Genome-Wide Mapping, Allelic Fingerprinting, and Haplotypes Validation Provide Insights Into the Genetic Control of Phenotypic Plasticity in Rice.

Plant density significantly impacts photosynthesis, crop growth, and yield, thereby shaping the [CO₂] fertilization effect and intricate physiological interactions in rice. An association panel of 171 rice genotypes was evaluated for physiological and yield-related traits, including the cumulative response index, under both normal planting density (NPD) and low planting density (LPD) conditions. LPD, serving as a proxy for elevated atmospheric [CO₂], significantly increased all trait values, except for harvest index, compared to NPD. A genome-wide association study identified 172 QTNs, including 12 associated with multiple traits under NPD or LPD conditions. Candidate gene mining and network analysis within QTN regions identified potential candidates such as OsHAK1, RGA1, OsalphaCA3, OsalphaCA4, OsalphaCA5, OsCYP38, and OsPIN1, influencing various physiological and yield-related traits under LPD conditions. A significant relationship between the percentage of favorable alleles in genotypes and their performance under different conditions was observed. Potential haplotypes were validated using genotypes identified with contrasting [CO₂] responses, grown under LPD and Free-Air [CO₂] Enrichment facility. These findings can aid in selectively breeding genotypes with favorable alleles or haplotypes to enhance [CO₂] responsiveness in rice. Incorporating greater phenotypic plasticity can help develop climate-smart rice varieties that increase grain yield and quality while mitigating losses from warming temperatures.