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Lin P, Chai J, Wang A, Zhong H, Wang K. High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing. Int J Mol Sci 2024; 25:8840. [PMID: 39201527 PMCID: PMC11354348 DOI: 10.3390/ijms25168840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
Camellia oleifera, an important tree species and source of edible oil in China, has received significant attention owing to the oil's high unsaturated fatty acid content, which has benefits for human health. However, the mechanisms underlying C. oleifera yield and oil quality are largely unknown. In this study, 180 F1 progenies were obtained from two parents with obvious differences in fruit- and oil-related traits. We constructed a high-density genetic map using a double digest restriction site-associated DNA sequencing (ddRAD-Seq) strategy in C. oleifera. This map spanned 3327 cM and anchored 2780 markers in 15 linkage groups (LGs), with an average marker interval of 1.20 cM. A total of 221 quantitative trait loci (QTLs) associated with fruit- and oil-related traits were identified across three years' worth of phenotypic data. Nine QTLs were detected simultaneously in at least two different years, located on LG02, LG04, LG05, LG06, and LG11, and explained 8.5-16.6% of the phenotypic variation in the corresponding traits, respectively. Seventeen major QTLs were obtained that explained 13.0-16.6% of the phenotypic variance. Eleven and five flanking SNPs of major QTLs for fruit- and oil-related traits were detected which could be used for marker-assisted selection in C. oleifera breeding programs. Furthermore, 202 potential candidate genes in QTL regions were identified based on the collinearity of the genetic map and the C. oleifera "CON" genome. A potential regulatory network controlling fruit development and oil biosynthesis was constructed to dissect the complex mechanism of oil accumulation. The dissection of these QTLs will facilitate the gene cloning underlying lipid synthesis and increase our understanding in order to enhance C. oleifera oil yield and quality.
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Affiliation(s)
- Ping Lin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Jingyu Chai
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Anni Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Huiqi Zhong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Kailiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
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Wang H, Cai X, Umer MJ, Xu Y, Hou Y, Zheng J, Liu F, Wang K, Chen M, Ma S, Yu J, Zhou Z. Genetic Analysis of Cotton Fiber Traits in Gossypium Hybrid Lines. PHYSIOLOGIA PLANTARUM 2024; 176:e14442. [PMID: 39030776 DOI: 10.1111/ppl.14442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/25/2024] [Indexed: 07/22/2024]
Abstract
Cotton plays a crucial role in the progress of the textile industry and the betterment of human life by providing natural fibers. In our study, we explored the genetic determinants of cotton architecture and fiber yield and quality by crossbreeding Gossypium hirsutum and Gossypium barbadense, creating a recombinant inbred line (RIL) population. Utilizing SNP markers, we constructed an extensive genetic map encompassing 7,730 markers over 2,784.2 cM. We appraised two architectural and seven fiber traits within six environments, identifying 58 QTLs, of which 49 demonstrated stability across these environments. These encompassed QTLs for traits such as lint percentage (LP), boll weight (BW), fiber strength (STRENGTH), seed index (SI), and micronaire (MIC), primarily located on chromosomes chr-A07, chr-D06, and chr-D07. Notably, chr-D07 houses a QTL region affecting SI, corroborated by multiple studies. Within this region, the genes BZIP043 and SEP2 were identified as pivotal, with SEP2 particularly showing augmented expression in developing ovules. These discoveries contribute significantly to marker-assisted selection, potentially elevating both the yield and quality of cotton fiber production. These findings provide valuable insights into marker-assisted breeding strategies, offering crucial information to enhance fiber yield and quality in cotton production.
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Affiliation(s)
- Heng Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China/ National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China
- Henan International Joint Laboratory of Cotton Biology, Anyang, Henan, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
- Henan International Joint Laboratory of Cotton Biology, Anyang, Henan, China
| | - Jie Zheng
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China/ National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China
- Henan International Joint Laboratory of Cotton Biology, Anyang, Henan, China
| | - Fang Liu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China/ National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Cotton Biology, Anyang, Henan, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
| | - Mengshan Chen
- Chinese Academy of Agricultural Science, Beijing, China
| | | | - Jingzhong Yu
- Standing Committee of the People's Congress of Jiangsu Province, Nanjing, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
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Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
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Xu M, Kong K, Miao L, He J, Liu T, Zhang K, Yue X, Jin T, Gai J, Li Y. Identification of major quantitative trait loci and candidate genes for seed weight in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:22. [PMID: 36688967 PMCID: PMC9870841 DOI: 10.1007/s00122-023-04299-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Four major quantitative trait loci for 100-seed weight were identified in a soybean RIL population under five environments, and the most likely candidate genes underlying these loci were identified. Seed weight is an important target of soybean breeding. However, the genes underlying the major quantitative trait loci (QTL) controlling seed weight remain largely unknown. In this study, a soybean population of 300 recombinant inbred lines (RILs) derived from a cross between PI595843 (PI) and WH was used to map the QTL and identify candidate genes for seed weight. The RIL population was genotyped through whole genome resequencing, and phenotyped for 100-seed weight under five environments. A total of 38 QTL were detected, and four major QTL, each explained at least 10% of the variation in 100-seed weight, were identified. Six candidate genes within these four major QTL regions were identified by analyses of their tissue expression patterns, gene annotations, and differential gene expression levels in soybean seeds during four developmental stages between two parental lines. Further sequence variation analyses revealed a C to T substitution in the first exon of the Glyma.19G143300, resulting in an amino acid change between PI and WH, and thus leading to a different predicted kinase domain, which might affect its protein function. Glyma.19G143300 is highly expressed in soybean seeds and encodes a leucine-rich repeat receptor-like protein kinase (LRR-RLK). Its predicted protein has typical domains of LRR-RLK family, and phylogenetic analyses reveled its similarity with the known LRR-RLK protein XIAO (LOC_Os04g48760), which is involved in controlling seed size. The major QTL and candidate genes identified in this study provide useful information for molecular breeding of new soybean cultivars with desirable seed weight.
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Affiliation(s)
- Mengge Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Keke Kong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Long Miao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jianbo He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Tengfei Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Kai Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Xiuli Yue
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Ting Jin
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
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Lu Q, Yu X, Wang H, Yu Z, Zhang X, Zhao Y. Quantitative trait locus mapping for important yield traits of a sorghum-sudangrass hybrid using a high-density single nucleotide polymorphism map. FRONTIERS IN PLANT SCIENCE 2022; 13:1098605. [PMID: 36605962 PMCID: PMC9808045 DOI: 10.3389/fpls.2022.1098605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The sorghum-sudangrass hybrid is a vital gramineous herbage.The F2 population was obtained to clarify genetic regularities among the traits of sorghum-sudangrass hybrids by bagging and selfing in the F1 generation using 'scattered ear sorghum' and 'red hull sudangrass.' This hybrid combines the characteristics of the strong resistance of parents, high yield, and good palatability and has clear heterosis. A thorough understanding of the genetic mechanisms of yield traits in sorghum-sudangrass hybrids is essential in improving their yield. Therefore, we conducted quantitative trait locus (QTL) mapping for plant height, stem diameter, tiller number, leaf number, leaf length, leaf width, and fresh weight of each plant in three different environments, using a high-density genetic linkage map based on single nucleotide polymorphism markers previously constructed by our team. A total of 55 QTLs were detected, uniformly distributed over the 10 linkage groups (LGs), with logarithm of odds values ranging between 2.5 and 7.1, which could explain the 4.9-52.44% phenotypic variation. Furthermore, 17 yield-related relatively high-frequency QTL (RHF-QTL) loci were repeatedly detected in at least two environments, with an explanatory phenotypic variation of 4.9-30.97%. No RHF-QTLs were associated with the tiller number. The genes within the confidence interval of RHF-QTL were annotated, and seven candidate genes related to yield traits were screened. Three QTL sites overlapping or adjacent to previous studies were detected by comparative analysis. We also found that QTL was enriched and that qLL-10-1 and qFW-10-4 were located at the same location of 25.81 cM on LG10. The results of this study provide a foundation for QTL fine mapping, candidate gene cloning, and molecular marker-assisted breeding of sorghum-sudangrass hybrids.
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Zhao Y, Zhai G, Li X, Tao H, Li L, He Y, Zhang X, Wang F, Hong G, Zhu Y. Metabolomics Reveals Nutritional Diversity among Six Coarse Cereals and Antioxidant Activity Analysis of Grain Sorghum and Sweet Sorghum. Antioxidants (Basel) 2022; 11:antiox11101984. [PMID: 36290708 PMCID: PMC9598553 DOI: 10.3390/antiox11101984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 11/29/2022] Open
Abstract
Coarse cereals are rich in dietary fiber, B vitamins, minerals, secondary metabolites, and other bioactive components, which exert numerous health benefits. To better understand the diversity of metabolites in different coarse cereals, we performed widely targeted metabolic profiling analyses of six popular coarse cereals, millet, coix, buckwheat, quinoa, oat, and grain sorghum, of which 768 metabolites are identified. Moreover, quinoa and buckwheat showed significantly different metabolomic profiles compared with other coarse cereals. Analysis of the accumulation patterns of common nutritional metabolites among six coarse cereals, we found that the accumulation of carbohydrates follows a conserved pattern in the six coarse cereals, while those of amino acids, vitamins, flavonoids, and lipids were complementary. Furthermore, the species-specific metabolites in each coarse cereal were identified, and the neighbor-joining tree for the six coarse cereals was constructed based on the metabolome data. Since sorghum contains more species-specific metabolites and occupies a unique position on the neighbor-joining tree, the metabolite differences between grain sorghum 654 and sweet sorghum LTR108 were finally compared specifically, revealing that LTR108 contained more flavonoids and had higher antioxidant activity than 654. Our work supports an overview understanding of nutrient value in different coarse cereals, which provides the metabolomic evidence for the healthy diet. Additionally, the superior antioxidant activity of sweet sorghum provides clues for its targeted uses.
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Affiliation(s)
- Yao Zhao
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
| | - Guowei Zhai
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xuetong Li
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Han Tao
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
| | - Linying Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
| | - Yuqing He
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
| | - Xueying Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
| | - Fulin Wang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Gaojie Hong
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs, Key Laboratory of Biotechnology in Plant Protection of Zhejiang Province, Hangzhou 310021, China
- Correspondence: (G.H.); (Y.Z.)
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence: (G.H.); (Y.Z.)
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Zhang J, Zhang F, Tian L, Ding Y, Qi J, Zhang H, Mu X, Ma Z, Xia L, Tang B. Molecular mapping of quantitative trait loci for 3 husk traits using genotyping by sequencing in maize ( Zea mays L.). G3 GENES|GENOMES|GENETICS 2022; 12:6659096. [PMID: 35944205 PMCID: PMC9526056 DOI: 10.1093/g3journal/jkac198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022]
Abstract
The maize (Zea mays L.) husk consists of multiple leaf layers and plays an important role in grain growth and development. Despite significant achievements in physiological and morphological research, few studies have focused on the detection of genetic loci underlying husk-related traits due to the lack of efficient tools. In this study, we constructed an ultra-high-density linkage map using genotyping by sequencing based on a recombinant inbred line population to estimate the genetic variance and heritability of 3 husk traits, i.e. husk length, husk width, and husk layer number in 3 field environments and the combined environment. The 3 husk traits showed broad phenotypic variation and high heritability; the broad-sense heritability (H2) was 0.92, 0.84, and 0.86. Twenty quantitative trait loci were consistently detected more than 1 environment, including 9 for husk length, 6 for husk width, and 5 for husk layer number. These loci were considered as stable quantitative trait loci. Based on the quantitative trait loci mapping in the recombinant inbred line population, qHL6 and qHN4 were detected across all environments and inferred to be reliable and major-effect quantitative trait loci for husk length and husk layer number, respectively. In addition, several predicted candidate genes were identified in the region of qHL6 and qHN4, of which 17 candidate genes potentially play a role in biological processes related to development process and energy metabolism. These results will be as a useful resource for performing functional studies aimed at understanding the molecular pathways involved in husk growth and development.
