IRAP and REMAP-based assessment of genetic diversity in chickpea collection from Iran

Abstract

Retrotransposons (RTN) make a significant contribution to the size, organization and genetic diversity of their host genomes. Several RTN families have been identified in chickpea (Cicer arietinum L.) and other closely related species. In the current research, integration activity and insertional polymorphism of the RTNs CARE1, Tms1Ret1, TPS and LORE were studied in 64 chickpea accessions collected in Iran using inter retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) techniques. Results indicated that all RTNs studied, are transpositionally active in chickpea genome and amplified scorable and polymorphic banding pattern. Among the RTN families used, the highest percentage of polymorphic loci (PPL) was produced by TPS family (81.82%). Totally, 129 loci were amplified using 18 IRAP and REMAP primers which 83 (64.34%) were polymorphic. The Dice genetic similarity coefficients among accessions ranged from 0.84 (accessions Tj48 and Ba4) to 0.98 (accessions Ka30 and Urm61), averaging 0.93. The parameters of expected heterozygosity (He), Shannon?s information index (I) and number of effective alleles (Ne) were the highest for Urmia accessions. Cluster analysis based on UPGMA algorithm and Dice similarity coefficient categorized the 64 accessions in 7 main groups. The mean Fst values of all groups except for groups IV and VII, were lower than 0.20, demonstrating no clear differentiation among the groups, no genetic structure of the studied chickpea collection and probably occurrences of gene flow among the origins. In conclusion, although RTN-based markers were able to differentiate the chickpea accessions but the measured relative genetic similarity among accessions were not correlated with geographical distances between places of their origins.