Abstract
Alfalfa (Medicago sativa L.) also called as queen of fodder or green gold, is the most important fodder crop grown in Ladakh region owing to its well adaptability to cold arid habitat (35000 m amsl). Three species of Medicago such as M. falcata, M. sativa and M. varia are found in Ladakh. Owing to little information available on population substructure and genetic diversity of alfalfa in the region, 45 accessions of Medicago sub species collected from Drass, Kargil and Leh regions of Ladakh were studied for molecular and morphological diversity. Observations recorded on 12 quantitative traits revealed presence of high genetic diversity among the sub-populations of alfalfa. The genotypes spread into 7 clusters based on D-2 statistic with maximum distance of 833.92 was observed between cluster VI and cluster V. Molecular characterization was carried out using 12 SSR markers. Analysis of molecular variance (AMOVA) revealed significant variation within population variance. Maximum PIC value was shown by the marker Afat-15 (0.74) and minimum by the marker MTIC-432 (0.54). The genotypes were grouped into five different clusters following UPGMA method: Small Fst values depicted minimum population sub-structure and greater sharing of gene pool among different sub-species. The. kind of information we generated on the molecular divergence in alfalfa populations of the region shows that there is a need to introduce novel Medicago species in the region and cross them with already existing inter-sub-species derivatives. Besides, population improvement programs should be initiated to improve the frequency of desirable alleles among and within sub-species.