The Ratio of A/A Mapping Identifies Chromosomal Regions Containing Known Photoprotection Recovery-Related Genes in Rice.

The rice, like other plants, undergoes photoprotection mode by increasing nonphotochemical quenching (NPQ) in high light intensity (> 1200 µmol ms PPFD), which attenuates photosystem II yield (φPSII) drastically. The plant remains in photoprotection mode even after light intensity becomes not stressful for an extended period. While there are significant differences in the time it takes for photoprotection to recover among different genotypes, its use is limited in plant breeding because measuring the chlorophyll fluorescence parameters in progressive actinic light after dark adaptation takes more than forty-five minutes per genotype. The study finds that instantly measured A/A ratio by five minutes in flag leaves of 25 diverse genotypes strongly associated with the φPSII differences between theoretical and actual, qPd and NPQ with R values 0.74, 0.65 and 0.60, respectively. In two consecutive years, GWAS of A/A ratio identified the regions with genes reported earlier for plant photoprotection recovery. Additionally, QTL analysis in a RIL population also identified the regions carrying known genes related to photoprotection. Thus, the A/A ratio can quickly phenotype many plants for easier introgression of the traits in popular cultivars. The identified genotypes, genes, and QTLs can be used to improve yield potential and allele mining.