Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping

Nadia Al-Tamimi, Chris Brien, Helena Oakey, Bettina Berger, Stephanie Saade, Yung Shwen Ho, Sandra M. Schmöckel, Mark Tester () and Sónia Negrão
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Nadia Al-Tamimi: King Abdullah University of Science and Technology (KAUST)
Chris Brien: University of South Australia, Phenomics and Bioinformatics Research Centre
Helena Oakey: King Abdullah University of Science and Technology (KAUST)
Bettina Berger: University of Adelaide, Australian Plant Phenomics Facility, The Plant Accelerator
Stephanie Saade: King Abdullah University of Science and Technology (KAUST)
Yung Shwen Ho: King Abdullah University of Science and Technology (KAUST)
Sandra M. Schmöckel: King Abdullah University of Science and Technology (KAUST)
Mark Tester: King Abdullah University of Science and Technology (KAUST)
Sónia Negrão: King Abdullah University of Science and Technology (KAUST)

Nature Communications, 2016, vol. 7, issue 1, 1-11

Abstract: Abstract High-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth and transpiration, yet are computationally economic. Here we develop such analyses and apply this to a rice population genotyped with a 700k SNP high-density array. Two rice diversity panels, indica and aus, containing a total of 553 genotypes, are phenotyped in waterlogged conditions. Using cubic smoothing splines to estimate plant growth and transpiration, we identify four time intervals that characterize the early responses of rice to salinity. Relative growth rate, transpiration rate and transpiration use efficiency (TUE) are analysed using a new association model that takes into account the interaction between treatment (control and salt) and genetic marker. This model allows the identification of previously undetected loci affecting TUE on chromosome 11, providing insights into the early responses of rice to salinity, in particular into the effects of salinity on plant growth and transpiration.

Date: 2016
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DOI: 10.1038/ncomms13342

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