Retroelement Insertional Polymorphism and Genetic Diversity in Medicago sativa Populations Revealed by IRAP and REMAP Markers

Retrotransposons (RTNs) are common components of plant genomes, showing activity at transcription and integration levels. Their abundance, dispersion, ubiquity, and ability to transpose make them useful as molecular markers. In this study, we used multilocus PCR-based techniques, inter-retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP) to study the integration events of native (Tms1Ret1) and non-native RTN (LORE1, LORE2, Tps12a, and Tps19) families in M. sativa genome. IRAP and REMAP markers derived from these RTNs were used to assess genetic diversity among and within 80 M. sativa genotypes belonging to eight populations. Results indicated the presence and transpositional activation of RTNs Tms1Ret1, LORE1, LORE2, and even Tps12a in M. sativa genome. REMAP analysis showed the insertion of studied RTN families near the microsatellites in M. sativa genome except for RTN Tps19. A total of 101 and 119 loci were amplified using 10 and 14 IRAP and REMAP primers, respectively. The number of polymorphic loci was 66 and 62 for IRAP and REMAP, respectively. Mantel test between IRAP and REMAP cophenetic matrices evidenced no significant correlation (r = 0.15). Although populations could be relatively differentiated based on IRAP + REMAP data, overall genetic differentiation among populations was low (PhiPT = 0.082, P = 0.0010). Analysis of molecular variance based on IRAP + REMAP analysis revealed the higher level of genetic variation within populations (92%) compared to among populations (8%). IRAP + REMAP-based cluster analysis of 80 M. sativa genotypes using complete linkage algorithm identified five heterotic groups that could be applied as crossing parents in M. sativa alfalfa breeding programs.