Genetic analysis of Lepidium spp. by SSR and ISSR molecular markers

Abstract Simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers were employed to evaluate the genetic diversity and population structure of 22 accessions belonging to three Lepidium species. Results revealed a high level of genetic diversity in the Lepidium accessions. A total of 58 bands were amplified by 11 ISSR primers, of which all were polymorphic, while 11 SSR primers produced 30 bands, of which 27 (90.0%) were polymorphic. The average values of polymorphism information content (PIC), marker index (MI), effective multiplex ratio (EMR) and percentage of polymorphic loci (PPL) in the ISSR markers were higher than those in SSRs, whereas higher values of number of effective alleles (Ne) and Shannon's information index (I) were observed by SSR markers. Based on the number of observed alleles (Na), Ne, I, expected heterozygosity (He) and PPL, the highest genetic diversity was found in L. draba followed by L. sativum by both markers. The analysis of molecular variance showed that higher allelic diversity within species than among species. The 22 Lepidium accessions grouped into three main clusters based on neighbor-joining (NJ) clustering and principal coordinate analysis (PCoA), and three (ISSR) or four (SSR and pooled data) sub-populations based on STRUCTURE analysis independent of their taxonomy. This is the first report of genetic diversity and relationships among accessions of L. sativum, L. draba and L. latifolium using SSR and ISSR markers. Therefore, these results can be utilized to improve these Lepidium species for various desired traits through molecular and hybridization breeding techniques.