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Linkage disequilibrium and association analysis of stripe rust resistance in wild emmer wheat (Triticum turgidum ssp. dicoccoides) population in Israel

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Rapid LD decay in wild emmer population from Israel allows high-resolution association mapping. Known and putative new stripe rust resistance genes were found.

Abstract

Genome-wide association mapping (GWAM) is becoming an important tool for the discovery and mapping of loci underlying trait variation in crops, but in the wild relatives of crops the use of GWAM has been limited. Critical factors for the use of GWAM are the levels of linkage disequilibrium (LD) and genetic diversity in mapped populations, particularly in those of self-pollinating species. Here, we report LD estimation in a population of 128 accessions of self-pollinating wild emmer, Triticum turgidum ssp. dicoccoides, the progenitor of cultivated wheat, collected in Israel. LD decayed fast along wild emmer chromosomes and reached the background level within 1 cM. We employed GWAM for the discovery and mapping of genes for resistance to three isolates of Puccinia striiformis, the causative agent of wheat stripe rust. The wild emmer population was genotyped with the wheat iSelect assay including 8643 gene-associated SNP markers (wheat 9K Infinium) of which 2,278 were polymorphic. The significance of association between stripe rust resistance and each of the polymorphic SNP was tested using mixed linear model implemented in EMMA software. The model produced satisfactory results and uncovered four significant associations on chromosome arms 1BS, 1BL and 3AL. The locus on 1BS was located in a region known to contain stripe rust resistance genes. These results show that GWAM is an effective strategy for gene discovery and mapping in wild emmer that will accelerate the utilization of this genetic resource in wheat breeding.

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Acknowledgments

This work was supported by grant No IS-4137-08 from the US-Israel BARD foundation, grants 2009-65300-05638 and 2011-68002-30029 (Triticeae-CAP) from the USDA National Institute of Food and Agriculture.

Conflict of interest

The authors declare no conflict of interest.

Ethical standards

The authors declare that ethical standards are met, and all the experiments comply with the current laws of the country in which they were performed.

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Authors and Affiliations

  1. The Institute for Cereal Crops Improvement, Tel-Aviv University, P.O. Box 39040, 69978, Tel Aviv, Israel

    Hanan Sela, Smadar Ezrati, Pnina Ben-Yehuda, Jacob Manisterski & Adina Breiman

  2. Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA

    Eduard Akhunov

  3. Department of Plant Sciences, University of California, Davis, CA, 95616, USA

    Jan Dvorak

  4. Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, 31905, Haifa, Israel

    Abraham Korol

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  1. Hanan Sela
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  2. Smadar Ezrati
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Correspondence to Hanan Sela.

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Communicated by Heiko C. Becker.

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Sela, H., Ezrati, S., Ben-Yehuda, P. et al. Linkage disequilibrium and association analysis of stripe rust resistance in wild emmer wheat (Triticum turgidum ssp. dicoccoides) population in Israel. Theor Appl Genet 127, 2453–2463 (2014). https://doi.org/10.1007/s00122-014-2389-5

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