucrose content. We further proposed that as per sugarcane transgenic experiments, ShN/AINV3.1 plays a positive role in increasing stalk number, plant height, and stalk diameter. These findings provide comprehensive resources for understanding the genetic basis of agronomic traits and will be beneficial to germplasm innovation, screening molecular markers, and future sugarcane cultivar improvement.
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Affiliation(s)
- Xuhui Li
- Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
| | - Xinglong Chen
- Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
| | - Junteng Fang
- Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Xiaomin Feng
- Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
| | - Xiangbo Zhang
- Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
| | - Huanzhang Lin
- Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Weiwei Chen
- Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
| | - Nannan Zhang
- Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
| | - Huiyi He
- Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
| | - Zhenghui Huang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Xiaoming Xue
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Yucong Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Lina Fan
- Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Ruiqiang Lai
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Zhenye Huo
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Mingyang Cui
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Guangyan Deng
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Chachar Zaid
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Yueping Su
- Zhanjiang Academy of Agricultural Sciences, Zhanjiang, Guangdong, 524094, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Agro-Bioresources, Guangxi University, Nanning, Guangxi, 530005, China
| | - Weijun Cai
- Zhanjiang Academy of Agricultural Sciences, Zhanjiang, Guangdong, 524094, China
| | - Yongwen Qi
- Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
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le Roux J, Jacob R, Fischer R, van der Vyver C. Identification and expression analysis of nuclear factor Y transcription factor genes under drought, cold and Eldana infestation in sugarcane (Saccharum spp. hybrid). Genes Genomics 2024; 46:927-940. [PMID: 38877289 PMCID: PMC11329523 DOI: 10.1007/s13258-024-01529-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND The Nuclear Factor Y (NF-Y) transcription factor (TF) gene family plays a crucial role in plant development and response to stress. Limited information is available on this gene family in sugarcane. OBJECTIVES To identify sugarcane NF-Y genes through bioinformatic analysis and phylogenetic association and investigate the expression of these genes in response to abiotic and biotic stress. METHODS Sugarcane NF-Y genes were identified using comparative genomics from functionally annotated Poaceae and Arabidopsis species. Quantitative PCR and transcriptome analysis assigned preliminary functional roles to these genes in response to water deficit, cold and African sugarcane borer (Eldana saccharina) infestation. RESULTS We identify 21 NF-Y genes in sugarcane. Phylogenetic analysis revealed three main branches representing the subunits with potential discrepancies present in the assignment of numerical names of some NF-Y putative orthologs across the different species. Gene expression analysis indicated that three genes, ShNF-YA1, A3 and B3 were upregulated and two genes, NF-YA4 and A7 were downregulated, while three genes were upregulated, ShNF-YB2, B3 and C4, in the plants exposed to water deficit and cold stress, respectively. Functional involvement of NF-Y genes in the biotic stress response were also detected where three genes, ShNF-YA6, A3 and A7 were downregulated in the early resistant (cv. N33) response to Eldana infestation whilst only ShNF-YA6 was downregulated in the susceptible (cv. N11) early response. CONCLUSIONS Our research findings establish a foundation for investigating the function of ShNF-Ys and offer candidate genes for stress-resistant breeding and improvement in sugarcane.
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Affiliation(s)
- Jancke le Roux
- Institute for Plant Biotechnology, Department of Genetics, University of Stellenbosch, Stellenbosch, 7602, South Africa
| | - Robyn Jacob
- South African Sugarcane Research Institute (SASRI), KwaZulu-Natal, P/Bag X02, Mount Edgecombe, Durban, 4300, South Africa
| | - Riëtte Fischer
- Institute for Plant Biotechnology, Department of Genetics, University of Stellenbosch, Stellenbosch, 7602, South Africa
| | - Christell van der Vyver
- Institute for Plant Biotechnology, Department of Genetics, University of Stellenbosch, Stellenbosch, 7602, South Africa.
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Oliveira GK, Barreto FZ, Balsalobre TWA, Chapola RG, Hoffmann HP, Carneiro MS. Molecular evaluation and phenotypic screening of brown and orange rust in Saccharum germplasm. PLoS One 2024; 19:e0307935. [PMID: 39078834 PMCID: PMC11288420 DOI: 10.1371/journal.pone.0307935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024] Open
Abstract
Brazil is the largest global producer of sugarcane and plays a significant role-supplier of sugar and bioethanol. However, diseases such as brown and orange rust cause substantial yield reductions and economic losses, due decrease photosynthesis and biomass in susceptible cultivars. Molecular markers associated with resistance genes, such as Bru1 (brown rust) and G1 (orange rust), could aid in predicting resistant genotypes. In this study, we sought to associate the phenotypic response of 300 sugarcane accessions with the genotypic response of Bru1 and G1 markers. The field trials were conducted in a randomized block design, and five six-month-old plants per plot were evaluated under natural disease conditions. Genotypic information about the presence or absence of Bru1 (haplotype 1) and G1 gene was obtained after extraction of genomic DNA and conventional PCR. Of the total accessions evaluated, 60.3% (181) showed resistance to brown rust in the field, and of these, 70.7% (128) had the Bru1 gene present. Considering the field-resistant accessions obtained from Brazilian breeding programs (116), the Bru1 was present in 77,6% of these accessions. While alternative resistance sources may exist, Bru1 likely confers enduring genetic resistance in current Brazilian cultivars. Regarding the phenotypic reaction to orange rust, the majority of accessions, 96.3% (288), were field resistant, and of these, 52.7% (152) carried the G1 marker. Although less efficient for predicting resistance when compared to Bru1, the G1 marker could be part of a quantitative approach when new orange rust resistance genes are described. Therefore, these findings showed the importance of Bru1 molecular markers for the early selection of resistant genotypes to brown rust by genetic breeding programs.
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Affiliation(s)
- Gleicy Kelly Oliveira
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Araras, SP, Brazil
| | - Fernanda Zatti Barreto
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Araras, SP, Brazil
| | | | | | - Hermann Paulo Hoffmann
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Araras, SP, Brazil
- Sugarcane Breeding Program of RIDESA/UFSCar, Araras, SP, Brazil
| | - Monalisa Sampaio Carneiro
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Araras, SP, Brazil
- Sugarcane Breeding Program of RIDESA/UFSCar, Araras, SP, Brazil
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Li Y, Lin P, You Q, Huang J, Yao W, Wang J, Zhang M. Identification of candidate single-nucleotide polymorphisms (SNPs) and genes associated with sugarcane leaf scald disease. Sci Rep 2024; 14:16214. [PMID: 39003420 PMCID: PMC11246479 DOI: 10.1038/s41598-024-67059-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024] Open
Abstract
Leaf scald, caused by Xanthomonas albilineans, is a severe disease affecting sugarcane worldwide. One of the most practical ways to control it is by developing resistant sugarcane cultivars. It is essential to identify genes associated with the response to leaf scald. A panel of 170 sugarcane genotypes was evaluated for resistance to leaf scald in field conditions for 2 years, followed by a 1-year greenhouse experiment. The phenotypic evaluation data showed a wide continuous distribution, with heritability values ranging from 0.58 to 0.84. Thirteen single nucleotide polymorphisms (SNPs) were identified, significantly associated with leaf scald resistance. Among these, eight were stable across multiple environments and association models. The candidate genes identified and validated based on RNA-seq and qRT-PCR included two genes that encode NB-ARC leucine-rich repeat (LRR)-containing domain disease-resistance protein. These findings provide a basis for developing marker-assisted selection strategies in sugarcane breeding programs.
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Affiliation(s)
- Yisha Li
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Pingping Lin
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Qian You
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Jiangfeng Huang
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Wei Yao
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Jianping Wang
- Agronomy Department, IFAS, University of Florida, Gainesville, FL, 32611, USA
| | - Muqing Zhang
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China.
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Mbo Nkoulou LF, Nkouandou YF, Ngalle HB, Cros D, Martin G, Molo T, Eya'a C, Essome C, Zandjanakou-Tachin M, Degbey H, Bell J, Achigan-Dako EG. Screening of Triploid Banana Population Under Natural and Controlled Black Sigatoka Disease for Genomic Selection. PLANT DISEASE 2024; 108:2006-2016. [PMID: 38243182 DOI: 10.1094/pdis-04-23-0741-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Black sigatoka disease (BSD) is the most important foliar threat in banana production, and breeding efforts against it should take advantage of genomic selection (GS), which has become one of the most explored tools to increase genetic gain, save time, and reduce selection costs. To evaluate the potential of GS in banana for BSD, 210 triploid accessions were obtained from the African Banana and Plantain Research Center to constitute a training population. The variability in the population was assessed at the phenotypic level using BSD- and agronomic-related traits and at the molecular level using single-nucleotide polymorphisms (SNPs). The analysis of variance showed a significant difference between accessions for almost all traits measured, although at the genomic group level, there was no significant difference for BSD-related traits. The index of non-spotted leaves among accessions ranged from 0.11 to 0.8. The accessions screening in controlled conditions confirmed the susceptibility of all genomic groups to BSD. The principal components analysis with phenotypic data revealed no clear diversity partition of the population. However, the structure analysis and the hierarchical clustering analysis with SNPs grouped the population into four clusters and two subpopulations, respectively. The field and laboratory screening of the banana GS training population confirmed that all genomic groups are susceptible to BSD but did not reveal any genetic structure, whereas SNP markers exhibited clear genetic structure and provided useful information in the perspective of applying GS.
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Affiliation(s)
- Luther Fort Mbo Nkoulou
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Laboratory of Crop Production, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
- Institute of Agricultural Research for Development, Mbalmayo Agricultural Research Centre (CRA-MB) Mbalmayo, Mbalmayo, Cameroon
- Centre de Recherche et d'Accompagnement des Producteurs Agro-pastoraux du Cameroun, Boumyebel, Cameroun
| | - Yacouba Fifen Nkouandou
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Hermine Bille Ngalle
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - David Cros
- Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Montpellier, France
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, F-34398 Montpellier, France
| | - Guillaume Martin
- Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Montpellier, France
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, F-34398 Montpellier, France
| | - Thierry Molo
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
- Centre de Recherche et d'Accompagnement des Producteurs Agro-pastoraux du Cameroun, Boumyebel, Cameroun
| | - Clement Eya'a
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
- Lipids analysis Laboratory, Institute of Agricultural Research for Development, Specialized Station for Oil Palm of La Dibamba, Douala, Cameroon
| | - Charles Essome
- Laboratory of Phytopathology and Crop Protection, Department of Plant Biology, University of Yaoundé I, 812, Yaoundé, Cameroon
| | - Martine Zandjanakou-Tachin
- School of Horticulture and Landscape Management (UNA), National University of Agriculture, Ketou, Republic of Benin
| | - Hervé Degbey
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Laboratory of Crop Production, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin
| | - Joseph Bell
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Enoch G Achigan-Dako
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Laboratory of Crop Production, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin
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Kumar T, Wang JG, Xu CH, Lu X, Mao J, Lin XQ, Kong CY, Li CJ, Li XJ, Tian CY, Ebid MHM, Liu XL, Liu HB. Genetic Engineering for Enhancing Sugarcane Tolerance to Biotic and Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:1739. [PMID: 38999579 PMCID: PMC11244436 DOI: 10.3390/plants13131739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024]
Abstract
Sugarcane, a vital cash crop, contributes significantly to the world's sugar supply and raw materials for biofuel production, playing a significant role in the global sugar industry. However, sustainable productivity is severely hampered by biotic and abiotic stressors. Genetic engineering has been used to transfer useful genes into sugarcane plants to improve desirable traits and has emerged as a basic and applied research method to maintain growth and productivity under different adverse environmental conditions. However, the use of transgenic approaches remains contentious and requires rigorous experimental methods to address biosafety challenges. Clustered regularly interspaced short palindromic repeat (CRISPR) mediated genome editing technology is growing rapidly and may revolutionize sugarcane production. This review aims to explore innovative genetic engineering techniques and their successful application in developing sugarcane cultivars with enhanced resistance to biotic and abiotic stresses to produce superior sugarcane cultivars.
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Affiliation(s)
- Tanweer Kumar
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
- Sugar Crops Research Institute, Agriculture, Fisheries and Co-Operative Department, Charsadda Road, Mardan 23210, Khyber Pakhtunkhwa, Pakistan
| | - Jun-Gang Wang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
| | - Chao-Hua Xu
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Xin Lu
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Jun Mao
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Xiu-Qin Lin
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Chun-Yan Kong
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Chun-Jia Li
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Xu-Juan Li
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Chun-Yan Tian
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Mahmoud H. M. Ebid
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
- Sugar Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Xin-Long Liu
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Hong-Bo Liu
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
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7
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Abbas Q, Wilhelm M, Kuster B, Poppenberger B, Frishman D. Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies. BMC Genomics 2024; 25:619. [PMID: 38898442 PMCID: PMC11186247 DOI: 10.1186/s12864-024-10521-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024] Open
Abstract
Plant genomics plays a pivotal role in enhancing global food security and sustainability by offering innovative solutions for improving crop yield, disease resistance, and stress tolerance. As the number of sequenced genomes grows and the accuracy and contiguity of genome assemblies improve, structural annotation of plant genomes continues to be a significant challenge due to their large size, polyploidy, and rich repeat content. In this paper, we present an overview of the current landscape in crop genomics research, highlighting the diversity of genomic characteristics across various crop species. We also assessed the accuracy of popular gene prediction tools in identifying genes within crop genomes and examined the factors that impact their performance. Our findings highlight the strengths and limitations of BRAKER2 and Helixer as leading structural genome annotation tools and underscore the impact of genome complexity, fragmentation, and repeat content on their performance. Furthermore, we evaluated the suitability of the predicted proteins as a reliable search space in proteomics studies using mass spectrometry data. Our results provide valuable insights for future efforts to refine and advance the field of structural genome annotation.
