A Whole Genome DArTseq and SNP Analysis for Genetic Diversity Assessment in Durum Wheat from Central Fertile Crescent

Abstract

Until now, little attention has been paid to the geographic distribution and evaluation of genetic diversity of durum wheat from the Central Fertile Crescent (modern-day Turkey and Syria). Turkey and Syria are considered as primary centers of wheat diversity, and thousands of locally adapted wheat landraces are still present in the farmers’ small fields. We planned this study to evaluate the genetic diversity of durum wheat landraces from the Central Fertile Crescent by genotyping based on DArTseq and SNP analysis. A total of 39,568 DArTseq and 20,661 SNP markers were used to characterize the genetic characteristic of 91 durum wheat land races. Clustering based on Neighbor joining analysis, principal coordinate as well as Bayesian model implemented in structure, clearly showed that the grouping pattern is not associated with the geographical distribution of the durum wheat due to the mixing of the Turkish and Syrian landraces. Significant correlation between DArTseq and SNP markers was observed in the Mantel test. However, we detected a non-significant relationship between geographical coordinates and DArTseq (r = -0.085) and SNP (r = -0.039) loci. These results showed that unconscious farmer selection and lack of the commercial varieties might have resulted in the exchange of genetic material and this was apparent in the genetic structure of durum wheat in Turkey and Syria. The genomic characterization presented here is an essential step towards a future exploitation of the available durum wheat genetic resources in genomic and breeding programs. The results of this study have also depicted a clear insight about the genetic diversity of wheat accessions from the Central Fertile Crescent.

Dowsing for salinity tolerance related genes in chickpea through genome wide association and in silico PCR analysis

“…However, a positive correlation between SNP and DArT assay was revealed by Mantel test with R 2 of 0.58 (FIGURE 10). Similar results were reported by Baloch et al, 167 in wheat, they spotted a correlation of 0.775 between DArT and SNP markers. Except for chromosomes 6 and 8, salinity tolerance associated genes were distributed across the chickpea genome (FIGURE 5).…”

Genetic Diversity and Population Structure of Mongolian Wheat Based on SSR Markers: Implications for Conservation and Management

“…Various studies have estimated genetic diversity and phylogenetic relationship among wheat genotypes (Chen et al 2012;Khan et al 2015;Zarei Abbasabad et al 2016;Baloch et al 2017). Similarly various methods have been used for surveying population structures (Khan et al 2014).…”

“…Recently, genotyping-by-sequencing (GBS) technology has been deployed to enable SNP discovery and genotyping (Elshire et al 2011). DArTseq and SNP markers based on GBS technology have been successfully applied for genetic diversity studies in wheat (Baloch et al 2017). As a gene bank possesses large numbers of accessions, this technology remains in laboratories because it needs special equipment and finical support.…”

Phenotypic Characterization of 183 Turkish Common Bean Accessions for Agronomic, Trading, and Consumer-Preferred Plant Characteristics for Breeding Purposes

“…In order to meet global food demands, there is need to harness plant genetic diversity. Characterization of genetic resources is a valid strategy in this regard because it helps to explore the genotypic and phenotypic variations that can be effectively utilized by the breeding community [4,5]. Nearly, 41,500 accessions of genus Phaseolus are present in the International Center for Tropical Agriculture (CIAT) [6]; additionally, there are hundreds of landraces present in farmer's fields in different bean growing countries.…”