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

Abstract

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

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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