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Kumaravel N, Ebinezer LB, Ashwin NMR, Franchin C, Battisti I, Carletti P, Ramesh Sundar A, Masi A, Malathi P, Viswanathan R, Arrigoni G. Comparative proteomics of sugarcane smut fungus - Sporisorium scitamineum unravels dynamic proteomic alterations during the dimorphic transition. J Proteomics 2024; 304:105230. [PMID: 38901800 DOI: 10.1016/j.jprot.2024.105230] [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: 12/11/2023] [Revised: 06/07/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
Life cycle of the dimorphic sugarcane smut fungi, Sporisorium scitamineum, involves recognition and mating of compatible saprophytic yeast-like haploid sporidia (MAT-1 and MAT-2) that upon fusion, develop into infective dikaryotic mycelia. Although the dimorphic transition is intrinsically linked with the pathogenicity and virulence of S. scitamineum, it has never been studied using a proteomic approach. In the present study, an iTRAQ-based comparative proteomic analysis of three distinct stages was carried out. The stages were: the dimorphic transition period - haploid sporidial stage (MAT-1 and MAT-2); the transition phase (24 h post co-culturing (hpc)) and the dikaryotic mycelial stage (48 hpc). Functional categorization of differentially abundant proteins showed that the most altered biological processes were energy production, primary metabolism, especially, carbohydrate, amino acid, fatty acid, followed by translation, post-translation and protein turnover. Several differentially abundant proteins (DAPs), especially in the dikaryotic mycelial stage were predicted as effectors. Taken together, key molecular mechanisms underpinning the dimorphic transition in S. scitamineum at the proteome level were highlighted. The catalogue of stage-specific and dimorphic transition-associated-proteins and potential effectors identified herein represents a list of potential candidates for defective mutant screening to elucidate their functional role in the dimorphic transition and pathogenicity in S. scitamineum. BIOLOGICAL SIGNIFICANCE: Being the first comparative proteomics analysis of S. scitamineum, this study comprehensively examined three pivotal life cycle stages of the pathogen: the non-pathogenic haploid phase, the transition phase, and the pathogenic dikaryotic mycelial stage. While previous studies have reported the sugarcane and S. scitamineum interactions, this study endeavored to specifically identify the proteins responsible for pathogenicity. By analyzing the proteomic alterations between the haploid and dikaryotic mycelial phases, the study revealed significant changes in metabolic pathway-associated proteins linked to energy production, notably oxidative phosphorylation, and the citrate cycle. Furthermore, this study successfully identified key metabolic pathways that undergo reprogramming during the transition from the non-pathogenic to the pathogenic stage. The study also deciphered the underlying mechanisms driving the morphological and physiological alterations crucial for the S. scitamineum virulence. By studying its life cycle stages, identifying the key metabolic pathways and stage-specific proteins, it provides unprecedented insights into the pathogenicity and potential avenues for intervention. As proteomics continues to advance, such studies pave the way for a deeper understanding of plant-pathogen interactions and the development of innovative strategies to mitigate the impact of devastating pathogens like S. scitamineum.
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Affiliation(s)
- Nalayeni Kumaravel
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Leonard Barnabas Ebinezer
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - N M R Ashwin
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; Biochemical Sciences Division, Council of Scientific and Industrial Research - National Chemical Laboratory, Pune 411008, Maharashtra, India.
| | - Cinzia Franchin
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy.
| | - Ilaria Battisti
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Amalraj Ramesh Sundar
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Palaniyandi Malathi
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Rasappa Viswanathan
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; Indian Council of Agricultural Research - Indian Institute of Sugarcane Research, Lucknow, Uttar Pradesh 226002, India.
| | - Giorgio Arrigoni
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy.
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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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Wu Q, Li Z, Yang J, Xu F, Fu X, Xu L, You C, Wang D, Su Y, Que Y. Deciphering the Atlas of Post-Translational Modification in Sugarcane. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37339007 DOI: 10.1021/acs.jafc.3c01886] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
In plants, lysine acetylation (Kac), 2-hydroxyisobutyrylation (Khib), and lysine lactylation (Kla), the three new types of post-translational modification (PTM), play very important roles in growth, development, and resistance to adverse environmental stresses. Herein, we report the first global acetylome, 2-hydroxyisobutyrylome, and lactylome in sugarcane. A total of 8573 Kac, 4637 Khib, and 215 Kla sites across 3903, 1507, and 139 modified proteins were identified. Besides, homology analyses revealed the Kac, Khib, and Kla sites on histones were conserved between sugarcane and rice or poplar. Functional annotations demonstrated that the Kac, Khib, and Kla proteins were mainly involved in energy metabolism. In addition, a number of modified transcription factors and stress-related proteins, which were constitutively expressed in different tissues of sugarcane and induced by drought, cold or Sporisorium scitamineum stress, were identified. Finally, a proposed working mode on how PTM functions in sugarcane was depicted. We thus concluded that PTM should play a role in sugarcane growth, development, and response to biotic and abiotic stresses, but the mechanisms require further investigation. The present study provided the all-new comprehensive profile of proteins Kac, Khib, and Kla and a new perspective to understand the molecular mechanisms of protein PTMs in sugarcane.
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Affiliation(s)
- Qibin Wu
- 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
| | - Jingtao Yang
- 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
| | - Fu Xu
- 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
| | - Xueqin Fu
- 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
| | - Liping Xu
- 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
| | - Chuihuai You
- College of Life Sciences, 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
- National Key Laboratory for Tropical Crop Breeding, Kaiyuan, Yunnan 661699, China
| | - Youxiong Que
- 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
- National Key Laboratory for Tropical Crop Breeding, Kaiyuan, Yunnan 661699, China
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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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Integrated Transcriptome and Metabolome Analysis to Identify Sugarcane Gene Defense against Fall Armyworm ( Spodoptera frugiperda) Herbivory. Int J Mol Sci 2022; 23:ijms232213712. [PMID: 36430189 PMCID: PMC9694286 DOI: 10.3390/ijms232213712] [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: 10/14/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2022] Open
Abstract
Sugarcane is the most important sugar crop, contributing ≥80% to total sugar production around the world. Spodoptera frugiperda is one of the main pests of sugarcane, potentially causing severe yield and sugar loss. The identification of key defense factors against S. frugiperda herbivory can provide targets for improving sugarcane resistance to insect pests by molecular breeding. In this work, we used one of the main sugarcane pests, S. frugiperda, as the tested insect to attack sugarcane. Integrated transcriptome and metabolomic analyses were performed to explore the changes in gene expression and metabolic processes that occurred in sugarcane leaf after continuous herbivory by S. frugiperda larvae for 72 h. The transcriptome analysis demonstrated that sugarcane pest herbivory enhanced several herbivory-induced responses, including carbohydrate metabolism, secondary metabolites and amino acid metabolism, plant hormone signaling transduction, pathogen responses, and transcription factors. Further metabolome analysis verified the inducement of specific metabolites of amino acids and secondary metabolites by insect herbivory. Finally, association analysis of the transcriptome and metabolome by the Pearson correlation coefficient method brought into focus the target defense genes against insect herbivory in sugarcane. These genes include amidase and lipoxygenase in amino acid metabolism, peroxidase in phenylpropanoid biosynthesis, and pathogenesis-related protein 1 in plant hormone signal transduction. A putative regulatory model was proposed to illustrate the sugarcane defense mechanism against insect attack. This work will accelerate the dissection of the mechanism underlying insect herbivory in sugarcane and provide targets for improving sugarcane variety resistance to insect herbivory by molecular breeding.
