Meng Shan, He Jianbo, Zhao Tuanjie, Xing Guangnan, Li Yan, Yang Shouping, Lu Jiangjie, Wang Yufeng, Gai Junyi
Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.
Theor Appl Genet. 2016 Aug;129(8):1557-76. doi: 10.1007/s00122-016-2724-0. Epub 2016 May 17.
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.
利用中国大豆地方品种群体（CSLRP）中一项创新的全基因组关联研究（GWAS），检测到44个数量性状基因座（QTL）的199个等位基因，它们对种子异黄酮含量（SIFC）变异的贡献率为72.2%，并将其整理成一个用于杂交设计和基因注释的QTL-等位基因矩阵。大豆的种子异黄酮含量对医疗保健非常重要。采用创新的限制性两阶段多位点全基因组关联研究程序（RTM-GWAS），对作为遗传资源库的中国大豆地方品种群体（CSLRP）的SIFC全基因组数量性状基因座（QTL）系统进行了研究。在四个环境下对366个地方品种进行了测试，并使用RAD-seq（限制性位点相关DNA测序）技术进行测序，以获得116,769个单核苷酸多态性（SNP），然后将其整理成29,119个SNP连锁不平衡块（SNPLDB）用于GWAS。在16条染色体上检测到的44个QTL的199个等位基因（解释了72.2%的总表型变异）以及CSLRP的等位基因效应（92个正向和107个负向）被整理成一个显示SIFC群体遗传结构的QTL-等位基因矩阵。除了全基因组标记的差异外，还发现了由于SIFC导致的生态区域间的额外差异。所有种质都包含正向和负向等位基因，这意味着群体内重组的潜力很大。从这些矩阵中预测了最佳杂交组合，显示出CSLRP中的超亲潜力。从检测到的QTL系统中，对与11个生物学过程相关的55个候选基因进行了χ²检验，作为一个SIFC候选基因系统。本研究利用创新的RTM-GWAS探索了全基因组SIFC QTL/基因系统，并发现了QTL-等位基因矩阵在最佳杂交设计以及群体遗传和基因组研究中的潜力，这可能为育种计划中在QTL和基因水平上匹配设计育种策略提供了一种解决方案。
