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Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping

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Rice Genome Engineering and Gene Editing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2238))

Abstract

Rice is the most salt-sensitive cereal, suffering yield losses above 50% with soil salinity of 6 dS/m. Thus, understanding the mechanisms of rice salinity tolerance is key to address food security. In this chapter, we provide guidelines to assess rice salinity tolerance using a high-throughput phenotyping platform (HTP) with digital imaging at seedling/early tillering stage and suggest improved analysis methods using stress indices. The protocols described here also include computer scripts for users to improve their experimental design, run genome-wide association studies (GWAS), perform multi-testing corrections, and obtain the Manhattan plots, enabling the identification of loci associated with salinity tolerance. Notably, the computer scripts provided here can be used for any stress or GWAS experiment and independently of HTP.

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Acknowledgments

Financial support from King Abdullah University of Science and Technology (KAUST) is gratefully acknowledged. Sónia Negrão thanks the financial support of University College Dublin (UCD) and UCD School of Biology and Environmental Science.

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Authors and Affiliations

  1. Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

    Nadia Al-Tamimi & Mark Tester

  2. School of Agriculture Food and Wine, University of Adelaide, Urrbrae, SA, Australia

    Helena Oakey

  3. School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland

    Sónia Negrão

Authors
  1. Nadia Al-Tamimi
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  2. Helena Oakey
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  3. Mark Tester
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  4. Sónia Negrão
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Corresponding author

Correspondence to Sónia Negrão .

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Editors and Affiliations

  1. Synthetic Biology, Biofuel and Genome Editing R&D, Reliance Industries Ltd, Navi Mumbai, Maharashtra, India

    Anindya Bandyopadhyay

  2. Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, CA, USA

    Roger Thilmony

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Al-Tamimi, N., Oakey, H., Tester, M., Negrão, S. (2021). Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping. In: Bandyopadhyay, A., Thilmony, R. (eds) Rice Genome Engineering and Gene Editing. Methods in Molecular Biology, vol 2238. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1068-8_23

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  • DOI: https://doi.org/10.1007/978-1-0716-1068-8_23

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1067-1

  • Online ISBN: 978-1-0716-1068-8

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