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

Published online by Cambridge University Press:  07 March 2016

Elham Zarei Abbasabad ,
Seyed Abolghasem Mohammadi ,
Mohammad Moghaddam  and
Mohammad Reza Jalal Kamali
Elham Zarei Abbasabad
Affiliation:
Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
Seyed Abolghasem Mohammadi*
Affiliation:
Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran Center of Excellence in Cereal Molecular Breeding, University of Tabriz, Tabriz, Iran
Mohammad Moghaddam
Affiliation:
Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran Center of Excellence in Cereal Molecular Breeding, University of Tabriz, Tabriz, Iran
Mohammad Reza Jalal Kamali
Affiliation:
CIMMYT (International Maize and Wheat Improvement Center), Karaj, Iran
*
*Corresponding author. E-mail: mohammadi@tabrizu.ac.ir
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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 r2 ≥ 0.01 and P ≤ 0.001 and six pair showed r2 ≥ 0.05 with P ≤ 0.001. LD clearly decays within the genetic distance of 40–60 cM with r2 ~ 0.05. The results of this study should provide valuable information for future association mapping using this wheat collection.

Keywords

gene diversitylinkage disequilibriummicrosatellite markerspopulation structure
Type
Research Article
Information
Plant Genetic Resources , Volume 15 , Issue 4 , August 2017 , pp. 327 - 334
Copyright
Copyright © NIAB 2016 

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