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
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...
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MDPI AG
2021-05-01
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| Online Access: | https://www.mdpi.com/2223-7747/10/6/1116 |
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| author | Vladimir Aleksandrov Tania Kartseva Ahmad M. Alqudah Konstantina Kocheva Krasimira Tasheva Andreas Börner Svetlana Misheva |
| author_facet | Vladimir Aleksandrov Tania Kartseva Ahmad M. Alqudah Konstantina Kocheva Krasimira Tasheva Andreas Börner Svetlana Misheva |
| author_sort | Vladimir Aleksandrov |
| collection | DOAJ |
| description | 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 (<i>r<sup>2</sup></i>), 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. |
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| last_indexed | 2024-03-10T10:49:48Z |
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| series | Plants |
| spelling | doaj.art-732c7973a951466797299195088659af2023-11-21T22:20:36ZengMDPI AGPlants2223-77472021-05-01106111610.3390/plants10061116Genetic Diversity, Linkage Disequilibrium and Population Structure of Bulgarian Bread Wheat Assessed by Genome-Wide Distributed SNP Markers: From Old Germplasm to Semi-Dwarf CultivarsVladimir Aleksandrov0Tania Kartseva1Ahmad M. Alqudah2Konstantina Kocheva3Krasimira Tasheva4Andreas Börner5Svetlana Misheva6Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev str., Block 21, 1113 Sofia, BulgariaInstitute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev str., Block 21, 1113 Sofia, BulgariaInstitute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Straße 3, 06120 Halle (Saale), GermanyInstitute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev str., Block 21, 1113 Sofia, BulgariaInstitute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev str., Block 21, 1113 Sofia, BulgariaLeibniz Institute of Plant Genetics and Crop Plants Research (IPK Gatersleben), Corrensstraße 3, Seeland, 06466 Gatersleben, GermanyInstitute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev str., Block 21, 1113 Sofia, BulgariaGenetic 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 (<i>r<sup>2</sup></i>), 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.https://www.mdpi.com/2223-7747/10/6/1116bread wheatgenetic diversitylinkage disequilibriummodern cultivarsold germplasmpopulation structure |
| spellingShingle | Vladimir Aleksandrov Tania Kartseva Ahmad M. Alqudah Konstantina Kocheva Krasimira Tasheva Andreas Börner Svetlana Misheva 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 Plants bread wheat genetic diversity linkage disequilibrium modern cultivars old germplasm population structure |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | bread wheat genetic diversity linkage disequilibrium modern cultivars old germplasm population structure |
| url | https://www.mdpi.com/2223-7747/10/6/1116 |
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