title: Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping.
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.
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Nadia
authors.initials: N
authors.lastname: Al-Tamimi
authors.affiliation: University of South Australia, Phenomics and Bioinformatics Research Centre, Adelaide, South Australia 5001, Australia.|University of Adelaide, Australian Plant Phenomics Facility, The Plant Accelerator, Urrbrae, South Australia 5064, Australia.
authors.forename: Chris
authors.identifier: 0000-0003-0581-1817
authors.initials: C
authors.lastname: Brien
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Helena
authors.initials: H
authors.lastname: Oakey
authors.affiliation: University of Adelaide, Australian Plant Phenomics Facility, The Plant Accelerator, Urrbrae, South Australia 5064, Australia.
authors.forename: Bettina
authors.initials: B
authors.lastname: Berger
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Saade
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Yung Shwen
authors.initials: YS
authors.lastname: Ho
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Sandra M
authors.initials: SM
authors.lastname: Schmöckel
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Mark
authors.identifier: 0000-0002-5085-8801
authors.initials: M
authors.lastname: Tester
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Sónia
authors.initials: S
authors.lastname: Negrão
mesh_terms: D018506:Gene Expression Regulation, Plant; D005819:Genetic Markers; D055106:Genome-Wide Association Study; D057166:High-Throughput Screening Assays; D012275:Oryza / Q000187:drug effects / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018526:Plant Transpiration; D054712:Salinity; D055049:Salt Tolerance / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D010940:Plant Proteins