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Affiliation(s)
- Jun Zhang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Henan Provincial Key Laboratory of Maize Biology, Zhengzhou 450003 , China
| | - Fengqi Zhang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Henan Provincial Key Laboratory of Maize Biology, Zhengzhou 450003 , China
| | - Lei Tian
- Henan Institute of Science and Technology for Development , Zhengzhou 450003, China
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University , Zhengzhou 450046, China
| | - Yong Ding
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Henan Provincial Key Laboratory of Maize Biology, Zhengzhou 450003 , China
| | - Jianshuang Qi
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Henan Provincial Key Laboratory of Maize Biology, Zhengzhou 450003 , China
| | - Hongfeng Zhang
- Henan Institute of Science and Technology for Development , Zhengzhou 450003, China
| | - Xinyuan Mu
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Henan Provincial Key Laboratory of Maize Biology, Zhengzhou 450003 , China
| | - Zhiyan Ma
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Henan Provincial Key Laboratory of Maize Biology, Zhengzhou 450003 , China
| | - Laikun Xia
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Henan Provincial Key Laboratory of Maize Biology, Zhengzhou 450003 , China
| | - Baojun Tang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Henan Provincial Key Laboratory of Maize Biology, Zhengzhou 450003 , China
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Somegowda VK, Prasad KVSV, Naravula J, Vemula A, Selvanayagam S, Rathore A, Jones CS, Gupta R, Deshpande SP. Genetic Dissection and Quantitative Trait Loci Mapping of Agronomic and Fodder Quality Traits in Sorghum Under Different Water Regimes. FRONTIERS IN PLANT SCIENCE 2022; 13:810632. [PMID: 35251083 PMCID: PMC8892184 DOI: 10.3389/fpls.2022.810632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/03/2022] [Indexed: 06/01/2023]
Abstract
Livestock provides an additional source of income for marginal cropping farmers, but crop residues that are used as a main source of animal feed are characteristically low in digestibility and protein content. This reduces the potential livestock product yield and quality. The key trait, which influences the quality and the cost of animal feed, is digestibility. In this study, we demonstrate that sorghum breeding can be directed to achieve genetic gains for both fodder biomass and digestibility without any trade-offs. The genotypic variance has shown significant differences for biomass across years (13,035 in 2016 and 3,395 in 2017) while in vitro organic matter digestibility (IVOMD) showed significant genotypic variation in 2016 (0.253) under drought. A range of agronomic and fodder quality traits was found to vary significantly in the population within both the control and drought conditions and across both years of the study. There was significant genotypic variance (σg2) and genotypic × treatment variance (σgxt2) in dry matter production in a recombinant inbred line (RIL) population in both study years, while there was only significant σg2 and σgxt2 in IVOMD under the control conditions. There was no significant correlation identified between biomass and digestibility traits under the control conditions, but there was a positive correlation under drought. However, a negative relation was observed between digestibility and grain yield under the control conditions, while there was no significant correlation under drought population, which was genotyped using the genotyping-by-sequencing (GBS) technique, and 1,141 informative single nucleotide polymorphism (SNP) markers were identified. A linkage map was constructed, and a total of 294 quantitative trait loci (QTLs) were detected, with 534 epistatic interactions, across all of the traits under study. QTL for the agronomic traits fresh and dry weight, together with plant height, mapped on to the linkage group (LG) 7, while QTL for IVOMD mapped on to LG1, 2, and 8. A number of genes previously reported to play a role in nitrogen metabolism and cell wall-related functions were found to be associated with these QTL.
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Affiliation(s)
- Vinutha K. Somegowda
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
- Department of Biotechnology, Vignan University, Vadlamudi, India
| | - Kodukula V. S. V. Prasad
- International Livestock Research Institute (ILRI), International Crops Research Institute for the Semi-arid Tropics Campus, Patancheru, India
| | - Jalaja Naravula
- Department of Biotechnology, Vignan University, Vadlamudi, India
| | - Anilkumar Vemula
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
| | | | - Abhishek Rathore
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
| | - Chris S. Jones
- International Livestock Research Institute (ILRI), International Crops Research Institute for the Semi-arid Tropics Campus, Patancheru, India
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
| | - Santosh P. Deshpande
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
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9
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Ou C, Sun T, Liu X, Li C, Li M, Wang X, Ren H, Zhao Z, Zhuang F. Detection of Chromosomal Segments Introgressed from Wild Species of Carrot into Cultivars: Quantitative Trait Loci Mapping for Morphological Features in Backcross Inbred Lines. PLANTS (BASEL, SWITZERLAND) 2022; 11:391. [PMID: 35161370 PMCID: PMC8840429 DOI: 10.3390/plants11030391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Cultivated carrot is thought to have been domesticated from a wild species, and various phenotypes developed through human domestication and selection over the past several centuries. Little is known about the genomic contribution of wild species to the phenotypes of present-day cultivars, although several studies have focused on identifying genetic loci that contribute to the morphology of storage roots. A backcross inbred line (BIL) population derived from a cross between the wild species Daucus carota ssp. carota "Songzi" and the orange cultivar "Amsterdam forcing" was developed. The morphological features in the BIL population became more diverse after several generations of selfing BC2F1 plants. Only few lines retained features of wild parent. Genomic resequencing of the two parental lines and the BILs resulted in 3,223,651 single nucleotide polymorphisms (SNPs), and 13,445 bin markers were generated using a sliding window approach. We constructed a genetic map with 2027 bins containing 154,776 SNPs; the total genetic distance was 1436.43 cM and the average interval between the bins was 0.71 cm. Five stable QTLs related to root length, root shoulder width, dry material content of root, and ratio of root shoulder width to root middle width were consistently detected on chromosome 2 in both years and explained 23.4-66.9% of the phenotypic variance. The effects of introgressed genomic segments from the wild species on the storage root are reported and will enable the identification of functional genes that control root morphological traits in carrot.
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Affiliation(s)
- Chenggang Ou
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Tingting Sun
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Xing Liu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Chengjiang Li
- Suzhou Academy of Agricultural Science, Suzhou 234000, China; (C.L.); (H.R.)
| | - Min Li
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Xuewei Wang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Huaifu Ren
- Suzhou Academy of Agricultural Science, Suzhou 234000, China; (C.L.); (H.R.)
| | - Zhiwei Zhao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Feiyun Zhuang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
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10
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Zhi X, Tao Y, Jordan D, Borrell A, Hunt C, Cruickshank A, Potgieter A, Wu A, Hammer G, George-Jaeggli B, Mace E. Genetic control of leaf angle in sorghum and its effect on light interception. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:801-816. [PMID: 34698817 DOI: 10.1093/jxb/erab467] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Developing sorghum genotypes adapted to different light environments requires understanding of a plant's ability to capture light, determined through leaf angle specifically. This study dissected the genetic basis of leaf angle in 3 year field trials at two sites, using a sorghum diversity panel (729 accessions). A wide range of variation in leaf angle with medium heritability was observed. Leaf angle explained 36% variation in canopy light extinction coefficient, highlighting the extent to which variation in leaf angle influences light interception at the whole-canopy level. This study also found that the sorghum races of Guinea and Durra consistently having the largest and smallest leaf angle, respectively, highlighting the potential role of leaf angle in adaptation to distinct environments. The genome-wide association study detected 33 quantitative trait loci (QTLs) associated with leaf angle. Strong synteny was observed with previously detected leaf angle QTLs in maize (70%) and rice (40%) within 10 cM, among which the overlap was significantly enriched according to χ2 tests, suggesting a highly consistent genetic control in grasses. A priori leaf angle candidate genes identified in maize and rice were found to be enriched within a 1-cM window around the sorghum leaf angle QTLs. Additionally, protein domain analysis identified the WD40 protein domain as being enriched within a 1-cM window around the QTLs. These outcomes show that there is sufficient heritability and natural variation in the angle of upper leaves in sorghum which may be exploited to change light interception and optimize crop canopies for different contexts.
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Affiliation(s)
- Xiaoyu Zhi
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - Andrew Borrell
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
| | - Alan Cruickshank
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
| | - Andries Potgieter
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Gatton, QLD, Australia
| | - Alex Wu
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD, Australia
| | - Graeme Hammer
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD, Australia
| | - Barbara George-Jaeggli
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
| | - Emma Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
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Chiluwal A, Perumal R, Poudel HP, Muleta K, Ostmeyer T, Fedenia L, Pokharel M, Bean SR, Sebela D, Bheemanahalli R, Oumarou H, Klein P, Rooney WL, Jagadish SVK. Genetic control of source-sink relationships in grain sorghum. PLANTA 2022; 255:40. [PMID: 35038036 DOI: 10.1007/s00425-022-03822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
QTL hotspots identified for selected source-sink-related traits provide the opportunity for pyramiding favorable alleles for improving sorghum productivity under diverse environments. A sorghum bi-parental mapping population was evaluated under six different environments at Hays and Manhattan, Kansas, USA, in 2016 and 2017, to identify genomic regions controlling source-sink relationships. The population consisted of 210 recombinant inbred lines developed from US elite post-flowering drought susceptible (RTx430) and a known post-flowering drought tolerant cultivar (SC35). Selected physiological traits related to source (effective quantum yield of photosystem II and chlorophyll index), sink (grain yield per panicle) and panicle neck diameter were recorded during grain filling. The results showed strong phenotypic and genotypic association between panicle neck diameter and grain yield per panicle during mid-grain filling and at maturity. Multiple QTL model revealed 5-12 including 2-5 major QTL for each trait. Among them 3, 7 and 8 QTL for quantum yield, panicle neck diameter and chlorophyll index, respectively, have not been identified previously in sorghum. Phenotypic variation explained by QTL identified across target traits ranged between 5.5 and 25.4%. Panicle neck diameter and grain yield per panicle were positively associated, indicating the possibility of targeting common co-localized QTL to improve both traits simultaneously through marker-assisted selection. Three major QTL hotspots, controlling multiple traits were identified on chromosome 1 (52.23-61.18 Mb), 2 (2.52-11.43 Mb) and 3 (1.32-3.95 Mb). The identified genomic regions and underlying candidate genes can be utilized in pyramiding favorable alleles for improving source-sink relationships in sorghum under diverse environments.
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Affiliation(s)
- Anuj Chiluwal
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, 67601, USA
| | - Hari P Poudel
- Agriculture and Agri-Food Canada, 5403 First Ave. South, Lethbridge, AB, T1J 4B1, Canada
| | - Kebede Muleta
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Troy Ostmeyer
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Lauren Fedenia
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Meghnath Pokharel
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Scott R Bean
- Grain Quality and Structure Research Unit, CGAHR, USDA-ARS, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - David Sebela
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Raju Bheemanahalli
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Halilou Oumarou
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Patricia Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - William L Rooney
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - S V Krishna Jagadish
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA.
