油菜主花序角果密度及其相关性状的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2018.06.002

摘要/Abstract

摘要： 【目的】油菜高产是育种工作的主要研究目标之一。角果密度、主花序有效角果数等性状与产量都有显著或极显著的正相关关系，是油菜高产育种考查的主要性状。为揭示油菜角果密度及其相关性状的遗传机理和分子机制奠定基础。【方法】以不同遗传背景和地理来源的213份甘蓝型油菜品种（系）构成的自然群体为研究对象，利用芸薹属60K Illumina Infinium SNP芯片对该群体进行基因型分型。分别于2015年和2016年在成熟期调查该群体主花序有效长和主花序有效角果数，计算主花序角果密度。利用Structure 2.3.4软件对该群体进行群体结构分析，Tassel 5.1.0软件分析亲缘关系和染色体连锁不平衡的衰减；然后基于最优模型对主花序角果密度及其相关性状进行全基因组关联分析（genome-wide association analysis，GWAS），依据关联SNP位点的LD区间序列，预测与性状相关的重要关联候选基因。【结果】群体结构分析显示，213份甘蓝型油菜分为P1和P2亚群，P1亚群包含50份材料（23.5%），P2亚群包含163份材料（76.5%），基本上和油菜的地理栽培属性一致；亲缘关系发现约89.74%材料之间的亲缘关系值小于0.2，其中约有59.91%材料的亲缘关系值为0。总体来看，整个自然群体材料之间的亲缘关系比较远。对A、C基因组进行连锁不平衡分析发现，A和C基因组的r2随着遗传距离的增加而下降，A基因组的衰减距离整体比C基因组的衰减距离小。GWAS分析两年数据共检测到17个SNP位点与主花序角果密度及其相关性状关联。其中与主花序角果密度和主花序有效长相关的SNP标记分别有7个和9个，并分别解释11.34%—15.96%和9.67%—13.10%的表型变异；与主花序有效角果数相关联的标记有1个，解释11.56%的表型变异。通过分析关联SNP位点的LD区间与甘蓝型油菜对应的区间序列，找到22个与主花序角果密度及其相关性状有关的候选基因，其中BnaA01g16940D、BnaC01g38800D和BnaA04g09170D等主要通过调控赤霉素和生长素等内源激素的合成和信号转导来控制主花序角果密度及其相关性状；BnaA01g16970D、BnaA03g29180D、BnaA03g29810D、BnaC01g39680D和 BnaC03g32770D通过对分生组织的调控来改变表型；BnaC09g18690D和 BnaC09g09210D等主要通过控制细胞分裂生长等过程改变表型。【结论】检测到17个SNP标记与油菜主花序角果密度、主花序有效长和主花序有效角果数关联，筛选出22个与主花序角果密度及其相关性状有关的候选基因。

关键词: 甘蓝型油菜, 主花序角果密度, 连锁不平衡, SNP, 全基因组关联分析

Abstract: 【Objective】 High yield of rapeseed (Brassica napus) has been regarded as one of the main research goals for breeders. Silique density, the number of valid siliques on racemes as well as them related traits, which are the main character to test yield level of rapeseed, have significant or extremely significant positive correlation with the yield. These results are helpful to further elucidate the genetic and molecular mechanisms of the siliques density and related traits of rapeseed. 【Method】 In this study, a natural populations contained 213 rapeseed cultivars (lines) with different genetic backgrounds were used to study genotyping via the Brassica 60 K Illumina Infinium SNP array. Valid length on racemes and valid silique on racemes were investigated at the fruit ripening stage in 2015 and 2016, respectively, at same time silique density on racemes was calculated. Furthermore, relative kinship and linkage disequilibrium of chromosome were analyzed by Tassel 5.1.0 software, and the population structure was analyzed using Structure 2.3.4 software. Then, based on the optimal model, important candidate genes related to traits were predicted by the genome-wide correlation analysis (GWAS) of the silique density on racemes and its component traits were conducted, according to the sequence of LD regions of the associated SNP array. 【Result】Population structure analysis showed that 213 varieties were divided into P1 and P2 subgroups, in which the P1 contained 50 varieties of rapeseed (23.5%) and the P2 contained 163 varieties of rapeseed (76.5%), and it was consistent with the geo-cultivation of rapeseed. Meanwhile, the results of phylogenetic relationship indicated that about 89.74% materials had kinship value less than 0.2, of which about 59.91% materials had almost little genetic kinship. Thus, it can be concluded that there was a relatively distant kinship among materials in this natural group. In addition, a linkage disequilibrium analysis of A and C genomes revealed that r2 of A and C genomes decreased with increasing genetic distance, and the attenuation distance of A genome is smaller than that of C genome. Based on the two-year data analyzed by GWAS, 17 SNP were detected to be significant correlation with the siliques density on racemes and its component traits. Among them, 7 and 9 SNPs associated with silique density and valid length on racemes, each of them explained 11.343%-15.96% and 9.67%-13.097% of phenotypic variation, respectively. And 1 SNP site was related to valid silique on racemes, explaining the phenotypic variation of 11.56%. 22 candidate genes associated with silique density on racemes and its component traits were found via the LD interval of the significant SNPs and corresponding interval sequences of Brassica napus. Specifically, some genes including BnaA01g16940D, BnaC01g38800D and so on controlled silique density on racemes and its component traits by regulating the synthesis and signal transduction of endogenous hormones such as GA and IAA. And some genes, such as BnaA01g16970D, BnaA03g29180D and so on, were related to regulate meristems development of floral while other genes, BnaC09g18690D and BnaC09g09210D were involved in division and cell growth of floral. 【Conclusion】 In this study, 17 SNPs were detected associated with the siliques density on racemes, the valid length on racemes and the valid silique on racemes. Furthermore, 22 candidate genes related to the siliques density on racemes and its component traits were screened out.

Key words: Brassica napus, silique density on racemes, linkage disequilibrium, SNP, genome-wide association analysis

任义英，崔翠，王倩，唐章林，徐新福，林呐，殷家明，李加纳，周清元. 油菜主花序角果密度及其相关性状的全基因组关联分析[J]. 中国农业科学, 2018, 51(6): 1020-1033.

REN YiYing, CUI Cui, WANG Qian, TANG ZhangLin, XU XinFu, LIN Na, YIN JiaMing, LI JiaNa, ZHOU QingYuan. Genome-Wide Association Analysis of Silique Density on Racemes and Its Component Traits in Brassica napus L.[J]. Scientia Agricultura Sinica, 2018, 51(6): 1020-1033.

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