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Wu Q, Su Y, Pan YB, Xu F, Zou W, Que B, Lin P, Sun T, Grisham MP, Xu L, Que Y. Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq. FRONTIERS IN PLANT SCIENCE 2022; 13:1035266. [PMID: 36311133 PMCID: PMC9608552 DOI: 10.3389/fpls.2022.1035266] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/27/2022] [Indexed: 06/01/2023]
Abstract
Sugarcane smut caused by Sporisorium scitamineum is one of the most severe fungal diseases worldwide. In this study, a cross was made between a smut-resistant variety YT93-159 and a smut-susceptible variety ROC22, and 312 progenies were obtained. Two bulks of progenies were then constructed, one consisted of 27 highly smut resistant progenies and the other 24 smut susceptible progenies. Total RNAs of the progenies of each bulk, were pooled and subject to bulked segregant RNA-sequence analysis (BSR-Seq). A total of 164.44 Gb clean data containing 2,341,449 SNPs and 64,999 genes were obtained, 7,295 of which were differentially expressed genes (DEGs). These DEGs were mainly enriched in stress-related metabolic pathways, including carbon metabolism, phenylalanine metabolism, plant hormone signal transduction, glutathione metabolism, and plant-pathogen interactions. Besides, 45,946 high-quality, credible SNPs, a 1.27 Mb region at Saccharum spontaneum chromosome Chr5B (68,904,827 to 70,172,982), and 129 candidate genes were identified to be associated with smut resistance. Among them, twenty-four genes, either encoding key enzymes involved in signaling pathways or being transcription factors, were found to be very closely associated with stress resistance. RT-qPCR analysis demonstrated that they played a positive role in smut resistance. Finally, a potential molecular mechanism of sugarcane and S. scitamineum interaction is depicted that activations of MAPK cascade signaling, ROS signaling, Ca2+ signaling, and PAL metabolic pathway and initiation of the glyoxalase system jointly promote the resistance to S. scitamineum in sugarcane. This study provides potential SNP markers and candidate gene resources for smut resistance breeding in sugarcane.
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Affiliation(s)
- Qibin Wu
- 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, 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, China
| | - Yong-Bao Pan
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA, United States
| | - Fu Xu
- 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, China
| | - Wenhui Zou
- 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, China
| | - Beibei Que
- 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, China
- International College, Fujian Agriculture and Forestry University, Fuzhou, 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, China
| | - Tingting Sun
- 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, China
| | - Michael P. Grisham
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA, United States
| | - Liping Xu
- 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, China
| | - Youxiong Que
- 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, China
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WGCNA Identifies a Comprehensive and Dynamic Gene Co-Expression Network That Associates with Smut Resistance in Sugarcane. Int J Mol Sci 2022; 23:ijms231810770. [PMID: 36142681 PMCID: PMC9506403 DOI: 10.3390/ijms231810770] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (susceptible) upon S. scitamineum infection. Data analysis revealed 20,273 (12,659 up-regulated and 7614 down-regulated) and 11,897 (7806 up-regulated and 4091 down-regulated) differentially expressed genes (DEGs) in YT93-159 and ROC22, respectively. A co-expression network was then constructed by weighted gene co-expression network analysis (WGCNA), which identified 5010 DEGs in 15 co-expressed gene modules. Four of the 15 modules, namely, Skyblue, Salmon, Darkorange, and Grey60, were significantly associated with smut resistance. The GO and KEGG enrichment analyses indicated that the DEGs involving in these four modules could be enriched in stress-related metabolic pathways, such as MAPK and hormone signal transduction, plant-pathogen interaction, amino acid metabolism, glutathione metabolism, and flavonoid, and phenylpropanoid biosynthesis. In total, 38 hub genes, including six from the Skyblue module, four from the Salmon module, 12 from the Darkorange module, and 16 from the Grey60 module, were screened as candidate hub genes by calculating gene connectivity in the corresponding network. Only 30 hub genes were amplifiable with RT-qPCR, of which 27 were up-regulated upon S. scitamineum infection. The results were consistent with the trend of gene expression in RNA-Seq, suggesting their positive roles in smut resistance. Interestingly, the expression levels of AOX, Cyb5, and LAC were higher in ROC22 than in YT93-159, indicating these three genes may act as negative regulators in response to S. scitamineum infection. This study revealed the transcriptome dynamics in sugarcane challenged by S. scitamineum infection and provided gene targets for smut resistance breeding in sugarcane.
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Infection by Pseudocercospora musae leads to an early reprogramming of the Musa paradisiaca defense transcriptome. 3 Biotech 2022; 12:177. [PMID: 35855477 PMCID: PMC9288577 DOI: 10.1007/s13205-022-03245-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 06/27/2022] [Indexed: 11/26/2022] Open
Abstract
Deep sequencing technologies such as RNA sequencing can help unravel mechanisms governing defense or resistance responses in plant-pathogen interactions. Several studies have been carried out to investigate the transcriptomic changes in Musa germplasm against Yellow Sigatoka disease, but the defense response of Musa paradisiaca has not been investigated so far. We carried out transcriptome sequencing of M. paradisiaca var. Kachkal infected with the pathogen Pseudocercospora musae and found that a vast set of genes were upregulated while many genes were downregulated in the resistant cultivar as a result of infection. After transcriptome assembly and differential gene expression analysis, 429 upregulated and 156 downregulated genes were filtered out (considering fold change ± 2, p < 0.01). Functional annotation of the differentially expressed genes (DEGs) enriched the upregulated genes into 49 gene ontology (GO) classes of biological processes (BP), 20 classes of molecular function (MF) and 9 classes of cellular component (CC). Similarly, the downregulated genes were classified into 35 GO classes of BP, 28 classes of MF and 6 classes of CC. The KEGG enrichment analysis revealed that the upregulated genes were most highly represented in 'metabolic' and 'biosynthesis of secondary metabolites' pathways. Additionally, 'plant hormone signal transduction', 'plant-pathogen interaction' and 'phenylpropanoid biosynthesis' pathways were also significantly enriched indicating their involvement in resistance responses against the pathogen. The RNA-seq analysis also depicts that a range of important defense-related genes are modulated as a result of infection, all of which are responsible for either mediating or activating resistance responses in the host. We studied and validated the expression profiles of ten important defense-related genes potentially involved in conferring resistance to the pathogen through qRT-PCR. Almost all the selected defense-related genes were found to be highly and significantly upregulated within 24 h post inoculation (hpi) and for some genes, the expression remained consistently high till the later time point of 72 hpi. These results, thus, indicate that the infection by P. musae leads to a rapid reprogramming of the defense transcriptome of the resistant banana cultivar. The defense-related genes identified to be modulated in response to infection are important not only for pathogen recognition and perception but also for activation and persistence of defense in the host. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03245-9.
