The effective increase of the rice breeding process for grain yield could be sustained by developing efficient tools to accelerate plant selection through the rapid determination of reliable predictors. Here, we have described different associations between grain yield and photosynthetic parameters simply and fast obtainable by a non-invasive technique in flag leaf during the anthesis stage. Among the analyzed photosynthetic parameters, the photosynthetic performance index (PIABS) stood out for its strong association with grain yield. A genome-wide association analysis determined in plants from a rice diversity panel at tillering stage indicated the presence of a quantitative trait locus on chromosome 9 characterized by a set of candidate chloroplastic genes with contrasting haplotypes for PIABS. An analysis of these haplotypes indicated a separation into two groups. One with haplotypes linked to high values of PIABS, which were associated almost exclusively withJaponicaspp. subpopulations, and another with haplotypes linked to low values of PIABS, which were associated exclusively withIndicaspp. subpopulations. Genotypes of theJaponicaspp. subpopulations showed high values in panicle weight, a yield components parameter, compared with theIndicaspp. subpopulations genotypes. The results of this work suggested that PIABScould be an early predictor of grain yield at the tillering stage in rice breeding processes.

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