Abstract
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.
Highlights
Arabidopsis thaliana is a naturally inbred plant, which means that all lines have nearly completely homozygous genomes
We developed a completely new branch to provide RNASeq expression profiles for thousands of samples and genes in AraPheno, as well as novel associations between knockout (KO) mutations and population-scale phenotypes in the AraGWAS Catalog
At the moment we only provide the expression data in AraPheno, but in principle, gene expression data could be treated as high-dimensional phenotypic data and could be used directly for Genome-wide association studies (GWAS) as well as for transcription-wide association studies (TWAS) [24], where the transcript abundances are treated as explanatory variables
Summary
Arabidopsis thaliana is a naturally inbred plant, which means that all lines have nearly completely homozygous genomes. We extended the GWAS analysis to compute associations between reported knockout (KO) mutations based on loss-of-function alleles of full genes [35] and all publicly available phenotypes in A. thaliana. For this purpose, we created additional views in the AraGWAS Catalog to report these results. When subsetting associations by those meeting various significance thresholds, we observed a significant enrichment in knockout alleles associated with increased trait values (greater number of positive  coefficients, Figure 2D–I) This observation may reflect the fact that reference gene models are based on the Col-0 genotype, which is relatively small and rapid cycling. Such results are consistent with previously observed biases in the direction of knockout effects [35,36] and motivate efforts to define gene functional allele state informed by diverse genotypes
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