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Li AM, He WZ, Wei JL, Chen ZL, Liao F, Qin CX, Pan YQ, Shang XK, Lakshmanan P, Wang M, Tan HW, Huang DL. Transcriptome Profiling Reveals Genes Related to Sex Determination and Differentiation in Sugarcane Borer (Chilo sacchariphagus Bojer). INSECTS 2022; 13:insects13060500. [PMID: 35735837 PMCID: PMC9225334 DOI: 10.3390/insects13060500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 01/27/2023]
Abstract
Simple Summary Chilo sacchariphagus Bojer is an important sugarcane pest globally. The identification of key genes associated with sex determination and differentiation will provide important basic information for the sterile insect technique control strategy. In this study, the comparative transcriptomic analysis of female and male adults revealed sex-biased gene expression, indicating putative genetic elements of sex determination and differentiation in this species. Abstract Chilo sacchariphagus Bojer is an important sugarcane pest globally. Along with genetic modification strategies, the sterile insect technique (SIT) has gained more attention as an environment-friendly method for pest control. The identification of key genes associated with sex determination and differentiation will provide important basic information for this control strategy. As such, the transcriptome sequencing of female and male adults was conducted in order to understand the sex-biased gene expression and molecular basis of sex determination and differentiation in this species. A total of 60,429 unigenes were obtained; among them, 34,847 genes were annotated. Furthermore, 11,121 deferentially expressed genes (DEGs) were identified, of which 8986 were male-biased and 2135 were female-biased genes. The male-biased genes were enriched for carbon metabolism, peptidase activity and transmembrane transport, while the female-biased genes were enriched for the cell cycle, DNA replication, and the MAPK signaling pathway. In addition, 102 genes related to sex-determination and differentiation were identified, including the protein toll, ejaculatory bulb-specific protein, fruitless, transformer-2, sex-lethal, beta-Catenin, sox, gata4, beta-tubulin, cytosol aminopeptidase, seminal fluid, and wnt4. Furthermore, transcription factors such as myb, bhlh and homeobox were also found to be potentially related to sex determination and differentiation in this species. Our data provide new insights into the genetic elements associated with sex determination and differentiation in Chilo sacchariphagus, and identified potential candidate genes to develop pest-control strategies.
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Affiliation(s)
- Ao-Mei Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Wei-Zhong He
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Ji-Li Wei
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- 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, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- 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, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- 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, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - You-Qiang Pan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xian-Kun Shang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Prakash Lakshmanan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400716, China
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD 4067, Australia
| | - Miao Wang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Hong-Wei Tan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
- Correspondence: (H.-W.T.); (D.-L.H.)
| | - Dong-Liang Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Nanning 530007, China; (A.-M.L.); (W.-Z.H.); (J.-L.W.); (Z.-L.C.); (F.L.); (C.-X.Q.); (Y.-Q.P.); (X.-K.S.); (P.L.); (M.W.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
- Correspondence: (H.-W.T.); (D.-L.H.)
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10
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Bhuiyan SA, Magarey RC, McNeil MD, Aitken KS. Sugarcane Smut, Caused by Sporisorium scitamineum, a Major Disease of Sugarcane: A Contemporary Review. PHYTOPATHOLOGY 2021; 111:1905-1917. [PMID: 34241540 DOI: 10.1094/phyto-05-21-0221-rvw] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sugarcane smut caused by the fungus Sporisorium scitamineum is one of the major diseases of sugarcane worldwide, causing significant losses in productivity and profitability of this perennial crop. Teliospores of this fungus are airborne, can travel long distances, and remain viable in hot and dry conditions for >6 months. The disease is easily recognized by its long whiplike sorus produced on the apex or side shoots of sugarcane stalks. Each sorus can release ≤100 million teliospores in a day; the spores are small (≤7.5 µ) and light and can survive in harsh environmental conditions. The airborne teliospores are the primary mode of smut spread around the world and across cane-growing regions. The most effective method of managing this disease is via resistant varieties. Because of the complex genomic makeup of sugarcane, selection for resistant traits is difficult in sugarcane breeding programs. In recent times, the application of molecular markers as a rapid tool of discarding susceptible genotypes early in the selection program has been investigated. Large effect resistance loci have been identified and have the potential to be used for marker-assisted selection to increase the frequency of resistant breeding lines in breeding programs. Recent developments in omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have contributed to our understanding and provided insights into the mechanism of resistance and susceptibility. This knowledge will further our understanding of smut and its interactions with sugarcane genotypes and aid in the development of durable resistant varieties.
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Affiliation(s)
- Shamsul A Bhuiyan
- Sugar Research Australia, Woodford, QLD 4514, Australia, and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | | | - Meredith D McNeil
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia
| | - Karen S Aitken
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia
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11
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Comparative expression analysis of potential pathogenicity-associated genes of high- and low-virulent Sporisorium scitamineum isolates during interaction with sugarcane. 3 Biotech 2021; 11:353. [PMID: 34249594 DOI: 10.1007/s13205-021-02893-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/10/2021] [Indexed: 02/05/2023] Open
Abstract
Sporisorium scitamineum is a teleomorphic, biotrophic fungus causing the globally prevalent sugarcane smut disease in sugarcane. The severity of the disease depends on two major factors, viz. degree of resistance in the host genotype and virulence level of the pathogen. Hence, in this study, temporal transcriptomic expression of potential pathogenicity-associated genes of two distinctly virulent S. scitamineum isolates, viz. SsV89101 (low virulent) and Ss97009 (high virulent) were analyzed during interaction with a smut susceptible sugarcane cv. Co 97009 at six different time intervals. The pathogenicity-associated genes profiled in this study comprises 14 plant cell wall degrading enzymes (PCWDEs) and ten candidates secreted effector protein-coding (CSEPs) genes. Absolute quantification of pathogen biomass and comparative expression profiling analyses of these pathogenicity-associated genes during host-pathogen interaction indicated that there was a significant variation between low and high virulent isolates. More precisely, the higher and early expression (24 hpi) of certain PCWDEs, viz. Chitinase-1 and Laccase, and the CSEPs, viz. SUC2, SRT1 and CMU1 during the colonization of high virulent isolate suggested that they might possibly play a major role in facilitating faster and successful pathogen ingress, and tissue colonization than the less-virulent isolate. Transcript expression profiling of Chitinase and Laccases were also in correlation with their corresponding enzyme activity assays. Comprehensively, this quantitative temporal expression analysis has provided critical insights into the early expression of pathogenicity-associated genes and their putative role in attributing to higher virulence. Moreover, this study provides valuable clues for the screening of candidate virulence determinants for further functional characterization of the test pathogen isolates used for the evaluation of smut resistance in breeding clones. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02893-7.
