COMPILE

COMPILE identifies and annotates candidate genes from Genome-Wide Association Studies (GWAS) to link significant quantitative trait loci (QTL) to genes and RNA regulatory elements across genomes.

Key Features:

• Mixed Linear Model-based GWAS: Executes GWAS using a Mixed Linear Model with population structure control without data compression to detect QTL.
• QTL-to-gene and RNA annotation: Links significant QTL to candidate genes and RNA regulatory elements across any genome.
• Homology matching: Matches identified maize genes to closest homologs in rice and Arabidopsis based on sequence similarity.
• Validation on trait datasets: Validated using published data for α-tocopherol biosynthesis and flowering time and applied to 274 maize genotypes from the Goodman Association Panel to identify loci for European Corn Borer resistance.
• Diverse candidate detection: Identifies candidate genes and non-coding RNAs involved in transcriptional regulation (WRKY and MYB-like factors), receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation.
• Performance characteristics: Provides relatively rapid data analysis enabling comparison of population size and compression to address limitations related to population diversity and size.

Scientific Applications:

• Agricultural genomics and plant biology: Mapping genes for traits such as disease resistance, biosynthesis pathways (including α-tocopherol), and developmental timing (flowering time) in crops such as maize.
• Resistance locus discovery: Identification of loci contributing to resistance against European Corn Borer larvae in the Goodman Association Panel.
• Cross-species functional inference: Facilitates transfer of annotations and candidate identification across species via homolog matching to rice and Arabidopsis.

Methodology:

Performs Mixed Linear Model GWAS with population structure control without data compression, links significant QTL to candidate genes and RNA regulatory elements, and matches maize genes to rice and Arabidopsis homologs by sequence similarity; applied to 274 maize genotypes and validated on published α-tocopherol biosynthesis and flowering time datasets.