@inbook{8a72379e2c764ca983e739a10852d568,
title = "Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping",
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.",
keywords = "Association mapping, Forward genetics, GWAS, High-throughput phenotyping, Plant imaging, Rice, Salinity, Statistical genetics",
author = "Nadia Al-Tamimi and Helena Oakey and Mark Tester and S{\'o}nia Negr{\~a}o",
note = "Funding Information: Financial support from King Abdullah University of Science and Technology (KAUST) is gratefully acknowledged. S{\'o}nia Negr{\~a}o thanks the financial support of University College Dublin (UCD) and UCD School of Biology and Environmental Science. Publisher Copyright: {\textcopyright} 2021, Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2021",
doi = "10.1007/978-1-0716-1068-8_23",
language = "English (US)",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "339--375",
booktitle = "Methods in Molecular Biology",
}