全基因组关联分析整合高通量基因组测序和表型分析是研究作物复杂性状遗传特性和功能基因挖掘的有效策略。近日，我院刘克德教授团队构建了一个包括4,542,011个 SNPs 和628,666 INDELs的油菜基因组变异图谱，并利用382万个多态性位点对芥酸含量、硫苷含量和种子含油量等三个控制油菜籽粒品质的重要性状进行GWAS分析，在多个环境条件下，分别检测到6，49和17个关联位点，对表型的贡献率分别为94.1%、40.1%和87.9% 。这些关联位点的等位变异不仅可以用于遗传改良，而且有助于挖掘功能基因。利用该方法，研究人员在染色体A8 和 C3上克隆到控制芥酸含量的功能基因FAE1，在染色体A9, C2 和 C9上克隆到控制硫苷含量的功能基因MYB28。此外，研究人员还克隆到4个新的控制硫苷含量和种子含油量的候选基因。该研究揭示了油菜品质性状的遗传结构，对油菜的遗传改良和分子育种具有重要的指导意义。相关研究进展发表在Plant Biotechnol J上。
Plant Biotechnol J, 19 December 2017
Dissection of the genetic architecture of three seed-quality traits and consequences for breeding in Brassica napus
Bo Wang, Zhikun Wu, Zhaohong Li, Qinghua Zhang, Jianlin Hu, Yingjie Xiao, Dongfang Cai, Jiangsheng Wu, Graham J King, Haitao Li, Kede Liu
Genome-wide association studies (GWASs) combining high-throughput genome resequencing and phenotyping can accelerate the dissection of genetic architecture and identification of genes for plant complex traits. In this study, we developed a rapeseed genomic variation map consisting of 4,542,011 SNPs and 628,666 INDELs. GWAS was performed for three seed-quality traits, including erucic acid content (EAC), glucosinolate content (GSC) and seed oil content (SOC) using 3.82 million polymorphisms in an association panel. Six, 49 and 17 loci were detected to be associated with EAC, GSC and SOC in multiple environments, respectively. The mean total contribution of these loci in each environment was 94.1% for EAC and 87.9% for GSC, notably higher than that for SOC (40.1%). A high correlation was observed between phenotypic variance and number of favorable alleles for associated loci, which will contribute to breeding improvement by pyramiding these loci. Furthermore, candidate genes were detected underlying associated loci, based on functional polymorphisms in gene regions where sequence variation was found to correlate with phenotypic variation. Our approach was validated by detection of well characterized FAE1 genes at each of two major loci for EAC on chromosomes A8 and C3, along with MYB28 genes at each of three major loci for GSC on chromosomes A9, C2 and C9. Four novel candidate genes were detected by correlation between GSC and SOC and observed sequence variation, respectively. The present study provides insights into the genetic architecture of three seed-quality traits, which would be useful for genetic improvement of B. napus.