Evaluation of genetic divergence and phylogenetic relationship using sequence-tagged microsatellite (STMS) sequences in Chickpea (Cicer arietinum L.) genotypes

Abstract

The current investigation was carried out to analyse the genetic diversity estimates between 125 chickpea genotypes using sequence-tagged microsatellite (STMS) markers. Thirty one STMS primers generated a total of 153 loci (an average of 4.94 loci per primer) out of which 129 loci were found to be polymorphic and 24 loci were monomorphic. The value of PIC varied from 0.128 to 0.783 while the resolving power varied from 0.912 to 4.768. The UPGMA generated dendrogram showed the grouping of all the 125 chickpea cultivars into two major clusters and one small cluster. An unbiased clustering of genotypes based on STRUCTURE program, without prior knowledge about the populations, clustered all the 125 genotypes into three major groups. Percentage of polymorphic loci using POPGENE analysis was 50.98, 58.82 and 96.73 for susceptible, resistant and miscellaneous genotypes, respectively. Genetic diversity analysis in terms of Shannon’s index and Nei’s gene diversity for resistant, susceptible, and miscellaneous cultivars revealed higher values for miscellaneous cultivars, indicating more variability among these cultivars in comparison to resistant and susceptible cultivars. AMOVA results among groups and among cultivars were 10 and 90%, respectively, while the estimated gene flow was 6.117. The overall Nei’s gene diversity (0.238) and Shannon’s information index (0.372) indicated high degree of genetic polymorphism revealed by the STMS molecular markers. So, genetic divergence in chickpea can provide useful indications in understanding species relationships and may help in developing effective breeding programs.

Keywords: Cicer arietinum, genetic polymorphism, molecular markers, analysis of molecular variance, gene flow.