Genetic Control of Plasticity in Root Morphology and Anatomy of Rice in Response to Water Deficit

• Published in: Plant physiology (Bethesda) Vol. 174; no. 4; pp. 2302 - 2315
• Main Authors: Kadam, Niteen N., Tamilselvan, Anandhan, Lawas, Lovely M.F., Quinones, Cherryl, Bahuguna, Rajeev N., Thomson, Michael J., Dingkuhn, Michael, Muthurajan, Raveendran, Struik, Paul C., Yin, Xinyou, Jagadisha, S.V. Krishna
• Format: Journal Article
• Language: English
• Published: United States American Society of Plant Biologists 01.08.2017
• Subjects: Centre for Crop Systems Analysis; Chromosome Mapping; Crop Physiology; ECOPHYSIOLOGY AND SUSTAINABILITY; Genetic Loci; Genome, Plant; Genome-Wide Association Study; Genotype; Linear Models; Linkage Disequilibrium - genetics; Oryza - anatomy & histology; Oryza - genetics; PE&RC; Phenotype; Plant Roots - anatomy & histology; Plant Roots - genetics; Principal Component Analysis; Quantitative Trait, Heritable; Water
• ISSN: 0032-0889; 1532-2548
• DOI: 10.1104/pp.17.00500

Elucidating the genetic control of rooting behavior under water-deficit stress is essential to breed climate-robust rice (Oryza sativa) cultivars. Using a diverse panel of 274 indica genotypes grown under control and water-deficit conditions during vegetative growth, we phenotyped 35 traits, mostly related to root morphology and anatomy, involving 45,000 root-scanning images and nearly 25,000 cross sections from the root-shoot junction. The phenotypic plasticity of these traits was quantified as the relative change in trait value under water-deficit compared with control conditions. We then carried out a genome-wide association analysis on these traits and their plasticity, using 45,608 high-quality single-nucleotide polymorphisms. One hundred four significant loci were detected for these traits under control conditions, 106 were detected under water-deficit stress, and 76 were detected for trait plasticity. We predicted 296 (control), 284 (water-deficit stress), and 233 (plasticity) a priori candidate genes within linkage disequilibrium blocks for these loci. We identified key a priori candidate genes regulating root growth and development and relevant alleles that, upon validation, can help improve rice adaptation to water-deficit stress.