Genetic dissection of photochemical efficiency under water-deficit stress in rice

Chlorophyll fluorescence (Chl-F) measurements together with non-invasive estimations of chlorophyll content, can be used to investigate functionally rich or poor photosystem II (PSII), relating to alterations in photosynthetic performances under different abiotic stresses. The aim was to identify genetic loci that control rice capacity to cope with different soil moisture conditions such as non-stress (control), water deficit and recovery during the reproductive stage. A genome-wide association study was performed for effective quantum yield of photosystem II (QY) and chlorophyll index across all three treatments. Accessions showed significant variability in traits within each treatment. A total of 43 genetic loci associated with QY and chlorophyll index were identified. Of the total genetic loci identified, 14 were for control, 13 for water-deficit stress and 16 for recovery responses. Interestingly, the majority of the identified genetic loci were co-localized either with chlorophyll synthesis or degradation pathways, components of PSII, transcription factors, protein kinases, transporters, kinases, and antioxidants genes. Favorable alleles and donor accessions found in our study would complement efforts aimed at stacking of traits. Moreover, our results provide promising genetic information for future validation and a potential resource for improving photochemical efficiency and subsequently enhancing carbon gain in rice under water-limited conditions.