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12
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Drought Tolerance and Application of Marker-Assisted Selection in Sorghum. BIOLOGY 2021; 10:biology10121249. [PMID: 34943164 PMCID: PMC8699005 DOI: 10.3390/biology10121249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 12/30/2022]
Abstract
Simple Summary Sorghum is a climate-resilient crop grown in limited rainfall areas globally. However, climate change has increased temperature and shortened rainfall durations, which has constrained crop yield. We reviewed mechanisms of drought tolerance and application of marker-assisted selection in sorghum. Marker-assisted selection uses DNA molecular markers to map quantitative trait loci (QTL) associated with stay-green. Stg1, Stg2, Stg3, Stg4, Stg3A, and Stg3B QTLs associated with stay-green and high yield, have been mapped in sorghum. These QTLs are used for introgression into the senescent sorghum varieties through marker-assisted backcrossing. Abstract Sorghum is an important staple food crop in drought prone areas of Sub-Saharan Africa, which is characterized by erratic rainfall with poor distribution. Sorghum is a drought-tolerant crop by nature with reasonable yield compared to other cereal crops, but such abiotic stress adversely affects the productivity. Some sorghum varieties maintain green functional leaves under post-anthesis drought stress referred to as stay-green, which makes it an important crop for food and nutritional security. Notwithstanding, it is difficult to maintain consistency of tolerance over time due to climate change, which is caused by human activities. Drought in sorghum is addressed by several approaches, for instance, breeding drought-tolerant sorghum using conventional and molecular technologies. The challenge with conventional methods is that they depend on phenotyping stay-green, which is complex in sorghum, as it is constituted by multiple genes and environmental effects. Marker assisted selection, which involves the use of DNA molecular markers to map QTL associated with stay-green, has been useful to supplement stay-green improvement in sorghum. It involves QTL mapping associated with the stay-green trait for introgression into the senescent sorghum varieties through marker-assisted backcrossing by comparing with phenotypic field data. Therefore, this review discusses mechanisms of drought tolerance in sorghum focusing on physiological, morphological, and biochemical traits. In addition, the review discusses the application of marker-assisted selection techniques, including marker-assisted backcrossing, QTL mapping, and QTL pyramiding for addressing post-flowering drought in sorghum.
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Wang L, Upadhyaya HD, Zheng J, Liu Y, Singh SK, Gowda CLL, Kumar R, Zhu Y, Wang YH, Li J. Genome-Wide Association Mapping Identifies Novel Panicle Morphology Loci and Candidate Genes in Sorghum. FRONTIERS IN PLANT SCIENCE 2021; 12:743838. [PMID: 34675951 PMCID: PMC8525895 DOI: 10.3389/fpls.2021.743838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Panicle morphology is an important trait in racial classification and can determine grain yield and other agronomic traits in sorghum. In this study, we performed association mapping of panicle length, panicle width, panicle compactness, and peduncle recurving in the sorghum mini core panel measured in multiple environments with 6,094,317 single nucleotide polymorphism (SNP) markers. We mapped one locus each on chromosomes 7 and 9 to recurving peduncles and eight loci for panicle length, panicle width, and panicle compactness. Because panicle length was positively correlated with panicle width, all loci for panicle length and width were colocalized. Among the eight loci, two each were on chromosomes 1, 2, and 6, and one each on chromosomes 8 and 10. The two loci on chromosome 2, i.e., Pm 2-1 and Pm 2-2, were detected in 7 and 5 out of 11 testing environments, respectively. Pm 2-2 colocalized with panicle compactness. Candidate genes were identified from both loci. The rice Erect Panicle2 (EP2) ortholog was among the candidate genes in Pm 2-2. EP2 regulates panicle erectness and panicle length in rice and encodes a novel plant-specific protein with unknown functions. The results of this study may facilitate the molecular identification of panicle morphology-related genes and the enhancement of yield and adaptation in sorghum.
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Affiliation(s)
- Lihua Wang
- College of Agriculture, Anhui Science and Technology University, Chuzhou, China
| | - Hari D. Upadhyaya
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheruvu, India
| | - Jian Zheng
- College of Agriculture, Anhui Science and Technology University, Chuzhou, China
| | - Yanlong Liu
- College of Agriculture, Anhui Science and Technology University, Chuzhou, China
| | - Shailesh Kumar Singh
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheruvu, India
| | - C. L. L. Gowda
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheruvu, India
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Yongqun Zhu
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, China
| | - Yi-Hong Wang
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Jieqin Li
- College of Agriculture, Anhui Science and Technology University, Chuzhou, China
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Kaur B, Sandhu KS, Kamal R, Kaur K, Singh J, Röder MS, Muqaddasi QH. Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects. PLANTS 2021; 10:plants10101989. [PMID: 34685799 PMCID: PMC8541486 DOI: 10.3390/plants10101989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022]
Abstract
Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.
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Affiliation(s)
- Balwinder Kaur
- Everglades Research and Education Center, University of Florida, 3200 E. Palm Beach Rd., Belle Glade, FL 33430, USA;
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Kawalpreet Kaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
- Correspondence: or
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15
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Zhao J, Li H, Xu Y, Yin Y, Huang T, Zhang B, Wang Y, Li Y, Cao Y, An W. A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.). BMC PLANT BIOLOGY 2021; 21:350. [PMID: 34303361 PMCID: PMC8306383 DOI: 10.1186/s12870-021-03115-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/22/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Lycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. However, genetic analysis of this plant and molecular breeding for quality improvement are limited by the lack of sufficient molecular markers. RESULTS In this study, two parental strains, 'Ningqi No. 1' (Lycium barbarum L.) and 'Yunnan Gouqi' (Lycium yunnanense Kuang et A.M. Lu), and 200 F1 hybrid individuals were resequenced for genetic analysis. In total, 8,507 well-selected SNPs were developed, and a high-density genetic map (NY map) was constructed with a total genetic distance of 2,122.24 cM. A consensus genetic map was established by integrating the NY map and a previously published genetic map (NC map) containing 15,240 SNPs, with a total genetic distance of 3,058.19 cM and an average map distance of 0.21 cM. The 12 pseudochromosomes of the Lycium reference genome were anchored using this consensus genetic map, with an anchoring rate of 64.3%. Moreover, weak collinearities between the consensus map and the pepper, potato, and tomato genomes were observed. Twenty-five stable QTLs were identified for leaf- and fruit-related phenotypes, including fruit weight, fruit longitude, leaf length, the fruit index, and the leaf index; these stable QTLs were mapped to four different linkage groups, with LOD scores ranging from 2.51 to 19.37 and amounts of phenotypic variance explained from 6.2% to 51.9%. Finally, 82 out of 188 predicted genes underlying stable QTLs for fruit-related traits were differentially expressed according to RNA-seq analysis. CONCLUSIONS A chromosome-level assembly can provide a foundation for further functional genomics research for wolfberry. The genomic regions of these stably expressed QTLs could be used as targets for further fine mapping and development of molecular markers for marker-assisted selection (MAS). The present study provided valuable information on saturated SNP markers and reliable QTLs for map-based cloning of functional genes related to yield and morphological traits in Lycium spp.
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Affiliation(s)
- Jianhua Zhao
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Haoxia Li
- Desertification Control Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd, Urumchi, 830022 China
| | - Yue Yin
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Ting Huang
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Bo Zhang
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Yajun Wang
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Yanlong Li
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Youlong Cao
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Wei An
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
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Sorghum as Biofuel Crop: Interdisciplinary Methods to Enhance Productivity (Botany, Genetics, Breeding, Seed Technology, and Bioengineering). Methods Mol Biol 2021. [PMID: 34009595 DOI: 10.1007/978-1-0716-1323-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Sorghum is a versatile crop cultivated since time immemorial. It fulfills the basic needs of mankind in the contest of food, feed, fodder, nutrition, and pharmaceutical uses. Now it adds one more paramount importance as a second-generation biofuel. It offers ethanol from grain, stem (sweet sorghum), and biomass (lignocellulose), and the previous one is discouraging because of food versus fuel conflict. However sorghum lignocellulosic biofuel are gaining momentum in order to conserve nature from depleting first-generation fuel. This chapter describes interdisciplinary approaches/methods involving understanding the genetics of biofuel traits, formulating suitable breeding strategies and seed enhancement techniques to achieve higher productivity in marginal lands in order to avoid food vs. fuel conflict, and finally realization of bioethanol by involving bioengineering process. Many reviews, worldwide researches, and policy papers accepted that sorghum has tremendous potential to be used as a crop of biofuel production.
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Genetic dissection of QTLs associated with spikelet-related traits and grain size in sorghum. Sci Rep 2021; 11:9398. [PMID: 33931706 PMCID: PMC8087780 DOI: 10.1038/s41598-021-88917-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Although spikelet-related traits such as size of anther, spikelet, style, and stigma are associated with sexual reproduction in grasses, no QTLs have been reported in sorghum. Additionally, there are only a few reports on sorghum QTLs related to grain size, such as grain length, width, and thickness. In this study, we performed QTL analyses of nine spikelet-related traits (length of sessile spikelet, pedicellate spikelet, pedicel, anther, style, and stigma; width of sessile spikelet and stigma; and stigma pigmentation) and six grain-related traits (length, width, thickness, length/width ratio, length/thickness ratio, and width/thickness ratio) using sorghum recombinant inbred lines. We identified 36 and 7 QTLs for spikelet-related traits and grain-related traits, respectively, and found that most sorghum spikelet organ length- and width-related traits were partially controlled by the dwarf genes Dw1 and Dw3. Conversely, we found that these Dw genes were not strongly involved in the regulation of grain size. The QTLs identified in this study aid in understanding the genetic basis of spikelet- and grain-related traits in sorghum.
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Liu M, He W, Zhang A, Zhang L, Sun D, Gao Y, Ni P, Ma X, Cui Z, Ruan Y. Genetic analysis of maize shank length by QTL mapping in three recombinant inbred line populations. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110767. [PMID: 33487352 DOI: 10.1016/j.plantsci.2020.110767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
In maize, the shank is a unique tissue linking the stem to the ear. Shank length (SL) mainly affects the transport of photosynthetic products to the ear and the dehydration of kernels via regulated husk morphology. The limited studies on SL revealed it is a highly heritable quantitative trait controlled by significant additive and additive-dominance effects. However, the genetic basis of SL remains unclear. In this study, we analyzed three maize recombinant inbred line (RIL) populations to elucidate the molecular mechanism underlying the SL. The data indicated the SL varied among the three RIL populations and was highly heritable. Additionally, the SL was positively correlated with the husk length (HL), husk number (HN), ear length (EL), and ear weight (EW) in the BY815/K22 (BYK) and CI7/K22 (CIK) RIL populations, but was negatively correlated with the husk width (HW) in the BYK RIL population. Moreover, 10 quantitative trait loci (QTL) for SL were identified in the three RIL populations, five of which were large-effect QTL. The percentage of the total phenotypic variation explained by the QTL for SL was 13.67 %, 20.45 %, and 30.81 % in the BY815/DE3 (BYD), BYK, and CIK RIL populations, respectively. Further analyses uncovered some genetic overlap between SL and EL, SL and ear row number (ERN), SL and cob weight (CW), and SL and HN. Unlike the large-effect QTL qSL BYK-2-2, which spanned the centromere, the other four large-effect QTL were delimited to a single peak bin via bin map. Furthermore, 2, 5, 6, and 12 genes associated with SL were identified for qSL BYK-2-1, qSL CIK-2-1, qSL CIK-9-1, and qSL CIK-9-2, respectively. Five of the candidate genes for SL may contribute to the hormone metabolism and sphingolipid biosynthesis regulating cell elongation, division, differentiation, and expansion. These results may be relevant for future studies on the genetic basis of SL and for the molecular breeding of maize based on marker-assisted selection to develop new varieties with an ideal SL.
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Affiliation(s)
- Meiling Liu
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wenshu He
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China; Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, Lleida, 25198, Spain
| | - Ao Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Lijun Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Daqiu Sun
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuan Gao
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Pengzun Ni
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xinglin Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhenhai Cui
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Yanye Ruan
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China.
