SSR analysis to assess genetic diversity and population structure in parthenocarpy cucumber (Cucumis sativus L.)

Abstract

The genetic diversity and population relationship was determined in 14 genotypes of parthenocarpic cucumber (Cucumis sativus L.) using simple sequence repeats (SSR) markers. In this study, fifty-nine SSR markers comprehensively showed polymorphism among cucumber genotypes. Total 252 alleles were identified with an average of 4.27 alleles per locus, while the polymorphism information content (PIC) of the primers ranged from 0.34 to 0.84 with a mean value of 0.62. The major allele frequency and heterozygosity ranged from 0.21 to 0.75 and from 0.43 to 0.89, respectively. Maximum major allele frequency was reported with primer Cs- Female-4, whereas the maximum value of polymorphic information content was found with the primer SSR11742. The dendrogram clustered genotypes into two main groups A and B with 8 and 6 genotypes, respectively. Jaccard’s similarity coefficient ranged from 0.63 to 0.86 with maximum similarity between genotypes DDPCG3 and PLP-1, whereas minimum similarity was observed between DDPCG8 and PLP Gy-1-08B. The population structure revealed three sub-populations with some admixtures. Principal coordinate analysis (PCoA) with SSR markers revealed that the genotypes were uniformly distributed across the two axes in both the plots with 41.76% of cumulative variation. The genetic divergence within indigenous genotypes allow genotypic identification, gene mapping and cloning for improvement in cucumber breeding.