Molecular diversity and genetic structure of rainfed durum wheat genotypes using SCoT markers

Selection- and conservation-based breeding programs require the study of genetic diversity. In this study, a collection of durum wheat consisting of 90 rainfed genotypes was subjected to the analysis of genetic diversity and population structure based on polymorphisms obtained from the Start Codon Targeted (SCoT) marker system. Out of 26 initial primers tested, 15 primers produced scorable polymorphism and were therefore, selected for further analyses. On average, 11.27 polymorphic fragments were observed for each primer per reaction. Polymorphism Information Content (PIC) ranged from 0.10 to 0.32 per locus with an average of 0.23 per primer. Resolving power (Rp) was varied from 0.98 to 5.80. The structure analysis classified the assessed population into 3 subpopulations. Besides, the Neighbor-Joining phylogenetic tree and Principal Coordinate Analysis separated genotypes into 3 and 5 distinct clusters. The Analysis of Molecular Variance (AMOVA) revealed high intra-population diversity. The gene flow index (Nm) indicated a relatively small probability of gene flow between the studied subsets. The Nei’s gene diversity (n), Shannon’s information index (I), and allele distribution statistics revealed that the individuals of subpopulation-2 had a significant capacity for genetic diversity. In conclusion, the studied SCoT primers had a high discriminating power and therefore, were efficient for evaluating genetic diversity in the durum wheat. The results of this study revealed the existence of a significant genetic diversity between the studied genotypes. Besides, the individuals of subpopulation-2 had a notable level of genetic diversity that can be used for various breeding purposes.