Fine mapping PsPS1, a gene controlling pod softness that defines market type in pea (Pisum sativum)

Pea is an important grain and vegetable crop with a large genome of similar to 4.45 Gb. The softness of pod is key to the quality of pea, yet the genes controlling softness remain unknown. Here, the pod softness phenotype was visually scored at the fully mature stage, which suggested that this trait was a composite trait governed by two genes. Bulked segregant analysis sequencing (BSA-Seq) using the soft- and hard-podded pools from the F-2 detected a strong peak of Delta (SNP-index) on chromosome 1 and a weaker peak on chromosome 5. The former was designated as PsPS1. Fine mapping using the F-2 delimited PsPS1 to a similar to 6 Mb genomic region. A set of interesting candidate genes including those encoding cell wall components were identified. Sequence variants analysis from a panel of pea accessions and qRT-PCR in immature pods of the parents suggested Psat1g150000 encoding a pectate lyase superfamily protein as a candidate gene. The results solidify the basis for cloning of the gene determining pod softness and marker-assisted selection for the trait improvement.