College of Agronomy and Biotechnology, Southwest University , Beibei, Chongqing 400715, People's Republic of China.
Nanchong Academy of Agricultural Sciences , Nanchong, Sichuan 637000, People's Republic of China.
J Agric Food Chem. 2017 Jul 5;65(26):5229-5237. doi: 10.1021/acs.jafc.7b01226. Epub 2017 Jun 26.
Seed coat color is an extremely important breeding characteristic of Brassica napus. To elucidate the factors affecting the genetic architecture of seed coat color, a genome-wide association study (GWAS) of seed coat color was conducted with a diversity panel comprising 520 B. napus cultivars and inbred lines. In total, 22 single-nucleotide polymorphisms (SNPs) distributed on 7 chromosomes were found to be associated with seed coat color. The most significant SNPs were found in 2014 near Bn-scaff_15763_1-p233999, only 43.42 kb away from BnaC06g17050D, which is orthologous to Arabidopsis thaliana TRANSPARENT TESTA 12 (TT12), an important gene involved in the transportation of proanthocyanidin precursors into the vacuole. Two of eight repeatedly detected SNPs can be identified and digested by restriction enzymes. Candidate gene mining revealed that the relevant regions of significant SNP loci on the A09 and C08 chromosomes are highly homologous. Moreover, a comparison of the GWAS results to those of previous quantitative trait locus (QTL) studies showed that 11 SNPs were located in the confidence intervals of the QTLs identified in previous studies based on linkage analyses or association mapping. Our results provide insights into the genetic basis of seed coat color in B. napus, and the beneficial allele, SNP information, and candidate genes should be useful for selecting yellow seeds in B. napus breeding.
油菜籽种皮颜色是一个极其重要的甘蓝型油菜品种选育特性。为了阐明影响种皮颜色遗传结构的因素，对一个由 520 个甘蓝型油菜品种和自交系组成的多样性群体进行了种皮颜色全基因组关联研究（GWAS）。共发现 22 个单核苷酸多态性（SNP）分布在 7 条染色体上与种皮颜色相关。在 2014 年，在 Bn-scaff_15763_1-p233999 附近发现了最显著的 SNP，距离拟南芥 TRANSPARENT TESTA 12（TT12）的同源基因 BnaC06g17050D 仅有 43.42kb，TT12 是一个参与原花青素前体向液泡运输的重要基因。8 个重复检测到的 SNP 中有 2 个可以通过限制酶进行鉴定和切割。候选基因挖掘表明，A09 和 C08 染色体上显著 SNP 位点的相关区域高度同源。此外，将 GWAS 结果与之前基于连锁分析或关联图谱的数量性状基因座（QTL）研究结果进行比较，发现 11 个 SNP 位于先前研究中鉴定的 QTL 置信区间内。我们的研究结果为油菜籽种皮颜色的遗传基础提供了深入的了解，有益等位基因、SNP 信息和候选基因应该对油菜籽黄色种子的选育有用。