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Affiliation(s)
- Qussai Abbas
- Chair of Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Munich Data Science Institute, Technical University of Munich, Garching, Germany
| | - Bernhard Kuster
- Munich Data Science Institute, Technical University of Munich, Garching, Germany
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Dmitrij Frishman
- Chair of Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
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Zhang C, Li Z, Sun T, Zang S, Wang D, Su Y, Wu Q, Que Y. Sugarcane ScCAX4 is a Negative Regulator of Resistance to Pathogen Infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:13205-13216. [PMID: 38809782 DOI: 10.1021/acs.jafc.4c00805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Calcium (Ca2+) is a second messenger in various physiological processes within plants. The significance of the Ca2+/H+ exchanger (CAX) has been established in facilitating Ca2+ transport in plants; however, disease resistance functions of the CAX gene remain elusive. In this study, we conducted sequence characterization and expression analysis for a sugarcane CAX gene, ScCAX4 (GenBank Accession Number: MW206380). In order to further investigate the disease resistance functions, this gene was then transiently overexpressed in Nicotiana benthamiana leaves, which were subsequently inoculated with Fusarium solani var. coeruleum. Results showed that ScCAX4 overexpression increased the susceptibility of N. benthamiana to pathogen infection by regulating the expression of genes related to salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) pathways, suggesting its negative role in disease resistance. Furthermore, we genetically transformed the ScCAX4 gene into N. benthamiana and obtained three positive T2 generation lines. Interestingly, the symptomatology of transgenic plants was consistent with that of transient overexpression after pathogen inoculation. Notably, the JA content in transgenic overexpression lines was significantly higher than that in the wild-type. RNA-seq revealed that ScCAX4 could mediate multiple signaling pathways, and the JA signaling pathway played a key role in modulating disease resistance. Finally, a regulatory model was depicted for the increased susceptibility to pathogen infection conferred by the ScCAX4 gene. This study provides genetic resources for sugarcane molecular breeding and the research direction for plant CAX genes.
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Affiliation(s)
- Chang Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenxiang Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tingting Sun
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youxiong Que
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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9
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Lohmaneeratana K, Leetanasaksakul K, Thamchaipenet A. Transcriptomic Profiling of Sugarcane White Leaf (SCWL) Canes during Maturation Phase. PLANTS (BASEL, SWITZERLAND) 2024; 13:1551. [PMID: 38891358 PMCID: PMC11174868 DOI: 10.3390/plants13111551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
Sugarcane white leaf (SCWL) disease, caused by Candidatus Phytoplasma sacchari, results in the most damage to sugarcane plantations. Some SCWL canes can grow unnoticed through the maturation phase, subsequently resulting in an overall low sugar yield, or they can be used accidentally as seed canes. In this work, 12-month-old SCWL and asymptomatic canes growing in the same field were investigated. An abundance of phytoplasma in SCWL canes affected growth and sugar content as well as alterations of transcriptomic profiles corresponding to several pathways that responded to the infection. Suppression of photosynthesis, porphyrin and chlorophyll metabolism, coupled with an increase in the expression of chlorophyllase, contributed to the reduction in chlorophyll levels and photosynthesis. Blockage of sucrose transport plausibly occurred due to the expression of sugar transporters in leaves but suppression in stalks, resulting in low sugar content in canes. Increased expression of genes associated with MAPK cascades, plant hormone signaling transduction, callose plug formation, the phenylpropanoid pathway, and calcium cascades positively promoted defense mechanisms against phytoplasma colonization by an accumulation of lignin and calcium in response to plant immunity. Significant downregulation of CPK plausibly results in a reduction in antioxidant enzymes and likely facilitates pathogen invasion, while expression of sesquiterpene biosynthesis possibly attracts the insect vectors for transmission, thereby enabling the spread of phytoplasma. Moreover, downregulation of flavonoid biosynthesis potentially intensifies the symptoms of SCWL upon challenge by phytoplasma. These SCWL sugarcane transcriptomic profiles describe the first comprehensive sugarcane-phytoplasma interaction during the harvesting stage. Understanding molecular mechanisms will allow for sustainable management and the prevention of SCWL disease-a crucial benefit to the sugar industry.
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Affiliation(s)
- Karan Lohmaneeratana
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Kantinan Leetanasaksakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand;
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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10
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Zou W, Sun T, Chen Y, Wang D, You C, Zang S, Lin P, Wu Q, Su Y, Que Y. Sugarcane ScOPR1 gene enhances plant disease resistance through the modulation of hormonal signaling pathways. PLANT CELL REPORTS 2024; 43:158. [PMID: 38822833 DOI: 10.1007/s00299-024-03241-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/21/2024] [Indexed: 06/03/2024]
Abstract
KEY MESSAGE Transgenic plants stably overexpressing ScOPR1 gene enhanced disease resistance by increasing the accumulation of JA, SA, and GST, as well as up-regulating the expression of genes related to signaling pathways. 12-Oxo-phytodienoate reductase (OPR) is an oxidoreductase that depends on flavin mononucleotide (FMN) and catalyzes the conversion of 12-oxophytodienoate (12-OPDA) into jasmonic acid (JA). It plays a key role in plant growth and development, and resistance to adverse stresses. In our previous study, we have obtained an OPR gene (ScOPR1, GenBank Accession Number: MG755745) from sugarcane. This gene showed positive responses to methyl jasmonate (MeJA), salicylic acid (SA), abscisic acid (ABA), and Sporisorium scitamineum, suggesting its potential for pathogen resistance. Here, in our study, we observed that Nicotiana benthamiana leaves transiently overexpressing ScOPR1 exhibited weaker disease symptoms, darker 3,3-diaminobenzidine (DAB) staining, higher accumulation of reactive oxygen species (ROS), and higher expression of hypersensitive response (HR) and SA pathway-related genes after inoculation with Ralstonia solanacearum and Fusarium solanacearum var. coeruleum. Furthermore, the transgenic N. benthamiana plants stably overexpressing the ScOPR1 gene showed enhanced resistance to pathogen infection by increasing the accumulation of JA, SA, and glutathione S-transferase (GST), as well as up-regulating genes related to HR, JA, SA, and ROS signaling pathways. Transcriptome analysis revealed that the specific differentially expressed genes (DEGs) in ScOPR1-OE were significantly enriched in hormone transduction signaling and plant-pathogen interaction pathways. Finally, a functional mechanism model of the ScOPR1 gene in response to pathogen infection was depicted. This study provides insights into the molecular mechanism of ScOPR1 and presents compelling evidence supporting its positive involvement in enhancing plant disease resistance.
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Affiliation(s)
- Wenhui Zou
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Tingting Sun
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Yao Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chuihuai You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Peixia Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Youxiong Que
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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11
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Fang J, Chai Z, Huang C, Huang R, Chen B, Yao W, Zhang M. Functional characterization of sugarcane ScFTIP1 reveals its role in Arabidopsis flowering. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108629. [PMID: 38626657 DOI: 10.1016/j.plaphy.2024.108629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 04/18/2024]
Abstract
The timing of floral transition is essential for reproductive success in flowering plants. In sugarcane, flowering time affects the production of sugar and biomass. Although the function of the crucial floral pathway integrators, FLOWERING LOCUS T (FT), in sugarcane, has been uncovered, the proteins responsible for FT export and the underlying mechanism remain unexplored. In this study, we identified a member of the multiple C2 domain and transmembrane region proteins (MCTPs) family in sugarcane, FT-interacting protein 1 (ScFTIP1), which was localized to the endoplasmic reticulum. Ectopic expression of ScFTIP1 in the Arabidopsis mutant ftip1-1 rescued the late-flowering phenotype. ScFTIP1 interacted with AtFT in vitro and in vivo assays. Additionally, ScFTIP1 interacted with ScFT1 and the floral inducer ScFT3. Furthermore, we found that the NAC member, ScNAC23, could directly bind to the ScFTIP1 promoter and negatively regulate its transcription. Overall, our findings revealed the function of ScFTIP1 and proposed a potential mechanism underlying flowering regulation in sugarcane.
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Affiliation(s)
- Jinlan Fang
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zhe Chai
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cuilin Huang
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Run Huang
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Wei Yao
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
| | - Muqing Zhang
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
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12
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Wu X, Cui Z, Li X, Yu Z, Lin P, Xue L, Khan A, Ou C, Deng Z, Zhang M, Yao W, Yu F. Identification and characterization of PAL genes involved in the regulation of stem development in Saccharum spontaneum L. BMC Genom Data 2024; 25:38. [PMID: 38689211 PMCID: PMC11061975 DOI: 10.1186/s12863-024-01219-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/12/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Saccharum spontaneum L. is a closely related species of sugarcane and has become an important genetic component of modern sugarcane cultivars. Stem development is one of the important factors for affecting the yield, while the molecular mechanism of stem development remains poorly understanding in S. spontaneum. Phenylalanine ammonia-lyase (PAL) is a vital component of both primary and secondary metabolism, contributing significantly to plant growth, development and stress defense. However, the current knowledge about PAL genes in S. spontaneum is still limited. Thus, identification and characterization of the PAL genes by transcriptome analysis will provide a theoretical basis for further investigation of the function of PAL gene in sugarcane. RESULTS In this study, 42 of PAL genes were identified, including 26 SsPAL genes from S. spontaneum, 8 ShPAL genes from sugarcane cultivar R570, and 8 SbPAL genes from sorghum. Phylogenetic analysis showed that SsPAL genes were divided into three groups, potentially influenced by long-term natural selection. Notably, 20 SsPAL genes were existed on chromosomes 4 and 5, indicating that they are highly conserved in S. spontaneum. This conservation is likely a result of the prevalence of whole-genome replications within this gene family. The upstream sequence of PAL genes were found to contain conserved cis-acting elements such as G-box and SP1, GT1-motif and CAT-box, which collectively regulate the growth and development of S. spontaneum. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that SsPAL genes of stem had a significantly upregulated than that of leaves, suggesting that they may promote the stem growth and development, particularly in the + 6 stem (The sixth cane stalk from the top to down) during the growth stage. CONCLUSIONS The results of this study revealed the molecular characteristics of SsPAL genes and indicated that they may play a vital role in stem growth and development of S. spontaneum. Altogether, our findings will promote the understanding of the molecular mechanism of S. spontaneum stem development, and also contribute to the sugarcane genetic improving.
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Affiliation(s)
- Xiaoqing Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Zetian Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Xinyi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Zehuai Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Pingping Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Li Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Abdullah Khan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Cailan Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Zuhu Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China.
| | - Fan Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China.
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13
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Zhang T, Huang W, Zhang L, Li DZ, Qi J, Ma H. Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages. Nat Commun 2024; 15:3305. [PMID: 38632270 PMCID: PMC11024178 DOI: 10.1038/s41467-024-47428-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.
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Affiliation(s)
- Taikui Zhang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Weichen Huang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ji Qi
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Hong Ma
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA.
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14
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Bao Y, Zhang Q, Huang J, Zhang S, Yao W, Yu Z, Deng Z, Yu J, Kong W, Yu X, Lu S, Wang Y, Li R, Song Y, Zou C, Xu Y, Liu Z, Yu F, Song J, Huang Y, Zhang J, Wang H, Chen B, Zhang X, Zhang M. A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution. Nat Commun 2024; 15:3041. [PMID: 38589412 PMCID: PMC11001919 DOI: 10.1038/s41467-024-47390-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/31/2024] [Indexed: 04/10/2024] Open
Abstract
Sugarcane is a vital crop with significant economic and industrial value. However, the cultivated sugarcane's ultra-complex genome still needs to be resolved due to its high ploidy and extensive recombination between the two subgenomes. Here, we generate a chromosomal-scale, haplotype-resolved genome assembly for a hybrid sugarcane cultivar ZZ1. This assembly contains 10.4 Gb genomic sequences and 68,509 annotated genes with defined alleles in two sub-genomes distributed in 99 original and 15 recombined chromosomes. RNA-seq data analysis shows that sugar accumulation-associated gene families have been primarily expanded from the ZZSO subgenome. However, genes responding to pokkah boeng disease susceptibility have been derived dominantly from the ZZSS subgenome. The region harboring the possible smut resistance genes has expanded significantly. Among them, the expansion of WAK and FLS2 families is proposed to have occurred during the breeding of ZZ1. Our findings provide insights into the complex genome of hybrid sugarcane cultivars and pave the way for future genomics and molecular breeding studies in sugarcane.
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Affiliation(s)
- Yixue Bao
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Qing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Jiangfeng Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Shengcheng Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zehuai Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zuhu Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Jiaxin Yu
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Weilong Kong
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Xikai Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Shan Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Yibin Wang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Ru Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Yuhan Song
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Chengwu Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Yuzhi Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zongling Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Fan Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Jiaming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Youzong Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Haifeng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
| | - Xingtan Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China.
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
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15
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Healey AL, Garsmeur O, Lovell JT, Shengquiang S, Sreedasyam A, Jenkins J, Plott CB, Piperidis N, Pompidor N, Llaca V, Metcalfe CJ, Doležel J, Cápal P, Carlson JW, Hoarau JY, Hervouet C, Zini C, Dievart A, Lipzen A, Williams M, Boston LB, Webber J, Keymanesh K, Tejomurthula S, Rajasekar S, Suchecki R, Furtado A, May G, Parakkal P, Simmons BA, Barry K, Henry RJ, Grimwood J, Aitken KS, Schmutz J, D'Hont A. The complex polyploid genome architecture of sugarcane. Nature 2024; 628:804-810. [PMID: 38538783 PMCID: PMC11041754 DOI: 10.1038/s41586-024-07231-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 02/23/2024] [Indexed: 04/06/2024]
Abstract
Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.