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12
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Transcriptional reprogramming of major defense-signaling pathways during defense priming and sugarcane-Colletotrichum falcatum interaction. Mol Biol Rep 2020; 47:8911-8923. [PMID: 33161528 DOI: 10.1007/s11033-020-05944-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/22/2020] [Indexed: 02/08/2023]
Abstract
Red rot caused by Colletotrichum falcatum poses a serious threat to sugarcane cultivation in many tropical and sub-tropical countries. Deciphering the molecular network of major defense-signaling pathways in sugarcane cultivars with varying red rot resistance is essential to elucidate the phenomenon of defense priming exerted by resistance inducers. Therefore, in this study, expression pattern of transcripts coding for major defense-signaling pathway regulatory genes was profiled during compatible and incompatible interactions and in response to defense priming using qRT-PCR. Candidate genes that were profiled are involved in or related to hypersensitive response and reactive oxygen species production (HR/ROS), salicylic acid (SA), and jasmonic acid/ethylene (JA/ET) pathways. For compatible and incompatible interactions, susceptible (CoC 671), field tolerant (Co 86032) and resistant (Co 93009) sugarcane cultivars were used, whereas for defense priming, benzothiadiazole (BTH) and the pathogen-associated molecular patterns (PAMPs) of C. falcatum viz., CfEPL1 (eliciting plant response-like) and CfPDIP1 (plant defense inducing protein) were used in CoC 671 cultivar. Results indicated that the master regulator of defense pathways, nonexpressor of pathogenesis-related genes 1 (NPR1) was highly upregulated in incompatible interactions (in both Co 86032 and Co 93009) than the compatible interaction along with SA pathway-associated genes. Similarly, in response to defense priming with BTH, CfEPL1 and CfPDIP1, only the SA pathway-associated genes showed considerable upregulation at 0 h post inoculation (hpi) and other intermittent time points. Overall, this study showed that SA-mediated defense pathway is the most predominant pathway reprogrammed during priming with BTH, CfEPL1 and CfPDIP1 and substantiated the earlier findings that these agents indeed induce systemic resistance against red rot of sugarcane.
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13
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Transcriptome analysis of the effect of GA 3 in sugarcane culm. 3 Biotech 2019; 9:376. [PMID: 31588400 DOI: 10.1007/s13205-019-1908-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/19/2019] [Indexed: 01/06/2023] Open
Abstract
Our earlier studies have indicated that GA3, being a growth hormone, increases internodal length, in turn increasing sink strength and improving sucrose accumulation in sugarcane. In this study, transcriptomic level analysis was carried out on internodal samples of a high sugar accumulating variety (CoLk 94184) of sugarcane, to determine the effect of exogenous application of GA3 vis a vis functional analysis of differentially expressing transcripts. Overall, a total of 201,184 transcripts were identified, with median contig length of 450 bp and N50 length of 1029 bp. Analyzing the data from control and GA3-treated canes, at 0.01 significance, a total of 1516 differentially expressing transcripts were identified in bottom internodes and 1589 in top internodes. A KEGG (enrichment) analysis grouped the transcripts into 153 plant-related functional categories. From among these, the transcripts which were functionally relevant to sugar metabolism and photosynthesis were sieved out. Starch and sucrose metabolizing genes showed maximum fold change of 5.0 and 3.0 among top and bottom internodal samples. A homology match using Blastx analysis tool yielded 65 transcripts/differentially expressed genes (DEGs) which were found to share homology with C4 plants like Saccharum, Sorghum and Zea mays. Differentially expressing transcripts from both top and bottom internodes were validated by qRT-PCR, indicating their importance in such study. Results also enriched sugarcane transcriptome resources useful for omics study in genus Saccharum and family Poaceae.
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Su Y, Xiao X, Ling H, Huang N, Liu F, Su W, Zhang Y, Xu L, Muhammad K, Que Y. A dynamic degradome landscape on miRNAs and their predicted targets in sugarcane caused by Sporisorium scitamineum stress. BMC Genomics 2019; 20:57. [PMID: 30658590 PMCID: PMC6339412 DOI: 10.1186/s12864-018-5400-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sugarcane smut is a fungal disease caused by Sporisorium scitamineum. Cultivation of smut-resistant sugarcane varieties is the most effective way to control this disease. The interaction between sugarcane and S. scitamineum is a complex network system. However, to date, there is no report on the identification of microRNA (miRNA) target genes of sugarcane in response to smut pathogen infection by degradome technology. RESULTS TaqMan qRT-PCR detection and enzyme activity determination showed that S. scitamineum rapidly proliferated and incurred significant enzyme activity changes in the reactive oxygen species metabolic pathway and phenylpropanoid metabolic pathway at 2 d and 5 d after inoculation, which was the best time points to study target gene degradation during sugarcane and S. scitamineum interaction. A total of 122.33 Mb of raw data was obtained from degradome sequencing analysis of YC05-179 (smut-resistant) and ROC22 (smut-susceptible) after inoculation. The Q30 of each sample was > 93%, and the sequence used for degradation site analysis exactly matched the sugarcane reference sequence. A total of 309 target genes were predicted in sugarcane, corresponding to 97 known miRNAs and 112 novel miRNAs, and 337 degradation sites, suggesting that miRNAs can efficiently direct cleavage at multiple sites in the predicted target mRNAs. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the predicted target genes were involved in various regulatory processes, such as signal transduction mechanisms, inorganic ion transport and metabolism, defense mechanisms, translation, posttranslational modifications, energy production and conversion, and glycerolipid metabolism. qRT-PCR analysis of the expression level of 13 predicted target genes and their corresponding miRNAs revealed that there was no obvious negative regulatory relationship between miRNAs and their target genes. In addition, a number of putative resistance-related target genes regulated by miRNA-mediated cleavage were accumulated in sugarcane during S. scitamineum infection, suggesting that feedback regulation of miRNAs may be involved in the response of sugarcane to S. scitamineum infection. CONCLUSIONS This study elucidates the underlying response of sugarcane to S. scitamineum infection, and also provides a resource for miRNAs and their predicted target genes for smut resistance improvement in sugarcane.
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Affiliation(s)
- Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xinhuan Xiao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Feng Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuye Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Khushi Muhammad
- Department of Genetics, Hazara University, Mansehra, 21300 Pakistan
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Wu Q, Gao S, Pan YB, Su Y, Grisham MP, Guo J, Xu L, Que Y. Heterologous expression of a Glyoxalase I gene from sugarcane confers tolerance to several environmental stresses in bacteria. PeerJ 2018; 6:e5873. [PMID: 30402355 PMCID: PMC6215438 DOI: 10.7717/peerj.5873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/01/2018] [Indexed: 01/02/2023] Open
Abstract
Glyoxalase I belongs to the glyoxalase system that detoxifies methylglyoxal (MG), a cytotoxic by-product produced mainly from triose phosphates. The concentration of MG increases rapidly under stress conditions. In this study, a novel glyoxalase I gene, designated as SoGloI was identified from sugarcane. SoGloI had a size of 1,091 bp with one open reading frame (ORF) of 885 bp encoding a protein of 294 amino acids. SoGloI was predicted as a Ni2+-dependent GLOI protein with two typical glyoxalase domains at positions 28-149 and 159-283, respectively. SoGloI was cloned into an expression plasmid vector, and the Trx-His-S-tag SoGloI protein produced in Escherichia coli was about 51 kDa. The recombinant E. coli cells expressing SoGloI compared to the control grew faster and tolerated higher concentrations of NaCl, CuCl2, CdCl2, or ZnSO4. SoGloI ubiquitously expressed in various sugarcane tissues. The expression was up-regulated under the treatments of NaCl, CuCl2, CdCl2, ZnSO4 and abscisic acid (ABA), or under simulated biotic stress conditions upon exposure to salicylic acid (SA) and methyl jasmonate (MeJA). SoGloI activity steadily increased when sugarcane was subjected to NaCl, CuCl2, CdCl2, or ZnSO4 treatments. Sub-cellular observations indicated that the SoGloI protein was located in both cytosol and nucleus. These results suggest that the SoGloI gene may play an important role in sugarcane's response to various biotic and abiotic stresses.
