title: Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method.
abstract: Flowering time and seed size are traits related to domestication. However, identification of domestication-related loci/genes of controlling the traits in soybean is rarely reported. In this study, we identified a total of 48 domestication-related loci based on RAD-seq genotyping of a natural population comprising 286 accessions. Among these, four on chromosome 12 and additional two on chromosomes 11 and 15 were associated with flowering time, and four on chromosomes 11 and 16 were associated with seed size. Of the five genes associated with flowering time and the three genes associated with seed size, three genes Glyma11g18720, Glyma11g15480 and Glyma15g35080 were homologous to Arabidopsis genes, additional five genes were found for the first time to be associated with these two traits. Glyma11g18720 and Glyma05g28130 were co-expressed with five genes homologous to flowering time genes in Arabidopsis, and Glyma11g15480 was co-expressed with 24 genes homologous to seed development genes in Arabidopsis. This study indicates that integration of population divergence analysis, genome-wide association study and expression analysis is an efficient approach to identify candidate domestication-related genes.
authors: State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
authors: Ling
authors: L
authors: Zhou
authors: State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
authors: Shi-Bo
authors: SB
authors: Wang
authors: BGI-Shenzhen, Shenzhen 518083, China.
authors: Jianbo
authors: J
authors: Jian
authors: State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
authors: Qing-Chun
authors: QC
authors: Geng
authors: State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
authors: Jia
authors: J
authors: Wen
authors: Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, USA.
authors: Qijian
authors: Q
authors: Song
authors: BGI-Shenzhen, Shenzhen 518083, China.
authors: Zhenzhen
authors: Z
authors: Wu
authors: College of Life Science, Linyi University, Linyi 276005, China.
authors: Guang-Jun
authors: GJ
authors: Li
authors: Crop Research Institute, Linyi Academy of Agricultural Sciences, Linyi 276012, China.
authors: Yu-Qin
authors: YQ
authors: Liu
authors: School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AR, United Kingdom.
authors: Jim M
authors: JM
authors: Dunwell
authors: State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
authors: Jin
authors: J
authors: Zhang
authors: State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
authors: Jian-Ying
authors: JY
authors: Feng
authors: State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
authors: Yuan
authors: Y
authors: Niu
authors: State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
authors: Li
authors: L
authors: Zhang
authors: State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
authors: Wen-Long
authors: WL
authors: Ren
authors: 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China [2] Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors: Yuan-Ming
authors: YM
authors: Zhang
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001947:Breeding; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000737:chemistry*; D035264:Flowers / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D060005:Genotyping Techniques; D010641:Phenotype; D040641:Quantitative Trait Loci; D012639:Seeds / Q000033:anatomy & histology / Q000235:genetics*; D013025:Glycine max / Q000033:anatomy & histology / Q000235:genetics*; D013997:Time Factors