Assessment of Genetic Diversity and Population Structure in Local Alfalfa Genotypes Using iPBS Molecular Markers

Abstract iPBS retrotransposon markers, in other words, inter-primer binding site markers based on retrotransposon, have been useful for the determination of genetic diversity in several plants. The study was evaluated by using 10 iPBS molecular markers the level of genetic diversity and genetic structure of alfalfa genotypes. A total of 280 alleles in 50 alfalfa genotypes (48 local genotypes and 2 commercial varieties) were obtained by 267 polymorphic markers with an average of 28 per locus, ranging from 9 to 41 alleles. The rate of polymorphism of the markers ranged from 86.36–100% with an average of 93.71%. The average number of polymorphic bands per marker was detected as 26.7. The mean PIC value and Dice's similarity were calculated between 0.14 and 0.50 respectively. The Results of UPGMA analysis, principal component analysis (PCA), and STRUCTURE demonstrated that the 50 alfalfa genotypes could be classified into 4 subpopulations, namely the Q1, Q2, Q3, and Q4. The Nei’s genetic distance ranged from 0.0121 to 0.0359. iPBS markers and alfalfa genotypes used in this study may be used in studies of alfalfa breeding and germplasm conservation.