Exploring novel SNPs and candidate genes associated with seed allometry in Pisum sativum L.

Abstract

Seed size is an important agronomic trait that indicates seed quality. In legumes, pods with equal and larger seeds remain the first preference of farmers and consumers. Genetic understanding related to seed size including seed allometric traits has been limited in the case of peas. To fill this void the findings presented here used the genome-wide association studies (GWAS) to identify novel candidate gene(s) putatively linked with seed size in Pisum sativum L. The study was conducted on 240 Pea Single Plant Plus Collection (PSPPC) panels of pea germplasm. Allometric traits measured included seed_length, seed_width, seed_thickness, seed_volume, seed_biomass, and seed_biomass by volume (SB_V). GWAS was performed using the Genome Association and Prediction Integrated Tool (GAPIT) on R-studio. The Bayesian information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model provided significant single nucleotide polymorphisms (SNPs) linked with all the seed allometric traits. When analyzed the genomic regions of these SNPs provided a list of candidate genes that may be related to seed size. The present study thus provides a list of significant SNPs and relevant genes viz. Psat2g072000 for seed_length, Psat4g104320 for seed_width, Psat6g125800 and Psat6g125840 for seed_thickness, Psat6g228320 for seed_volume, Psat2g143920 for seed_biomass, and Psat2g120400 for SB_V which may prove useful in the improvement of pea seed size using breeding programs or CRISPR intervention. Understanding the genetic basis of seed size could lead to crop development with desirable seed characteristics, such as equal and larger-sized seeds with maximum yield and higher nutritional content.