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Affiliation(s)
- Qibin Wu
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Shiwu Gao
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Yong-Bao Pan
- USDA-ARS, Sugarcane Research Unit, Houma, LA, USA
| | - Yachun Su
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | | | - Jinlong Guo
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Liping Xu
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Youxiong Que
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
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16
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Sánchez-Elordi E, Contreras R, de Armas R, Benito MC, Alarcón B, de Oliveira E, Del Mazo C, Díaz-Peña EM, Santiago R, Vicente C, Legaz ME. Differential expression of SofDIR16 and SofCAD genes in smut resistant and susceptible sugarcane cultivars in response to Sporisorium scitamineum. JOURNAL OF PLANT PHYSIOLOGY 2018; 226:103-113. [PMID: 29753910 DOI: 10.1016/j.jplph.2018.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 05/25/2023]
Abstract
Proteomic profiling of the stalk of a smut resistant and a susceptible sugarcane cultivars revealed the presence of dirigent and dirigent-like proteins in abundance in the pool of high molecular mass (HMMG) and mid-molecular mass (MMMG) glycoproteins, produced as part of the defensive response to the fungal smut pathogen. Quantitative RT-PCR analysis showed that expression levels of SofDIR16 (sugarcane dirigent16) and SofCAD (sugarcane cinnamyl alcohol dehydrogenase) were higher in the smut resistant My 55-14 cultivar than in the sensitive B 42231 cultivar prior to infection. Inoculation with fungal sporidia or water decreased the level of SofCAD transcripts in My 55-14, indicating that regulation of SofCAD expression does not take part of the specific response to smut infection. In contrast, SofDIR16 expression was almost nullified in My 55-14 after inoculation with fungal sporidia, but not after water injection. It is proposed that the decreased expression of dirigent proteins induces the formation of lignans, which are involved in the defense response of the smut resistant My 55-14 cultivar.
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Affiliation(s)
- Elena Sánchez-Elordi
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Roberto Contreras
- Department of Genetics, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | | | - Mario C Benito
- Department of Genetics, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Borja Alarcón
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Eliandre de Oliveira
- Plataforma de Proteómica, Parc Cientific de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Carlos Del Mazo
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Eva M Díaz-Peña
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Rocío Santiago
- Department of Biochemistry and Department of Geographical Sciences, Universidade Federal de Pernambuco, Recife, Brazil
| | - Carlos Vicente
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - María E Legaz
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain.
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17
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Huang N, Ling H, Liu F, Su Y, Su W, Mao H, Zhang X, Wang L, Chen R, Que Y. Identification and evaluation of PCR reference genes for host and pathogen in sugarcane-Sporisorium scitamineum interaction system. BMC Genomics 2018; 19:479. [PMID: 29914370 PMCID: PMC6006842 DOI: 10.1186/s12864-018-4854-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 06/06/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sugarcane (Saccharum L. plant) is an important crop for sugar and bio-energy production around the world. Among sugarcane diseases, smut caused by Sporisorium scitamineum is one of the major fungal diseases causing severe losses to the sugarcane industry. The use of PCR reference genes is essential to the normalization of data on gene expression involving the sugarcane-S. scitamineum interaction system; however, no report that addresses criteria in selecting these reference genes has been published to date. RESULTS In this study, 10 sugarcane genes and eight S. scitamineum genes were selected as candidate PCR reference genes in the sugarcane-S. scitamineum interaction system. The stability and reliability of these 18 candidate genes were analyzed in smut-resistant (NCo376) and -susceptible (YC71-374) genotypes using the statistical algorithms geNorm, NormFinder, BestKeeper, and deltaCt method. Subsequently, the relative expression levels of the sugarcane chitinase I-3 gene and S. scitamineum chorismate mutase gene were determined to validate the applicability of these sugarcane and S. scitamineum PCR reference genes, respectively. We finally found that the acyl-CoA dehydrogenase gene (ACAD), serine/arginine repetitive matrix protein 1 gene (SARMp1), or their combination (ACAD + SARMp1) could be utilized as the most suitable reference genes for normalization of sugarcane gene expression in sugarcane bud tissues after S. scitamineum infection. Similarly, the inosine 5'-monophosphate dehydrogenase gene (S10), the SEC65-signal recognition particle subunit gene (S11), or their combination (S10 + S11) were suitable for normalization of S. scitamineum gene expression in sugarcane bud tissues. CONCLUSIONS The PCR reference genes ACAD, SARMp1, S10, and S11 may be employed in gene transcriptional studies involving the sugarcane-S. scitamineum interaction system.
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Affiliation(s)
- Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Feng Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Huaying Mao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xu Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ling Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Rukai Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Guangxi Collaborative Innovation Center of Sugarcane Industry, Guangxi University, Nanning, 530005 China
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Analysis of the resistance mechanisms in sugarcane during Sporisorium scitamineum infection using RNA-seq and microscopy. PLoS One 2018; 13:e0197840. [PMID: 29795614 PMCID: PMC5993111 DOI: 10.1371/journal.pone.0197840] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/09/2018] [Indexed: 02/03/2023] Open
Abstract
Smut caused by biotrophic fungus Sporisorium scitamineum is a major disease of cultivated sugarcane that can cause considerable yield losses. It has been suggested in literature that there are at least two types of resistance mechanisms in sugarcane plants: an external resistance, due to chemical or physical barriers in the sugarcane bud, and an internal resistance governed by the interaction of plant and fungus within the plant tissue. Detailed molecular studies interrogating these two different resistance mechanisms in sugarcane are scarce. Here, we use light microscopy and global expression profiling with RNA-seq to investigate these mechanisms in sugarcane cultivar CP74-2005, a cultivar that possibly possesses both internal and external defence mechanisms. A total of 861 differentially expressed genes (DEGs) were identified in a comparison between infected and non-infected buds at 48 hours post-inoculation (hpi), with 457 (53%) genes successfully annotated using BLAST2GO software. This includes genes involved in the phenylpropanoid pathway, cell wall biosynthesis, plant hormone signal transduction and disease resistance genes. Finally, the expression of 13 DEGs with putative roles in S. scitamineum resistance were confirmed by quantitative real-time reverse transcription PCR (qRT-PCR) analysis, and the results were consistent with the RNA-seq data. These results highlight that the early sugarcane response to S. scitamineum infection is complex and many of the disease response genes are attenuated in sugarcane cultivar CP74-2005, while others, like genes involved in the phenylpropanoid pathway, are induced. This may point to the role of the different disease resistance mechanisms that operate in cultivars such as CP74-2005, whereby the early response is dominated by external mechanisms and then as the infection progresses, the internal mechanisms are switched on. Identification of genes underlying resistance in sugarcane will increase our knowledge of the sugarcane-S. scitamineum interaction and facilitate the introgression of new resistance genes into commercial sugarcane cultivars.