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Ranganatha HM, Lohithaswa HC, Pandravada A. Mapping and Validation of Major Quantitative Trait Loci for Resistance to Northern Corn Leaf Blight Along With the Determination of the Relationship Between Resistances to Multiple Foliar Pathogens of Maize ( Zea mays L.). Front Genet 2021; 11:548407. [PMID: 33584784 PMCID: PMC7878677 DOI: 10.3389/fgene.2020.548407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
Among various foliar diseases affecting maize yields worldwide, northern corn leaf blight (NCLB) is economically important. The genetics of resistance was worked out to be quantitative in nature thereby suggesting the need for the detection of quantitative trait loci (QTL) to initiate effective marker-aided breeding strategies. From the cross CML153 (susceptible) × SKV50 (resistant), 344 F2 : 3 progenies were derived and screened for their reaction to NCLB during the rainy season of 2013 and 2014. The identification of QTL affecting resistance to NCLB was carried out using the genetic linkage map constructed with 194 polymorphic SNPs and the disease data recorded on F2 : 3 progeny families. Three QTL for NCLB resistance were detected on chromosomes 2, 5, and 8 with the QTL qNCLB-8-2 explaining the highest phenotypic variation of 16.34% followed by qNCLB-5 with 10.24%. QTL for resistance to sorghum downy mildew (SDM) and southern corn rust (SCR) were also identified from one season phenotypic data, and the co-location of QTL for resistance to three foliar diseases was investigated. QTL present in chromosome bins 8.03, 5.03, 5.04, and 3.04 for resistance to NCLB, SDM, and SCR were co-localized, indicating their usefulness for the pyramiding of quantitative resistance to multiple foliar pathogens. Marker-assisted selection was practiced in the crosses CM212 × SKV50, HKI162 × SKV50, and CML153 × SKV50 employing markers linked to major QTL on chromosomes 8, 2, and 10 for NCLB, SDM, and SCR resistance, respectively. The populations were advanced to F6 stage to derive multiple disease-resistant inbred lines. Out of the 125 lines developed, 77 lines were tested for their combining ability and 39 inbred lines exhibited high general combining ability with an acceptable level of resistance to major diseases.
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Affiliation(s)
- Hosahally Muddrangappa Ranganatha
- Department of Genetics and Plant Breeding, College of Agriculture - Mandya, University of Agricultural Sciences, Bengaluru, Bengaluru, India
| | - Hirenallur Chandappa Lohithaswa
- Department of Genetics and Plant Breeding, College of Agriculture - Mandya, University of Agricultural Sciences, Bengaluru, Bengaluru, India
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Dissecting the Genetic Architecture of Biofuel-Related Traits in a Sorghum Breeding Population. G3-GENES GENOMES GENETICS 2020; 10:4565-4577. [PMID: 33051261 PMCID: PMC7718745 DOI: 10.1534/g3.120.401582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In sorghum [Sorghum bicolor (L.) Moench], hybrid cultivars for the biofuel industry are desired. Along with selection based on testcross performance, evaluation of the breeding population per se is also important for the success of hybrid breeding. In addition to additive genetic effects, non-additive (i.e., dominance and epistatic) effects are expected to contribute to the performance of early generations. Unfortunately, studies on early generations in sorghum breeding programs are limited. In this study, we analyzed a breeding population for bioenergy sorghum, which was previously developed based on testcross performance, to compare genomic selection models both trained on and evaluated for the per se performance of the 3rd generation S0 individuals. Of over 200 ancestral inbred accessions in the base population, only 13 founders contributed to the 3rd generation as progenitors. Compared to the founders, the performances of the population per se were improved for target traits. The total genetic variance within the S0 generation progenies themselves for all traits was mainly additive, although non-additive variances contributed to each trait to some extent. For genomic selection, linear regression models explicitly considering all genetic components showed a higher predictive ability than other linear and non-linear models. Although the number and effect distribution of underlying loci was different among the traits, the influence of priors for marker effects was relatively small. These results indicate the importance of considering non-additive effects for dissecting the genetic architecture of early breeding generations and predicting the performance per se.
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Zou G, Zhai G, Yan S, Li S, Zhou L, Ding Y, Liu H, Zhang Z, Zou J, Zhang L, Chen J, Xin Z, Tao Y. Sorghum qTGW1a encodes a G-protein subunit and acts as a negative regulator of grain size. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5389-5401. [PMID: 32497208 DOI: 10.1093/jxb/eraa277] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Grain size is a major determinant of grain yield in sorghum and other cereals. Over 100 quantitative trait loci (QTLs) of grain size have been identified in sorghum. However, no gene underlying any grain size QTL has been cloned. Here, we describe the fine mapping and cloning of one grain size QTL. From an F8 recombinant inbred line population derived from a cross between inbred lines 654 and LTR108, we identified 44 grain size QTLs. One QTL, qTGW1a, was detected consistently on the long arm of chromosome 1 in the span of 4 years. Using the extreme recombinants from an F2:3 fine-mapping population, qTGW1a was delimited within a ~33 kb region containing three predicted genes. One of them, SORBI_3001G341700, predicted to encode a G-protein γ subunit and homologous to GS3 in rice, is likely to be the causative gene for qTGW1a. qTGW1a appears to act as a negative regulator of grain size in sorghum. The functional allele of the putatively causative gene of qTGW1a from inbred line 654 decreased grain size, plant height, and grain yield in transgenic rice. Identification of the gene underlying qTGW1a advances our understanding of the regulatory mechanisms of grain size in sorghum and provides a target to manipulate grain size through genome editing.
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Affiliation(s)
- Guihua Zou
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guowei Zhai
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Song Yan
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Sujuan Li
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lengbo Zhou
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yanqing Ding
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Heqin Liu
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhipeng Zhang
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Jianqiu Zou
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Liyi Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Junping Chen
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Zhanguo Xin
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Yuezhi Tao
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Li S, Zhang C, Lu M, Yang D, Qian Y, Yue Y, Zhang Z, Jin F, Wang M, Liu X, Liu W, Li X. QTL mapping and GWAS for field kernel water content and kernel dehydration rate before physiological maturity in maize. Sci Rep 2020; 10:13114. [PMID: 32753586 PMCID: PMC7403598 DOI: 10.1038/s41598-020-69890-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/20/2020] [Indexed: 11/09/2022] Open
Abstract
Kernel water content (KWC) and kernel dehydration rate (KDR) are two main factors affecting maize seed quality and have a decisive influence on the mechanical harvest. It is of great importance to map and mine candidate genes related to KWCs and KDRs before physiological maturity in maize. 120 double-haploid (DH) lines constructed from Si287 with low KWC and JiA512 with high KWC were used as the mapping population. KWCs were measured every 5 days from 10 to 40 days after pollination, and KDRs were calculated. A total of 1702 SNP markers were used to construct a linkage map, with a total length of 1,309.02 cM and an average map distance of 0.77 cM. 10 quantitative trait loci (QTLs) and 27 quantitative trait nucleotides (QTNs) were detected by genome-wide composite interval mapping (GCIM) and multi-locus random-SNP-effect mixed linear model (mrMLM), respectively. One and two QTL hotspot regions were found on Chromosome 3 and 7, respectively. Analysis of the Gene Ontology showed that 2 GO terms of biological processes (BP) were significantly enriched (P ≤ 0.05) and 6 candidate genes were obtained. This study provides theoretical support for marker-assisted breeding of mechanical harvest variety in maize.
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Affiliation(s)
- Shufang Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Chunxiao Zhang
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Ming Lu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Deguang Yang
- College of Agronomy, Northeast Agricultural University, Harbin, 150030, China
| | - Yiliang Qian
- Maize Research Center, Anhui Academy of Agricultural Science, Hefei, 230001, China
| | - Yaohai Yue
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Zhijun Zhang
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Fengxue Jin
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Min Wang
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Xueyan Liu
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Wenguo Liu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China.
| | - Xiaohui Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China.
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Lin X, Armstrong M, Baker K, Wouters D, Visser RGF, Wolters PJ, Hein I, Vleeshouwers VGAA. RLP/K enrichment sequencing; a novel method to identify receptor-like protein (RLP) and receptor-like kinase (RLK) genes. THE NEW PHYTOLOGIST 2020; 227:1264-1276. [PMID: 32285454 PMCID: PMC7383770 DOI: 10.1111/nph.16608] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/27/2020] [Indexed: 05/29/2023]
Abstract
The identification of immune receptors in crop plants is time-consuming but important for disease control. Previously, resistance gene enrichment sequencing (RenSeq) was developed to accelerate mapping of nucleotide-binding domain and leucine-rich repeat containing (NLR) genes. However, resistances mediated by pattern recognition receptors (PRRs) remain less utilized. Here, our pipeline shows accelerated mapping of PRRs. Effectoromics leads to precise identification of plants with target PRRs, and subsequent RLP/K enrichment sequencing (RLP/KSeq) leads to detection of informative single nucleotide polymorphisms that are linked to the trait. Using Phytophthora infestans as a model, we identified Solanum microdontum plants that recognize the apoplastic effectors INF1 or SCR74. RLP/KSeq in a segregating Solanum population confirmed the localization of the INF1 receptor on chromosome 12, and led to the rapid mapping of the response to SCR74 to chromosome 9. By using markers obtained from RLP/KSeq in conjunction with additional markers, we fine-mapped the SCR74 receptor to a 43-kbp G-LecRK locus. Our findings show that RLP/KSeq enables rapid mapping of PRRs and is especially beneficial for crop plants with large and complex genomes. This work will enable the elucidation and characterization of the nonNLR plant immune receptors and ultimately facilitate informed resistance breeding.
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Affiliation(s)
- Xiao Lin
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Miles Armstrong
- Cell and Molecular SciencesThe James Hutton InstituteDundeeDD2 5DAUK
| | - Katie Baker
- Cell and Molecular SciencesThe James Hutton InstituteDundeeDD2 5DAUK
| | - Doret Wouters
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Richard G. F. Visser
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Pieter J. Wolters
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Ingo Hein
- Cell and Molecular SciencesThe James Hutton InstituteDundeeDD2 5DAUK
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeDD2 5DAUK
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Zhou L, Wang C, Gao X, Ding Y, Cheng B, Zhang G, Cao N, Xu Y, Shao M, Zhang L. Genome-wide variations analysis of sorghum cultivar Hongyingzi for brewing Moutai liquor. Hereditas 2020; 157:19. [PMID: 32410666 PMCID: PMC7227080 DOI: 10.1186/s41065-020-00130-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/14/2020] [Indexed: 11/28/2022] Open
Abstract
Background Hongyingzi is a sorghum (Sorghum bicolor L. Moench) cultivar for brewing Moutai liquor. For an overall understanding of the whole genome of Hongyingzi, we performed whole-genome resequencing technology to reveal its comprehensive variations. Results Compared with the BTx623 reference genome, we uncovered 1,885,774 single nucleotide polymorphisms (SNPs), 309,381 small fragments insertions and deletions (Indels), 31,966 structural variations (SVs), and 217,273 copy number variations (CNVs). These alterations conferred 29,614 gene variations. It was also predicted that 35 gene variations were related to the multidrug and toxic efflux (MATE) transporter, chalcone synthase (CHS), ATPase isoform 10 (AHA10) transporter, dihydroflavonol-4-reductase (DFR), the laccase 15 (LAC15), flavonol 3′-hydroxylase (F3′H), flavanone 3-hydroxylase (F3H), O-methyltransferase (OMT), flavonoid 3′5′ hydroxylase (F3′5′H), UDP-glucose:sterol-glucosyltransferase (SGT), flavonol synthase (FLS), and chalcone isomerase (CHI) involved in the tannin synthesis. Conclusions These results would provide theoretical supports for the molecular markers developments and gene function studies related to the tannin synthesis, and the genetic improvement of liquor-making sorghum based on the genome editing technology.
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Affiliation(s)
- Lingbo Zhou
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Can Wang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Xu Gao
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Yanqing Ding
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Bin Cheng
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Guobing Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Ning Cao
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Yan Xu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Mingbo Shao
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Liyi Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China.
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Jaganathan D, Bohra A, Thudi M, Varshney RK. Fine mapping and gene cloning in the post-NGS era: advances and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1791-1810. [PMID: 32040676 PMCID: PMC7214393 DOI: 10.1007/s00122-020-03560-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/29/2020] [Indexed: 05/18/2023]
Abstract
Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genome-wide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.
