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Whole-genome diversity, population structure and linkage disequilibrium analysis of globally diverse wheat genotypes using genotyping-by-sequencing DArTseq platform

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Abstract

In this study, 129 wheat genotypes from globally diverse origins were genotyped using DArTseq (SilicoDArT and SNP) markers. After filtering markers for quality-filtering, 14,270 SilicoDArTs and 6484 SNPs were retained and used for genetic diversity, population structure and linkage disequilibrium analyses. The highest number of SilicoDArT and SNP markers mapped on genome A and B compared to genome D. In both marker types, polymorphism information content (PIC) values ranged from 0.1 to 0.5, while > 0.80% of SilicoDArTs and > 0.44% SNPs showed PIC value more than median (0.25%). Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped wheat genotypes into three and four clusters, respectively. Principal component analysis and discriminant analysis of principal component results showed highly match with cluster and population structure analysis. Linkage disequilibrium (LD) was more extensive in both marker types, while graphical display of LD decay for both marker types showed that LD declined in the region close to 15 kbp, where r2-values corresponded to r2 = 0.16. Overall, our genetic diversity analysis showed high level of variation in studied wheat genotypes, even though there was no relationship between wheat grouping and origins. This might be attributed to admixture level that occurred during long-term natural selection of wheat genotypes in different parts of the world. Highly diverse wheat genotypes used in this study may possess unique genes and are useful sources in breeding programs to improve grain yield and quality.

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Acknowledgements

The study was conducted as a part of PhD thesis of first author and supported by Islamic Azad University, Sanandaj Branch, Iran. We are grateful to Iranian Cereal Research Institute for providing wheat genotypes used in this study.

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Authors and Affiliations

  1. College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran

    Mojgan Mahboubi & Reza Talebi

  2. Department of Biotechnology, College of Agriculture, Isfahan University of Technology, PO Box 8415683111, Isfahan, Iran

    Rahim Mehrabi

  3. Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahed University, Tehran, Iran

    Amir Mohammad Naji

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  1. Mojgan Mahboubi
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  2. Rahim Mehrabi
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  4. Reza Talebi
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Correspondence to Reza Talebi.

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Mahboubi, M., Mehrabi, R., Naji, A.M. et al. Whole-genome diversity, population structure and linkage disequilibrium analysis of globally diverse wheat genotypes using genotyping-by-sequencing DArTseq platform. 3 Biotech 10, 48 (2020). https://doi.org/10.1007/s13205-019-2014-z

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