Genetic diversity and population structure analysis in tetraploid wheat (Triticum turgidum spp) germplasm from Ethiopia based on DArTSeq markers

Genetic diversity and population structure analysis is vital for germplam conservation and efficient utilization. A set of 188 tetraploid wheat (Triticum turgidum spp) genotypes, including 166 landraces and 22 improved cultivars, were genotyped using high density genotyping by sequencing by diversity arrays technology sequencing. We investigated the genetic diversity and population structure for the study panel as well as the landraces, separately based on 10,349 DArTSeq markers distributed across A and B genomes. The whole tetraploid wheat study panel was clustered into two populations: pop1 and pop2 comprising 150 landraces and three released cultivars and 19 released cultivars and 12 landraces, respectively. Further population structure analysis of the tetraploid wheat landraces revealed two subgroups of the landraces. Population structure based on the analysis of molecular variance (AMOVA) revealed significant (P < 0.001) variation between populations and within populations for both the study panels and the landraces. Total variation within population (88%, 97%) was higher than total variation between populations (12%, 3%) for both study panel and the landraces. The AMOVA result was also verified by the population structure analysis based on genetic differentiation (Fst), which was reported to be little (Fst = 0.028) and moderate (Fst = 0.117) for the landraces and the study panel, respectively, thereby implying no significant differentiation among populations. The lower genetic differentiation led to more gene flow in the study panel (Nm = 1.891) and in the landraces (Nm = 8,612) which is an indication of more gene exchange preventing genetic differentiation among populations implying a low level of diversity among subpopulations, that was confirmed by the AMOVA result. The genetic indices of the study panel revealed that pop2 (I = 0.523, Ne = 1.612, He = 0.353, uHe = 0.359) was more diverse than pop1 (I = 0.415, Ne = 1.423, He = 0.263, uHe = 0.264), which comprised of 98.04% landraces along with 1.96% released cultivars. Likewise, pop2 (I = 0.432, Ne = 1.442, He = 0.276, uHe = 0.277) of the landraces was more diverse than Pop1 (I = 1.380, Ne = 1.380, He = 0.234, uHe = 0.236). Furthermore, principal component analysis (PCA) of the tetraploid wheat study panel grouped the released cultivars together and the landraces separately. However, PCA of the landraces did not show clear groupings. The first two components together explained 77% (PC1 = 65%, PC2 = 12%) and 68% (PC1 = 48%, PC2 = 20%) of the total variation in the tetraploid wheat study panel and landraces, respectively. The total number of different alleles in pop1 (4762, 4624) and pop2 (4708, 4760) were revealed in the study panel and the landraces, respectively. 127 genotypes were reported to have one or more private alleles at 755 loci, an indication of key adaptive genes at these loci to be exploited in breeding program. In conclusion, high genetic diversity was detected in Ethiopian tetraploid wheat germplasm, which could be utilized for future wheat breeding program. Furthermore, the higher genetic variation observed within populations than between populations reveal that more attention should be given to individual accessions within populations to explore the existing genetic diversity.