Deciphering genetic diversity and population structure in ex-situ conserved Brassica rapa var. yellow sarson germplasm using morphological traits and simple sequence repeat (SSR) markers

Brassica rapa (2n = 20, AA) is consumed as vegetable, fodder and oilseed crop. Oilseed type B. rapa species occupy important place after B. juncea in India. So, present study was carried out to study genetic diversity and population structure in 136 yellow sarson germplasm using 17 morphological traits and 99 simple sequence repeat (SSR) markers. A good frequency for most of the morphological traits was reported. At species level, morphological markers exhibited maximum polymorphism (61.89%) as compared to SSR markers (46.67%). Analysis of molecular variance (AMOVA) revealed significant differences among populations based on different markers. However, SSR markers (PhiPT = 0.040, p-value = 0.010) revealed more variation between populations as compared to morphological traits. On the basis of pooled markers, indigenous lines showed highest expected heterozygosity (He = 0.20) and polymorphism (P = 87.96%). Both markers revealed lowest Nei’s genetic distance (GD) between advanced breeding lines and indigenous lines (Morph GD = 0.01, SSR GD = 0.01). Furthermore, optimum three clusters (K = 3) were deciphered in yellow sarson germplasm based on principal coordinates analysis (PCoA), AMOVA and population structure analysis. PCoA and AMOVA could be used in addition to delta K and LnPd in deciding optimum number of clusters in structure analysis. Information of present study will be useful in selection of suitable traits and SSR markers for characterization, conservation and utilization of yellow sarson germplasm. Likewise, inclusion of more number of morphological characters, seed biochemical parameters and genotyping by sequencing would be helpful in gaining more understanding on genetic variability and diversity of these traits in yellow sarson.