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.

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Drought stress is a prominent and persisting constraint for sustaining global rice (Oryza sativa L.) production. Priming with mild drought can be effective in reducing the impact of severe terminal drought stress affecting seed set and grain filling in rice. The cultivars N22 (drought tolerant), NSIC Rc222 and IR64 (high yielding, drought sensitive) were tested for short-term mild drought priming before flowering and subsequently exposed to severe drought stress either at the highly sensitive flowering or at the early grain filling stage under greenhouse conditions. Drought stress increased oxidative damage and reduced photosynthesis and sink enzymatic activity, ultimately reducing seed set (20–46%) and grain yield (22–68%) across cultivars. However, priming with mild drought significantly reduced oxidative damage, and increased photosynthesis, stomatal conductance and enzymatic activity, contributing to improved sink strength, thereby significantly reducing seed set (7–18%) and grain yield (12–59%) losses. The higher activity of key enzymes associated with sink strength such as cell wall invertase and sucrose synthase in primed plants probably reduced drought-induced losses at the grain filling stage. The findings support mild drought priming before flowering as a promising strategy for reducing yield penalty by providing partial protection against subsequent severe terminal drought stress. However, application of mild drought priming at the field level would need further investigation.