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Affiliation(s)
- A L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - O Garsmeur
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - J T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Shengquiang
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - J Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - C B Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - N Piperidis
- Sugar Research Australia, Te Kowai, Queensland, Australia
| | - N Pompidor
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - V Llaca
- Corteva Agriscience, Johnston, IA, USA
| | - C J Metcalfe
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - J Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - P Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - J W Carlson
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Y Hoarau
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- ERCANE, Sainte-Clotilde, La Réunion, France
| | - C Hervouet
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - C Zini
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - A Dievart
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - A Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - M Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - L B Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - J Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - K Keymanesh
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Tejomurthula
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Rajasekar
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, USA
| | - R Suchecki
- CSIRO Agriculture and Food, Urrbrae, South Australia, Australia
| | - A Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - G May
- Corteva Agriscience, Johnston, IA, USA
| | | | - B A Simmons
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - K Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, Queensland, Australia
| | - J Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - K S Aitken
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - J Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - A D'Hont
- CIRAD, UMR AGAP Institut, Montpellier, France.
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
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Dijoux J, Rio S, Hervouet C, Garsmeur O, Barau L, Dumont T, Rott P, D'Hont A, Hoarau JY. Unveiling the predominance of Saccharum spontaneum alleles for resistance to orange rust in sugarcane using genome-wide association. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:81. [PMID: 38478168 DOI: 10.1007/s00122-024-04583-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/14/2024] [Indexed: 04/16/2024]
Abstract
KEY MESSAGE Six QTLs of resistance to sugarcane orange rust were identified in modern interspecific hybrids by GWAS. For five of them, the resistance alleles originated from S. spontaneum. Altogether, they efficiently predict disease resistance. Sugarcane orange rust (SOR) is a threatening emerging disease in many sugarcane industries worldwide. Improving the genetic resistance of commercial cultivars remains the most promising solution to control this disease. In this study, an association panel of 568 modern interspecific sugarcane hybrids (Saccharum officinarum x S. spontaneum) from Réunion's breeding program was evaluated for its resistance to SOR under natural conditions of infection. Two genome-wide association studies (GWAS) were conducted between disease reactions and 183,842 single nucleotide polymorphism (SNP) markers obtained by targeted genotyping-by-sequencing. Five resistance quantitative trait loci (QTLs), named Oru1, Oru2, Oru3, Oru4 and Oru5, were identified using a single-locus GWAS (SL-GWAS). These five QTLs all originated from the species S. spontaneum. A multi-locus GWAS (ML-GWAS) uncovered an additional but less significant resistance QTL named Oru6, which originated from S. officinarum. All six QTLs had a moderate to major phenotypic effect on disease resistance. Prediction accuracy estimated with linear regression models based on each of the five QTLs identified by SL-GWAS was between 0.16-0.41. Altogether, these five QTLs provided a relatively high prediction accuracy of 0.60. In comparison, accuracies obtained with six genome-wide prediction models (i.e., GBLUP, Bayes-A, Bayes-B, Bayes-C, Bayesian Lasso and RKHS) reached only 0.65. The good prediction accuracy of disease resistance provided by the QTLs and the predominant S. spontaneum origin of their resistance alleles pave the way for effective marker-assisted breeding strategies.
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Affiliation(s)
- Jordan Dijoux
- eRcane, 29 rue d'Emmerez de Charmoy, 97490, Sainte-Clotilde, La Réunion, France
- CIRAD, UMR PHIM, F-34398, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Simon Rio
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Olivier Garsmeur
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Laurent Barau
- eRcane, 29 rue d'Emmerez de Charmoy, 97490, Sainte-Clotilde, La Réunion, France
| | - Thomas Dumont
- eRcane, 29 rue d'Emmerez de Charmoy, 97490, Sainte-Clotilde, La Réunion, France
| | - Philippe Rott
- CIRAD, UMR PHIM, F-34398, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jean-Yves Hoarau
- eRcane, 29 rue d'Emmerez de Charmoy, 97490, Sainte-Clotilde, La Réunion, France.
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
- CIRAD, UMR AGAP Institut, F-97494, Sainte-Clotilde, La Réunion, France.
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Roopendra K, Priyanka, Chandra A, Akhter Y, Saxena S. Transcriptome scale analysis to decode the differential sucrose accumulation mechanisms in sugarcane under the effect of gibberellin. PHYSIOLOGIA PLANTARUM 2024; 176:e14290. [PMID: 38634341 DOI: 10.1111/ppl.14290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 04/19/2024]
Abstract
In the present study, we analyzed GA3 (gibberellin)-treated sugarcane samples at the transcriptomic level to elucidate the differential expression of genes that influence sucrose accumulation. Previous research has suggested that GA3 application can potentially delay sink saturation by enhancing sink strength and demand, enabling the accommodation of more sucrose. To investigate the potential role of GA-induced modification of sink capacity in promoting higher sucrose accumulation, we sought to unravel the differential expression of transcripts and analyze their functional annotation. Several genes homologous to the sugar-phosphate/phosphate translocator, UTP-glucose-1-phosphate uridylyltransferase, and V-ATPases (vacuolar-type H+ ATPase) were identified as potentially associated with the increased sucrose content observed. A differentially expressed transcript was found to be identical to the mRNA of an unknown protein. Homology-based bioinformatics analysis suggested it to be a hydrolase enzyme, which could potentially act as a stimulator of sucrose buildup. The database of differentially expressed transcripts obtained in this study under the influence of GA3 represents a valuable addition to the sugarcane transcriptomics and functional genomics knowledge base.
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Affiliation(s)
- Kriti Roopendra
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India
- Division of Plant Physiology and Biochemistry, ICAR-Indian Institute of Sugarcane Research, Lucknow, India
| | - Priyanka
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Amaresh Chandra
- Division of Plant Physiology and Biochemistry, ICAR-Indian Institute of Sugarcane Research, Lucknow, India
| | - Yusuf Akhter
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Sangeeta Saxena
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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18
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Cao Z, An Y, Lu Y. Altered N6-Methyladenosine Modification Patterns and Transcript Profiles Contributes to Cognitive Dysfunction in High-Fat Induced Diabetic Mice. Int J Mol Sci 2024; 25:1990. [PMID: 38396669 PMCID: PMC10889299 DOI: 10.3390/ijms25041990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
N6-methyladenosine (m6A) constitutes the paramount post-transcriptional modification within eukaryotic mRNA. This modification is subjected to stimulus-dependent regulation within the central nervous system of mammals, being influenced by sensory experiences, learning processes, and injuries. The patterns of m6A methylation within the hippocampal region of diabetes cognitive impairment (DCI) has not been investigated. A DCI model was established by feeding a high-fat diet to C57BL/6J mice. m6A and RNA sequencing was conducted to profile the m6A-tagged transcripts in the hippocampus. Methylated RNA immunoprecipitation with next-generation sequencing and RNA sequencing analyses yielded differentially m6A-modified and expressed genes in the hippocampus of DCI mice, which were enriched in pathways involving synaptic transmission and axonal guidance. Mechanistic analyses revealed a remarkable change in m6A modification levels through alteration of the mRNA expression of m6A methyltransferases (METTL3 and METTL14) and demethylase (FTO) in the hippocampus of DCI mice. We identified a co-mediated specific RNA regulatory strategy that broadens the epigenetic regulatory mechanism of RNA-induced neurodegenerative disorders associated with metabolic and endocrine diseases.
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Affiliation(s)
- Zhaoming Cao
- School of Nursing, Peking University, Beijing 100191, China;
| | - Yu An
- Endocrinology Department, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China;
| | - Yanhui Lu
- School of Nursing, Peking University, Beijing 100191, China;
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19
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Prado GS, Rocha DC, dos Santos LN, Contiliani DF, Nobile PM, Martinati-Schenk JC, Padilha L, Maluf MP, Lubini G, Pereira TC, Monteiro-Vitorello CB, Creste S, Boscariol-Camargo RL, Takita MA, Cristofani-Yaly M, de Souza AA. CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane. FRONTIERS IN PLANT SCIENCE 2024; 14:1331258. [PMID: 38259920 PMCID: PMC10801916 DOI: 10.3389/fpls.2023.1331258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
Gene editing technologies have opened up the possibility of manipulating the genome of any organism in a predicted way. CRISPR technology is the most used genome editing tool and, in agriculture, it has allowed the expansion of possibilities in plant biotechnology, such as gene knockout or knock-in, transcriptional regulation, epigenetic modification, base editing, RNA editing, prime editing, and nucleic acid probing or detection. This technology mostly depends on in vitro tissue culture and genetic transformation/transfection protocols, which sometimes become the major challenges for its application in different crops. Agrobacterium-mediated transformation, biolistics, plasmid or RNP (ribonucleoprotein) transfection of protoplasts are some of the commonly used CRISPR delivery methods, but they depend on the genotype and target gene for efficient editing. The choice of the CRISPR system (Cas9, Cas12), CRISPR mechanism (plasmid or RNP) and transfection technique (Agrobacterium spp., PEG solution, lipofection) directly impacts the transformation efficiency and/or editing rate. Besides, CRISPR/Cas technology has made countries rethink regulatory frameworks concerning genetically modified organisms and flexibilize regulatory obstacles for edited plants. Here we present an overview of the state-of-the-art of CRISPR technology applied to three important crops worldwide (citrus, coffee and sugarcane), considering the biological, methodological, and regulatory aspects of its application. In addition, we provide perspectives on recently developed CRISPR tools and promising applications for each of these crops, thus highlighting the usefulness of gene editing to develop novel cultivars.
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Affiliation(s)
- Guilherme Souza Prado
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
| | - Dhiôvanna Corrêia Rocha
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Lucas Nascimento dos Santos
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Danyel Fernandes Contiliani
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Paula Macedo Nobile
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
| | | | - Lilian Padilha
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Mirian Perez Maluf
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Greice Lubini
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Tiago Campos Pereira
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Silvana Creste
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Marco Aurélio Takita
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
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Vignesh P, Mahadevaiah C, Selvamuthu K, Mahadeva Swamy HK, Sreenivasa V, Appunu C. Comparative genome-wide characterization of salt responsive micro RNA and their targets through integrated small RNA and de novo transcriptome profiling in sugarcane and its wild relative Erianthus arundinaceus. 3 Biotech 2024; 14:24. [PMID: 38162015 PMCID: PMC10756875 DOI: 10.1007/s13205-023-03867-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024] Open
Abstract
Soil salinity and saline irrigation water are major constraints in sugarcane affecting the production of cane and sugar yield. To understand the salinity induced responses and to identify novel genomic resources, integrated de novo transcriptome and small RNA sequencing in sugarcane wild relative, Erianthus arundinaceus salt tolerant accession IND 99-907 and salt-sensitive sugarcane genotype Co 97010 were performed. A total of 362 known miRNAs belonging to 62 families and 353 miRNAs belonging to 63 families were abundant in IND 99-907 and Co 97010 respectively. The miRNA families such as miR156, miR160, miR166, miR167, miR169, miR171, miR395, miR399, miR437 and miR5568 were the most abundant with more than ten members in both genotypes. The differential expression analysis of miRNA reveals that 221 known miRNAs belonging to 48 families and 130 known miRNAs belonging to 42 families were differentially expressed in IND 99-907 and Co 97010 respectively. A total of 12,693 and 7982 miRNA targets against the monoploid mosaic genome and a total of 15,031 and 12,152 miRNA targets against the de novo transcriptome were identified for differentially expressed known miRNAs of IND 99-907 and Co 97010 respectively. The gene ontology (GO) enrichment analysis of the miRNA targets revealed that 24, 12 and 14 enriched GO terms (FDR < 0.05) for biological process, molecular function and cellular component respectively. These miRNAs have many targets that associated in regulation of biotic and abiotic stresses. Thus, the genomic resources generated through this study are useful for sugarcane crop improvement through biotechnological and advanced breeding approaches. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03867-7.
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Affiliation(s)
- Palanisamy Vignesh
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - Channappa Mahadevaiah
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
- ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bangalore, 560089 India
| | - Kannan Selvamuthu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | | | - Venkatarayappa Sreenivasa
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - Chinnaswamy Appunu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
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Khanbo S, Somyong S, Phetchawang P, Wirojsirasak W, Ukoskit K, Klomsa-ard P, Pootakham W, Tangphatsornruang S. A SNP variation in the Sucrose synthase ( SoSUS) gene associated with sugar-related traits in sugarcane. PeerJ 2023; 11:e16667. [PMID: 38111652 PMCID: PMC10726748 DOI: 10.7717/peerj.16667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/20/2023] Open
Abstract
Background Sugarcane (Saccharum spp.) is an economically significant crop for both the sugar and biofuel industries. Breeding sugarcane cultivars with high-performance agronomic traits is the most effective approach for meeting the rising demand for sugar and biofuels. Molecular markers associated with relevant agronomic traits could drastically reduce the time and resources required to develop new sugarcane varieties. Previous sugarcane candidate gene association analyses have found single nucleotide polymorphism (SNP) markers associated with sugar-related traits. This study aims to validate these associated SNP markers of six genes, including Lesion simulating disease 1 (LSD), Calreticulin (CALR), Sucrose synthase 1 (SUS1), DEAD-box ATP-dependent RNA helicase (RH), KANADI1 (KAN1), and Sodium/hydrogen exchanger 7 (NHX7), in a diverse population in 2-year and two-location evaluations. Methods After genotyping of seven targeted SNP markers was performed by PCR Allelic Competitive Extension (PACE) SNP genotyping, the association with sugar-related traits and important cane yield component traits was determined on a set of 159 sugarcane genotypes. The marker-trait relationships were validated and identified by both t-test analysis and an association analysis based on the general linear model. Results The mSoSUS1_SNPCh10.T/C and mSoKAN1_SNPCh7.T/C markers that were designed from the SUS1 and KAN1 genes, respectively, showed significant associations with different amounts of sugar-related traits and yield components. The mSoSUS1_SNPCh10.T/C marker was found to have more significant association with sugar-related traits, including pol, CCS, brix, fiber and sugar yield, with p values of 6.08 × 10-6 to 4.35 × 10-2, as well as some cane yield component traits with p values of 1.61 × 10-4 to 3.35 × 10-2. The significant association is consistent across four environments. Conclusion Sucrose synthase (SUS) is considered a crucial enzyme involved in sucrose metabolism. This marker is a high potential functional marker that may be used in sugarcane breeding programs to select superior sugarcane with good fiber and high sugar contents.
