GWAS剖析拟南芥镁相关位点以及水稻同源基因

发布时间：2018-04-21 13:02

本文选题：全基因组关联分析(GWAS) + 高镁相关位点　；参考：《中国农业科学院》2017年博士后论文

【摘要】：深度的全基因组关联分析方法Open GWAS algorithm(OATH)为响应遗传学界的开源趋势,我们开发了一种新的线性回归方法用于全基因组关联分析研究(GWAS),我们将其命名为开放GWAS算法(OATH)。该算法可以在不需要个体水平数据的情况下,仅使用自然汇总统计(NSS),不仅能完整的重现单一实验模型的报告结果,还能生成被掩藏或者未报道的其他模型下的结果。使用NSS,我们可以1、重复出于使用个体水平数据同样精确度的GWAS结果,2、恢复出未报道的使用任何组合协变量的结果,3、深度评估结果,比如分析p值得方差,进而得出一个更加可靠的评估结果,如同我们使用3种供镁条件下的42个拟南芥表型数据所展示的结果。此外,OATH方法可以用于多中心联合的GWAS meta研究,可以极大的提高GWAMA研究的灵活性。OATH的原型已在软件 GEnetic Analysis Repository(GEAR,https://github.com/gc5k/GEAR)中实现。拟南芥不同生态型对高镁的响应某些蛇纹石土壤或半干旱地区土壤中的高镁是作物生长发育的重要障碍。然而高镁稳态下植物适应的具体遗传位点和机理尚未很好的了解。利用388份收集自世界各地的拟南芥生态型材料和约25万个SNP的基因型数据,我们成功的找到了 109和74个分别在正常镁(1OOOuM)和高镁(1OOOOuM)与营养性状相关的基因位点。超过90%的SNP与营养表型有关,仅有2个SNP同时在正常镁和高镁条件下被定位到。在高镁下发现一个与植株Ca浓度表型强相关的SNP位于候选基因Atlg60420(6tNRX1)中。进一步的研究显示,相较于野生型,Atnrx1突变体在高镁供应下具有较高的胞内钙浓度,较长的主根和积累更多的鲜重。这表明AtNRX1基因特异性的负向调节Ca的吸收和植株生长。此外,GWAS找到的其它SNP位点将有助于确定早期营养相关的生物标志基因和分组育种标记从而帮助开发镁营养高效作物。水稻镁相关同源基因挖掘针对拟南芥中定位的镁相关的基因位点,我们利用水稻基因组信息,比对后鉴定了一些水稻同源基因。通过GWAS定位,我们一共613个显著SNP位点区段,并预测筛选了 431个候选基因。通过同源比对,寻找在水稻中的直系同源基因,最终一共找到424个水稻同源基因。已克隆基因表明通过GWAS定位发现的表型关联基因至少部分可以通过同源比对分析在水稻中找到相似功能的基因。此外,进一步分析了剩余未克隆的水稻基因的表达以及其与表型的关系,发现种子萌发和鲜重以及上胚轴长度的基因以及钠和钙含量的基因存在较为可能的同源基因。
[Abstract]:Open GWAS algorithm (OATH), in response to the open source trend of the genetic community, has developed a new linear regression method for whole genome association analysis (GWAS). We named it as an open GWAS algorithm (OATH). This algorithm can only be made without the need for individual level data. Natural summary statistics (NSS) can not only reproduce the results of the single experimental model completely, but also generate the results under other models that are hidden or unreported. Using NSS, we can 1, repeat out of the GWAS results using the same accuracy of the individual level data, 2, and restore the unreported results of using any combinatorial covariance, 3 The results of the depth assessment, such as the analysis of the P worth of variance, and then a more reliable evaluation result, like the results shown in the 42 Arabidopsis phenotypic data of 3 kinds of magnesium supply conditions. In addition, the OATH method can be used in the multi center joint GWAS meta study, which can greatly improve the prototype of the flexibility.OATH of GWAMA research. It has been implemented in the software GEnetic Analysis Repository (GEAR, https://github.com/gc5k/GEAR). The high magnesium response to high magnesium in different ecotypes of Arabidopsis thaliana is an important obstacle to the growth and development of crops. However, the specific genetic sites and mechanisms of plant adaptation in high magnesium steady state are not very good. With 388 copies of Arabidopsis ecotype materials and about 250 thousand SNP genotype data collected from all over the world, we have successfully found 109 and 74 gene loci related to normal magnesium (1OOOuM) and high magnesium (1OOOOuM). More than 90% of SNP is associated with nutritional phenotypes, and only 2 SNP at the same time in normal magnesium and high magnesium Under high magnesium, a strong correlation between Ca concentration and SNP was found in the candidate gene Atlg60420 (6tNRX1). Further studies showed that, compared to the wild type, the Atnrx1 mutant had higher intracellular calcium concentration, longer main root and more fresh weight under the high magnesium supply. This indicated that the AtNRX1 gene was specific. Sexual negative regulation of Ca absorption and plant growth. In addition, the other SNP sites found by GWAS will help to identify early nutrition related biomarker genes and group breeding markers to help develop magnesium nutritive crops. Rice genome information was identified and some rice homologous genes were identified. Through GWAS location, we had 613 significant SNP loci segments and predicted and screened 431 candidate genes. Through homologous alignment, we searched for the direct homologous genes in rice, and finally found 424 rice homologous genes. The cloned genes showed that the gene was located by GWAS. The present phenotypic associated genes may at least partially find similar genes in Rice by homologous comparison. In addition, the expression of the remaining uncloned rice genes and their relationship with the phenotype are further analyzed. The genes of seed germination and fresh weight and the length of the hypocotyl, as well as the genes of sodium and calcium content are found to exist. Possible homologous genes.

【学位授予单位】：中国农业科学院
【学位级别】：博士后
【学位授予年份】：2017
【分类号】：Q943.2

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