Genetic diversity and population structure analysis of Durum wheat (Triticum turgidum L.) genotypes using whole genome DArTseq-generated SilicoDArT markers

Abstract

Objective Durum wheat (Triticum turgidum) with an average annual production of 40 million tons, is the tenth most important and common crop grown worldwide. The aim of this study was to analysis the genetic diversity and population structure of durum wheat genotypes for knowledge and apply in future genomic studies using SilicoDArT markers generated by DarTseq. Materials and Methods The DNA of 94 durum wheat genotypes were extracted by CTAB method from fresh leaves. The quality and quantity of extracted DNA were measured using spectrophotometer and adjusted to 50 ng / μl. The DNA samples were processed at Diversity Array Technology Pty, Ltd, Australia (https://www.diversityarrays.com) for DArTseq analyses using genotyping by sequencing Platform. Genetic diversity and population structure analysis were performed on the remaining 7882 markers using: Power Markerv.3.25, DARwinver 5.0, STRUCTURE2.1., GenAlexv. 6.41 and Rv3.2.3 software. Results The amount of polymorphic information content (PIC) of SilicoDArT markers ranged from 0.023 to 0.499 with an average of 0.38. The mean reproducibility and call rate of sequences in all linkage groups were above 0.98 and 0.92, respectively. The number of mapped SilicoDArT markers varied from 300 markers in the linkage group (Chr1A) to 853 markers in the linkage group (Chr7B). Chromosome size covered by SilicoDArT markers ranged from 829200 kbp in the linkage group (Chr3B) to 589293.786 kbp in the linkage group (Chr1A). The results of cluster analysis by Neighbor-Joining (NJ) method, population structure and discriminant analysis of principal components were highly consistent with each other and clearly divided the studied genotypes into four distinct groups. Genetic diversity among populations was primarily within the population (76.36 vs. 23.64%). Conclusions The relatively high number of subpopulations and the presence of high genetic diversity among and within populations were the characteristics of studied durum wheat genotypes in this study. Therefore, considering the loss of 84% genetic diversity of durum wheat during the early domestication processes, these populations can be used as a valuable resource in basic and applied research in breeding projects.

Keywords

• durum wheat
• linkage group
• marker
• polymorphism
• population