Identification of candidate region and diagnostic KASP markers associated with earliness in Pea through BSA-Seq Approach
The Garden pea, a temperate crop belonging to the Leguminosae family, is valued for its early maturation, making it economically beneficial. Early maturity varieties, which complete their growth cycle in approximately 80-90 days, fit well within the cropping sequence of rice, wheat, and maize, providing an extra source of income. The high market demand of early maturing pea varieties in India is due to their early availability in market resulting in higher prices. Mapping the quantitative trait loci associated with earliness is essential for elucidating the genetic factors that influence the maturity period in peas. This study seeks to investigate the genetics of earliness and identify the QTL for this trait in the F2 population employing the BSA-Seq method coupled with whole genome sequencing. We phenotyped 120 F2 individuals developed from a cross between early-maturing, MatarAgeta-10 and late-maturing, Punjab-89 pea varieties. Phenotypic analysis revealed that earliness follows a monogenic recessive inheritance pattern, which was designated as the locus pel-1. To map this locus, we selected 10 early-maturing and 10 late-maturing homozygous F2 individuals for the whole genome resequencing. Utilizing a customized bioinformatics pipeline, we identified two regions on chromosome 2 and 7 associated with earliness. A novel QTL for earliness, named qPSE7 was discovered on chromosome 7, spanning from 418.4 Mb to 424.9 Mb. Out of 907 SNPs identified within the 6.5 Mb region of the QTL qPSE7, 23 SNPs were validated as KASP markers in the F2 population. Among these markers, PS423028253 showed a significant association with the earliness trait with distance of 1.7cM. This novel QTL along with KASP markers identified can be utilized for marker-assisted selection in pea breeding programs and will aid in the identification of the linked gene in future studies.