Developing Breeders' Tools: Identifying and Visualising Genotype-to-Phenotype Associations in the Common Pea and Its Wild Relatives

Peas (Pisum sativum) are an important crop plant and are important for food security. These cool season legumes are the second most important family of crops and are high in protein making them important for food and animal fodder. Furthermore, peas are useful in crop rotation as they can symbiotically fix nitrogen, reducing the need for fertiliser.

John Innes Pisum Collection is a well-characterised collection of peas, holding approximately 3,600 accessions. Previous work with retrotransposon-based insertion polymorphism markers (RBIP) used characterised the collection into 3 distinct groups: cultivar, landrace and wild material.

We sampled a statistically representative core collection across all 3 groups of the 3,600 accessions for phenotypic and sequence analysis. Biological replicates were sown in field and glasshouse environments. To quantify phenotypic traits we have imaged and measured several phenotypes of interest: seed weight, plant height, leaflet margin and pod length, width and apex. We have focused primarily on seed weight, as it is a highly heritable trait of interest to pea breeders.

The Pea genome is large and highly repetitive and currently has no reference. To tackle this issue we used Genotyping-by-sequencing (GbS), a reduced representative sequence approach to generate a high-density marker panel of SNPs without a reference at low cost.

Here we present, a quantitative phenotypic analysis across wild and domesticated pea material, and in combination with the GbS sequencing data, this contributes to a wider Genome-Wide Association Study (GWAS) to identify candidate regions for the associated genotypes.