Genome-wide InDel marker development and application of Cucurbita pepo L.

DONG Jiamei; YANG Yongzhao; SUN Liuqing; LU Qiuchen; CHEN Wanlu; WU Zhe; DUAN Ying; LEI Fengjin; WANG Changlin; BO Kailiang

doi:10.16861/j.cnki.zggc.2025.0461

Abstract：Pumpkin(Cucurbita pepo L.)is an important vegetable crops with rich genetic diversity,diverse use,and high economic value.To systematically develop genome-wide InDel markers,two accessions from different subspecies-Jin-GL(C.pepo ssp.texana)and HM-S2(C.pepo ssp.pepo)-were subjected to resequencing.Five polymorphic InDel locis were selected and successfully validated on each chromosome,resulting in a total of 100 pairs primers.Polymorphism evalua-tion using 81 pumpkin germplasms revealed broad genetic backgrounds among the tested material,with an average Shan-non's genetic diversity index of 1.00,and high marker polymorphism,as indicated by an average polymorphism informa-tion content(PIC)of 0.56.Cluster analysis via the unweighted pair group method with arithmetic mean(UPGMA)classi-fied the 81 germplasms into four gourps at a genetic similarity coefficient of 0.65.Group Ⅰ comprised 45 accessions,pri-marily vining ornamental types of ssp.texana.Group Ⅱ contained 34 accessions,representing cultivated types of ssp.pepo.Group Ⅲ contained one wild accession of C.foetidissima and group Ⅳ consisted of one C.maxima accession.Ten mark-ers with the highest polymorphism were selected from 100 polymorphic InDel markers to construct a fingerprinting.Final-ly,cluster analysis was performed on 237 commercial C.pepo varieties(and hybrids)using the 100 pairs of primers.The results showed that at the genetic distance of 0.08 did seed-types exhibit a tendency to form a distinct group.Furthermore,most varieties(hybrids)of both flesh-type and seed-type exhibit a trend of narrow genetic background.This study provides a theoretical basis for the genetic diversity analysis of C.pepo germplasm resources and the development of new cultivar.