AraPheno

AraPheno provides a centralized database of phenotypic, genotypic, and RNA-Seq expression data for Arabidopsis thaliana to support genotype–phenotype analyses and genome-wide association studies (GWAS).

Key Features:

• Extensive phenotypic dataset: Phenotypes for over 1,000 Arabidopsis thaliana natural inbred lines are curated for genetic analysis.
• RNA-Seq integration: RNA-Seq expression data are available for hundreds of accessions covering expression information for over 28,000 genes.
• Knockout mutation associations: Catalogued associations between knockout mutations and phenotypic traits enable functional genomics investigations.
• Imputed genotype matrices: Genotype imputation has been performed to produce imputed genotype matrices used for GWAS.
• Complementary AraGWAS Catalog: A manually curated and standardized collection of marker–trait associations for phenotypes from AraPheno is maintained in the AraGWAS Catalog.

Scientific Applications:

• Genome-wide association studies (GWAS): Use of imputed genotype matrices and extensive phenotype data to identify genetic loci associated with traits.
• Functional genomics: Analysis of knockout mutation–trait associations to investigate gene function and genetic effects on phenotype.
• Gene expression analysis: Integration of RNA-Seq data with phenotypes to link expression variation to trait variation and regulatory mechanisms.
• Comparative genetics: Comparison of phenotypic and genetic variation across A. thaliana lines to study trait diversity and evolutionary patterns.

Methodology:

Genotype imputation producing imputed genotype matrices, integration of RNA-Seq expression datasets for accessions, and genome-wide association studies (GWAS) using the imputed genotypes and phenotypes.