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Unraveling the Genetic Complexities in Gene Set of Sugarcane Red Rot Pathogen Colletotrichum falcatum Through Transcriptomic Approach. SUGAR TECH 2017. [DOI: 10.1007/s12355-017-0529-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Su Y, Zhang Y, Huang N, Liu F, Su W, Xu L, Ahmad W, Wu Q, Guo J, Que Y. Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection. BMC Genomics 2017; 18:325. [PMID: 28438123 PMCID: PMC5404671 DOI: 10.1186/s12864-017-3716-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 04/21/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Sugarcane smut caused by Sporisorium scitamineum leads to a significant reduction in cane yield and sucrose content. MicroRNAs (miRNAs) play an important role in regulating plant responses to biotic stress. The present study was the first to use two sugarcane genotypes, YA05-179 (smut-resistant) and ROC22 (smut-susceptible), to identify differentially expressed miRNAs in sugarcane challenged with S. scitamineum by using high-throughput sequencing. RESULTS The predicted target gene number corresponding to known differentially expressed miRNAs in YA05-179 was less than that in ROC22, however most of them were in common. Expression of differential miRNAs under S. scitamineum challenge was mostly downregulated, with similar trends in the two varieties. Gene ontology (GO) analysis showed that the target gene classification of known miRNAs was similar to that of the newly identified miRNAs. These were mainly associated with cellular processes and metabolic processes in the biological process category, as well as combination and catalytic activity in the molecular function category. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these predicted target genes involved in a series of physiological and biochemical pathways or disease resistance-related physiological metabolism and signal transduction pathways, suggesting that the molecular interaction mechanism between sugarcane and S. scitamineum was a complex network system. These findings also showed certain predicted target genes of miR5671, miR5054, miR5783, miR5221, and miR6478 play roles in the mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, and plant-pathogen interaction. Quantitative real-time PCR (qRT-PCR) analysis showed that majority of the known miRNAs and its predicted target genes followed a negatively regulated mode. Seven out of eight predicted target genes showed identical expression after 12 h treatment and reached the highest degree of matching at 48 h, indicating that the regulatory role of miRNAs on the target genes in sugarcane was maximized at 48 h after S. scitamineum challenge. CONCLUSIONS Taken together, our findings serve as evidence for the association of miRNA expression with the molecular mechanism underlying the pathogenesis of sugarcane smut, particularly on the significance of miRNA levels in relation to the cultivation of smut-resistant sugarcane varieties.
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Affiliation(s)
- Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuye Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Feng Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Waqar Ahmad
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Marques JPR, Appezzato-da-Glória B, Piepenbring M, Massola Jr NS, Monteiro-Vitorello CB, Vieira MLC. Sugarcane smut: shedding light on the development of the whip-shaped sorus. ANNALS OF BOTANY 2017; 119:815-827. [PMID: 27568298 PMCID: PMC5378185 DOI: 10.1093/aob/mcw169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/13/2016] [Accepted: 06/07/2016] [Indexed: 05/18/2023]
Abstract
Background and Aims Sugarcane smut is caused by the fungus Sporisorium scitamineum (Ustilaginales/Ustilaginomycotina/Basidiomycota), which is responsible for losses in sugarcane production worldwide. Infected plants show a profound metabolic modification resulting in the development of a whip-shaped structure (sorus) composed of a mixture of plant tissues and fungal hyphae. Within this structure, ustilospores develop and disseminate the disease. Despite the importance of this disease, a detailed histopathological analysis of the plant-pathogen interaction is lacking. Methods The whip-shaped sorus was investigated using light microscopy, scanning and transmission electron microscopy, histochemical tests and epifluorescence microscopy coupled with deconvolution. Key Results Sorus growth is mediated by intercalary meristem activity at the base of the sorus, where the fungus causes partial host cell wall degradation and formation of intercellular spaces. Sporogenesis in S. scitamineum is thallic, with ustilospore initials in intercalary or terminal positions, and mostly restricted to the base of the sorus. Ustilospore maturation is centrifugal in relation to the ground parenchyma and occurs throughout the sorus median region. At the apex of the sorus, the fungus produces sterile cells and promotes host cell detachment. Hyphae are present throughout the central axis of the sorus (columella). The plant cell produces callose around the intracellular hyphae as well as inside the papillae at the infection site. Conclusions The ontogeny of the whip-shaped sorus suggests that the fungus can cause the acropetal growth in the intercalary meristem. The sporogenesis of S. scitamineum was described in detail, demonstrating that the spores are formed exclusively at the base of the whip. Light was also shed on the nature of the sterile cells. The presence of the fungus alters the host cell wall composition, promotes its degradation and causes the release of some peripheral cells of the sorus. Finally, callose was observed around fungal hyphae in infected cells, suggesting that deposition of callose by the host may act as a structural response to fungal infection.
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Affiliation(s)
- João Paulo R. Marques
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, 13418-900 Piracicaba, Brazil
- Departamento de Ciências Biológicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, 13418-900 Piracicaba, Brazil
| | - Beatriz Appezzato-da-Glória
- Departamento de Ciências Biológicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, 13418-900 Piracicaba, Brazil
| | - Meike Piepenbring
- Department of Mycology, Cluster for Integrative Fungal Research (IPF), Goethe-Universität Frankfurt am Main, D-60438 Frankfurt am Main, Germany
| | - Nelson S. Massola Jr
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, 13418-900 Piracicaba, Brazil
| | - Claudia B. Monteiro-Vitorello
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, 13418-900 Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, 13418-900 Piracicaba, Brazil
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Schaker PDC, Peters LP, Cataldi TR, Labate CA, Caldana C, Monteiro-Vitorello CB. Metabolome Dynamics of Smutted Sugarcane Reveals Mechanisms Involved in Disease Progression and Whip Emission. FRONTIERS IN PLANT SCIENCE 2017; 8:882. [PMID: 28620397 PMCID: PMC5450380 DOI: 10.3389/fpls.2017.00882] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/10/2017] [Indexed: 05/02/2023]
Abstract
Sugarcane smut disease, caused by the biotrophic fungus Sporisorium scitamineum, is characterized by the development of a whip-like structure from the plant meristem. The disease causes negative effects on sucrose accumulation, fiber content and juice quality. The aim of this study was to exam whether the transcriptomic changes already described during the infection of sugarcane by S. scitamineum result in changes at the metabolomic level. To address this question, an analysis was conducted during the initial stage of the interaction and through disease progression in a susceptible sugarcane genotype. GC-TOF-MS allowed the identification of 73 primary metabolites. A set of these compounds was quantitatively altered at each analyzed point as compared with healthy plants. The results revealed that energetic pathways and amino acid pools were affected throughout the interaction. Raffinose levels increased shortly after infection but decreased remarkably after whip emission. Changes related to cell wall biosynthesis were characteristic of disease progression and suggested a loosening of its structure to allow whip growth. Lignin biosynthesis related to whip formation may rely on Tyr metabolism through the overexpression of a bifunctional PTAL. The altered levels of Met residues along with overexpression of SAM synthetase and ACC synthase genes suggested a role for ethylene in whip emission. Moreover, unique secondary metabolites antifungal-related were identified using LC-ESI-MS approach, which may have potential biomarker applications. Lastly, a putative toxin was the most important fungal metabolite identified whose role during infection remains to be established.
