POTAGE

POTAGE organizes genomic and expression data to enable identification of candidate genes underlying quantitative trait loci in hexaploid wheat (Triticum aestivum).

Key Features:

• Data integration: Integrates Chromosome Survey Sequences, gene predictions, and RNA-Seq expression data for Triticum aestivum.
• POPSEQ ordering: Applies the population sequencing (POPSEQ) approach to order sequences along chromosomes, providing chromosomal context.
• QTL candidate linkage: Links ordered sequence data with gene predictions and expression to support identification of candidate genes for quantitative trait loci (QTL).
• Expression and annotation integration: Combines RNA-Seq expression data with functional annotations to assist gene prioritization.
• Species focus: Targets analysis in hexaploid wheat (Triticum aestivum) and enables comparison with orthologs in related cereals.

Scientific Applications:

• QTL gene discovery: Facilitates discovery of candidate genes underlying QTL in hexaploid wheat.
• Gene prioritization: Prioritizes genes within mapped intervals using RNA-Seq expression and functional annotation evidence.
• Trait investigation: Has been applied to investigate pre-harvest sprouting and seed dormancy, including identification of TaMKK3 as a candidate gene and comparison with the barley ortholog.

Methodology:

Integrates Chromosome Survey Sequences, gene predictions, and RNA-Seq expression data and orders sequences along chromosomes using the population sequencing (POPSEQ) approach.