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Genome-Wide Association Studies (GWAS) in Cereals

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Accelerated Breeding of Cereal Crops

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Abstract

The advent of high-throughput next-generation sequencing technologies in the last decade, coupled with its substantial decrease in cost in the recent years and development of complementary array-based genotyping platforms, has revolutionized the generation of genome-wide markers and propelled several statistical methods for unearthing marker-phenotype association. This chapter provides an outline of the conceptual principles and steps of methods widely used for genome-wide association studies (GWAS) in cereals. Specifically, we focussed on presenting practical steps, starting from assembling populations suitable for phenotyping, genotyping platforms, estimation of population structure from genome-wide markers, estimation of linkage disequilibrium (LD), and methods of GWAS. We also highlighted the available sources of cereal genome assemblies and major software packages used for GWAS, namely, TASSEL-5.0, PLINK, and GAPIT-3.0.

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Authors and Affiliations

  1. Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Chile

    Braulio J. Soto-Cerda

  2. Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada

    Akshaya Vasudevan

  3. Department of Biology, University of Ottawa, Ottawa, ON, Canada

    Akshaya Vasudevan

  4. Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada

    André Laroche & Raja Ragupathy

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  1. Braulio J. Soto-Cerda
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  2. Akshaya Vasudevan
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  3. André Laroche
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  4. Raja Ragupathy
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Correspondence to Raja Ragupathy .

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Editors and Affiliations

  1. Agriculture and Agri-Food Canada, Morden, MB, Canada

    Andriy Bilichak

  2. Agriculture and Agri-Food Canada, Lethbridge, AB, Canada

    John D. Laurie

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Soto-Cerda, B.J., Vasudevan, A., Laroche, A., Ragupathy, R. (2022). Genome-Wide Association Studies (GWAS) in Cereals. In: Bilichak, A., Laurie, J.D. (eds) Accelerated Breeding of Cereal Crops. Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1526-3_4

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  • DOI: https://doi.org/10.1007/978-1-0716-1526-3_4

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1525-6

  • Online ISBN: 978-1-0716-1526-3

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