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Affiliation(s)
- Supaporn Khanbo
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Suthasinee Somyong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Phakamas Phetchawang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | | | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Pathumtani, Thailand
| | - Peeraya Klomsa-ard
- Mitr Phol Innovation and Research Center, Phu Khiao, Chaiyaphum, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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22
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Zhao J, Li S, Xu Y, Ahmad N, Kuang B, Feng M, Wei N, Yang X. The subgenome Saccharum spontaneum contributes to sugar accumulation in sugarcane as revealed by full-length transcriptomic analysis. J Adv Res 2023; 54:1-13. [PMID: 36781019 DOI: 10.1016/j.jare.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
INTRODUCTION Modern sugarcane cultivars (Saccharum spp. hybrids) derived from crosses between S. officinarum and S. spontaneum, with high-sugar traits and excellent stress tolerance inherited respectively. However, the contribution of the S. spontaneum subgenome to sucrose accumulation is still unclear. OBJECTIVE To compensate for the absence of a high-quality reference genome, a transcriptome analysis method is needed to analyze the molecular basis of differential sucrose accumulation in sugarcane hybrids and to find clues to the contribution of the S. spontaneum subgenome to sucrose accumulation. METHODS PacBio full-length sequencing was used to complement genome annotation, followed by the identification of differential genes between the high and low sugar groups using differential alternative splicing analysis and differential expression analysis. At the subgenomic level, the factors responsible for differential sucrose accumulation were investigated from the perspective of transcriptional and post-transcriptional regulation. RESULTS A full-length transcriptome annotated at the subgenomic level was provided, complemented by 263,378 allele-defined transcript isoforms and 139,405 alternative splicing (AS) events. Differential alternative splicing (DA) analysis and differential expression (DE) analysis identified differential genes between high and low sugar groups and explained differential sucrose accumulation factors by the KEGG pathways. In some gene models, different or even opposite expression patterns of alleles from the same gene were observed, reflecting the potential evolution of these alleles toward novel functions in polyploid sugarcane. Among DA and DE genes in the sucrose source-sink complex pathway, we found some alleles encoding sucrose accumulation-related enzymes derived from the S. spontaneum subgenome were differentially expressed or had DA events between the two contrasting sugarcane hybrids. CONCLUSION Full-length transcriptomes annotated at the subgenomic level could better characterize sugarcane hybrids, and the S. spontaneum subgenome was found to contribute to sucrose accumulation.
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Affiliation(s)
- Jihan Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Sicheng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yuzhi Xu
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Nazir Ahmad
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China
| | - Bowen Kuang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Mengfan Feng
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ni Wei
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China.
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23
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Li X, Li Y, Wei A, Wang Z, Huang H, Huang Q, Yang L, Gao Y, Zhu G, Liu Q, Li Y, Wei S, Wei D. Integrated transcriptomic and proteomic analyses of two sugarcane (Saccharum officinarum Linn.) varieties differing in their lodging tolerance. BMC PLANT BIOLOGY 2023; 23:601. [PMID: 38030995 PMCID: PMC10685470 DOI: 10.1186/s12870-023-04622-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Lodging seriously affects sugarcane stem growth and sugar accumulation, reduces sugarcane yield and sucrose content, and impedes mechanization. However, the molecular mechanisms underlying sugarcane lodging tolerance remain unclear. In this study, comprehensive transcriptomic and proteomic analyses were performed to explore the differential genetic regulatory mechanisms between upright (GT42) and lodged (GF98-296) sugarcane varieties. RESULTS The stain test showed that GT42 had more lignin and vascular bundles in the stem than GF98-296. The gene expression analysis revealed that the genes that were differentially expressed between the two varieties were mainly involved in the phenylpropanoid pathway at the growth stage. The protein expression analysis indicated that the proteins that were differentially expressed between the two varieties were related to the synthesis of secondary metabolites, the process of endocytosis, and the formation of aminoacyl-tRNA. Time-series analysis revealed variations in differential gene expression patterns between the two varieties, whereas significant protein expression trends in the two varieties were largely consistent, except for one profile. The expression of CYP84A, 4CL, and CAD from the key phenylpropanoid biosynthetic pathway was enhanced in GT42 at stage 2 but suppressed in GF98-296 at the growth stage. Furthermore, the expression of SDT1 in the nicotinate and nicotinamide metabolism was enhanced in GT42 cells but suppressed in GF98-296 cells at the growth stage. CONCLUSION Our findings provide reference data for mining lodging tolerance-related genes that are expected to facilitate the selective breeding of sugarcane varieties with excellent lodging tolerance.
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Affiliation(s)
- Xiang Li
- Guangxi Subtropical Crops Research Institute, Nanning, 530002, China
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yijie Li
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Ailin Wei
- Baise Institue of Agricultural Sciences, Baise, 533612, China
| | - Zeping Wang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Hairong Huang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Quyan Huang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Litao Yang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yijing Gao
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Guanghu Zhu
- Center for Applied Mathematics of Guangxi (GUET), Guilin, 541004, China
| | - Qihuai Liu
- Center for Applied Mathematics of Guangxi (GUET), Guilin, 541004, China
| | - Yangrui Li
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Shaolong Wei
- Guangxi Subtropical Crops Research Institute, Nanning, 530002, China.
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Debin Wei
- Baise Institue of Agricultural Sciences, Baise, 533612, China.
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24
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Yadav S, Ross EM, Wei X, Powell O, Hivert V, Hickey LT, Atkin F, Deomano E, Aitken KS, Voss-Fels KP, Hayes BJ. Optimising clonal performance in sugarcane: leveraging non-additive effects via mate-allocation strategies. FRONTIERS IN PLANT SCIENCE 2023; 14:1260517. [PMID: 38023905 PMCID: PMC10667552 DOI: 10.3389/fpls.2023.1260517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Mate-allocation strategies in breeding programs can improve progeny performance by harnessing non-additive genetic effects. These approaches prioritise predicted progeny merit over parental breeding value, making them particularly appealing for clonally propagated crops such as sugarcane. We conducted a comparative analysis of mate-allocation strategies, exploring utilising non-additive and heterozygosity effects to maximise clonal performance with schemes that solely consider additive effects to optimise breeding value. Using phenotypic and genotypic data from a population of 2,909 clones evaluated in final assessment trials of Australian sugarcane breeding programs, we focused on three important traits: tonnes of cane per hectare (TCH), commercial cane sugar (CCS), and Fibre. By simulating families from all possible crosses (1,225) with 50 progenies each, we predicted the breeding and clonal values of progeny using two models: GBLUP (considering additive effects only) and extended-GBLUP (incorporating additive, non-additive, and heterozygosity effects). Integer linear programming was used to identify the optimal mate-allocation among selected parents. Compared to breeding value-based approaches, mate-allocation strategies based on clonal performance yielded substantial improvements, with predicted progeny values increasing by 57% for TCH, 12% for CCS, and 16% for fibre. Our simulation study highlights the effectiveness of mate-allocation approaches that exploit non-additive and heterozygosity effects, resulting in superior clonal performance. However, there was a notable decline in additive gain, particularly for TCH, likely due to significant epistatic effects. When selecting crosses based on clonal performance for TCH, the inbreeding coefficient of progeny was significantly lower compared to random mating, underscoring the advantages of leveraging non-additive and heterozygosity effects in mitigating inbreeding depression. Thus, mate-allocation strategies are recommended in clonally propagated crops to enhance clonal performance and reduce the negative impacts of inbreeding.
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Affiliation(s)
- Seema Yadav
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Elizabeth M. Ross
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Xianming Wei
- Sugar Research Australia, Mackay, QLD, Australia
| | - Owen Powell
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Valentin Hivert
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Felicity Atkin
- Sugar Research Australia, Meringa Gordonvale, QLD, Australia
| | - Emily Deomano
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Karen S. Aitken
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QlD, Australia
| | - Kai P. Voss-Fels
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
- Department of Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Ben J. Hayes
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
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Chemelewski R, McKinley BA, Finlayson S, Mullet JE. Epicuticular wax accumulation and regulation of wax pathway gene expression during bioenergy Sorghum stem development. FRONTIERS IN PLANT SCIENCE 2023; 14:1227859. [PMID: 37936930 PMCID: PMC10626490 DOI: 10.3389/fpls.2023.1227859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/11/2023] [Indexed: 11/09/2023]
Abstract
Bioenergy sorghum is a drought-tolerant high-biomass C4 grass targeted for production on annual cropland marginal for food crops due primarily to abiotic constraints. To better understand the overall contribution of stem wax to bioenergy sorghum's resilience, the current study characterized sorghum stem cuticular wax loads, composition, morphometrics, wax pathway gene expression and regulation using vegetative phase Wray, R07020, and TX08001 genotypes. Wax loads on sorghum stems (~103-215 µg/cm2) were much higher than Arabidopsis stem and leaf wax loads. Wax on developing sorghum stem internodes was enriched in C28/30 primary alcohols (~65%) while stem wax on fully developed stems was enriched in C28/30 aldehydes (~80%). Scanning Electron Microscopy showed minimal wax on internodes prior to the onset of elongation and that wax tubules first appear associated with cork-silica cell complexes when internode cell elongation is complete. Sorghum homologs of genes involved in wax biosynthesis/transport were differentially expressed in the stem epidermis. Expression of many wax pathway genes (i.e., SbKCS6, SbCER3-1, SbWSD1, SbABCG12, SbABCG11) is low in immature apical internodes then increases at the onset of stem wax accumulation. SbCER4 is expressed relatively early in stem development consistent with accumulation of C28/30 primary alcohols on developing apical internodes. High expression of two SbCER3 homologs in fully elongated internodes is consistent with a role in production of C28/30 aldehydes. Gene regulatory network analysis aided the identification of sorghum homologs of transcription factors that regulate wax biosynthesis (i.e., SbSHN1, SbWRI1/3, SbMYB94/96/30/60, MYS1) and other transcription factors that could regulate and specify expression of the wax pathway in epidermal cells during cuticle development.
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Affiliation(s)
- Robert Chemelewski
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, United States
| | - Brian A. McKinley
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, United States
| | - Scott Finlayson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - John E. Mullet
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, United States
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26
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Wirojsirasak W, Songsri P, Jongrungklang N, Tangphatsornruang S, Klomsa-ard P, Ukoskit K. A Large-Scale Candidate-Gene Association Mapping for Drought Tolerance and Agronomic Traits in Sugarcane. Int J Mol Sci 2023; 24:12801. [PMID: 37628982 PMCID: PMC10454574 DOI: 10.3390/ijms241612801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Dissection of the genetic loci controlling drought tolerance traits with a complex genetic inheritance is important for drought-tolerant sugarcane improvement. In this study, we conducted a large-scale candidate gene association study of 649 candidate genes in a sugarcane diversity panel to identify genetic variants underlying agronomic traits and drought tolerance indices evaluated in plant cane and ratoon cane under water-stressed (WS) and non-stressed (NS) environments. We identified 197 significant marker-trait associations (MTAs) in 141 candidate genes associated with 18 evaluated traits with the Bonferroni correction threshold (α = 0.05). Out of the total, 95 MTAs in 78 candidate genes and 62 MTAs in 58 candidate genes were detected under NS and WS conditions, respectively. Most MTAs were found only in specific water regimes and crop seasons. These MTAs explained 7.93-30.52% of phenotypic variation. Association mapping results revealed that 34, 59, and 104 MTAs involved physiological and molecular adaptation, phytohormone metabolism, and drought-inducible genes. They identified 19 pleiotropic genes associated with more than one trait and many genes related to drought tolerance indices. The genetic and genomic resources identified in this study will enable the combining of yield-related traits and sugar-related traits with agronomic value to optimize the yield of sugarcane cultivars grown under drought-stressed and non-stressed environments.
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Affiliation(s)
- Warodom Wirojsirasak
- Department of Biotechnology, Faculty of Science and Technology, Rangsit Campus, Thammasat University, Pathum Thani 12120, Thailand;
- Mitr Phol Innovation and Research Center, Chaiyaphum 36110, Thailand;
| | - Patcharin Songsri
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (P.S.); (N.J.)
- Northeast Thailand Cane and Sugar Research Center, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Nakorn Jongrungklang
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (P.S.); (N.J.)
