Analysis of single nucleotide polymorphism and simple sequence repeat markers for the estimates of genetic diversity by using two oilseed Brassica napus populations carrying genome contents of Brassica oleracea

Abstract

Reliable estimates of genetic diversity among the accessions in a breeding population is important knowledge for use in breeding. Among the different types of molecular markers, single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) are largely used by breeders; however, our knowledge of the reliability of the estimates of genetic diversity based on these two types of markers in multiple populations is limited. In this study, a doubled haploid (DH) and an inbred population developed from Brassica napus × Brassica oleracea interspecific crosses were used for comparative analysis of these two types of markers. The estimates based on SNP and SSR markers showed a stronger correlation in the inbred population which was expected to carry greater genetic diversity as compared to the DH population. This inference was also evident from the analysis of different diversity groups (least, intermediate, and most similar) of these two populations for significant difference between the groups for six agronomic and seed quality traits, where this analysis failed to differentiate the diversity groups of the DH population for any of the traits. However, both marker types could differentiate the diversity groups of the inbred population for several traits. Furthermore, the six sub-populations of the inbred population could also be differentiated by both marker types. Thus, the results demonstrate the greater utility of the SSR and SNP markers in a genetically diverse population. This knowledge can be used while grouping a breeding population for diversity groups; however, caution needs to be taken while using the markers in a genetically narrow population.