title: Detecting the QTL-allele system of seed isoflavone content in Chinese soybean landrace population for optimal cross design and gene system exploration.
abstract: Utilizing an innovative GWAS in CSLRP, 44 QTL 199 alleles with 72.2 % contribution to SIFC variation were detected and organized into a QTL-allele matrix for cross design and gene annotation. The seed isoflavone content (SIFC) of soybeans is of great importance to health care. The Chinese soybean landrace population (CSLRP) as a genetic reservoir was studied for its whole-genome quantitative trait loci (QTL) system of the SIFC using an innovative restricted two-stage multi-locus genome-wide association study procedure (RTM-GWAS). A sample of 366 landraces was tested under four environments and sequenced using RAD-seq (restriction-site-associated DNA sequencing) technique to obtain 116,769 single nucleotide polymorphisms (SNPs) then organized into 29,119 SNP linkage disequilibrium blocks (SNPLDBs) for GWAS. The detected 44 QTL 199 alleles on 16 chromosomes (explaining 72.2 % of the total phenotypic variation) with the allele effects (92 positive and 107 negative) of the CSLRP were organized into a QTL-allele matrix showing the SIFC population genetic structure. Additional differentiation among eco-regions due to the SIFC in addition to that of genome-wide markers was found. All accessions comprised both positive and negative alleles, implying a great potential for recombination within the population. The optimal crosses were predicted from the matrices, showing transgressive potentials in the CSLRP. From the detected QTL system, 55 candidate genes related to 11 biological processes were χ (2)-tested as an SIFC candidate gene system. The present study explored the genome-wide SIFC QTL/gene system with the innovative RTM-GWAS and found the potentials of the QTL-allele matrix in optimal cross design and population genetic and genomic studies, which may have provided a solution to match the breeding by design strategy at both QTL and gene levels in breeding programs.
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.
authors.forename: Shan
authors.initials: S
authors.lastname: Meng
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.
authors.forename: Jianbo
authors.initials: J
authors.lastname: He
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.|Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Tuanjie
authors.initials: T
authors.lastname: Zhao
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.|Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Guangnan
authors.initials: G
authors.lastname: Xing
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.|Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.|Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Shouping
authors.initials: S
authors.lastname: Yang
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.
authors.forename: Jiangjie
authors.initials: J
authors.lastname: Lu
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.|National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. sri@njau.edu.cn.|National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China. sri@njau.edu.cn.|Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China. sri@njau.edu.cn.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. sri@njau.edu.cn.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. sri@njau.edu.cn.
authors.forename: Junyi
authors.initials: J
authors.lastname: Gai
mesh_terms: D000483:Alleles; D018744:DNA, Plant / Q000235:genetics; D056726:Genetic Association Studies; D005828:Genetics, Population; D006239:Haplotypes; D007529:Isoflavones / Q000737:chemistry*; D015810:Linkage Disequilibrium; D010641:Phenotype; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012639:Seeds / Q000737:chemistry*; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000737:chemistry / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D007529:Isoflavones