Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments
Pod dehiscence (shattering) is the main cause of serious yield loss during the soybean mechanical harvesting process. A better understanding of the genetic architecture and molecular mechanisms of pod dehiscence is of great significance for soybean breeding. In this study, genome-wide association an...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-06-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2019.00811/full |
| _version_ | 1828289385261432832 |
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| author | Dezhou Hu Guizhen Kan Wei Hu Yali Li Derong Hao Xiao Li Hui Yang Hui Yang Zhongyi Yang Xiaohong He Fang Huang Deyue Yu Deyue Yu |
| author_facet | Dezhou Hu Guizhen Kan Wei Hu Yali Li Derong Hao Xiao Li Hui Yang Hui Yang Zhongyi Yang Xiaohong He Fang Huang Deyue Yu Deyue Yu |
| author_sort | Dezhou Hu |
| collection | DOAJ |
| description | Pod dehiscence (shattering) is the main cause of serious yield loss during the soybean mechanical harvesting process. A better understanding of the genetic architecture and molecular mechanisms of pod dehiscence is of great significance for soybean breeding. In this study, genome-wide association analysis (GWAS) with NJAU 355K SoySNP array was performed to detect single nucleotide polymorphisms (SNPs) associated with pod dehiscence in an association panel containing 211 accessions across five environments. A total of 163 SNPs were identified as significantly associated with pod dehiscence. Among these markers, 136 SNPs identified on chromosome 16 were located in the known QTL qPDH1. One, one, three, eleven, three, one, three, three and one SNPs were distributed on chromosome 1, 4, 6, 8, 9, 11, 17, 18, and 20, respectively. Favorable SNPs and six haplotypes were identified based on ten functional SNPs; among those Hap2 and Hap3 were considered as optimal haplotypes. In addition, based on GWAS results, the candidate gene Glyma09g06290 was identified. Quantitative real-time PCR (qRT-PCR) results and polymorphism analysis suggested that Glyma09g06290 might be involved in pod dehiscence. Furthermore, a derived cleaved amplified polymorphic sequences (dCAPS) marker for Glyma09g06290 was developed. Overall, the loci and genes identified in this study will be helpful in breeding soybean accessions resistant to pod dehiscence. |
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| id | doaj.art-c10e9b81581047daaa6a0740dea8ec49 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T10:20:01Z |
| publishDate | 2019-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-c10e9b81581047daaa6a0740dea8ec492022-12-22T02:50:32ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-06-011010.3389/fpls.2019.00811458232Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple EnvironmentsDezhou Hu0Guizhen Kan1Wei Hu2Yali Li3Derong Hao4Xiao Li5Hui Yang6Hui Yang7Zhongyi Yang8Xiaohong He9Fang Huang10Deyue Yu11Deyue Yu12National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, ChinaNational Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, ChinaNational Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, ChinaNational Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, ChinaJiangsu Yanjiang Institute of Agricultural Sciences, Nantong, ChinaNational Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, ChinaNational Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, ChinaSchool of Life Sciences, Guangzhou University, Guangzhou, ChinaNational Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, ChinaNational Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, ChinaNational Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, ChinaNational Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, ChinaSchool of Life Sciences, Guangzhou University, Guangzhou, ChinaPod dehiscence (shattering) is the main cause of serious yield loss during the soybean mechanical harvesting process. A better understanding of the genetic architecture and molecular mechanisms of pod dehiscence is of great significance for soybean breeding. In this study, genome-wide association analysis (GWAS) with NJAU 355K SoySNP array was performed to detect single nucleotide polymorphisms (SNPs) associated with pod dehiscence in an association panel containing 211 accessions across five environments. A total of 163 SNPs were identified as significantly associated with pod dehiscence. Among these markers, 136 SNPs identified on chromosome 16 were located in the known QTL qPDH1. One, one, three, eleven, three, one, three, three and one SNPs were distributed on chromosome 1, 4, 6, 8, 9, 11, 17, 18, and 20, respectively. Favorable SNPs and six haplotypes were identified based on ten functional SNPs; among those Hap2 and Hap3 were considered as optimal haplotypes. In addition, based on GWAS results, the candidate gene Glyma09g06290 was identified. Quantitative real-time PCR (qRT-PCR) results and polymorphism analysis suggested that Glyma09g06290 might be involved in pod dehiscence. Furthermore, a derived cleaved amplified polymorphic sequences (dCAPS) marker for Glyma09g06290 was developed. Overall, the loci and genes identified in this study will be helpful in breeding soybean accessions resistant to pod dehiscence.https://www.frontiersin.org/article/10.3389/fpls.2019.00811/fullsoybeanpod dehiscenceGWAShaplotype analysisGlyma09g06290polymorphism analysis |
| spellingShingle | Dezhou Hu Guizhen Kan Wei Hu Yali Li Derong Hao Xiao Li Hui Yang Hui Yang Zhongyi Yang Xiaohong He Fang Huang Deyue Yu Deyue Yu Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments Frontiers in Plant Science soybean pod dehiscence GWAS haplotype analysis Glyma09g06290 polymorphism analysis |
| title | Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments |
| title_full | Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments |
| title_fullStr | Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments |
| title_full_unstemmed | Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments |
| title_short | Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments |
| title_sort | identification of loci and candidate genes responsible for pod dehiscence in soybean via genome wide association analysis across multiple environments |
| topic | soybean pod dehiscence GWAS haplotype analysis Glyma09g06290 polymorphism analysis |
| url | https://www.frontiersin.org/article/10.3389/fpls.2019.00811/full |
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