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Affiliation(s)
- Deepa Jaganathan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Abhishek Bohra
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
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Wang F, Zhang J, Chen Y, Zhang C, Gong J, Song Z, Zhou J, Wang J, Zhao C, Jiao M, Liu A, Du Z, Yuan Y, Fan S, Zhang J. Identification of candidate genes for key fibre-related QTLs and derivation of favourable alleles in Gossypium hirsutum recombinant inbred lines with G. barbadense introgressions. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:707-720. [PMID: 31446669 PMCID: PMC7004909 DOI: 10.1111/pbi.13237] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/15/2019] [Indexed: 05/02/2023]
Abstract
Fine mapping QTLs and identifying candidate genes for cotton fibre-quality and yield traits would be beneficial to cotton breeding. Here, we constructed a high-density genetic map by specific-locus amplified fragment sequencing (SLAF-seq) to identify QTLs associated with fibre-quality and yield traits using 239 recombinant inbred lines (RILs), which was developed from LMY22 (a high-yield Gossypium hirsutumL. cultivar) × LY343 (a superior fibre-quality germplasm with G. barbadenseL. introgressions). The genetic map spanned 3426.57 cM, including 3556 SLAF-based SNPs and 199 SSR marker loci. A total of 104 QTLs, including 67 QTLs for fibre quality and 37 QTLs for yield traits, were identified with phenotypic data collected from 7 environments. Among these, 66 QTLs were co-located in 19 QTL clusters on 12 chromosomes, and 24 QTLs were detected in three or more environments and determined to be stable. We also investigated the genomic components of LY343 and their contributions to fibre-related traits by deep sequencing the whole genome of LY343, and we found that genomic components from G. hirsutum races (which entered LY343 via its G. barbadense parent) contributed more favourable alleles than those from G. barbadense. We further identified six putative candidate genes for stable QTLs, including Gh_A03G1147 (GhPEL6), Gh_D07G1598 (GhCSLC6) and Gh_D13G1921 (GhTBL5) for fibre-length QTLs and Gh_D03G0919 (GhCOBL4), Gh_D09G1659 (GhMYB4) and Gh_D09G1690 (GhMYB85) for lint-percentage QTLs. Our results provide comprehensive insight into the genetic basis of the formation of fibre-related traits and would be helpful for cloning fibre-development-related genes as well as for marker-assisted genetic improvement in cotton.
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Affiliation(s)
- Furong Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Chuanyun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Juwu Gong
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhangqiang Song
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Juan Zhou
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Jingjing Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Chengjie Zhao
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Mengjia Jiao
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Aiying Liu
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhaohai Du
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Youlu Yuan
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Shoujin Fan
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
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Jiang S, Yang C, Xu Q, Wang L, Yang X, Song X, Wang J, Zhang X, Li B, Li H, Li Z, Li W. Genetic Dissection of Germinability under Low Temperature by Building a Resequencing Linkage Map in japonica Rice. Int J Mol Sci 2020; 21:ijms21041284. [PMID: 32074988 PMCID: PMC7072905 DOI: 10.3390/ijms21041284] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/06/2020] [Accepted: 02/13/2020] [Indexed: 12/17/2022] Open
Abstract
Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature germination (LTG) ability can significantly accelerate cold-tolerant rice breeding to ensure the wide application of rice cultivation through the direct seeding method. In this study, we identified 11 QTLs for LTG using 144 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant variety, Lijiangxintuanheigu (LTH), and a cold-sensitive variety, Shennong265 (SN265). By resequencing two parents and RIL lines, a high-density bin map, including 2,828 bin markers, was constructed using 123,859 single-nucleotide polymorphisms (SNPs) between two parents. The total genetic distance corresponding to all 12 chromosome linkage maps was 2,840.12 cm. Adjacent markers were marked by an average genetic distance of 1.01 cm, corresponding to a 128.80 kb physical distance. Eight and three QTL alleles had positive effects inherited from LTH and SN265, respectively. Moreover, a pleiotropic QTL was identified for a higher number of erected panicles and a higher grain number on Chr-9 near the previously cloned DEP1 gene. Among the LTG QTLs, qLTG3 and qLTG7b were also located at relatively small genetic intervals that define two known LTG genes, qLTG3-1 and OsSAP16. Sequencing comparisons between the two parents demonstrated that LTH possesses qLTG3-1 and OsSAP16 genes, and SN-265 owns the DEP1 gene. These comparison results strengthen the accuracy and mapping resolution power of the bin map and population. Later, fine mapping was done for qLTG6 at 45.80 kb through four key homozygous recombinant lines derived from a population with 1569 segregating plants. Finally, LOC_Os06g01320 was identified as the most possible candidate gene for qLTG6, which contains a missense mutation and a 32-bp deletion/insertion at the promoter between the two parents. LTH was observed to have lower expression levels in comparison with SN265 and was commonly detected at low temperatures. In conclusion, these results strengthen our understanding of the impacts of cold temperature stress on seed vigor and germination abilities and help improve the mechanisms of rice breeding programs to breed cold-tolerant varieties.
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Affiliation(s)
- Shukun Jiang
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
- Correspondence: (S.J.); (Z.L.); (W.L.)
| | - Chao Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (C.Y.); (X.S.)
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang 110866, China; (Q.X.); (J.W.)
| | - Lizhi Wang
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
| | - Xianli Yang
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
| | - Xianwei Song
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (C.Y.); (X.S.)
| | - Jiayu Wang
- Rice Research Institute of Shenyang Agricultural University, Shenyang 110866, China; (Q.X.); (J.W.)
| | - Xijuan Zhang
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
| | - Bo Li
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
| | - Hongyu Li
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163000, China;
| | - Zhugang Li
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
- Correspondence: (S.J.); (Z.L.); (W.L.)
| | - Wenhua Li
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
- Correspondence: (S.J.); (Z.L.); (W.L.)
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Wei J, Chen Y, Wang W. A High-Density Genetic Linkage Map and QTL Mapping for Sex and Growth-Related Traits of Large-Scale Loach ( Paramisgurnus dabryanus). Front Genet 2019; 10:1023. [PMID: 31708968 PMCID: PMC6823184 DOI: 10.3389/fgene.2019.01023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/24/2019] [Indexed: 12/30/2022] Open
Abstract
Large-scale loach (Paramisgurnus dabryanus) is a commercially important species in East Asia; however, the cultured population that exhibited degradation of germplasm resource cannot meet the market needs, and the genome resources for P. dabryanus are still lacking. In this study, the first high-density genetic map of P. dabryanus was constructed using 15,830 SNP markers based on high-throughput sequencing with an improved SLAF-seq strategy. The quantitative trait locus (QTL) mapping for sex, growth, and morphology traits was performed for the first time. The genetic map spanned 4,657.64 cM in length with an average inter-marker distance of 0.30 cM. QTL mapping and association analysis identified eight QTLs of growth traits, nine QTLs of morphology traits, and five QTLs of sex-related traits, respectively. Interestingly, the most significant QTLs for almost all the traits were concentrated on the same linkage group LG11. Seven candidate markers and 12 potentially key genes, which were associated with sex determination and growth, were identified within the overlapped QTL regions on LG11. Further, the first genome survey analysis of P. dabryanus was performed which represents the first step toward fully decoding the P. dabryanus genome. The genome scaffolds were anchored to the high-density linkage map, spanning 960.27 Mb of P. dabryanus reference genome. The collinearity analysis revealed a high level of collinearity between the genetic map and the reference genome of P. dabryanus. Moreover, a certain degree of homology was observed between large-scale loach and zebrafish using comparative genomic analysis. The constructed high-density genetic map was an important basis for QTL fine mapping, genome assembly, and genome comparison. The present study will provide a valuable resource for future marker-assisted breeding, and further genetic and genomic researches in P. dabryanus.
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Affiliation(s)
- Jin Wei
- Key Lab of Agricultural Animal Genetics, College of Fisheries, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Yuanyuan Chen
- Key Lab of Agricultural Animal Genetics, College of Fisheries, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Weimin Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
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Cao Y, Li S, Chen G, Wang Y, Bhat JA, Karikari B, Kong J, Gai J, Zhao T. Deciphering the Genetic Architecture of Plant Height in Soybean Using Two RIL Populations Sharing a Common M8206 Parent. PLANTS 2019; 8:plants8100373. [PMID: 31561497 PMCID: PMC6843848 DOI: 10.3390/plants8100373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/09/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022]
Abstract
Plant height (PH) is an important agronomic trait that is closely related to soybean yield and quality. However, it is a complex quantitative trait governed by multiple genes and is influenced by environment. Unraveling the genetic mechanism involved in PH, and developing soybean cultivars with desirable PH is an imperative goal for soybean breeding. In this regard, the present study used high-density linkage maps of two related recombinant inbred line (RIL) populations viz., MT and ZM evaluated in three different environments to detect additive and epistatic effect quantitative trait loci (QTLs) as well as their interaction with environments for PH in Chinese summer planting soybean. A total of eight and 12 QTLs were detected by combining the composite interval mapping (CIM) and mixed-model based composite interval mapping (MCIM) methods in MT and ZM populations, respectively. Among these QTLs, nine QTLs viz., QPH-2, qPH-6-2MT, QPH-6, qPH-9-1ZM, qPH-10-1ZM, qPH-13-1ZM, qPH-16-1MT, QPH-17 and QPH-19 were consistently identified in multiple environments or populations, hence were regarded as stable QTLs. Furthermore, Out of these QTLs, three QTLs viz., qPH-4-2ZM, qPH-15-1MT and QPH-17 were novel. In particular, QPH-17 could detect in both populations, which was also considered as a stable and major QTL in Chinese summer planting soybean. Moreover, eleven QTLs revealed significant additive effects in both populations, and out of them only six showed additive by environment interaction effects, and the environment-independent QTLs showed higher additive effects. Finally, six digenic epistatic QTLs pairs were identified and only four additive effect QTLs viz., qPH-6-2MT, qPH-19-1MT/QPH-19, qPH-5-1ZM and qPH-17-1ZM showed epistatic effects. These results indicate that environment and epistatic interaction effects have significant influence in determining genetic basis of PH in soybean. These results would not only increase our understanding of the genetic control of plant height in summer planting soybean but also provide support for implementing marker assisted selection (MAS) in developing cultivars with ideal plant height as well as gene cloning to elucidate the mechanisms of plant height.
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Affiliation(s)
- Yongce Cao
- MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China.
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Science, Yan'an University, Yan'an 716000, China.
| | - Shuguang Li
- MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Guoliang Chen
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Science, Yan'an University, Yan'an 716000, China.
| | - Yanfeng Wang
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Science, Yan'an University, Yan'an 716000, China.
| | - Javaid Akhter Bhat
- MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Benjamin Karikari
- MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiejie Kong
- MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Junyi Gai
- MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tuanjie Zhao
- MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China.
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Sorghum as a Novel Crop for Central Europe: Using a Broad Diversity Set to Dissect Temperate-Adaptation. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9090535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sorghum (Sorghum bicolor L. Moench) is a promising novel crop for Central Europe. However, enhancements in cold tolerance and early maturity are essential for a successful adaptation to cooler climates. We scored a broad sorghum diversity set (n = 338) for early chilling tolerance, high-latitude adaptation, and bioenergy related agronomical traits in multi-environment trials. Our results show a high phenotypic variation and medium to high heritabilities for most traits, indicating that a robust breeding progress is feasible. Several public accessions with a good adaptation to cooler climates were identified, which can serve as valuable base material for sorghum breeding in temperate areas. Genome-wide association studies reveal a polygenic (quantitative) character for most of the traits, confirming previous studies. Hence, for practical breeding, it will be difficult to conduct efficient marker-assisted selection for temperate-adaptation traits in genetically diverse material.
