Genomic region associated with pod color variation in pea (Pisum sativum)

Pea (Pisum sativum) was chosen as the research material by Gregor Mendel to discover the laws of inheritance. Out of seven traits studied by Mendel, genes controlling three traits including pod shape, pod color, and flower position have not been identified to date. With the aim to identify the genomic region controlling pod color, we determined the genome sequence of a pea line with yellow pods. Genome sequence reads obtained using a nanopore sequencing technology were assembled into 117,981 contigs that spanned 3.3 Gb in length and showed an N50 value of 51.2 kb.

Using single nucleotide polymorphisms (SNPs) detected in a pea mapping population, these contigs were genetically anchored to the publicly available pseudomolecule sequences of the pea genome. Subsequent genetic and association analyses identified a genomic region responsible for pea pod color. At this genomic location, genes encoding 3’ exoribonucleases were selected as potential candidates controlling pod color, based on DNA sequencing and transcriptome analysis of green and yellow pod lines.

The results presented in this study are expected to accelerate pan-genome studies in pea and facilitate the identification of the gene controlling one of the traits studied by Mendel.