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Affiliation(s)
- Patricia D. C. Schaker
- Department of Genetics, “Luiz de Queiroz”' College of Agriculture, University of São PauloSão Paulo, Brazil
| | - Leila P. Peters
- Department of Genetics, “Luiz de Queiroz”' College of Agriculture, University of São PauloSão Paulo, Brazil
| | - Thais R. Cataldi
- Department of Genetics, “Luiz de Queiroz”' College of Agriculture, University of São PauloSão Paulo, Brazil
| | - Carlos A. Labate
- Department of Genetics, “Luiz de Queiroz”' College of Agriculture, University of São PauloSão Paulo, Brazil
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology LaboratorySão Paulo, Brazil
- Max Planck Partner Group at Brazilian Bioethanol Science and Technology LaboratorySão Paulo, Brazil
| | - Claudia B. Monteiro-Vitorello
- Department of Genetics, “Luiz de Queiroz”' College of Agriculture, University of São PauloSão Paulo, Brazil
- *Correspondence: Claudia B. Monteiro-Vitorello
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23
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Barnabas L, Ashwin NMR, Kaverinathan K, Trentin AR, Pivato M, Sundar AR, Malathi P, Viswanathan R, Rosana OB, Neethukrishna K, Carletti P, Arrigoni G, Masi A, Agrawal GK, Rakwal R. Proteomic analysis of a compatible interaction between sugarcane and Sporisorium scitamineum. Proteomics 2016; 16:1111-22. [PMID: 26857420 DOI: 10.1002/pmic.201500245] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 01/05/2016] [Accepted: 02/02/2016] [Indexed: 02/05/2023]
Abstract
Smut caused by Sporisorium scitamineum is one of the important diseases of sugarcane with global significance. Despite the intriguing nature of sugarcane, S. scitamineum interaction, several pertinent aspects remain unexplored. This study investigates the proteome level alterations occurring in the meristem of a S. scitamineum infected susceptible sugarcane cultivar at whip emergence stage. Differentially abundant proteins were identified by 2DE coupled with MALDI-TOF/TOF-MS. Comprehensively, 53 sugarcane proteins identified were related to defence, stress, metabolism, protein folding, energy, and cell division; in addition, a putative effector of S. scitamineum, chorismate mutase, was identified. Transcript expression vis-à-vis the activity of phenylalanine ammonia lyase was relatively higher in the infected meristem. Abundance of seven candidate proteins in 2D gel profiles was in correlation with its corresponding transcript expression levels as validated by qRT-PCR. Furthermore, this study has opened up new perspectives on the interaction between sugarcane and S. scitamineum.
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Affiliation(s)
- Leonard Barnabas
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - N M R Ashwin
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - K Kaverinathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Anna Rita Trentin
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Micaela Pivato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - A Ramesh Sundar
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - P Malathi
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - R Viswanathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - O B Rosana
- Bioinformatics Center, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - K Neethukrishna
- Bioinformatics Center, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Giorgio Arrigoni
- Proteomics Center of Padova University, Padova, Italy.,Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.,GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.,GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal.,Tsukuba International Academy for Sport Studies (TIAS) and Faculty of Health and Sport Sciences, University of Tsukuba, Ibaraki, Japan
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24
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Su Y, Xu L, Wang Z, Peng Q, Yang Y, Chen Y, Que Y. Comparative proteomics reveals that central metabolism changes are associated with resistance against Sporisorium scitamineum in sugarcane. BMC Genomics 2016; 17:800. [PMID: 27733120 PMCID: PMC5062822 DOI: 10.1186/s12864-016-3146-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 10/05/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Sugarcane smut, which is caused by Sporisorium scitamineum, has been threatening global sugarcane production. Breeding smut resistant sugarcane varieties has been proven to be the most effective method of controlling this particular disease. However, a lack of genome information of sugarcane has hindered the development of genome-assisted resistance breeding programs. Furthermore, the molecular basis of sugarcane response to S. scitamineum infection at the proteome level was incomplete and combining proteomic and transcriptional analysis has not yet been conducted. RESULTS We identified 273 and 341 differentially expressed proteins in sugarcane smut-resistant (Yacheng05-179) and susceptible (ROC22) genotypes at 48 h after inoculation with S. scitamineum by employing an isobaric tag for relative and absolute quantification (iTRAQ). The proteome quantitative data were then validated by multiple reaction monitoring (MRM). The integrative analysis showed that the correlations between the quantitative proteins and the corresponding genes that was obtained in our previous transcriptome study were poor, which were 0.1502 and 0.2466 in Yacheng05-179 and ROC22, respectively, thereby revealing a post-transcriptional event during Yacheng05-179-S. scitamineum incompatible interaction and ROC22-S. scitamineum compatible interaction. Most differentially expressed proteins were closely related to sugarcane smut resistance such as beta-1,3-glucanase, peroxidase, pathogenesis-related protein 1 (PR1), endo-1,4-beta-xylanase, heat shock protein, and lectin. Ethylene and gibberellic acid pathways, phenylpropanoid metabolism and PRs, such as PR1, PR2, PR5 and PR14, were more active in Yacheng05-179, which suggested of their possible roles in sugarcane smut resistance. However, calcium signaling, reactive oxygen species, nitric oxide, and abscisic acid pathways in Yacheng05-179 were repressed by S. scitamineum and might not be crucial for defense against this particular pathogen. CONCLUSIONS These results indicated complex resistance-related events in sugarcane-S. scitamineum interaction, and provided novel insights into the molecular mechanism underlying the response of sugarcane to S. scitamineum infection.
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Affiliation(s)
- Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhuqing Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qiong Peng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuting Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yun Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Guangxi Collaborative Innovation Center of Sugarcane Industry, Guangxi University, Nanning, 530005 China
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Schaker PDC, Palhares AC, Taniguti LM, Peters LP, Creste S, Aitken KS, Van Sluys MA, Kitajima JP, Vieira MLC, Monteiro-Vitorello CB. RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease. PLoS One 2016; 11:e0162237. [PMID: 27583836 PMCID: PMC5008620 DOI: 10.1371/journal.pone.0162237] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/21/2016] [Indexed: 11/25/2022] Open
Abstract
Sugarcane smut disease is caused by the biotrophic fungus Sporisorium scitamineum. The disease is characterized by the development of a whip-like structure from the primary meristems, where billions of teliospores are produced. Sugarcane smut also causes tillering and low sucrose and high fiber contents, reducing cane productivity. We investigated the biological events contributing to disease symptoms in a smut intermediate-resistant sugarcane genotype by examining the transcriptional profiles (RNAseq) shortly after inoculating the plants and immediately after whip emission. The overall picture of disease progression suggests that premature transcriptional reprogramming of the shoot meristem functions continues until the emergence of the whip. The guidance of this altered pattern is potentially primarily related to auxin mobilization in addition to the involvement of other hormonal imbalances. The consequences associated with whip emission are the modulation of typical meristematic functions toward reproductive organ differentiation, requiring strong changes in carbon partitioning and energy production. These changes include the overexpression of genes coding for invertases and trehalose-6P synthase, as well as other enzymes from key metabolic pathways, such as from lignin biosynthesis. This is the first report describing changes in the transcriptional profiles following whip development, providing a hypothetical model and candidate genes to further study sugarcane smut disease progression.