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Han J, Han D, Guo Y, Yan H, Wei Z, Tian Y, Qiu L. QTL mapping pod dehiscence resistance in soybean (Glycine max L. Merr.) using specific-locus amplified fragment sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2253-2272. [PMID: 31161230 PMCID: PMC6647749 DOI: 10.1007/s00122-019-03352-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 04/25/2019] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE We constructed a high-density genetic linkage map comprising 4,593 SLAF markers using specific-locus amplified fragment sequencing and identified six quantitative trait loci for pod dehiscence resistance in soybean. Pod dehiscence is necessary for propagation in wild soybean (Glycine soja). It is a major component causing yield losses in cultivated soybean, however, and thus, cultivated soybean varieties have been artificially selected for resistance to pod dehiscence. Detecting quantitative trait loci (QTLs) related to pod dehiscence is required for molecular marker-assisted selection for breeding new varieties with pod dehiscence resistance. In this study, we constructed a high-density genetic linkage map using 260 recombinant inbred lines derived from the cultivars of Heihe 43 (pod-indehiscent) (ZDD24325) and Heihe 18 (pod-dehiscent) (ZDD23620). The map contained 4953 SLAF markers spanning 1478.86 cM on 20 linkage groups with an average distance between adjacent markers of 0.53 cM. In total, six novel QTLs related to pod dehiscence were mapped using inclusive composite interval mapping, explaining 7.22-24.44% of the phenotypic variance across 3 years, including three stable QTLs (qPD01, qPD05-1 and qPD08-1), that had been validated by developing CAPS/dCAPS markers. Based on the SNP/Indel and significant differential expression analyses of two parents, seven genes were selected as candidate genes for future study. The high-density map, three stable QTLs and their molecular markers will be helpful for map-based cloning of pod dehiscence resistance genes and marker-assisted selection of pod dehiscence resistance in soybean breeding.
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Affiliation(s)
- Jianan Han
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Dezhi Han
- Institute of Soybean Research, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China
| | - Yong Guo
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Hongrui Yan
- Institute of Soybean Research, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China
| | - Zhongyan Wei
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Yu Tian
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Lijuan Qiu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China.
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Zhang X, Hina A, Song S, Kong J, Bhat JA, Zhao T. Whole-genome mapping identified novel "QTL hotspots regions" for seed storability in soybean (Glycine max L.). BMC Genomics 2019; 20:499. [PMID: 31208334 PMCID: PMC6580613 DOI: 10.1186/s12864-019-5897-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 06/11/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Seed aging in soybean is a serious challenge for agronomic production and germplasm preservation. However, its genetic basis remains largely unclear in soybean. Unraveling the genetic mechanism involved in seed aging, and enhancing seed storability is an imperative goal for soybean breeding. The aim of this study is to identify quantitative trait loci (QTLs) using high-density genetic linkage maps of soybean for seed storability. In this regard, two recombinant inbred line (RIL) populations derived from Zhengyanghuangdou × Meng 8206 (ZM6) and Linhefenqingdou × Meng 8206 (LM6) crosses were evaluated for three seed-germination related traits viz., germination rate (GR), normal seedling length (SL) and normal seedling fresh weight (FW) under natural and artificial aging conditions to map QTLs for seed storability. RESULTS A total of 34 QTLs, including 13 QTLs for GR, 11 QTLs for SL and 10 QTLs for FW, were identified on 11 chromosomes with the phenotypic variation ranged from 7.30 to 23.16% under both aging conditions. All these QTLs were novel, and 21 of these QTLs were clustered in five QTL-rich regions on four different chromosomes viz., Chr3, Chr5, Chr17 &Chr18, among them the highest concentration of seven and six QTLs were found in "QTL hotspot A" (Chr17) and "QTL hotspot B" (Chr5), respectively. Furthermore, QTLs within all the five QTL clusters are linked to at least two studied traits, which is also supported by highly significant correlation between the three germination-related traits. QTLs for seed-germination related traits in "QTL hotspot B" were found in both RIL populations and aging conditions, and also QTLs underlying "QTL hotspot A" are identified in both RIL populations under artificial aging condition. These are the stable genomic regions governing the inheritance of seed storability in soybean, and will be the main focus for soybean breeders. CONCLUSION This study uncovers the genetic basis of seed storability in soybean. The newly identified QTLs provides valuable information, and will be main targets for fine mapping, candidate gene identification and marker-assisted breeding. Hence, the present study is the first report for the comprehensive and detailed investigation of genetic architecture of seed storability in soybean.
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Affiliation(s)
- Xi Zhang
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Aiman Hina
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shiyu Song
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiejie Kong
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Javaid Akhter Bhat
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tuanjie Zhao
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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Karikari B, Li S, Bhat JA, Cao Y, Kong J, Yang J, Gai J, Zhao T. Genome-Wide Detection of Major and Epistatic Effect QTLs for Seed Protein and Oil Content in Soybean Under Multiple Environments Using High-Density Bin Map. Int J Mol Sci 2019; 20:E979. [PMID: 30813455 PMCID: PMC6412760 DOI: 10.3390/ijms20040979] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/01/2019] [Accepted: 02/19/2019] [Indexed: 01/25/2023] Open
Abstract
Seed protein and oil content are the two important traits determining the quality and value of soybean. Development of improved cultivars requires detailed understanding of the genetic basis underlying the trait of interest. However, it is prerequisite to have a high-density linkage map for precisely mapping genomic regions, and therefore the present study used high-density genetic map containing 2267 recombination bin markers distributed on 20 chromosomes and spanned 2453.79 cM with an average distance of 1.08 cM between markers using restriction-site-associated DNA sequencing (RAD-seq) approach. A recombinant inbred line (RIL) population of 104 lines derived from a cross between Linhefenqingdou and Meng 8206 cultivars was evaluated in six different environments to identify main- and epistatic-effect quantitative trait loci (QTLs)as well as their interaction with environments. A total of 44 main-effect QTLs for protein and oil content were found to be distributed on 17 chromosomes, and 15 novel QTL were identified for the first time. Out of these QTLs, four were major and stable QTLs, viz., qPro-7-1, qOil-8-3, qOil-10-2 and qOil-10-4, detected in at least two environments plus combined environment with R² values >10%. Within the physical intervals of these four QTLs, 111 candidate genes were screened for their direct or indirect involvement in seed protein and oil biosynthesis/metabolism processes based on gene ontology and annotation information. Based on RNA sequencing (RNA-seq) data analysis, 15 of the 111 genes were highly expressed during seed development stage and root nodules that might be considered as the potential candidate genes. Seven QTLs associated with protein and oil content exhibited significant additive and additive × environment interaction effects, and environment-independent QTLs revealed higher additive effects. Moreover, three digenic epistatic QTLs pairs were identified, and no main-effect QTLs showed epistasis. In conclusion, the use of a high-density map identified closely linked flanking markers, provided better understanding of genetic architecture and candidate gene information, and revealed the scope available for improvement of soybean quality through marker assisted selection (MAS).
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Affiliation(s)
- Benjamin Karikari
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shuguang Li
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an 223001, China.
| | - Javaid Akhter Bhat
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yongce Cao
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
- College of Life Science, Yan'an University, Yan'an 716000, China.
| | - Jiejie Kong
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiayin Yang
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an 223001, China.
| | - Junyi Gai
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tuanjie Zhao
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
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Cao Z, Guo Y, Yang Q, He Y, Fetouh MI, Warner RM, Deng Z. Genome-wide identification of quantitative trait loci for important plant and flower traits in petunia using a high-density linkage map and an interspecific recombinant inbred population derived from Petunia integrifolia and P. axillaris. HORTICULTURE RESEARCH 2019; 6:27. [PMID: 30729017 PMCID: PMC6355904 DOI: 10.1038/s41438-018-0091-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/19/2018] [Indexed: 05/26/2023]
Abstract
Petunia is a very important flower in the global floriculture industry and has played a critical role as a model in plant genetic studies. Owing to limited genetic variability in commercial germplasm, development of novel petunia phenotypes and new varieties has become increasingly difficult. To enrich petunia germplasm and facilitate genetic improvement, it is important to explore genetic variation in progenitor species that may contain highly valuable genes/alleles. In this study, an interspecific recombinant inbred population (168 recombinant inbreds) derived from Petunia integrifolia × P. axillaris were phenotyped for days to anthesis (DTA), flower count (Flower_C), flower diameter (Flower_D), flower length (Flower_L), plant height (Plant_H), plant spread (Plant_S), and plant size (Plant_Z) in 2014 and 2015. Transgressive segregation was observed for all traits in both years. The broad-sense heritability on a 2-year basis varied from 0.38 (Flower_C) to 0.82 (Flower_L). Ten QTL were consistently identified in both years and by two mapping strategies [multiple QTL mapping (MQM) in MapQTL and inclusive composite interval mapping (ICIM) in IciMapping]. Major QTL explained up to 30.2, 35.5, and 47.1% of the total phenotypic variation for Plant_S, Flower_L, and Flower_D, respectively. These findings should be of significant values for introgression of desirable genes from wild petunias into commercial varieties and future genetic improvement of this important flower.
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Affiliation(s)
- Zhe Cao
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, IFAS, University of Florida, 14625 County Road 672, Wimauma, FL 33598 USA
| | - Yufang Guo
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Qian Yang
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, IFAS, University of Florida, 14625 County Road 672, Wimauma, FL 33598 USA
| | - Yanhong He
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, Hubei China
| | - Mohammed I. Fetouh
- Department of Horticulture, Faculty of Agriculture, Tanta University, Tanta, 31527 Egypt
| | - Ryan M. Warner
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, IFAS, University of Florida, 14625 County Road 672, Wimauma, FL 33598 USA
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Malmberg MM, Barbulescu DM, Drayton MC, Shinozuka M, Thakur P, Ogaji YO, Spangenberg GC, Daetwyler HD, Cogan NOI. Evaluation and Recommendations for Routine Genotyping Using Skim Whole Genome Re-sequencing in Canola. FRONTIERS IN PLANT SCIENCE 2018; 9:1809. [PMID: 30581450 PMCID: PMC6292936 DOI: 10.3389/fpls.2018.01809] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/21/2018] [Indexed: 05/25/2023]
Abstract
Whole genome sequencing offers genome wide, unbiased markers, and inexpensive library preparation. With the cost of sequencing decreasing rapidly, many plant genomes of modest size are amenable to skim whole genome resequencing (skim WGR). The use of skim WGR in diverse sample sets without the use of imputation was evaluated in silico in 149 canola samples representative of global diversity. Fastq files with an average of 10x coverage of the reference genome were used to generate skim samples representing 0.25x, 0.5x, 1x, 2x, 3x, 4x, and 5x sequencing coverage. Applying a pre-defined list of SNPs versus de novo SNP discovery was evaluated. As skim WGR is expected to result in some degree of insufficient allele sampling, all skim coverage levels were filtered at a range of minimum read depths from a relaxed minimum read depth of 2 to a stringent read depth of 5, resulting in 28 list-based SNP sets. As a broad recommendation, genotyping pre-defined SNPs between 1x and 2x coverage with relatively stringent depth filtering is appropriate for a diverse sample set of canola due to a balance between marker number, sufficient accuracy, and sequencing cost, but depends on the intended application. This was experimentally examined in two sample sets with different genetic backgrounds: 1x coverage of 1,590 individuals from 84 Australian spring type four-parent crosses aimed at maximizing diversity as well as one commercial F1 hybrid, and 2x coverage of 379 doubled haploids (DHs) derived from a subset of the four-parent crosses. To determine optimal coverage in a simpler genetic background, the DH sample sequence coverage was further down sampled in silico. The flexible and cost-effective nature of the protocol makes it highly applicable across a range of species and purposes.
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Affiliation(s)
- M. Michelle Malmberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | | | - Michelle C. Drayton
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Maiko Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Preeti Thakur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Yvonne O. Ogaji
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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Genome-Wide Search for Quantitative Trait Loci Controlling Important Plant and Flower Traits in Petunia Using an Interspecific Recombinant Inbred Population of Petunia axillaris and Petunia exserta. G3-GENES GENOMES GENETICS 2018; 8:2309-2317. [PMID: 29764961 PMCID: PMC6027870 DOI: 10.1534/g3.118.200128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting of 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia.