- Northeast Thailand Cane and Sugar Research Center, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | | | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Rangsit Campus, Thammasat University, Pathum Thani 12120, Thailand;
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27
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Thirugnanasambandam PP, Singode A, Thalambedu LP, Athiappan S, Krishnasamy M, Purakkal SV, Govind H, Furtado A, Henry R. Long read transcriptome sequencing of a sugarcane hybrid and its progenitors, Saccharum officinarum and S. spontaneum. FRONTIERS IN PLANT SCIENCE 2023; 14:1199748. [PMID: 37662143 PMCID: PMC10469502 DOI: 10.3389/fpls.2023.1199748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/17/2023] [Indexed: 09/05/2023]
Abstract
Commercial sugarcane hybrids are derivatives from Saccharum officinarum and Saccharum spontaneum hybrids containing the full complement of S. officinarum and a few S. spontaneum chromosomes and recombinants with favorable agronomic characters from both the species. The combination of the two sub-genomes in varying proportions in addition to the recombinants presents a challenge in the study of gene expression and regulation in the hybrid. We now report the transcriptome analysis of the two progenitor species and a modern commercial sugarcane hybrid through long read sequencing technology. Transcripts were profiled in the two progenitor species S. officinarum (Black Cheribon), and S. spontaneum (Coimbatore accession) and a recent high yielding, high sugar variety Co 11015. The composition and contribution of the progenitors to a hybrid with respect to sugar, biomass, and disease resistance were established. Sugar related transcripts originated from S. officinarum while several stress and senescence related transcripts were from S. spontaneum in the hybrid. The hybrid had a higher number of transcripts related to sugar transporters, invertases, transcription factors, trehalose, UDP sugars, and cellulose than the two progenitor species. Both S. officinarum and the hybrid had an abundance of novel genes like sugar phosphate translocator, while S. spontaneum had just one. In general, the hybrid shared a larger number of transcripts with S. officinarum than with S. spontaneum, reflecting the genomic contribution, while the progenitors shared very few transcripts between them. The common isoforms among the three genotypes and unique isoforms specific to each genotype indicate that there is a high scope for improvement of the modern hybrids by utilizing novel gene isoforms from the progenitor species.
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Affiliation(s)
| | - Avinash Singode
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Millets Research, Hyderabad, Telangana, India
| | | | - Selvi Athiappan
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Mohanraj Krishnasamy
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | | | - Hemaprabha Govind
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
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28
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Yu RM, Zhang N, Zhang BW, Liang Y, Pang XX, Cao L, Chen YD, Zhang WP, Yang Y, Zhang DY, Pang EL, Bai WN. Genomic insights into biased allele loss and increased gene numbers after genome duplication in autotetraploid Cyclocarya paliurus. BMC Biol 2023; 21:168. [PMID: 37553642 PMCID: PMC10408227 DOI: 10.1186/s12915-023-01668-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Autopolyploidy is a valuable model for studying whole-genome duplication (WGD) without hybridization, yet little is known about the genomic structural and functional changes that occur in autopolyploids after WGD. Cyclocarya paliurus (Juglandaceae) is a natural diploid-autotetraploid species. We generated an allele-aware autotetraploid genome, a chimeric chromosome-level diploid genome, and whole-genome resequencing data for 106 autotetraploid individuals at an average depth of 60 × per individual, along with 12 diploid individuals at an average depth of 90 × per individual. RESULTS Autotetraploid C. paliurus had 64 chromosomes clustered into 16 homologous groups, and the majority of homologous chromosomes demonstrated similar chromosome length, gene numbers, and expression. The regions of synteny, structural variation and nonalignment to the diploid genome accounted for 81.3%, 8.8% and 9.9% of the autotetraploid genome, respectively. Our analyses identified 20,626 genes (69.18%) with four alleles and 9191 genes (30.82%) with one, two, or three alleles, suggesting post-polyploid allelic loss. Genes with allelic loss were found to occur more often in proximity to or within structural variations and exhibited a marked overlap with transposable elements. Additionally, such genes showed a reduced tendency to interact with other genes. We also found 102 genes with more than four copies in the autotetraploid genome, and their expression levels were significantly higher than their diploid counterparts. These genes were enriched in enzymes involved in stress response and plant defense, potentially contributing to the evolutionary success of autotetraploids. Our population genomic analyses suggested a single origin of autotetraploids and recent divergence (~ 0.57 Mya) from diploids, with minimal interploidy admixture. CONCLUSIONS Our results indicate the potential for genomic and functional reorganization, which may contribute to evolutionary success in autotetraploid C. paliurus.
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Affiliation(s)
- Rui-Min Yu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Ning Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yu Liang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiao-Xu Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lei Cao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yi-Dan Chen
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Wei-Ping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yang Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Er-Li Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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Islam MS, Corak K, McCord P, Hulse-Kemp AM, Lipka AE. A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane. FRONTIERS IN PLANT SCIENCE 2023; 14:1205999. [PMID: 37600177 PMCID: PMC10433174 DOI: 10.3389/fpls.2023.1205999] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023]
Abstract
The sugarcane ratooning ability (RA) is the most important target trait for breeders seeking to enhance the profitability of sugarcane production by reducing the planting cost. Understanding the genetics governing the RA could help breeders by identifying molecular markers that could be used for genomics-assisted breeding (GAB). A replicated field trial was conducted for three crop cycles (plant cane, first ratoon, and second ratoon) using 432 sugarcane clones and used for conducting genome-wide association and genomic prediction of five sugar and yield component traits of the RA. The RA traits for economic index (EI), stalk population (SP), stalk weight (SW), tonns of cane per hectare (TCH), and tonns of sucrose per hectare (TSH) were estimated from the yield and sugar data. A total of six putative quantitative trait loci and eight nonredundant single-nucleotide polymorphism (SNP) markers were associated with all five tested RA traits and appear to be unique. Seven putative candidate genes were colocated with significant SNPs associated with the five RA traits. The genomic prediction accuracies for those tested traits were moderate and ranged from 0.21 to 0.36. However, the models fitting fixed effects for the most significant associated markers for each respective trait did not give any advantages over the standard models without fixed effects. As a result of this study, more robust markers could be used in the future for clone selection in sugarcane, potentially helping resolve the genetic control of the RA in sugarcane.
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Affiliation(s)
| | - Keo Corak
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC, United States
| | - Per McCord
- Sugarcane Field Station, USDA-ARS, Canal Point, FL, United States
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, United States
| | - Amanda M. Hulse-Kemp
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC, United States
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, IL, United States
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Sichel V, Sarah G, Girollet N, Laucou V, Roux C, Roques M, Mournet P, Cunff LL, Bert P, This P, Lacombe T. Chimeras in Merlot grapevine revealed by phased assembly. BMC Genomics 2023; 24:396. [PMID: 37452318 PMCID: PMC10347889 DOI: 10.1186/s12864-023-09453-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Chimerism is the phenomenon when several genotypes coexist in a single individual. Used to understand plant ontogenesis they also have been valorised through new cultivar breeding. Viticulture has been taking economic advantage out of chimeras when the variant induced an important modification of wine type such as berry skin colour. Crucial agronomic characters may also be impacted by chimeras that aren't identified yet. Periclinal chimera where the variant has entirely colonised a cell layer is the most stable and can be propagated through cuttings. In grapevine, leaves are derived from both meristem layers, L1 and L2. However, lateral roots are formed from the L2 cell layer only. Thus, comparing DNA sequences of roots and leaves allows chimera detection. In this study we used new generation Hifi long reads sequencing, recent bioinformatics tools and trio-binning with parental sequences to detect periclinal chimeras on 'Merlot' grapevine cultivar. Sequencing of cv. 'Magdeleine Noire des Charentes' and 'Cabernet Franc', the parents of cv. 'Merlot', allowed haplotype resolved assembly. Pseudomolecules were built with a total of 33 to 47 contigs and in few occasions a unique contig for one chromosome. This high resolution allowed haplotype comparison. Annotation was transferred from PN40024 VCost.v3 to all pseudomolecules. After strong selection of variants, 51 and 53 'Merlot' specific periclinal chimeras were found on the Merlot-haplotype-CF and Merlot-haplotype-MG respectively, 9 and 7 been located in a coding region. A subset of positions was analysed using Molecular Inversion Probes (MIPseq) and 69% were unambiguously validated, 25% are doubtful because of technological noise or weak depth and 6% invalidated. These results open new perspectives on chimera detection as an important resource to improve cultivars through clonal selection or breeding.
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Affiliation(s)
- V. Sichel
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
| | - G. Sarah
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - N. Girollet
- EGFV, Université de Bordeaux, Bordeaux-Sciences Agro, INRAe, ISVV, 210 Chemin de Leysotte, F-33882 Villenave d’Ornon, France
| | - V. Laucou
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - C. Roux
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - M. Roques
- Institut Français de la Vigne et du Vin, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - P. Mournet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMR AGAP Institut, CIRAD, Montpellier, F-34398 France
| | - L. Le Cunff
- Institut Français de la Vigne et du Vin, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - P.F. Bert
- EGFV, Université de Bordeaux, Bordeaux-Sciences Agro, INRAe, ISVV, 210 Chemin de Leysotte, F-33882 Villenave d’Ornon, France
| | - P. This
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - T. Lacombe
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
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Wang L, Yeo S, Lee M, Endah S, Alhuda NA, Yue GH. Combination of GWAS and F ST-based approaches identified loci associated with economic traits in sugarcane. Mol Genet Genomics 2023:10.1007/s00438-023-02040-2. [PMID: 37289230 DOI: 10.1007/s00438-023-02040-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/28/2023] [Indexed: 06/09/2023]
Abstract
Sugarcane is a globally important plant for both sugar and biofuel production. Although conventional breeding has played an important role in increasing the productivity of sugarcane, it takes a long time to achieve breeding goals such as high yield and resistant to diseases. Molecular breeding, including marker-assisted breeding and genomic selection, can accelerate genetic improvement by selecting elites at the seedling stage with DNA markers. However, only a few DNA markers associated with important traits were identified in sugarcane. The purpose of this study was to identify DNA markers associated with sugar content, stalk diameter, and sugarcane top borer resistance. The sugarcane samples with trait records were genotyped using the restriction site-associated DNA sequencing (RADseq) technology. Using FST analysis and genome-wide association study (GWAS), a total of 9, 23 and 9 DNA variants (single nucleotide polymorphisms (SNPs)/insertions and deletions (indels)) were associated with sugar content, stalk diameter, and sugarcane top borer resistance, respectively. The identified genetic variants were on different chromosomes, suggesting that these traits are complex and determined by multiple genetic factors. These DNA markers identified by both approaches have the potential to be used in selecting elite clones at the seeding stage in our sugarcane breeding program to accelerate genetic improvement. Certainly, it is essential to verify the reliability of the identified DNA markers associated with traits before they are used in molecular breeding in other populations.
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Affiliation(s)
- Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Shadame Yeo
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - May Lee
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - S Endah
- Research and Development, PT Gunung Madu Plantations, KM 90 Terusan Nunyai, Central Lampung, Lampung, 34167, Indonesia
| | - N A Alhuda
- Research and Development, PT Gunung Madu Plantations, KM 90 Terusan Nunyai, Central Lampung, Lampung, 34167, Indonesia
| | - G H Yue
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore.
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Miller S, Rønager A, Holm R, Fontanet-Manzaneque JB, Caño-Delgado AI, Bjarnholt N. New methods for sorghum transformation in temperate climates. AOB PLANTS 2023; 15:plad030. [PMID: 37396498 PMCID: PMC10308921 DOI: 10.1093/aobpla/plad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 06/02/2023] [Indexed: 07/04/2023]
Abstract
Sorghum (Sorghum bicolor) is an emerging cereal crop in temperate climates due to its high drought tolerance and other valuable traits. Genetic transformation is an important tool for the improvement of cereals. However, sorghum is recalcitrant to genetic transformation which is almost only successful in warmer climates. Here, we test the application of two new techniques for sorghum transformation in temperate climates, namely transient transformation by Agrobacterium tumefaciens-mediated agroinfiltration and stable transformation using gold particle bombardment and leaf whorls as explants. We optimized the transient transformation method, including post-infiltration incubation of plants in the dark and using Agrobacterium grown on plates with a high cell density (OD600 = 2.0). Expression of the green fluorescence protein (GFP)-tagged endogenous sorghum gene SbDHR2 was achieved with low transformation efficiency, and our results point out a potential weakness in using this approach for localization studies. Furthermore, we succeeded in the production of callus and somatic embryos from leaf whorls, although no genetic transformation was accomplished with this method. Both methods show potential, even if they seem to be influenced by climatic conditions and therefore need further optimization to be applied routinely in temperate climates.
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Affiliation(s)
- Sara Miller
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksbergs, Denmark
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Asta Rønager
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksbergs, Denmark
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Rose Holm
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksbergs, Denmark
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Juan B Fontanet-Manzaneque
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB (Cerdanyola del Vallès), 08193 Barcelona, Spain
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Li AM, Liao F, Wang M, Chen ZL, Qin CX, Huang RQ, Verma KK, Li YR, Que YX, Pan YQ, Huang DL. Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors. Int J Mol Sci 2023; 24:ijms24108913. [PMID: 37240257 DOI: 10.3390/ijms24108913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Sugarcane, a C4 plant, provides most of the world's sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the potential to be grown in arid and semi-arid regions if its stress tolerance can be improved. Modern sugarcane cultivars which exhibit a greater extent of polyploidy and agronomically important traits, such as high sugar concentration, biomass production, and stress tolerance, are regulated by complex mechanisms. Molecular techniques have revolutionized our understanding of the interactions between genes, proteins, and metabolites, and have aided in the identification of the key regulators of diverse traits. This review discusses various molecular techniques for dissecting the mechanisms underlying the sugarcane response to biotic and abiotic stresses. The comprehensive characterization of sugarcane's response to various stresses will provide targets and resources for sugarcane crop improvement.
