title: Establishment of a 100-seed weight quantitative trait locus-allele matrix of the germplasm population for optimal recombination design in soybean breeding programmes.
abstract: A representative sample comprising 366 accessions from the Chinese soybean landrace population (CSLRP) was tested under four growth environments for determination of the whole-genome quantitative trait loci (QTLs) system of the 100-seed weight trait (ranging from 4.59g to 40.35g) through genome-wide association study (GWAS). A total of 116 769 single nucleotide polymorphisms (SNPs) were identified and organized into 29 121 SNP linkage disequilibrium blocks (SNPLDBs) to fit the property of multiple alleles/haplotypes per locus in germplasm. An innovative two-stage GWAS was conducted using a single locus model for shrinking the marker number followed by a multiple loci model utilizing a stepwise regression for the whole-genome QTL identification. In total, 98.45% of the phenotypic variance (PV) was accounted for by four large-contribution major QTLs (36.33%), 51 small-contribution major QTLs (43.24%), and a number of unmapped minor QTLs (18.88%), with the QTL×environment variance representing only 1.01% of the PV. The allele numbers of each QTL ranged from two to 10. A total of 263 alleles along with the respective allele effects were estimated and organized into a 263×366 matrix, giving the compact genetic constitution of the CSLRP. Differentiations among the ecoregion matrices were found. No landrace had alleles which were all positive or all negative, indicating a hidden potential for recombination. The optimal crosses within and among ecoregions were predicted, and showed great transgressive potential. From the QTL system, 39 candidate genes were annotated, of which 26 were involved with the gene ontology categories of biological process, cellular component, and molecular function, indicating that diverse genes are involved in directing the 100-seed weight.
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, Jiangsu 210095, China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu 210095, China National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China Institute of Agricultural Sciences in Jiangsu Coastal Areas, Yancheng, Jiangsu 224002, China.
authors.forename: Yinghu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, Jiangsu 210095, China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu 210095, China National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Jianbo
authors.initials: J
authors.lastname: He
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, Jiangsu 210095, China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu 210095, China National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, Jiangsu 210095, China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu 210095, China National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Guangnan
authors.initials: G
authors.lastname: Xing
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, Jiangsu 210095, China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu 210095, China National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Jinming
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, Jiangsu 210095, China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu 210095, China National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, Jiangsu 210095, China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu 210095, China National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Shouping
authors.initials: S
authors.lastname: Yang
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
authors.forename: R G
authors.initials: RG
authors.lastname: Palmer
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, Jiangsu 210095, China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu 210095, China National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China tjzhao@njau.edu.cn sri@njau.edu.cn.
authors.forename: Tuanjie
authors.initials: T
authors.lastname: Zhao
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, Jiangsu 210095, China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, Jiangsu 210095, China National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China tjzhao@njau.edu.cn sri@njau.edu.cn.
authors.forename: Junyi
authors.initials: J
authors.lastname: Gai
mesh_terms: D002681:China; D004777:Environment; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D000069600:Plant Breeding / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D013025:Glycine max / Q000235:genetics*
keywords: 100-seed weight; Chinese soybean landrace population (CSLRP); QTL–allele matrix; SNP linkage disequilibrium block (SNPLDB); gene ontology (GO) analysis; genome-wide association study (GWAS); soybean [Glycine max (L.) Merr.].