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High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis

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Abstract

Durum wheat (Triticum turgidum var. durum Desf.) is a major world crop that is grown primarily in areas of the world that experience periodic drought, and therefore, breeding climate-resilient durum wheat is a priority. High-throughput single nucleotide polymorphism (SNP) genotyping techniques have greatly increased the power of linkage and association mapping analyses for bread wheat, but as yet there is no durum wheat-specific platform available. In this study, we evaluate the new 384HT Wheat Breeders Array for its usefulness in tetraploid wheat breeding by genotyping a breeding population of F6 hybrids, derived from multiple crosses between T. durum cultivars and wild and cultivated emmer wheat accessions. Using a combined linkage and association mapping approach, we generated a genetic map including 1345 SNP markers, and identified markers linked to 6 QTLs for coleoptile length (2), heading date (1), anthocyanin accumulation (1) and osmotic stress tolerance (2). We also developed a straightforward approach for combining genetic data from multiple families of limited size that will be useful for evaluating and mapping pre-existing breeding material.

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Acknowledgements

This work was supported by the 1003 Primary Subjects R&D Funding Program of TÜBİTAK (The Scientific and Technological Research Council of Turkey, Grant no: 113O116) and by the General Directorate of Agriculture Research and Policy, Republic of Turkey Ministry of Food, Agriculture and Livestock (Grant no: TAGEM/TA/12/03/01/001). The authors thank İpek Özdemir for technical assistance with DNA isolation. We also thank the Wheat Improvement Strategic Programme (WISP) for designing the SNPs used on the Axiom array and making the marker information publicly available.

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Authors and Affiliations

  1. SU Nanotechnology Research and Application Centre, Sabanci University, 34956, Tuzla, İstanbul, Turkey

    Stuart J. Lucas

  2. Breeding and Genetics, Field Crops Central Research Institute, Ankara, Turkey

    Ayten Salantur & Selami Yazar

  3. Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey

    Hikmet Budak

  4. 412 Leon Johnson Hall, Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA

    Hikmet Budak

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  1. Stuart J. Lucas
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  2. Ayten Salantur
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  3. Selami Yazar
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  4. Hikmet Budak
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Correspondence to Stuart J. Lucas or Hikmet Budak.

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Lucas, S.J., Salantur, A., Yazar, S. et al. High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis. Funct Integr Genomics 17, 667–685 (2017). https://doi.org/10.1007/s10142-017-0563-y

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