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

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dc.contributor.authorAl-Tamimi, N.
dc.contributor.authorBrien, C.
dc.contributor.authorOakey, H.
dc.contributor.authorBerger, B.
dc.contributor.authorSaade, S.
dc.contributor.authorHo, Y.
dc.contributor.authorSchmöckel, S.
dc.contributor.authorTester, M.
dc.contributor.authorNegrão, S.
dc.date.issued2016
dc.description.abstractHigh-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.
dc.description.statementofresponsibilityNadia Al-Tamimi, Chris Brien, Helena Oakey, Bettina Berger, Stephanie Saade, Yung Shwen Ho, Sandra M. Schmöckel, Mark Tester and Sónia Negrão
dc.identifier.citationNature Communications, 2016; 7(1):13342-1-13342-11
dc.identifier.doi10.1038/ncomms13342
dc.identifier.issn2041-1723
dc.identifier.issn2041-1723
dc.identifier.orcidBrien, C. [0000-0003-0581-1817]
dc.identifier.orcidOakey, H. [0000-0003-1057-7615]
dc.identifier.orcidBerger, B. [0000-0003-1195-4478]
dc.identifier.urihttp://hdl.handle.net/2440/102678
dc.language.isoen
dc.publisherNature Publishing Group
dc.rights© The Author(s) 2016. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
dc.source.urihttps://doi.org/10.1038/ncomms13342
dc.subjectPlant Proteins
dc.subjectGenetic Markers
dc.subjectPlant Transpiration
dc.subjectGene Expression Regulation, Plant
dc.subjectSalinity
dc.subjectGenome-Wide Association Study
dc.subjectHigh-Throughput Screening Assays
dc.subjectOryza
dc.subjectSalt Tolerance
dc.titleSalinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping
dc.typeJournal article
pubs.publication-statusPublished

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