Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan

Abstract

Landraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high-yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north-eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping-by-sequencing of studied landraces after quality control provided 4897 high-quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using model-based STRUCTURE analysis and cluster-based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub-populations compared with the variation observed as a whole between sub-populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro-climatic conditions prevalent within the north-eastern agro-ecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro-climatic conditions within the agro-climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north-eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses.

Exploration of the Genetic Diversity of Solina Wheat and Its Implication for Grain Quality

“…Even though the final datasets were significantly reduced, high-quality SNP markers have remained widely distributed abroad the three genomes, as shown in Supplementary Table S2. Genome D and the homoeologous chromosomes of the fourth group were characterized by the lowest number of markers; this result is in accordance with those of other authors [22][23][24] who analyzed Spanish, Iranian, and Afghan common wheat landraces with the same DArTseq approach. The limited diversity of D genome may be originated from the "recent" introgression occurred with Aegilops tauschii (2n = DD), the common wheat D-genome donor, and the relative genetic bottleneck [27].…”

“…Recent works in this field demonstrated how geography was the main effect driving the genetic diversity [22,24], even though others did not find any geographical effect on genetics [20,23]. In this study, β-coefficients, calculated by MLR, clearly demonstrated how a geographic effect existed between Clu1 and Clu2.…”

“…In order to unravel the genetic structure and breeding history lying behind landraces, a genome-wide approach is needed; thanks to modern high-throughput technologies, such as DarTseq (Diversity Arrays Technology sequence), researchers can efficiently genotype thousands of genomic loci in parallel with a relative low cost [19]. Recently, DarTseq has been applied in complex polyploid crops, such as wheat, to find unexplored loci in landraces and elite wheats [20][21][22][23][24]. Using this technology, Sansaloni and co-workers [25] analyzed the genetic structure of 56,342 hexaploid wheat accessions with 85,531 single nucleotide polymorphism (SNP) markers, proving that the modern cultivars occupied only a little portion of the total genetic diversity space; thus landraces show a high unexplored biodiversity worthwhile of being studied and protected.…”

Exploring the Genetic Diversity and Population Structure of Wheat Landrace Population Conserved at ICARDA Genebank

“…The understanding of the population structure is crucial for further downstream analysis, for example, genome-wide association studies (GWAS). The evaluation of genetic diversity also provides vital information which can help in the preservation strategies and broadening of the genetic base of crops ( Eltaher et al, 2018 ; Tehseen et al, 2021a ). The presence of subpopulations in the panel can be attributed to the selection of desirable traits and genetic drift ( Kumar et al, 2020 ).…”

“…The fixation index (Fst) is used to measure the genetic differentiation among the populations ( Tehseen et al, 2021a ). An Fst value of 0.15 and more predicts the presence of a significant genetic differentiation in the subpopulations ( Frankham et al, 2002 ).…”