Analysis of genetic diversity, population structure and linkage disequilibrium in Iranian wheat landraces using SSR markers

• Published in: Plant genetic resources: characterization and utilization 2017-08, Vol.15 (4), p.327-334
• Main Authors: Zarei Abbasabad, Elham, Mohammadi, Seyed Abolghasem, Moghaddam, Mohammad, Jalal Kamali, Mohammad Reza
• Format: Article
• Language: English
• Subjects: Alleles; Assaying; Biotechnology; Bread; Colleges & universities; Corn; Decay; Deoxyribonucleic acid; DNA; Gene loci; Gene mapping; Genetic distance; Genetic diversity; Genetic markers; Genomes; Genomics; Genotype & phenotype; Germplasm; Information dissemination; Linkage disequilibrium; Mapping; Markers; Microsatellites; Polymorphism; Population; Population genetics; Population structure; Software; Spring (season); Subpopulations; Wheat; Winter
• ISSN: 1479-2621; 1479-263X
• DOI: 10.1017/S1479262115000684

Population structure and linkage disequilibrium (LD) were investigated in a set of 395 bread wheat landraces including 154 spring, 193 winter, two facultative wheat and 46 unknown growth type collected from different geographical regions of Iran. A total of 53 microsatellite markers distributed in three genomes of wheat were assayed for polymorphism. The 312 polymorphic alleles were served to estimate population structure and analyse the genome-wide LD. The number of alleles ranged from 2 to 18 with an average of 5.89 alleles/locus. Mean of polymorphic information content was 0.6 with a range of 0.15–0.86 and gene diversity varied from 0.16 to 0.88 with an average of 0.64. The population of landraces was highly structured and based on distance-and model-based cluster analyses the 395 landraces were assigned into eight subpopulations: SG1–SG8. Population structure estimates based on simple sequence repeat (SSR) marker data were quantified in a Q matrix and used in calculation of LD between pair of markers. A low overall LD level found in 12–13% (166) of the SSR marker pairs showed significant pairwise LD in r 2 ≥ 0.01 and P ≤ 0.001 and six pair showed r 2 ≥ 0.05 with P ≤ 0.001. LD clearly decays within the genetic distance of 40–60 cM with r 2 ~ 0.05. The results of this study should provide valuable information for future association mapping using this wheat collection.