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Affiliation(s)
- Ao-Mei Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Fen Liao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Miao Wang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Zhong-Liang Chen
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Cui-Xian Qin
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Ruo-Qi Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Krishan K Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - You-Xiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - You-Qiang Pan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Dong-Liang Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
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34
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Moura Dias H, Vieira AP, de Jesus EM, de Setta N, Barros G, Van Sluys MA. Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane. PeerJ 2023; 11:e14973. [PMID: 37214086 PMCID: PMC10194071 DOI: 10.7717/peerj.14973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 02/07/2023] [Indexed: 05/24/2023] Open
Abstract
De novo synthesis of thiamine (vitamin B1) in plants depends on the action of thiamine thiazole synthase, which synthesizes the thiazole ring, and is encoded by the THI1 gene. Here, we investigated the evolution and diversity of THI1 in Poaceae, where C4 and C3 photosynthetic plants co-evolved. An ancestral duplication of THI1 is observed in Panicoideae that remains in many modern monocots, including sugarcane. In addition to the two sugarcane copies (ScTHI1-1 and ScTHI1-2), we identified ScTHI1-2 alleles showing differences in their sequence, indicating divergence between ScTHI1-2a and ScTHI1-2b. Such variations are observed only in the Saccharum complex, corroborating the phylogeny. At least five THI1 genomic environments were found in Poaceae, two in sugarcane, M. sinensis, and S. bicolor. The THI1 promoter in Poaceae is highly conserved at 300 bp upstream of the start codon ATG and has cis-regulatory elements that putatively bind to transcription factors associated with development, growth, development and biological rhythms. An experiment set to compare gene expression levels in different tissues across the sugarcane R570 life cycle showed that ScTHI1-1 was expressed mainly in leaves regardless of age. Furthermore, ScTHI1 displayed relatively high expression levels in meristem and culm, which varied with the plant age. Finally, yeast complementation studies with THI4-defective strain demonstrate that only ScTHI1-1 and ScTHI1-2b isoforms can partially restore thiamine auxotrophy, albeit at a low frequency. Taken together, the present work supports the existence of multiple origins of THI1 harboring genomic regions in Poaceae with predicted functional redundancy. In addition, it questions the contribution of the levels of the thiazole ring in C4 photosynthetic plant tissues or potentially the relevance of the THI1 protein activity.
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Affiliation(s)
| | | | | | - Nathalia de Setta
- Botanica/IB, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
- Universidade Federal do ABC, Sao Bernardo do Campo, Sao Paulo, Brazil
| | - Gesiele Barros
- Botanica/IB, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
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Shen QQ, Wang TJ, Wang JG, He LL, Zhao TT, Zhao XT, Xie LY, Qian ZF, Wang XH, Liu LF, Chen SY, Zhang SZ, Li FS. The SsWRKY1 transcription factor of Saccharum spontaneum enhances drought tolerance in transgenic Arabidopsis thaliana and interacts with 21 potential proteins to regulate drought tolerance in S. spontaneum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107706. [PMID: 37119548 DOI: 10.1016/j.plaphy.2023.107706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/28/2023] [Accepted: 04/13/2023] [Indexed: 05/01/2023]
Abstract
In this study, we characterized a WRKY family member gene, SsWRKY1, which is located in the nucleus and contains multiple stress-related cis-acting elements. In addition, constructed SsWRKY1-overexpressing Arabidopsis thaliana had higher antioxidant enzyme activity and proline content under drought stress conditions, with lower malondialdehyde content and reactive oxygen species (ROS) accumulation, and the expression levels of six stress-related genes were significantly upregulated. This indicates that the overexpression of SsWRKY1 in Arabidopsis thaliana improves resistance to drought stress. SsWRKY1 does not have transcriptional autoactivation activity in yeast cells. The yeast two-hybrid (Y2H) system and the S. spontaneum cDNA library were used to screen 21 potential proteins that interact with SsWRKY1, and the interaction between SsWRKY1 and ATAF2 was verified by GST pull-down assay. In summary, our results indicate that SsWRKY1 plays an important role in the response to drought stress and provide initial insights into the molecular mechanism of SsWRKY1 in response to drought stress.
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Affiliation(s)
- Qing-Qing Shen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Tian-Ju Wang
- Institute for Bio-resources Research and Development of Central Yunnan Plateau, Chuxiong Normal University, Chuxiong, Yunnan, 675000, People's Republic of China
| | - Jun-Gang Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, People's Republic of China
| | - Li-Lian He
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Ting-Ting Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, People's Republic of China
| | - Xue-Ting Zhao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Lin-Yan Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Zhen-Feng Qian
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Xian-Hong Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Lu-Feng Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Shu-Ying Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China
| | - Shu-Zhen Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, People's Republic of China.
| | - Fu-Sheng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China; Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China.
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36
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Calvez L, Dereeper A, Perdereau A, Mournet P, Miranda M, Bruyère S, Hufnagel B, Froelicher Y, Lemainque A, Morillon R, Ollitrault P. Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks. PLANTS (BASEL, SWITZERLAND) 2023; 12:1630. [PMID: 37111854 PMCID: PMC10146282 DOI: 10.3390/plants12081630] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Sexual breeding at the tetraploid level is a promising strategy for rootstock breeding in citrus. Due to the interspecific origin of most of the conventional diploid citrus rootstocks that produced the tetraploid germplasm, the optimization of this strategy requires better knowledge of the meiotic behavior of the tetraploid parents. This work used Genotyping By Sequencing (GBS) data from 103 tetraploid hybrids to study the meiotic behavior and generate a high-density recombination landscape for their tetraploid intergenic Swingle citrumelo and interspecific Volkamer lemon progenitors. A genetic association study was performed with root architecture traits. For citrumelo, high preferential chromosome pairing was revealed and led to an intermediate inheritance with a disomic tendency. Meiosis in Volkamer lemon was more complex than that of citrumelo, with mixed segregation patterns from disomy to tetrasomy. The preferential pairing resulted in low interspecific recombination levels and high interspecific heterozygosity transmission by the diploid gametes. This meiotic behavior affected the efficiency of Quantitative Trait Loci (QTL) detection. Nevertheless, it enabled a high transmission of disease and pest resistance candidate genes from P. trifoliata that are heterozygous in the citrumelo progenitor. The tetrazyg strategy, using doubled diploids of interspecific origin as parents, appears to be efficient in transferring the dominant traits selected at the parental level to the tetraploid progenies.
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Affiliation(s)
- Lény Calvez
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Alexis Dereeper
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Aude Perdereau
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, F-91000 Evry, France; (A.P.)
| | - Pierre Mournet
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
| | - Maëva Miranda
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
| | - Saturnin Bruyère
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Barbara Hufnagel
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Yann Froelicher
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-20230 San Giuliano, France
| | - Arnaud Lemainque
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, F-91000 Evry, France; (A.P.)
| | - Raphaël Morillon
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
| | - Patrick Ollitrault
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
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Mbo Nkoulou LF, Tchinda Ninla LA, Cros D, Martin G, Ndiang Z, Houegban J, Ngalle HB, Bell JM, Achigan-Dako EG. Analysis of genetic diversity and agronomic variation in banana sub-populations for genomic selection under drought stress in southern Benin. Gene 2023; 859:147210. [PMID: 36681099 DOI: 10.1016/j.gene.2023.147210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
In the perspective of investigating genomic selection (GS) among Musa genotypes in West and Central Africa, banana accessions were phenotyped under natural drought stress in Benin and genotyped using genotyping by sequencing. Sixty-one (61) accessions grouped into three major genomic groups AAA, AAB and ABB and those without genomic affiliation information were used. Variation within the population was determined by phenotypic variables while population structure and clustering analysis were carried out to understand the genetic diversity at the molecular level. Among the genomic groups evaluated, the group AAB showed the best performance for fruit weight at maturity, (3.41 ± 1.99 kg) and for plant height (198.46 ± 12.66 cm). At the accession level, HD 117 S1 and NIA 27 showed the best plant height (263.16 ± 20.98 cm) and the best fruit weight at maturity (9.43 ± 0.0 kg) respectively. Phenotypic data did not reveal clear genetic diversity among accessions; however, the genetic diversity was conspicuous at the molecular level using 5000 markers. The affiliations of local accessions in genomic groups were determined for the first time based on the phenotypic and molecular data obtained in this study. The knowledge generated allows the possibility to apply GS in banana.
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Affiliation(s)
- Luther Fort Mbo Nkoulou
- Unit of Genetics, Biotechnology, and Seed Science (GBioS), Laboratory of Phytotechnics, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin; Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Po. Box 812, Yaoundé, Cameroon; Institute of Agricultural Research for Development, Mbalmayo Agricultural Research Centre (CRAM) Mbalmayo, Cameroon.
| | | | - David Cros
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, F-34398 Montpellier, France; Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, Univ. Montpellier, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, F-34398 Montpellier, France
| | - Guillaume Martin
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, F-34398 Montpellier, France; Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, Univ. Montpellier, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, F-34398 Montpellier, France
| | - Zenabou Ndiang
- Department of Plant Biology and Physiology, Faculty of Science, University of Douala, Po. Box 24157, Douala, Cameroon
| | - Jordan Houegban
- Unit of Genetics, Biotechnology, and Seed Science (GBioS), Laboratory of Phytotechnics, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin
| | - Hermine Bille Ngalle
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Po. Box 812, Yaoundé, Cameroon
| | - Joseph Martin Bell
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Po. Box 812, Yaoundé, Cameroon
| | - Enoch G Achigan-Dako
- Unit of Genetics, Biotechnology, and Seed Science (GBioS), Laboratory of Phytotechnics, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin.
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Wang T, Wang B, Hua X, Tang H, Zhang Z, Gao R, Qi Y, Zhang Q, Wang G, Yu Z, Huang Y, Zhang Z, Mei J, Wang Y, Zhang Y, Li Y, Meng X, Wang Y, Pan H, Chen S, Li Z, Shi H, Liu X, Deng Z, Chen B, Zhang M, Gu L, Wang J, Ming R, Yao W, Zhang J. A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus. NATURE PLANTS 2023; 9:554-571. [PMID: 36997685 DOI: 10.1038/s41477-023-01378-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/21/2023] [Indexed: 06/19/2023]
Abstract
A diploid genome in the Saccharum complex facilitates our understanding of evolution in the highly polyploid Saccharum genus. Here we have generated a complete, gap-free genome assembly of Erianthus rufipilus, a diploid species within the Saccharum complex. The complete assembly revealed that centromere satellite homogenization was accompanied by the insertions of Gypsy retrotransposons, which drove centromere diversification. An overall low rate of gene transcription was observed in the palaeo-duplicated chromosome EruChr05 similar to other grasses, which might be regulated by methylation patterns mediated by homologous 24 nt small RNAs, and potentially mediating the functions of many nucleotide-binding site genes. Sequencing data for 211 accessions in the Saccharum complex indicated that Saccharum probably originated in the trans-Himalayan region from a diploid ancestor (x = 10) around 1.9-2.5 million years ago. Our study provides new insights into the origin and evolution of Saccharum and accelerates translational research in cereal genetics and genomics.
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Affiliation(s)
- Tianyou Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Baiyu Wang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Xiuting Hua
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ruiting Gao
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Yiying Qi
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University, Yancheng, China
| | - Zehuai Yu
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Yongji Huang
- Institute of Oceanography, Marine Biotechnology Center, Minjiang University, Fuzhou, China
| | - Zhe Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Mei
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhao Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yixing Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yihan Li
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Xue Meng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongjun Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haoran Pan
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuqi Chen
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Li
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihong Shi
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinlong Liu
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianping Wang
- Department of Agronomy, University of Florida, Gainesville, FL, USA
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
| | - Jisen Zhang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
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Manimekalai R, Selvi A, Narayanan J, Vannish R, Shalini R, Gayathri S, Rabisha VP. Comparative physiological and transcriptome analysis in cultivated and wild sugarcane species in response to hydrogen peroxide-induced oxidative stress. BMC Genomics 2023; 24:155. [PMID: 36973642 PMCID: PMC10045617 DOI: 10.1186/s12864-023-09218-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Sugarcane is an important energy crop grown worldwide,supplementing various renewable energy sources. Cultivated and wild sugarcane species respond differently to biotic and abiotic stresses. Generally, wild species are tolerant to various abiotic stresses. In the present study, the physiological and molecular responses of cultivated and wild sugarcane species to oxidative stress at the transcriptional levels were compared. Transcriptional responses were determined using RNAseq. The representative RNA-seq transcript values were validated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and confirmed through physiological responses. RESULTS Oxidative stress causes leaf-rolling and -tip drying in cultivated sugarcane, but the wild species are tolerant. Higher chlorophyll fluorescence was observed in the wild species than that in the cultivated varieties under stress. Wild species can maintain a higher chlorophyll stability index than the cultivated species, which was confirmed by the lower transcripts of the chlorophyllase gene in the wild species than that in the cultivated variety. Transcription factor genes (NAC, MYB, and WRKY) were markedly expressed in response to oxidative stress, revealing their involvement in stress tolerance. The analysis revealed synchronized expression of acetyl-transferase, histone2A, cellulose synthase, and secondary cell wall biosynthetic genes in the wild species. The validation of selected genes and 15 NAC transcription factors using RT-qPCR revealed that their expression profiles were strongly correlated with RNA-seq. To the best of our knowledge, this is the first report on the oxidative stress response in cultivated and wild sugarcane species. CONCLUSION Physiological and biochemical changes in response to oxidative stress markedly differ between cultivated and wild sugarcane species. The differentially expressed stress-responsive genes are grouped intothe response to oxidative stress, heme-binding, peroxidase activity, and metal ion binding categories. Chlorophyll maintenance is a stress tolerance response enhanced by the differential regulation of the chlorophyllase gene.There is a considerable difference in the chlorophyll stability index between wild and cultivated varieties. We observed a substantial regulation of secondary wall biosynthesis genes in the wild species compared with that in the cultivated variety, suggesting differences in stress tolerance mechanisms.
