Identification and validation of KASP markers for the non-parchment trait in edible podded pea

The non-parchment layer trait in edible podded pea inhibits the formation of sclerenchymatous tissue in the pod wall which makes the pods edible in nature. In the present study, genetics and genomic region (s) controlling non-parchment layer trait was studied in edible podded pea. Inheritance study from the cross, Honey Snap × Punjab-89 showed that it was governed by single major recessive gene along with certain modifiers. Putative genomic regions associated with the non-parchment layer were identified using BSA seq approach where two extreme phenotypic pools were constructed by identifying extreme plants for the given trait. Downstream analysis through QTLseqr identified one major genomic region of 60 Mb located at 592.56 to 652.84 Mb on chromosome 5 and was designated as "qNpp5.1" which is at the same locus as V gene. Within this region, 26 KASP markers were developed and out of which 11 showed polymorphism in two parents and two bulks. The phenotypic and genotypic data from 257 F₃ population was used to construct linkage map using QTL IciMapping, that narrowed down the qNpp5.1 region to 12 Mb flanked by Psp618703255 and Psp606633411 KASP markers on Chr05. The QTL qNpp5.1 was identified at LOD 19.51 and explained 28.31% of the total phenotypic variation showing additive and dominant effects of 0.64 and - 0.08, respectively. The closely linked KASP marker Psp618703255 was able to predict 80-85% of plants accurately in a diverse panel of P. sativum var. hortense, P. sativum var. macrocarpon, P. sativum var. saccharatum and BC₁F₂ population derived from cross Punjab-89 X (Honey Snap X Punjab-89). Thus, these findings are useful for marker assisted selection (MAS) to accelerate the non-parchment layer breeding programs in edible podded pea.