State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Lekai South Street 2596, Baoding City, 071001, Hebei Province, People's Republic of China.
Theor Appl Genet. 2022 Jul;135(7):2341-2351. doi: 10.1007/s00122-022-04116-w. Epub 2022 May 19.
A soybean natural population was genotyped by deep re-sequencing and phenotyped for six seed size- and shape-related traits under six environments to identify closely associated SNPs and candidate genes. Seed size and shape are important determining factors for soybean yield formation, while their genetic basis and molecular mechanism are still largely unknown, which seriously constrains the increasing of soybean yield at present. In view of this, a natural population was genotyped via the deep re-sequencing technique (~ 20 ×) and phenotyped for six related traits under six environments. In total, 154 SNPs were closely associated with seed length across diverse environments, and 323, 483, 565, 394 and 2038 SNPs were closely associated with seed width, seed diameter, seed circumference, seed area and ratio of length to width under multiple environments. Moreover, 98.70%, 96.28%, 48.24%, 85.13%, 97.21% and 98.58% of them were further demonstrated by the BLUP and mean values of the related traits. Furthermore, 218 genes flanking the associated SNPs on chromosomes 6 and 10 were analyzed for DNA mutations and RNA expressions through SNP alleles and transcriptome data, simultaneously. The candidate genes, Glyma.10G035200 (Sn1-specific diacylglycerol lipase), Glyma.10G035400 (transcription factor) and Glyma.10G058200 (phenylalanine ammonia-lyase), were discovered to relate with the seed size and shape for their different DNA sequences or differential RNA expressions among soybean varieties at five seed developmental stages. Thus, these closely associated SNPs and related genes provide novel insights and useful information for the seed size and shape genetic basis dissection and breeding improvement in soybean.
一个大豆自然群体通过深度重测序进行了基因型分析，并在六个环境下对六个与种子大小和形状相关的性状进行了表型分析，以鉴定紧密相关的 SNP 和候选基因。种子大小和形状是大豆产量形成的重要决定因素，但其遗传基础和分子机制在很大程度上仍然未知，这严重限制了目前大豆产量的提高。鉴于此，利用深度重测序技术（~20×）对一个自然群体进行了基因型分析，并在六个环境下对六个相关性状进行了表型分析。总共发现 154 个 SNP 与不同环境下的种子长度密切相关，323、483、565、394 和 2038 个 SNP 与种子宽度、种子直径、种子周长、种子面积和长宽比在多个环境下密切相关。此外，相关性状的 BLUP 和平均值进一步验证了 98.70%、96.28%、48.24%、85.13%、97.21%和 98.58%的 SNP。此外，通过 SNP 等位基因和转录组数据，对位于染色体 6 和 10 上的相关 SNP 侧翼的 218 个基因进行了 DNA 突变和 RNA 表达分析。候选基因 Glyma.10G035200（Sn1 特异性二酰基甘油脂肪酶）、Glyma.10G035400（转录因子）和 Glyma.10G058200（苯丙氨酸解氨酶），由于其在五个种子发育阶段不同的大豆品种间的 DNA 序列或差异 RNA 表达与种子大小和形状有关，因此被发现与种子大小和形状有关。因此，这些紧密相关的 SNP 和相关基因为大豆种子大小和形状遗传基础解析和改良提供了新的见解和有用信息。
