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

abstract

  • 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) similar to 0.05. The results of this study should provide valuable information for future association mapping using this wheat collection.

publication date

  • 2017
  • 2017