Genome-wide mapping, allelic fingerprinting, and haplotypes validation provide insights into the genetic control of carbon dioxide responsiveness in rice

Plant density significantly impacts photosynthesis, canopy structure, crop growth, and yield, thereby shaping the [CO ] 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 [CO ], significantly increased all trait values, except for harvest index, compared to NPD. For the genome-wide association study, 386,817 high-quality SNPs were considered, employing both single-locus and multi-locus models, which collectively identified 172 QTNs, including 12 QTNs associated with at least two different traits under NPD or LPD conditions. A significant r­elationship between the percentage of favorable alleles in the genotypes and their performance under NPD and LPD conditions was observed. Potential haplotypes were validated using genotypes with contrasting [CO ] responses, grown under LPD and Free-Air CO Enrichment facility. These findings can enable efforts to selectively breed genotypes with favorable alleles and/or superior haplotypes for enhancing [CO ] responsiveness in rice. Climate smart rice varieties, with increased [CO ] responsiveness, have the potential to simultaneously enhance grain yield and quality while mitigating losses induced by high night temperatures.