Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping

Nadia Al-Tamimi, Helena Oakey, Mark Tester, Sónia Negrão*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

5 Scopus citations


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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages37
StatePublished - 2021

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Association mapping
  • Forward genetics
  • GWAS
  • High-throughput phenotyping
  • Plant imaging
  • Rice
  • Salinity
  • Statistical genetics

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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