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Affiliation(s)
- Patricia D. C. Schaker
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Alessandra C. Palhares
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Lucas M. Taniguti
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Leila P. Peters
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Silvana Creste
- Instituto Agronômico de Campinas, Centro de Cana, Ribeirão Preto, São Paulo, Brazil
| | - Karen S. Aitken
- CSIRO Agriculture, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Maria L. C. Vieira
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Claudia B. Monteiro-Vitorello
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
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Barnabas L, Ramadass A, Amalraj RS, Palaniyandi M, Rasappa V. Sugarcane proteomics: An update on current status, challenges, and future prospects. Proteomics 2016; 15:1658-70. [PMID: 25641866 DOI: 10.1002/pmic.201400463] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/27/2014] [Accepted: 01/09/2015] [Indexed: 12/23/2022]
Abstract
Sugarcane is one of the most important commercial crops cultivated worldwide for the production of crystal sugar, ethanol, and other related by-products. Unlike other comparable monocots like sorghum, maize, and rice, sugarcane genome by virtue of its polyploidy nature remains yet to be fully deciphered. Proteomics-an established complementary tool to genomics is at its infancy in sugarcane as compared to the other monocots. However, with the surge in genomics research accomplished by next-generation sequencing platforms, sugarcane proteomics has gained momentum. This review summarizes the available literature from 1970 to 2014, which ensures a comprehensive coverage on sugarcane proteomics-a topic first of its kind to be reviewed. We herewith compiled substantial contributions in different areas of sugarcane proteomics, which include abiotic and biotic stresses, cell wall, organelle, and structural proteomics. The past decade has witnessed a paradigm shift in the pace with which sugarcane proteomics is progressing, as evident by the number of research publications. In addition to extensively reviewing the progress made thus far, we intend to highlight the scope in sugarcane proteomics, with an aspiration to instigate focused research on sugarcane to harness its full potential for the human welfare.
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Affiliation(s)
- Leonard Barnabas
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Ashwin Ramadass
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Ramesh Sundar Amalraj
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Malathi Palaniyandi
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Viswanathan Rasappa
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
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Viswanathan R, Prasanth CN, Malathi P, Sundar AR. Draft Genome Sequence of Colletotrichum falcatum - A Prelude on Screening of Red Rot Pathogen in Sugarcane. J Genomics 2016; 4:1-3. [PMID: 26958090 PMCID: PMC4780119 DOI: 10.7150/jgen.13585] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Colletotrichum falcatum, a concealed fungal ascomycete causes red rot, which is a serious disease in sugarcane. It infects economically important stalk tissues, considered as store house of sugar in sugarcane. The study is to find genetic complexities of C. falcatum in establishing this as a stalk infecting pathogen and to decipher the unique lifestyle of this pathogen using NGS technology. We report the draft genome of C. falcatum of about 48.16 Mb in size with 12,270 genes. The genome sequences were compared with other fungal species which revealed that C. falcatum is closely related to C. graminicola and C.sublineola the causal organisms of anthracnose in maize and sorghum. These results brought a new revelation to explore the lifestyle of this unique pathogen which is specialized to infect sugarcane stalk tissues in detail.
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Affiliation(s)
- Rasappa Viswanathan
- Plant Pathology Section, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | | | - Palaniyandi Malathi
- Plant Pathology Section, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Amalraj Ramesh Sundar
- Plant Pathology Section, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
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Que Y, Su Y, Guo J, Wu Q, Xu L. A global view of transcriptome dynamics during Sporisorium scitamineum challenge in sugarcane by RNA-Seq. PLoS One 2014; 9:e106476. [PMID: 25171065 PMCID: PMC4149577 DOI: 10.1371/journal.pone.0106476] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/07/2014] [Indexed: 11/17/2022] Open
Abstract
Sugarcane smut caused by Sporisorium scitamineum is a critical fungal disease in the sugarcane industry. However, molecular mechanistic studies of pathological response of sugarcane to S. scitamineum are scarce and preliminary. Here, transcriptome analysis of sugarcane disease induced by S. scitamineum at 24, 48 and 120 h was conducted, using an S. scitamineum-resistant and -susceptible genotype (Yacheng05-179 and “ROC”22). The reliability of Illumina data was confirmed by real-time quantitative PCR. In total, transcriptome sequencing of eight samples revealed gene annotations of 65,852 unigenes. Correlation analysis of differentially expressed genes indicated that after S. scitamineum infection, most differentially expressed genes and related metabolic pathways in both sugarcane genotypes were common, covering most biological activities. However, expression of resistance-associated genes in Yacheng05-179 (24–48 h) occurred earlier than those in “ROC”22 (48–120 h), and more transcript expressions were observed in the former, suggesting resistance specificity and early timing of these genes in non-affinity sugarcane and S. scitamineum interactions. Obtained unigenes were related to cellular components, molecular functions and biological processes. From these data, functional annotations associated with resistance were obtained, including signal transduction mechanisms, energy production and conversion, inorganic ion transport and metabolism, and defense mechanisms. Pathway enrichment analysis revealed that differentially expressed genes are involved in plant hormone signal transduction, flavonoid biosynthesis, plant-pathogen interaction, cell wall fortification pathway and other resistance-associated metabolic pathways. Disease inoculation experiments and the validation of invitro antibacterial activity of the chitinase gene ScChi show that this sugarcane chitinase gene identified through RNA-Seq analysis is relevant to plant-pathogen interactions. In conclusion, expression data here represent the most comprehensive dataset available for sugarcane smut induced by S. scitamineum and will serve as a resource for finally unraveling the molecular mechanisms of sugarcane responses to S. scitamineum.
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Affiliation(s)
- Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Xu L, Lu Y, You Q, Liu X, Grisham MP, Pan Y, Que Y. Biogeographical variation and population genetic structure of Sporisorium scitamineum in Mainland China: insights from ISSR and SP-SRAP markers. ScientificWorldJournal 2014; 2014:296020. [PMID: 24772015 PMCID: PMC3977103 DOI: 10.1155/2014/296020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 02/04/2014] [Indexed: 11/17/2022] Open
Abstract
A total of 100 Sporisorium scitamineum isolates were investigated by inter simple sequence repeat (ISSR) and single primer-sequence related amplified polymorphism (SP-SRAP) markers. These isolates were clearly assorted into three distinct clusters regardless of method used: either cluster analysis or by principal component analysis (PCA) of the ISSR, SP-SRAP, or ISSR + SP-SRAP data set. The total gene diversity (H t) and gene diversity between subpopulations (H s) were estimated to be 0.34 to 0.38 and 0.22 to 0.29, respectively, by analyzing separately the ISSR and SP-SRAP data sets, and to be 0.26-0.36 by analyzing ISSR + SP-SRAP data set. The gene diversity attributable to differentiation among populations (G st) was estimated to be 0.35 and 0.22, and the gene flow (Nm) was 0.94 and 1.78, respectively, when analyzing separately ISSR and SP-SRAP data set, and was 0.27 and 1.33, respectively, when analyzing ISSR + SP-SRAP data set. Our study showed that there is considerable genetic variation in the analyzed 100 isolates, and the environmental heterogeneity has played an important role for this observed high degree of variation. The genetic differentiation of sugarcane smut fungus depends to a large extent on the heterogeneity of their habitats and is the result of long-term adaptations of pathogens to their ecological environments.
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Affiliation(s)
- Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yunhai Lu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qian You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaolan Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | | | - Yongbao Pan
- USDA-ARS, Sugarcane Research Unit, Houma, LA 70360, USA
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China
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