AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana
AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana
复制标题
AraPheno 和 AraGWAS Catalog 2020：主要数据库更新，包括拟南芥 RNA-Seq 和敲除突变数据
DOI：
10.1093/nar/gkz925
复制
发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Grimm, Dominik G.
中科院分区：
文献类型：
--
作者：
Togninalli, Matteo;Seren, Uemit;Grimm, Dominik G.
全基因组关联研究（GWAS）是研究基因型-表型关系和更深入地了解性状变异背后的遗传结构不可或缺的。模式植物拟南芥的不同基因座和各种性状之间的大量遗传关联已经被成功地发现并发表。这一成功以及免费提供1,000多个不同自然近交系的完整基因组和表型数据，导致了几个数据库的开发。AraPheno（https：arapheno.1001genomes.org）作为A. thaliana，而AraGWAS Catalog（https：//aragwas.1001genomes. org）提供了一个公开可用的、手动策划的和标准化的标记-性状关联集合，用于来自AraPheno的所有可用表型。在这次重大更新中，我们将介绍这两个平台的下一代，包括新的数据、功能和工具。我们纳入了敲除突变与所有AraPheno性状之间关联的新结果。此外，AraPheno已经扩展到显示数百个品种的RNA-Seq数据，为这些品种提供超过28000个基因的表达信息。所有数据，包括用于GWAS的插补基因型矩阵，都可以通过相应的数据库轻松下载。
Genome-wide association studies (GWAS) are integral for studying genotype-phenotype relationships and gaining a deeper understanding of the genetic architecture underlying trait variation. A plethora of genetic associations between distinct loci and various traits have been successfully discovered and published for the model plant Arabidopsis thaliana. This success and the free availability of full genomes and phenotypic data for more than 1,000 different natural inbred lines led to the development of several data repositories. AraPheno (https://arapheno.1001genomes.org ) serves as a central repository of population-scale phenotypes in A. thaliana, while the AraGWAS Catalog (https://aragwas.1001genomes. org ) provides a publicly available, manually curated and standardized collection of marker-trait associations for all available phenotypes from AraPheno. In this major update, we introduce the next generation of both platforms, including new data, features and tools. We included novel results on associations between knockout-mutations and all AraPheno traits. Furthermore, AraPheno has been extended to display RNA-Seq data for hundreds of accessions, providing expression information for over 28 000 genes for these accessions. All data, including the imputed genotype matrix used for GWAS, are easily downloadable via the respective databases.