National Center for Soybean Improvement/National Key laboratory of Crop Genetics and Germplasm enhancement, Key laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
BMC Genet. 2019 Mar 29;20(1):39. doi: 10.1186/s12863-019-0737-9.
The 100-pod fresh weight (PFW), 100-seed fresh weight (SFW), 100-seed dry weight (SDW) and moisture content of fresh seeds (MCFS) at the R6 stage are crucial factors for vegetable soybean yield. However, the genetic basis of yield at the R6 stage remains largely ambiguous in soybean.
To better understand the molecular mechanism underlying yield, we investigated four yield-related traits of 133 soybean landraces in two consecutive years and conducted a genome-wide association study (GWAS) using 82,187 single nucleotide polymorphisms (SNPs). The GWAS results revealed a total of 14, 15, 63 and 48 SNPs for PFW, SFW, SDW and MCFS, respectively. Among these markers, 35 SNPs were repeatedly identified in all evaluated environments (2015, 2016, and the average across the two years), and most co-localized with yield-related QTLs identified in previous studies. AX-90496773 and AX-90460290 were large-effect markers for PFW and MCFS, respectively. The two markers were stably identified in all environments and tagged to linkage disequilibrium (LD) blocks. Six potential candidate genes were predicted in LD blocks; five of them showed significantly different expression levels between the extreme materials with large PFW or MCFS variation at the seed development stage. Therefore, the five genes Glyma.16g018200, Glyma.16g018300, Glyma.05g243400, Glyma.05g244100 and Glyma.05g245300 were regarded as candidate genes associated with PFW and MCFS.
These results provide useful information for the development of functional markers and exploration of candidate genes in vegetable soybean high-yield breeding programs.
R6 期的百荚鲜重（PFW）、百粒鲜重（SFW）、百粒干重（SDW）和鲜籽含水量（MCFS）是蔬菜大豆产量的关键因素。然而，大豆在 R6 期的产量遗传基础在很大程度上仍不清楚。
为了更好地理解产量的分子机制，我们在连续两年内研究了 133 份大豆地方品种的四个产量相关性状，并使用 82187 个单核苷酸多态性（SNP）进行了全基因组关联研究（GWAS）。GWAS 结果共鉴定出 PFW、SFW、SDW 和 MCFS 的 14、15、63 和 48 个 SNP。在这些标记中，35 个 SNP 在所有评估环境中（2015 年、2016 年和两年的平均值）均被重复鉴定，且大多数与之前研究中鉴定出的与产量相关的 QTL 共定位。AX-90496773 和 AX-90460290 分别是 PFW 和 MCFS 的大效应标记。这两个标记在所有环境中均稳定鉴定，并与连锁不平衡（LD）块相关。在 LD 块中预测到了六个潜在的候选基因；其中五个在种子发育阶段具有较大 PFW 或 MCFS 变异的极端材料之间表现出显著不同的表达水平。因此，Glyma.16g018200、Glyma.16g018300、Glyma.05g243400、Glyma.05g244100 和 Glyma.05g245300 这五个基因被认为是与 PFW 和 MCFS 相关的候选基因。
这些结果为蔬菜大豆高产育种计划中功能标记的开发和候选基因的探索提供了有用的信息。