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Affiliation(s)
- R Manimekalai
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India.
| | - A Selvi
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
| | - Jini Narayanan
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
| | - Ram Vannish
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
| | - R Shalini
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
| | - S Gayathri
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
| | - V P Rabisha
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
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Ravikiran KT, Thribhuvan R, Sheoran S, Kumar S, Kushwaha AK, Vineeth TV, Saini M. Tailoring crops with superior product quality through genome editing: an update. PLANTA 2023; 257:86. [PMID: 36949234 DOI: 10.1007/s00425-023-04112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.
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Affiliation(s)
- K T Ravikiran
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Lucknow, Uttar Pradesh, India
| | - R Thribhuvan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India
| | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India.
| | - Sandeep Kumar
- ICAR-Indian Institute of Natural Resins and Gums, Ranchi, Jharkhand, India
| | - Amar Kant Kushwaha
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh, India
| | - T V Vineeth
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Bharuch, Gujarat, India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Banerjee N, Khan MS, Swapna M, Yadav S, Tiwari GJ, Jena SN, Patel JD, Manimekalai R, Kumar S, Dattamajuder SK, Kapur R, Koebernick JC, Singh RK. QTL mapping and identification of candidate genes linked to red rot resistance in sugarcane. 3 Biotech 2023; 13:82. [PMID: 36778768 PMCID: PMC9911584 DOI: 10.1007/s13205-023-03481-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/13/2023] [Indexed: 02/12/2023] Open
Abstract
Sugarcane (Saccharum species hybrid) is one of the most important commercial crops cultivated worldwide for products like white sugar, bagasse, ethanol, etc. Red rot is a major sugarcane disease caused by a hemi-biotrophic fungus, Colletotrichum falcatum Went., which can potentially cause a reduction in yield up to 100%. Breeding for red rot-resistant sugarcane varieties has become cumbersome due to its complex genome and frequent generation of new pathotypes of red rot fungus. In the present study, a genetic linkage map was developed using a selfed population of a popular sugarcane variety CoS 96268. A QTL linked to red rot resistance (qREDROT) was identified, which explained 26% of the total phenotypic variation for the trait. A genotype-phenotype network analysis performed to account for epistatic interactions, identified the key markers involved in red rot resistance. The differential expression of the genes located in the genomic region between the two flanking markers of the qREDROT as well as in the vicinity of the markers identified through the genotype-phenotype network analysis in a set of contrasting genotypes for red rot infection further confirmed the mapping results. Further, the expression analysis revealed that the plant defense-related gene coding 26S protease regulatory subunit is strongly associated with the red rot resistance. The findings can help in the screening of disease resistant genotypes for developing red rot-resistant varieties of sugarcane. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03481-7.
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Affiliation(s)
- Nandita Banerjee
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Mohammad Suhail Khan
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - M. Swapna
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Sonia Yadav
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Gopal Ji Tiwari
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Satya N. Jena
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Jinesh D. Patel
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - R. Manimekalai
- Biotechnology Lab, Sugarcane Breeding Institute, Coimbatore, 641007 India
| | - Sanjeev Kumar
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - S. K. Dattamajuder
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Raman Kapur
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Jenny C. Koebernick
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - Ram K. Singh
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
- Present Address: Crop Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001 India
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Song Z, Wang L, Lee M, Yue GH. The evolution and expression of stomatal regulators in C3 and C4 crops: Implications on the divergent drought tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1100838. [PMID: 36818875 PMCID: PMC9929459 DOI: 10.3389/fpls.2023.1100838] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/02/2023] [Indexed: 06/18/2023]
Abstract
Drought stress is a major environmental hazard. Stomatal development is highly responsive to abiotic stress and has been used as a cellular marker for drought-tolerant crop selection. C3 and C4 crops have evolved into different photosynthetic systems and physiological responses to water deficits. The genome sequences of maize, sorghum, and sugarcane make it possible to explore the association of the stomatal response to drought stress with the evolution of the key stomatal regulators. In this study, phylogenic analysis, gene expression analysis and stomatal assay under drought stress were used to investigate the drought tolerance of C3 and C4 plants. Our data shows that C3 and C4 plants exhibit different drought responses at the cellular level. Drought represses the growth and stomatal development of C3 crops but has little effect on that of C4 plants. In addition, stomatal development is unresponsive to drought in drought-tolerant C3 crops but is repressed in drought-tolerant C4 plants. The different developmental responses to drought in C3 and C4 plants might be associated with the divergent expression of their SPEECHLESS genes. In particular, C4 crops have evolved to generate multiple SPEECHLESS homologs with different genetic structure and expression levels. Our research provides not only molecular evidence that supports the evolutionary history of C4 from C3 plants but also a possible molecular model that controls the cellular response to abiotic stress in C3 and C4 crops.
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Affiliation(s)
- Zhuojun Song
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
| | - Le Wang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
| | - May Lee
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Xu Z, Kong R, An D, Zhang X, Li Q, Nie H, Liu Y, Su J. Evaluation of a Sugarcane ( Saccharum spp.) Hybrid F 1 Population Phenotypic Diversity and Construction of a Rapid Sucrose Yield Estimation Model for Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:647. [PMID: 36771730 PMCID: PMC9919227 DOI: 10.3390/plants12030647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/17/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Sugarcane is the major sugar-producing crop worldwide, and hybrid F1 populations are the primary populations used in breeding. Challenged by the sugarcane genome's complexity and the sucrose yield's quantitative nature, phenotypic selection is still the most commonly used approach for high-sucrose yield sugarcane breeding. In this study, a hybrid F1 population containing 135 hybrids was constructed and evaluated for 11 traits (sucrose yield (SY) and its related traits) in a randomized complete-block design during two consecutive growing seasons. The results revealed that all the traits exhibited distinct variation, with the coefficient of variation (CV) ranging from 0.09 to 0.35, the Shannon-Wiener diversity index (H') ranging between 2.64 and 2.98, and the broad-sense heritability ranging from 0.75 to 0.84. Correlation analysis revealed complex correlations between the traits, with 30 trait pairs being significantly correlated. Eight traits, including stalk number (SN), stalk diameter (SD), internode length (IL), stalk height (SH), stalk weight (SW), Brix (B), sucrose content (SC), and yield (Y), were significantly positively correlated with sucrose yield (SY). Cluster analysis based on the 11 traits divided the 135 F1 hybrids into three groups, with 55 hybrids in Group I, 69 hybrids in Group II, and 11 hybrids in Group III. The principal component analysis indicated that the values of the first four major components' vectors were greater than 1 and the cumulative contribution rate reached 80.93%. Based on the main component values of all samples, 24 F1 genotypes had greater values than the high-yielding parent 'ROC22' and were selected for the next breeding stage. A rapid sucrose yield estimation equation was established using four easily measured sucrose yield-related traits through multivariable linear stepwise regression. The model was subsequently confirmed using 26 sugarcane cultivars and 24 F1 hybrids. This study concludes that the sugarcane F1 population holds great genetic diversity in sucrose yield-related traits. The sucrose yield estimation model, ySY=2.01xSN+8.32xSD+0.79xB+3.44xSH-47.64, can aid to breed sugarcane varieties with high sucrose yield.
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Affiliation(s)
- Zhijun Xu
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
- Zhanjiang Experiment Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524031, China
- Guangdong Modern Agriculture (Cultivated Land Conservation and Water-Saving Agriculture) Industrial Technology Research and Development Center, Zhanjiang 524031, China
- Zhanjiang Experimental and Observation Station for National Long-Term Agricultural Green Development, Zhanjiang 524031, China
| | - Ran Kong
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Dongsheng An
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
- Zhanjiang Experiment Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524031, China
- Guangdong Modern Agriculture (Cultivated Land Conservation and Water-Saving Agriculture) Industrial Technology Research and Development Center, Zhanjiang 524031, China
- Zhanjiang Experimental and Observation Station for National Long-Term Agricultural Green Development, Zhanjiang 524031, China
| | - Xuejiao Zhang
- Zhanjiang Experiment Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524031, China
- Guangdong Modern Agriculture (Cultivated Land Conservation and Water-Saving Agriculture) Industrial Technology Research and Development Center, Zhanjiang 524031, China
| | - Qibiao Li
- Zhanjiang Experiment Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524031, China
- Guangdong Modern Agriculture (Cultivated Land Conservation and Water-Saving Agriculture) Industrial Technology Research and Development Center, Zhanjiang 524031, China
| | - Huzi Nie
- Agro-Tech Extension Center of Guangdong Province, Guangzhou 510520, China
| | - Yang Liu
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
- Zhanjiang Experiment Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524031, China
- College of Modern Agriculture, Jiaxing Vocational and Technical College, Jiaxing 314036, China
| | - Junbo Su
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
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Shang H, Fang L, Qin L, Jiang H, Duan Z, Zhang H, Yang Z, Cheng G, Bao Y, Xu J, Yao W, Zhang M. Genome-wide identification of the class III peroxidase gene family of sugarcane and its expression profiles under stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1101665. [PMID: 36794222 PMCID: PMC9924293 DOI: 10.3389/fpls.2023.1101665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/09/2023] [Indexed: 06/01/2023]
Abstract
INTRODUCTION Plant-specific Class III peroxidases (PRXs) play a crucial role in lignification, cell elongation, seed germination, and biotic and abiotic stresses. METHODS The class III peroxidase gene family in sugarcane were identified by bioinformatics methods and realtime fluorescence quantitative PCR. RESULTS Eighty-two PRX proteins were characterized with a conserved PRX domain as members of the class III PRX gene family in R570 STP. The ShPRX family genes were divided into six groups by the phylogenetic analysis of sugarcane, Saccharum spontaneum, sorghum, rice, and Arabidopsis thaliana. The analysis of promoter cis-acting elements revealed that most ShPRX family genes contained cis-acting regulatory elements involved in ABA, MeJA, light responsiveness, anaerobic induction, and drought inducibility. An evolutionary analysis indicated that ShPRXs was formed after Poaceae and Bromeliaceae diverged, and tandem duplication events played a critical role in the expansion of ShPRX genes of sugarcane. Purifying selection maintained the function of ShPRX proteins. SsPRX genes were differentially expressed in stems and leaves at different growth stages in S. spontaneum. However, ShPRX genes were differentially expressed in the SCMV-inoculated sugarcane plants. A qRT-PCR analysis showed that SCMV, Cd, and salt could specifically induce the expression of PRX genes of sugarcane. DISCUSSION These results help elucidate the structure, evolution, and functions of the class III PRX gene family in sugarcane and provide ideas for the phytoremediation of Cd-contaminated soil and breeding new sugarcane varieties resistant to sugarcane mosaic disease, salt, and Cd stresses.
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Affiliation(s)
- Heyang Shang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Linqi Fang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Lifang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Hongtao Jiang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Zhenzhen Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Hai Zhang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zongtao Yang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guangyuan Cheng
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yixue Bao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Jingsheng Xu
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Muqing Zhang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
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Mason PJ, Hoang NV, Botha FC, Furtado A, Marquardt A, Henry RJ. Organ-specific expression of genes associated with the UDP-glucose metabolism in sugarcane (Saccharum spp. hybrids). BMC Genomics 2023; 24:18. [PMID: 36639618 PMCID: PMC9840354 DOI: 10.1186/s12864-023-09124-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The importance of uridine 5'-diphosphate glucose (UDP-G) synthesis and degradation on carbon (C) partitioning has been indicated in several studies of plant systems, whereby the kinetic properties and abundance of involved enzymes had a significant effect upon the volume of C moving into the hemicellulose, cellulose and sucrose pools. In this study, the expression of 136 genes belonging to 32 gene families related to UDP-G metabolism was studied in 3 major sugarcane organs (including leaf, internode and root) at 6 different developmental stages in 2 commercial genotypes. RESULTS Analysis of the genes associated with UDP-G metabolism in leaves indicated low expression of sucrose synthase, but relatively high expression of invertase genes, specifically cell-wall invertase 4 and neutral acid invertase 1-1 and 3 genes. Further, organs that are primarily responsible for sucrose synthesis or bioaccumulation, i.e., in source organs (mature leaves) and storage sink organs (mature internodes), had very low expression of sucrose, cellulose and hemicellulose synthesis genes, specifically sucrose synthase 1 and 2, UDP-G dehydrogenase 5 and several cellulose synthase subunit genes. Gene expression was mostly very low in both leaf and mature internode samples; however, leaves did have a comparatively heightened invertase and sucrose phosphate synthase expression. Major differences were observed in the transcription of several genes between immature sink organs (roots and immature internodes). Gene transcription favoured utilisation of UDP-G toward insoluble and respiratory pools in roots. Whereas, there was comparatively higher expression of sucrose synthetic genes, sucrose phosphate synthase 1 and 4, and comparatively lower expression of many genes associated with C flow to insoluble and respiratory pools including myo-Inositol oxygenase, UDP-G dehydrogenase 4, vacuolar invertase 1, and several cell-wall invertases in immature internodes. CONCLUSION This study represents the first effort to quantify the expression of gene families associated with UDP-G metabolism in sugarcane. Transcriptional analysis displayed the likelihood that C partitioning in sugarcane is closely related to the transcription of genes associated with the UDP-G metabolism. The data presented may provide an accurate genetic reference for future efforts in altering UDP-G metabolism and in turn C partitioning in sugarcane.
