Establishment of a 100-seed weight quantitative trait locus-allele matrix of the germplasm population for optimal recombination design in soybean breeding programmes.
Establishment of a 100-seed weight quantitative trait locus-allele matrix of the germplasm population for optimal recombination design in soybean breeding programmes.
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DOI：
10.1093/jxb/erv342
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发表时间：
2015-09
影响因子：
6.9
通讯作者：
Yinghu Zhang;Jianbo He;Yufeng Wang;G. Xing;Jinming Zhao;Yan Li;Shouping Yang;Reid G. Palmer
中科院分区：
文献类型：
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作者：
Yinghu Zhang;Jianbo He;Yufeng Wang;G. Xing;Jinming Zhao;Yan Li;Shouping Yang;Reid G. Palmer
采用全基因组关联研究（GWAS）方法，对中国大豆地方品种（CSLRP） 366份代表性样品在4种生长环境下的100粒重性状（4.59g ~ 40.35g）的全基因组数量性状位点（qtl）系统进行了检测。共鉴定出116 769个单核苷酸多态性（SNP），并将其组织成29 121个SNP连锁不平衡块（snpldb），以适应种质资源中每个位点的多等位基因/单倍型的特性。利用单位点模型减少标记数量，然后利用逐步回归的多位点模型进行全基因组QTL鉴定，进行了创新的两阶段GWAS。总体而言，4个大贡献主要qtl（36.33%）、51个小贡献主要qtl（43.24%）和若干未定位的次要qtl（18.88%）占表型方差（PV）的98.45%，其中QTL×environment方差仅占PV的1.01%。每个QTL的等位基因数在2 ~ 10之间。对263个等位基因及其各自的等位基因效应进行了估计，并组织成263×366矩阵，给出了CSLRP紧凑的遗传结构。生态区域基质之间存在差异。没有地方品种的等位基因全部为正或全部为负，这表明存在潜在的重组潜力。预测了区域内和区域间的最优杂交组合，显示出较大的海侵潜力。在QTL系统中，共标注了39个候选基因，其中26个涉及生物过程、细胞成分和分子功能等基因本体类别，说明百粒重的调控涉及多种基因。
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.