Genetic control of rice root morphology and anatomy

34 Elucidating the genetic control of rooting behaviour under water-deficit stress is essential to 35 breed climate-robust rice cultivars. Using a diverse panel of 274 indica genotypes grown 36 under control and water-deficit conditions during vegetative growth, we phenotyped 35 traits, 37 mostly related to root morphology and anatomy, involving ~45,000 root scanning images and 38 nearly ~25,000 cross-sections from the root-shoot junction. Phenotypic plasticity of these 39 traits was quantified as the relative change in trait value under water-deficit compared to 40 control conditions. We then carried out a genome-wide association analysis on these traits 41 and their plasticity, using 45,608 high quality SNPs. One hundred four significant loci were 42 detected for these traits under control condition, 106 were detected under water-deficit stress, 43 and 76 were detected for trait plasticity. We predicted 296 (control), 284 (water-deficit stress) 44 and 233 (plasticity) a priori candidate genes within linkage disequilibrium (LD) blocks for 45 these loci. We identified key a priori candidate genes regulating root growth and 46 development and relevant alleles that upon validation can help improve rice adaptation to 47 water-deficit stress. 48