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Tornqvist CE, Taylor M, Jiang Y, Evans J, Buell CR, Kaeppler SM, Casler MD. Quantitative Trait Locus Mapping for Flowering Time in a Lowland × Upland Switchgrass Pseudo-F2 Population. THE PLANT GENOME 2018; 11. [PMID: 30025023 DOI: 10.3835/plantgenome2017.10.0093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Flowering is an important developmental event in switchgrass (), as the time to complete the life cycle affects overall biomass accumulation. The objective of this study was to generate a linkage map using single nucleotide polymorphism (SNP) markers to identify quantitative trait loci (QTL) associated with flowering time. A pseudo-F population was created by crossing two siblings derived from an initial cross between the lowland population Ellsworth and the upland cultivar Summer. Heading and anthesis dates were collected for 2 yr at two locations: DeKalb, IL and Lafayette, IN. Nine QTL for flowering time were detected, two of which were heading-associated, four anthesis-associated, and three associated with both heading and anthesis. One QTL on linkage group (LG) 2a was detected for heading and anthesis in each location and year when environments were analyzed separately, and in a combined analysis across both locations and years. The effect on heading and anthesis of the QTL on LG 2a ranged from 4 to 13 and 5 to 9 d, respectively, depending on environment. Our findings validate QTL for switchgrass flowering time from previous research and identified additional QTL. Based on the switchgrass reference genome version 1.1, flowering time gene homologs reside near the LG 2a QTL and include PSEUDO RESPONSE REGULATOR 5, SUPPRESSOR OF FRIGIDA 4, and APETALA 1, respectively involved in the circadian clock, vernalization, and floral meristem identity. Markers linked to the QTL can be used to improve the efficiency of breeding switchgrass for delayed flowering to increase biomass yield.
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Zhang Y, Wang L, Gao Y, Li D, Yu J, Zhou R, Zhang X. Genetic dissection and fine mapping of a novel dt gene associated with determinate growth habit in sesame. BMC Genet 2018; 19:38. [PMID: 29902971 PMCID: PMC6003200 DOI: 10.1186/s12863-018-0614-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As an important oil crop, growth habit of sesame (Sesamum indicum L.) is naturally indeterminate, which brings about asynchronous maturity of capsules and causes loss of yield. RESULTS The genetic basis of determinate growth habit in sesame was investigated by classical genetic analysis through multiple populations, results revealed that it was controlled by an unique recessive gene. The genotyping by sequencing (GBS) approach was employed for high-throughput SNP identification and genotyping in the F2 population, then a high density bin map was constructed, the map was 1086.403 cM in length, which consisted of 1184 bins (13,679 SNPs), with an average of 0.918 cM between adjacent bins. Based on bin mapping in conjunction with SSR markers analysis in targeted region, the novel sesame determinacy gene was mapped on LG09 in a genome region of 41 kb. CONCLUSIONS This study dissected genetic basis of determinate growth habit in sesame, constructed a new high-density bin map and mapped a novel determinacy gene. Results of this study demonstrate that we employed an optimized approach to get fine-accuracy, high-resolution and high-efficiency mapping result in sesame. The findings provided important foundation for sesame determinacy gene cloning and were expected to be applied in breeding for cultivars suited to mechanized production.
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Affiliation(s)
- Yanxin Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Yuan Gao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Donghua Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Jingyin Yu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China.
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Shu J, Liu Y, Zhang L, Li Z, Fang Z, Yang L, Zhuang M, Zhang Y, Lv H. QTL-seq for rapid identification of candidate genes for flowering time in broccoli × cabbage. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:917-928. [PMID: 29305701 DOI: 10.1007/s00122-017-3047-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/17/2017] [Indexed: 05/27/2023]
Abstract
A major QTL controlling early flowering in broccoli × cabbage was identified by marker analysis and next-generation sequencing, corresponding to GRF6 gene conditioning flowering time in Arabidopsis. Flowering is an important agronomic trait for hybrid production in broccoli and cabbage, but the genetic mechanism underlying this process is unknown. In this study, segregation analysis with BC1P1, BC1P2, F2, and F2:3 populations derived from a cross between two inbred lines "195" (late-flowering) and "93219" (early flowering) suggested that flowering time is a quantitative trait. Next, employing a next-generation sequencing-based whole-genome QTL-seq strategy, we identified a major genomic region harboring a robust flowering time QTL using an F2 mapping population, designated Ef2.1 on cabbage chromosome 2 for early flowering. Ef2.1 was further validated by indel (insertion or deletion) marker-based classical QTL mapping, explaining 51.5% (LOD = 37.67) and 54.0% (LOD = 40.5) of the phenotypic variation in F2 and F2:3 populations, respectively. Combined QTL-seq and classical QTL analysis narrowed down Ef1.1 to a 228-kb genomic region containing 29 genes. A cabbage gene, Bol024659, was identified in this region, which is a homolog of GRF6, a major gene regulating flowering in Arabidopsis, and was designated BolGRF6. qRT-PCR study of the expression level of BolGRF6 revealed significantly higher expression in the early flowering genotypes. Taken together, our results provide support for BolGRF6 as a possible candidate gene for early flowering in the broccoli line 93219. The identified candidate genomic regions and genes may be useful for molecular breeding to improve broccoli and cabbage flowering times.
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Affiliation(s)
- Jinshuai Shu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Yumei Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China.
| | - Lili Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Zhansheng Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
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Cai Z, Cheng Y, Ma Z, Liu X, Ma Q, Xia Q, Zhang G, Mu Y, Nian H. Fine-mapping of QTLs for individual and total isoflavone content in soybean (Glycine max L.) using a high-density genetic map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:555-568. [PMID: 29159422 DOI: 10.1007/s00122-017-3018-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 11/04/2017] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE Fifteen stable QTLs were identified using a high-density soybean genetic map across multiple environments. One major QTL, qIF5-1, contributing to total isoflavone content explained phenotypic variance 49.38, 43.27, 46.59, 45.15 and 52.50%, respectively. Soybeans (Glycine max L.) are a major source of dietary isoflavones. To identify novel quantitative trait loci (QTL) underlying isoflavone content, and to improve the accuracy of marker-assisted breeding in soybean, a valuable mapping population comprised of 196 F7:8-10 recombinant inbred lines (RILs, Huachun 2 × Wayao) was utilized to evaluate individual and total isoflavone content in plants grown in four different environments in Guangdong. A high-density genetic linkage map containing 3469 recombination bin markers based on 0.2 × restriction site-associated DNA tag sequencing (RAD-seq) technology was used to finely map QTLs for both individual and total isoflavone contents. Correlation analyses showed that total isoflavone content, and that of five individual isoflavone, was significantly correlated across the four environments. Based on the high-density genetic linkage map, a total of 15 stable quantitative trait loci (QTLs) associated with isoflavone content across multiple environments were mapped onto chromosomes 02, 05, 07, 09, 10, 11, 13, 16, 17, and 19. Further, one of them, qIF5-1, localized to chromosomes 05 (38,434,171-39,045,620 bp) contributed to almost all isoflavone components across all environments, and explained 6.37-59.95% of the phenotypic variance, especially explained 49.38, 43.27, 46.59, 45.15 and 52.50% for total isoflavone. The results obtained in the present study will pave the way for a better understanding of the genetics of isoflavone accumulation and reveals the scope available for improvement of isoflavone content through marker-assisted selection.
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Affiliation(s)
- Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China
| | - Zhuwen Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Xinguo Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China
| | - Qiuju Xia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086, People's Republic of China
| | - Gengyun Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086, People's Republic of China
| | - Yinghui Mu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China.
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China.
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Lai X, Yan L, Lu Y, Schnable JC. Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:843-855. [PMID: 29265526 DOI: 10.1111/tpj.13806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/27/2017] [Accepted: 12/04/2017] [Indexed: 05/14/2023]
Abstract
The domestication of diverse grain crops from wild grasses was a result of artificial selection for a suite of overlapping traits producing changes referred to in aggregate as 'domestication syndrome'. Parallel phenotypic change can be accomplished by either selection on orthologous genes or selection on non-orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many 'classic' domestication genes identified through quantitative trait locus mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization part of domestication targeted small and largely non-overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.
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Affiliation(s)
- Xianjun Lai
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lang Yan
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
- Laboratory of Functional Genome and Application of Potato, Xichang College, Liangshan, 615000, China
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - James C Schnable
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
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Wang B, Liu H, Liu Z, Dong X, Guo J, Li W, Chen J, Gao C, Zhu Y, Zheng X, Chen Z, Chen J, Song W, Hauck A, Lai J. Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays). BMC PLANT BIOLOGY 2018; 18:17. [PMID: 29347909 PMCID: PMC5774087 DOI: 10.1186/s12870-018-1233-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/14/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Plant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested. RESULTS Here, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs). Accurately mapping of well studied genes P1, pl1 and r1 underlying silk color demonstrated the map quality. After QTL analysis, a total of 51 loci were mapped for six PATs. Although all of them belong to minor effect alleles, the lengths of the QTL intervals, with a minimum and median of 1.03 and 3.40 Mb respectively, were remarkably reduced as compared with previous reports using smaller size of population or small number of markers. Several genes with known function in maize were shown to be overlapping with or close neighboring to these QTL peaks, including na1, td1, d3 for plant height, ra1 for tassel branch number, and zfl2 for tassel length. To further confirm our mapping results, a plant height QTL, qPH1a, was verified by an introgression lines (ILs). CONCLUSIONS We demonstrated a method for high resolution mapping of minor effect QTLs in maize, and the resulted comprehensive QTLs for PATs are valuable for maize molecular breeding in the future.
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Affiliation(s)
- Baobao Wang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Han Liu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Zhipeng Liu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Xiaomei Dong
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Jinjie Guo
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Wei Li
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Jing Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Chi Gao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Yanbin Zhu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Xinmei Zheng
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Zongliang Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Andrew Hauck
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
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Scheben A, Batley J, Edwards D. Revolution in Genotyping Platforms for Crop Improvement. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 164:37-52. [PMID: 29356847 DOI: 10.1007/10_2017_47] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the past decade, the application of high-throughput sequencing to crop genotyping has given rise to novel platforms capable of genotyping tens of thousands of genome-wide DNA markers. Coupled with the decreasing costs of sequencing, this rapid increase in markers allows accelerated and highly accurate genotyping of entire crop populations and diversity sets using single nucleotide polymorphisms (SNPs). These revolutionary advances accelerate crop improvement by facilitating a more precise connection of phenotype to genotype through association studies, linkage mapping and diversity analysis. The platforms driving the advances in genotyping are array technologies and genotyping by sequencing (GBS) methods, which include both low-coverage whole genome resequencing (skim sequencing) and reduced representation sequencing (RRS) approaches. Here, we outline and compare these genotyping platforms and provide a perspective on the promising future of crop genotyping. While SNP arrays provide high quality, simple handling, and unchallenging analysis, the lower cost of RRS and the greater data volume produced by skim sequencing suggest that use of GBS will become more prevalent in crop genomics as sequencing costs decrease and data analysis becomes more streamlined. Graphical Abstract.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia. .,Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
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Wang B, Zhu Y, Zhu J, Liu Z, Liu H, Dong X, Guo J, Li W, Chen J, Gao C, Zheng X, E L, Lai J, Zhao H, Song W. Identification and Fine-Mapping of a Major Maize Leaf Width QTL in a Re-sequenced Large Recombinant Inbred Lines Population. FRONTIERS IN PLANT SCIENCE 2018; 9:101. [PMID: 29487604 PMCID: PMC5816676 DOI: 10.3389/fpls.2018.00101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/18/2018] [Indexed: 05/11/2023]
Abstract
Leaf width (LW) influences canopy architecture of population-cultured maize and can thus contribute to density breeding. In previous studies, almost all maize LW-related mutants have extreme effect on leaf development or accompanied unfavorable phenotypes. In addition, the identification of quantitative trait loci (QTLs) has been resolution-limited, with cloning and fine-mapping rarely performed. Here, we constructed a bin map for 670 recombinant inbred lines (RILs) using ∼1.2 billion 100-bp re-sequencing reads. QTL analysis of the LW trait directly narrowed the major effect QTL, qLW4, to a ∼270-kb interval. A fine-mapping population and near-isogenic lines (NILs) were quickly constructed using a key RIL harboring heterozygous genotypes across the qLW4 region. A recombinant-derived progeny testing strategy was subsequently used to further fine-map qLW4 to a 55-kb interval. Examination of NILs revealed that qLW4 has a completely dominant effect on LW, with no additional effect on leaf length. Candidate gene analysis suggested that this locus may be a novel LW controlling allele in maize. Our findings demonstrate the advantage of large-population high-density bin mapping, and suggest a strategy for efficiently fine-mapping or even cloning of QTLs. These results should also be helpful for further dissection of the genetic mechanism of LW variation, and benefit maize density breeding.
