True hybridity analysis using genome-wide hypervariable SSR markers in pomegranate

Abstract

A total of 25 SSR primers were screened on 37 putative F1s derived from the five different crosses. Identified cross specific highly informative SSRs primers, i.e., 14 for the first cross, 10 for the second, 12 for the third and 6 each for fourth and fifth crosses. For the first cross Bhagwa × Daru 17, four primers (HvSSRT_375, NRCP_SSR9, NRCP_SSR12 and NRCP_SSR92) were found to be highly informative with higher 100% hybrid purity index (HPI), PIC (~0.52), and observed heterozygosity (Ho, range 0.87–0.93) values, and two F1s namely H1 and H2 were found to be highly heterotic with a heterozygosity index (HI) of 92.85%. Similarly, for Bhagwa × Nana, three primers (HvSSRT_375, HvSSRT_605 and NRCP_SSR19) had higher HPI (70%–100%), PIC (0.52–0.69), and Ho (0.75–0.33) values, and three F1s H1, H2, and H4 had 70% (HI). For Bhagwa × IC318712, four SSRs (HvSSRT_254, HvSSRT_348, HvSSRT_826 and NRCP_SSR95) had higher Ho (~0.83), HPI (100%) and PIC (~0.52) values, and four F1s H2, H7, H9, and H10 showed 91.66% (HI). For Bhagwa × Nayana, HvSSRT_605, HvSSRT_826, and HvSSRT_432, and for Ganesh × Nayana, HVSSRT_375, HVSSRT_605, and HvSSRT_826 were found informative. These markers will be highly useful in developing maps of populations.