Genetic Diversity, Linkage Disequilibrium and Population Structure of Bulgarian Bread Wheat Assessed by Genome-Wide Distributed SNP Markers: From Old Germplasm to Semi-Dwarf Cultivars

Abstract

Genetic diversity and population structure are key resources for breeding purposes and genetic studies of important agronomic traits in crops. In this study, we described SNP-based genetic diversity, linkage disequilibrium and population structure in a panel of 179 bread wheat advanced cultivars and old accessions from Bulgaria, using an optimized wheat 25K Infinium iSelect array. Out of 19,019 polymorphic SNPs, 17,968 had а known chromosome position on the A (41%), B (42%) and D (11%) genome, and 6% were not assigned to any chromosome. Homoeologous group 4, in particular chromosome 4D, was the least polymorphic. In the total population, the Nei’s gene diversity was within the range 0.1-0.5, and the polymorphism information content ranged from 0.1 to 0.4. Significant differences between the old and modern collections were revealed with respect to the linkage disequilibrium (LD): the average values for LD (r2), the percentage of the locus pairs in LD and the LD decay were 0.64, 16% and 3.3 for the old germplasm, and 0.43, 30% and 4.1 for the modern releases, respectively. Structure and k-means clustering algorithm divided the panel into three groups. The old accessions formed a distinct subpopulation. The cluster analysis further distinguished the modern releases according to the geographic region and genealogy. Gene exchange was evidenced mainly between the subpopulations of contemporary cultivars. The achieved understanding of the genetic diversity and structure of the Bulgarian wheat population and distinctiveness of the old germplasm could be of interest for breeders developing cultivars with improved characteristics. The obtained knowledge about SNP informativeness and the LD estimation are worthwhile for selecting markers and for considering the composition of a population in association mapping studies of traits of interest.

Genetic Variants Associated with Long-Terminal Repeats Can Diagnostically Classify Cannabis Varieties

“…This likely drove the observed increase in the relative value, given the inherent increase in genetic diversity of a seed grown plant, compared to clonal plants derived from cuttings. Overall, the average genetic distance values obtained for the remaining varieties were consistently low when compared to other studies in wheat, which describe D values from 0.1 to 0.5 across roughly 150 wheat accessions [ 14 , 15 ]. Nevertheless, this analysis highlighted the limited genetic distance between the Cannabis varieties CBD1 and CBD2 in particular, and to a lesser degree, the Motavation and Blue Venom varieties.…”

Growth responses and genetic variation among highly ecologically diverse spring wheat genotypes grown under seawater stress

“…The DNA of the 80 genotypes was sent to Trait Genetics (Gatersleben, Germany) for genotyping-by-sequencing using a 25K Infinium iSelect array. Extensive details on the development of the 25K wheat Infinium array were reported by Aleksandrov et al (2021). The array genotyping revealed 21,450 singlenucleotide polymorphisms (SNP) markers that were used to calculate the genetic distance among the selected genotypes using the R-package "ade4" as described by Dray and Dufour (2007).…”

Genotyping-by-Sequencing Based Molecular Genetic Diversity of Pakistani Bread Wheat (Triticum aestivum L.) Accessions

“…Results of this study were consistent with the findings of Chao et al (2010 ) and Ladejobi et al (2018 ) reported the LD decay of 6.4, 4.5, 4, and 4.98 Mbp for A, B, D, and whole-genome, respectively. Aleksandrov et al (2021) performed a study on Bulgarian bread wheat germplasm to dissect the population structure and linkage disequilibrium on two populations, including one population of old germplasm and one set of modern semi-dwarf cultivars. Old germplasm showed an LD decay of 3.6, 3.3, 3.1, and 3.3 Mb in subgenomes A, B, and D and the whole-genome, respectively.…”