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Li J, Tang W, Zhang YW, Chen KN, Wang C, Liu Y, Zhan Q, Wang C, Wang SB, Xie SQ, Wang L. Genome-Wide Association Studies for Five Forage Quality-Related Traits in Sorghum ( Sorghum bicolor L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1146. [PMID: 30186292 PMCID: PMC6111974 DOI: 10.3389/fpls.2018.01146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/18/2018] [Indexed: 05/20/2023]
Abstract
Understanding the genetic function of the forage quality-related traits, including crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose (HC), and cellulose (CL) contents, is essential for the identification of forage quality genes and selection of effective molecular markers in sorghum. In this study, we genotyped 245 sorghum accessions by 85,585 single-nucleotide polymorphisms (SNPs) and obtained the phenotypic data from four environments. The SNPs and phenotypic data were applied to multi-locus genome-wide association studies (GWAS) with the mrMLM software. A total of 42 SNPs were identified to be associated with the five forage quality-related traits. Moreover, three and two quantitative trait nucleotides (QTNs) were simultaneously detected among them by three and two multi-locus methods, respectively. One QTN on chromosome 5 was found to be associated simultaneously with CP, NDF, and ADF. Furthermore, 3, 2, 2, 5, and 2 candidate genes were identified to be responsible for CP, NDF, ADF, HC, and CL contents, respectively. These results provided insightful information of the forage quality-related traits and would facilitate the genetic improvement of sorghum forage quality in the future.
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Affiliation(s)
- Jieqin Li
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Weijie Tang
- College of Horticulture, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Ya-Wen Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kai-Ning Chen
- College of Horticulture, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chenchen Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yanlong Liu
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Qiuwen Zhan
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Chunming Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Shi-Bo Wang
- College of Horticulture, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Shang-Qian Xie
- College of Horticulture, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- *Correspondence: Shang-Qian Xie
| | - Lihua Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
- Lihua Wang
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Hussain W, Baenziger PS, Belamkar V, Guttieri MJ, Venegas JP, Easterly A, Sallam A, Poland J. Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat. Sci Rep 2017; 7:16394. [PMID: 29180623 PMCID: PMC5703991 DOI: 10.1038/s41598-017-16006-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 11/06/2017] [Indexed: 11/17/2022] Open
Abstract
Winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) were used to develop a recombinant inbred population with future goals of identifying genomic regions associated with drought tolerance. To precisely map genomic regions, high-density linkage maps are a prerequisite. In this study genotyping-by- sequencing (GBS) was used to construct the high-density linkage map. The map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. The constructed linkage map revealed strong collinearity in marker order across 21 chromosomes with POPSEQ-v2.0, which was based on a high-density linkage map. The reliability of the linkage map for QTL mapping was demonstrated by co-localizing the genes to previously mapped genomic regions for two highly heritable traits, chaff color, and leaf cuticular wax. Applicability of linkage map for QTL mapping of three quantitative traits, flag leaf length, width, and area, identified 21 QTLs in four environments, and QTL expression varied across the environments. Two major stable QTLs, one each for flag leaf length (Qfll.hww-7A) and flag leaf width (Qflw.hww-5A) were identified. The map constructed will facilitate QTL and fine mapping of quantitative traits, map-based cloning, comparative mapping, and in marker-assisted wheat breeding endeavors.
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Affiliation(s)
- Waseem Hussain
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - P Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Mary J Guttieri
- USDA, Agricultural Research Service, Center for Grain and Animal Health Research, Hard Winter Wheat Genetics Research Unit, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - Jorge P Venegas
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Amanda Easterly
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526, Assiut, Egypt
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
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Yan S, Li S, Zhai G, Lu P, Deng H, Zhu S, Huang R, Shao J, Tao Y, Zou G. Molecular cloning and expression analysis of duplicated polyphenol oxidase genes reveal their functional differentiations in sorghum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:23-30. [PMID: 28818380 DOI: 10.1016/j.plantsci.2017.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/22/2017] [Accepted: 07/03/2017] [Indexed: 05/13/2023]
Abstract
Polyphenol oxidase (PPO) is believed to play a role in plant growth, reproduction, and resistance to pathogens and pests. PPO causes browning of grains in cereals. In this study, genetic mapping of sorghum grain for phenol color reaction (PHR) was performed using a recombinant inbred line population. Only one locus was detected between SSR markers SM06072 and Xtxp176 on chromosome 6. Two linked orthologous genes (Sb06PPO1 and Sb06PPO2) within the mapped region were discovered and cloned. Transformation experiments using Nipponbare (a PHR negative rice cultivar) showed that Sb06PPO1 from LTR108 and two Sb06PPO2 alleles from both varieties could complement Nipponbare, whereas Sb06PPO1 from 654 could not. Subsequent quantitative real-time PCR (qPCR) experiments showed that Sb06PPO1 and Sb06PPO2 functioned diversely, Sb06PPO1 was mainly expressed in young panicles before flowering. Sb06PPO2 was strongly expressed in flowering panicles, especially in hulls and branches at filling stage. Moreover, the expression of Sb06PPO1 was found to be significantly up-regulated by exogenous ABA and salt, whereas Sb06PPO2 was not changed significantly, further demonstrating functional differentiation between the two genes.
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Affiliation(s)
- Song Yan
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China; Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.
| | - Sujuan Li
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.
| | - Guowei Zhai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.
| | - Ping Lu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Hui Deng
- College of Agriculture, Yangzhou University, Jiangsu 225009, China.
| | - Shan Zhu
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.
| | - Renliang Huang
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.
| | - Jianfeng Shao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.
| | - Yuezhi Tao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.
| | - Guihua Zou
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.
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Gelli M, Konda AR, Liu K, Zhang C, Clemente TE, Holding DR, Dweikat IM. Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum. BMC PLANT BIOLOGY 2017; 17:123. [PMID: 28697783 PMCID: PMC5505042 DOI: 10.1186/s12870-017-1064-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/25/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Quantitative trait loci (QTLs) detected in one mapping population may not be detected in other mapping populations at all the time. Therefore, before being used for marker assisted breeding, QTLs need to be validated in different environments and/or genetic backgrounds to rule out statistical anomalies. In this regard, we mapped the QTLs controlling various agronomic traits in a recombinant inbred line (RIL) population in response to Nitrogen (N) stress and validated these with the reported QTLs in our earlier study to find the stable and consistent QTLs across populations. Also, with Illumina RNA-sequencing we checked the differential expression of gene (DEG) transcripts between parents and pools of RILs with high and low nitrogen use efficiency (NUE) and overlaid these DEGs on to the common validated QTLs to find candidate genes associated with N-stress tolerance in sorghum. RESULTS An F7 RIL population derived from a cross between CK60 (N-stress sensitive) and San Chi San (N-stress tolerant) inbred sorghum lines was used to map QTLs for 11 agronomic traits tested under different N-levels. Composite interval mapping analysis detected a total of 32 QTLs for 11 agronomic traits. Validation of these QTLs revealed that of the detected, nine QTLs from this population were consistent with the reported QTLs in earlier study using CK60/China17 RIL population. The validated QTLs were located on chromosomes 1, 6, 7, 8, and 9. In addition, root transcriptomic profiling detected 55 and 20 differentially expressed gene (DEG) transcripts between parents and pools of RILs with high and low NUE respectively. Also, overlay of these DEG transcripts on to the validated QTLs found candidate genes transcripts for NUE and also showed the expected differential expression. For example, DEG transcripts encoding Lysine histidine transporter 1 (LHT1) had abundant expression in San Chi San and the tolerant RIL pool, whereas DEG transcripts encoding seed storage albumin, transcription factor IIIC (TFIIIC) and dwarfing gene (DW2) encoding multidrug resistance-associated protein-9 homolog showed abundant expression in CK60 parent, similar to earlier study. CONCLUSIONS The validated QTLs among different mapping populations would be the most reliable and stable QTLs across germplasm. The DEG transcripts found in the validated QTL regions will serve as future candidate genes for enhancing NUE in sorghum using molecular approaches.
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Affiliation(s)
- Malleswari Gelli
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Anji Reddy Konda
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
| | - Kan Liu
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | - Thomas E Clemente
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
| | - David R Holding
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
| | - Ismail M Dweikat
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
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Lopez JR, Erickson JE, Munoz P, Saballos A, Felderhoff TJ, Vermerris W. QTLs Associated with Crown Root Angle, Stomatal Conductance, and Maturity in Sorghum. THE PLANT GENOME 2017; 10. [PMID: 28724080 DOI: 10.3835/plantgenome2016.04.0038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Three factors that directly affect the water inputs in cropping systems are root architecture, length of the growing season, and stomatal conductance to water vapor (). Deeper-rooted cultivars will perform better under water-limited conditions because they can access water stored deeper in the soil profile. Reduced limits transpiration rate () and thus throughout the vegetative phase conserves water that may be used during grain filling in water-limited environments. Additionally, growing early-maturing varieties in regions that rely on soil-stored water is a key water management strategy. To further our understanding of the genetic basis underlying root depth, growing season length, and we conducted a quantitative trait locus (QTL) study. A QTL for crown root angle (a proxy for root depth) new to sorghum was identified in chromosome 3. For , a QTL in chromosome seven was identified. In a follow-up field study it was determined that the QTL for was associated with reduced but not with net carbon assimilation rate () or shoot biomass. No differences in guard-cell length or stomatal density were observed among the lines, leading to the conclusion that the observed differences in must be explained by partial stomatal closure. The well-studied maturity gene was identified in the QTL for maturity. The transgressive segregation of the population was explained by the possible interaction of with other loci. Finally, the most probable position of the genes underlying the QTLs and candidate genes were proposed.
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Mathur S, Umakanth AV, Tonapi VA, Sharma R, Sharma MK. Sweet sorghum as biofuel feedstock: recent advances and available resources. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:146. [PMID: 28603553 PMCID: PMC5465577 DOI: 10.1186/s13068-017-0834-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/30/2017] [Indexed: 05/08/2023]
Abstract
Sweet sorghum is a promising target for biofuel production. It is a C4 crop with low input requirements and accumulates high levels of sugars in its stalks. However, large-scale planting on marginal lands would require improved varieties with optimized biofuel-related traits and tolerance to biotic and abiotic stresses. Considering this, many studies have been carried out to generate genetic and genomic resources for sweet sorghum. In this review, we discuss various attributes of sweet sorghum that make it an ideal candidate for biofuel feedstock, and provide an overview of genetic diversity, tools, and resources available for engineering and/or marker-assisting breeding of sweet sorghum. Finally, the progress made so far, in identification of genes/quantitative trait loci (QTLs) important for agronomic traits and ongoing molecular breeding efforts to generate improved varieties, has been discussed.
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Affiliation(s)
- Supriya Mathur
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - A. V. Umakanth
- Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - V. A. Tonapi
- Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Rita Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manoj K. Sharma
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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