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Affiliation(s)
- Patrick J. Mason
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation (QAAFI), Level 2, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia
| | - Nam V. Hoang
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation (QAAFI), Level 2, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia ,grid.4818.50000 0001 0791 5666Wageningen University and Research (WUR), PO Box 9101, Wageningen, 6700 HB The Netherlands
| | - Frederik C. Botha
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation (QAAFI), Level 2, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia
| | - Agnelo Furtado
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation (QAAFI), Level 2, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia
| | - Annelie Marquardt
- grid.1003.20000 0000 9320 7537Commonwealth Scientific and Industrial Research Organisation (CSIRO), Level 3, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia
| | - Robert J. Henry
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation (QAAFI), Level 2, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia
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Molina C, Aguirre NC, Vera PA, Filippi CV, Puebla AF, Poltri SNM, Paniego NB, Acevedo A. ddRADseq-mediated detection of genetic variants in sugarcane. PLANT MOLECULAR BIOLOGY 2023; 111:205-219. [PMID: 36367622 DOI: 10.1007/s11103-022-01322-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
KEY MESSAGE The article presents an optimization of the key parameters for the identification of SNPs in sugarcane using a GBS protocol based on two Illumina NextSeq and NovaSeq platforms. Sugarcane (Saccharum sp.), a world-wide known feedstock for sugar production, bioethanol, and energy, has an extremely complex genome, being highly polyploid and aneuploid. A double-digestion restriction site-associated DNA sequencing protocol (ddRADseq) was tested in four commercial sugarcane hybrids and one high-fibre biotype for the detection of single nucleotide polymorphisms (SNPs). In this work we tested two Illumina sequencing platforms, read size (70 vs. 150 bp), different sequencing coverage per individual (medium and high coverage), and single-reads versus paired-end reads. We also explored different variant calling strategies (with and without reference genome) and filtering schemes [combining two minor allele frequencies (MAFs) with three depth of coverage thresholds]. For the discovery of a large number of novel SNPs in sugarcane, we recommend longer size and paired-end reads, medium sequencing coverage per individual and Illumina platform NovaSeq6000 for a cost-effective approach, and filter parameters of lower MAF and higher depth coverages thresholds. Although the de novo analysis retrieved more SNPs, the reference-based method allows downstream characterization of variants. For the two best performing matrices, the number of SNPs per chromosome correlated positively with chromosome length, demonstrating the presence of variants throughout the genome. Multivariate comparisons, with both matrices, showed closer relationships among commercial hybrids than with the high-fibre biotype. Functional analysis of the SNPs demonstrated that more than half of them landed within regulatory regions, whereas the other half affected coding, intergenic and intronic regions. Allelic distances values were lower than 0.07 when analysing two replicated genotypes, confirming the protocol robustness.
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Affiliation(s)
- Catalina Molina
- Instituto de Suelos, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Natalia Cristina Aguirre
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
| | - Pablo Alfredo Vera
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
| | - Carla Valeria Filippi
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Andrea Fabiana Puebla
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
| | - Susana Noemí Marcucci Poltri
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
| | - Norma Beatriz Paniego
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), formerly Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Buenos Aires, Argentina
| | - Alberto Acevedo
- Instituto de Suelos, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina.
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Meng Z, Wang F, Xie Q, Li R, Shen H, Li H. Reconstruction of karyotypic evolution in Saccharum spontaneum species by comparative oligo-FISH mapping. BMC PLANT BIOLOGY 2022; 22:599. [PMID: 36539690 PMCID: PMC9764494 DOI: 10.1186/s12870-022-04008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Karyotype dynamics driven by chromosomal rearrangements has long been considered as a fundamental question in the evolutionary genetics. Saccharum spontaneum, the most primitive and complex species in the genus Saccharum, has reportedly undergone at least two major chromosomal rearrangements, however, its karyotypic evolution remains unclear. RESULTS In this study, four representative accessions, i.e., hypothetical diploid sugarcane ancestor (sorghum, x = 10), Sa. spontaneum Np-X (x = 10, tetraploid), 2012-46 (x = 9, hexaploid) and AP85-441 (x = 8, tetraploid), were selected for karyotype evolution studies. A set of oligonucleotide (oligo)-based barcode probes was developed based on the sorghum genome, which allowed universal identification of all chromosomes from sorghum and Sa. spontaneum. By comparative FISH assays, we reconstructed the karyotype evolutionary history and discovered that although chromosomal rearrangements resulted in greater variation in relative lengths of some chromosomes, all chromosomes maintained a conserved metacentric structure. Additionally, we found that the barcode oligo probe was not applicable for chromosome identification in both Sa. robustum and Sa. officinarum species, suggesting that sorghum is more distantly related to Sa. robustum and Sa. officinarum compared with Sa. spontaneum species. CONCLUSIONS Our study demonstrated that the barcode oligo-FISH is an efficient tool for chromosome identification and karyotyping research, and expanded our understanding of the karyotypic and chromosomal evolution in the genus Saccharum.
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Affiliation(s)
- Zhuang Meng
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Fei Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Rong Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Haitao Shen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
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Morais ERDC, de Medeiros NMC, da Silva FL, de Sousa IAL, de Oliveira IGB, Meneses CHSG, Scortecci KC. Redox homeostasis at SAM: a new role of HINT protein. PLANTA 2022; 257:12. [PMID: 36520227 DOI: 10.1007/s00425-022-04044-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
ScHINT1 was identified at sugarcane SAM using subtractive libraries. Here, by bioinformatic tools, two-hybrid approach, and biochemical assays, we proposed that its role might be associated to control redox homeostasis. Such control is important for plant development and flowering transition, and this is ensured with some protein partners such as PAL and SBT that interact with ScHINT1. The shoot apical meristem transition from vegetative to reproductive is a crucial step for plants. In sugarcane (Saccharum spp.), this process is not well known, and it has an important impact on production due to field reduction. In view of this, ScHINT1 (Sugarcane HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN) was identified previously by subtractive cDNA libraries using Shoot Apical Meristem (SAM) by our group. This protein is a member of the HIT superfamily that was composed of hydrolase with an AMP site ligation. To better understand the role of ScHINT1 in sugarcane flowering, here its function in SAM was characterized using different approaches such as bioinformatics, two-hybrid assays, transgenic plants, and biochemical assays. ScHINT1 was conserved in plants, and it was grouped into four clades (HINT1, HINT2, HINT3, and HINT4). The 3D model proposed that ScHINT1 might be active as it was able to ligate to AMP subtract. Moreover, the two-hybrid approach identified two protein interactions: subtilase and phenylalanine ammonia-lyase. The evolutionary tree highlighted the relationships that each sequence has with specific subfamilies and different proteins. The 3D models constructed reveal structure conservation when compared with other PDB-related crystals, which indicates probable functional activity for the sugarcane models assessed. The interactome analysis showed a connection to different proteins that have antioxidative functions in apical meristems. Lastly, the transgenic plants with 35S::ScHINT1_AS (anti-sense orientation) produced more flowers than wild-type or 35S::ScHINT1_S (sense). Alpha-tocopherol and antioxidant enzymes measurement showed that their levels were higher in 35S::ScHINT_S plants than in 35S::ScHINT1_AS or wild-type plants. These results proposed that ScHINT1 might have an important role with other proteins in orchestrating this complex network for plant development and flowering.
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Affiliation(s)
- Emanoelly Roberta de Carvalho Morais
- Departamento de Biologia Celular e Genética - Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
- Programa de Pós-Graduação em Bioquímica e Biologia Molecular, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
| | - Nathalia Maira Cabral de Medeiros
- Departamento de Biologia Celular e Genética - Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
- Programa de Pós-Graduação em Bioquímica e Biologia Molecular, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
| | - Francinaldo Leite da Silva
- Departamento de Biologia Celular e Genética - Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
| | - Isabel Andrade Lopes de Sousa
- Departamento de Biologia Celular e Genética - Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
- Programa de Pós-Graduação em Bioquímica e Biologia Molecular, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
| | - Izamara Gesiele Bezerra de Oliveira
- Departamento de Biologia - Centro de Ciências Biológicas e da Saúde/Programa de Pós-Graduação em Ciências Agrárias, Universidade Estadual da Paraíba, Rua Baraúnas, 351, Bairro Universitário, Campina Grande, PB, 58429-500, Brazil
| | - Carlos Henrique Salvino Gadelha Meneses
- Departamento de Biologia - Centro de Ciências Biológicas e da Saúde/Programa de Pós-Graduação em Ciências Agrárias, Universidade Estadual da Paraíba, Rua Baraúnas, 351, Bairro Universitário, Campina Grande, PB, 58429-500, Brazil
| | - Katia Castanho Scortecci
- Departamento de Biologia Celular e Genética - Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil.
- Programa de Pós-Graduação em Bioquímica e Biologia Molecular, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil.
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Wang D, Qin L, Wu M, Zou W, Zang S, Zhao Z, Lin P, Guo J, Wang H, Que Y. Identification and characterization of WAK gene family in Saccharum and the negative roles of ScWAK1 under the pathogen stress. Int J Biol Macromol 2022; 224:1-19. [PMID: 36481328 DOI: 10.1016/j.ijbiomac.2022.11.300] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
Wall-associated kinase (WAK) is widely involved in signal transduction, reproductive growth, responses to pathogen infection and metal ion stress in plants. In this study, 19, 12, and 37 SsWAK genes were identified in Saccharum spontaneum, Saccharum hybrid and Sorghum bicolor, respectively. Phylogenetic tree showed that they could be divided into three groups. These WAK genes contained multiple cis-acting elements related to stress, growth and hormone response. RNA-seq analysis demonstrated that SsWAK genes were constitutively expressed in different sugarcane tissues and involved in response to smut pathogen (Sporisorium scitamineum) stress. Additionally, ScWAK1 (GenBank Accession No. OP479864), was then isolated from sugarcane cultivar ROC22. It was highly expressed in leaves and roots and its expression could be induced under SA and MeJA stress. Besides, ScWAK1 was significantly downregulated in both smut-resistant and susceptible sugarcane cultivars in response to S. scitamineum infection. ScWAK1 was a membrane protein without self-activating activity. Furthermore, transient expression of ScWAK1 in Nicotiana benthamiana enhanced the susceptibility of tobacco to the inoculation of Ralstonia solanacearum and Fusarium solani var. coeruleum, suggesting its negative role in disease resistance. The present study reveals the origin, distribution and evolution of WAK gene family and provides potential gene resources for sugarcane molecular breeding.
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Affiliation(s)
- Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Liqian Qin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Mingxing Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Peixia Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Hengbo Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
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50
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Shearman JR, Pootakham W, Sonthirod C, Naktang C, Yoocha T, Sangsrakru D, Jomchai N, Tongsima S, Piriyapongsa J, Ngamphiw C, Wanasen N, Ukoskit K, Punpee P, Klomsa-ard P, Sriroth K, Zhang J, Zhang X, Ming R, Tragoonrung S, Tangphatsornruang S. A draft chromosome-scale genome assembly of a commercial sugarcane. Sci Rep 2022; 12:20474. [PMID: 36443360 PMCID: PMC9705387 DOI: 10.1038/s41598-022-24823-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Sugarcane accounts for a large portion of the worlds sugar production. Modern commercial cultivars are complex hybrids of S. officinarum, S. spontaneum, and several other Saccharum species, resulting in an auto-allopolyploid with 8-12 copies of each chromosome. The current genome assembly gold standard is to generate a long read assembly followed by chromatin conformation capture sequencing to scaffold. We used the PacBio RSII and chromatin conformation capture sequencing to sequence and assemble the genome of a South East Asian commercial sugarcane cultivar, known as Khon Kaen 3. The Khon Kaen 3 genome assembled into 104,477 contigs totalling 7 Gb, which scaffolded into 56 pseudochromosomes containing 5.2 Gb of sequence. Genome annotation produced 242,406 genes from 30,927 orthogroups. Aligning the Khon Kaen 3 genome sequence to S. officinarum and S. spontaneum revealed a high level of apparent recombination, indicating a chimeric assembly. This assembly error is explained by high nucleotide identity between S. officinarum and S. spontaneum, where 91.8% of S. spontaneum aligns to S. officinarum at 94% identity. Thus, the subgenomes of commercial sugarcane are so similar that using short reads to correct long PacBio reads produced chimeric long reads. Future attempts to sequence sugarcane must take this information into account.
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Affiliation(s)
- Jeremy R. Shearman
- grid.425537.20000 0001 2191 4408National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Wirulda Pootakham
- grid.425537.20000 0001 2191 4408National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chutima Sonthirod
- grid.425537.20000 0001 2191 4408National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chaiwat Naktang
- grid.425537.20000 0001 2191 4408National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thippawan Yoocha
- grid.425537.20000 0001 2191 4408National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- grid.425537.20000 0001 2191 4408National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Nukoon Jomchai
- grid.425537.20000 0001 2191 4408National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sissades Tongsima
- grid.425537.20000 0001 2191 4408National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Jittima Piriyapongsa
- grid.425537.20000 0001 2191 4408National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chumpol Ngamphiw
- grid.425537.20000 0001 2191 4408National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Nanchaya Wanasen
- grid.425537.20000 0001 2191 4408National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Kittipat Ukoskit
- grid.412434.40000 0004 1937 1127Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathum Thani Thailand
| | - Prapat Punpee
- grid.425537.20000 0001 2191 4408National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand ,Crop Production, Mitr Phol Innovation and Research Center, Pathum Thani, Thailand
| | - Peeraya Klomsa-ard
- Crop Production, Mitr Phol Innovation and Research Center, Pathum Thani, Thailand
| | - Klanarong Sriroth
- Crop Production, Mitr Phol Innovation and Research Center, Pathum Thani, Thailand
| | - Jisen Zhang
- grid.256111.00000 0004 1760 2876Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Xingtan Zhang
- grid.256111.00000 0004 1760 2876Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Ray Ming
- grid.256111.00000 0004 1760 2876Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Somvong Tragoonrung
- grid.425537.20000 0001 2191 4408National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- grid.425537.20000 0001 2191 4408National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
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