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 a 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.
Highlights
In the present SNP-based study, we compared the levels of diversity between the two collections, and we found significant though slight differences, both gene diversity (GD) and polymorphism information content (PIC) having higher scores within the old accessions (Table 1)
Seven accessions of the old germplasm corresponded by definition to landraces or selections from landraces from different regions of Bulgaria, and 44 entries were releases of early purposeful breeding based on crosses between local and foreign accessions before the era of semi-dwarfism
The current study explored the extent of genetic diversity, linkage disequilibrium (LD) and the presence of genetic structures in a panel of 179 bread wheat old accessions and advanced cultivars collected or developed in the Eastern European country Bulgaria using SNP markers
Summary
Bread wheat (Triticum aestivum, L.) is an important strategic crop for food security globally. In Bulgaria, bread wheat is the major cereal crop grown on 1.0 to 1.3 million ha land area, with an average annual production of 5.1 million tonnes, and an average grain yield of 4.2 tonnes/ha (data for the last 10 years according to Annual Reports of the Ministry of Agriculture, Food and Forestry). The early breeding activities in Bulgaria date back to the beginning of the 20th century when the relatively homogeneous selections made within landraces and, later, crosses involving local and foreign accessions have brought up the first cultivars. In the 1960s, the science-based wheat breeding was launched with the introduction of alleles for reduced height or semi-dwarfism (initially Rht, later Rht-B1b/d) and plant adaptability alleles for vernalization response, Vrn; photoperiod response, Ppd, and frost tolerance, Fr) [1,2]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
