Analysis of genetic diversity and structure in a genebank collection of red clover (Trifolium pratense L.) using SSR markers

Abstract

AbstractGenetic diversity of a red clover global collection was assessed using 36 simple sequence repeat (SSR) primers representing all seven linkage groups (LGs). The number of fragments amplified ranged from 1 to 6 for all the primers. Primer RCS0060 detected highest number of fragments, whereas four SSRs viz., RCS0899, RCS1594, TPSSR40 and RCS6927 amplified single fragment. Size range of amplicons generated by all the primers varied from 100 to 400 bp. Polymorphism information content values ranged from 0.301 to 0.719 with an average value of 0.605. LG wise diversity analysis showed that LG 3 was most diverse (I = 0.65, Ht = 0.44), whereas LG-1 showed minimum diversity (I = 0.48, Ht = 0.26) for the microsatellites used. Bayesian model-based clustering inferred three genetically distinct populations in the red clover germplasm holding and showed considerable admixture in individuals within clusters. Neighbour-joining analysis showed intermixing of accessions within groups. Principal component analysis plot complemented the clustering shown by Structure and distinguished three populations to greater extent. Analysis of molecular variance showed that 91% of the genetic variation was residing within populations, while 9% variation was among populations. Overall, the results showed that a high level of genetic diversity is prevailing in this worldwide collection of red clover, which can be exploited for its genetic improvement through breeding approaches.