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Genome-wide association analysis of aluminum tolerance related traits in rapeseed ( Brassica napus L.) during germination
Genetic Resources and Crop Evolution ( IF 2 ) Pub Date : 2020-08-02 , DOI: 10.1007/s10722-020-00989-2
Huanhuan Gao , Sang Ye , Jiayi Wu , Liuyan Wang , Ruili Wang , Wei Lei , Lijiao Meng , Fang Yuan , Qingyuan Zhou , Cui Cui

With the increasing acidification of soil, aluminum (Al) toxicity has become one of the most important stress factors affecting seed germination quality and crop yield. To investigate the Al tolerance on seed germination, genome-wide association analysis (GWAS) of 19,949 SNPs with genome-wide coverage was used to identify the candidate genes, which were potentially related to germinate traits of rapeseed (Brassica napus L.) under Al stress. In the experiment, 169 rapeseed cultivars (lines) were treated with AlCl3 solution of 90 ppm, and distilled water was added to the control. At the 7th day, the phenotype data, including root length and dry weight, were measured and calculated. Using the TASSEL software, Al tolerance related traits were explored in rapeseed under germination with a 60 K Brassica Illumina® Infinium SNP array. Then, the structure of the population was analyzed with the STRUCTURE software, and the genetic relationship and LD attenuation were analyzed with the software TASSEL, respectively. The GWAS of relative root length (RRL) and relative dry weight (RDW) with SNP markers were carried out under the optimal model. Meanwhile, the candidate genes were predicted based on the LD interval sequence of the associated SNP locus. Subsequently, the homologous genes of rapeseed related to Al tolerance in the target genome region were screened in Arabidopsis thaliana (L.) Heynh. The results showed that 13 SNPs were significantly associated with these two traits. Among them, 8 SNPs were significantly associated with RRL and located on chromosomes A03, A07, A09, A10, C05, C06, and C09, respectively. Five SNPs were significantly associated with RDW and located on chromosomes A03, A04, A10, C05, and C07, respectively. Afterward, fifty-nine candidate genes related to Al tolerance were identified in the LD region of these SNP loci. Four of these genes were involved in the growth regulation about organic acid, ten were involved in growth-regulating substance, eleven were related to oxidative stress, and nineteen were involved in carbon and nitrogen metabolism. The results of this study provided a theoretical basis for Al tolerance in rapeseed and laid out a foundation for further functional verification of genes and cultivation of new Al tolerant rapeseed varieties.



中文翻译:

油菜发芽过程中铝耐性相关性状的全基因组关联分析

随着土壤酸化程度的增加,铝(Al)的毒性已成为影响种子发芽质量和作物产量的最重要的胁迫​​因素之一。为了研究铝对种子发芽的耐受性,使用全基因组覆盖的19,949个SNP的全基因组关联分析(GWAS)来识别候选基因,这些基因可能与铝下油菜(Brassica napus L.)的发芽性状有关强调。在实验中,用AlCl 3处理了169个油菜品种(品系)将90ppm溶液和蒸馏水加入到对照中。在第7天,测量并计算表型数据,包括根长和干重。使用TASSEL软件,Al耐受性相关性状的油菜籽进行了探讨下萌发了60K的甘蓝Illumina公司®Infinium SNP阵列。然后,使用STRUCTURE软件分析种群的结构,并使用TASSEL软件分析种群的遗传关系和LD衰减。在最佳模型下进行了具有SNP标记的相对根长(RRL)和相对干重(RDW)的GWAS。同时,基于相关SNP基因座的LD间隔序列预测候选基因。随后,在拟南芥中筛选了与目标基因组区域中耐铝性相关的油菜同源基因(L.)Heynh。结果表明13个SNP与这两个性状显着相关。其中,有8个SNP与RRL显着相关,分别位于A03,A07,A09,A10,C05,C06和C09染色体上。五个SNP与RDW显着相关,分别位于A03,A04,A10,C05和C07染色体上。之后,在这些SNP基因座的LD区域中鉴定了与Al耐受性有关的59个候选基因。其中有四个基因参与了有机酸的生长调节,有十个涉及生长调节物质,有十一个与氧化应激有关,有十九个参与碳氮代谢。

更新日期:2020-08-02
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