Chlorophyll fluorescence analysis in diverse rice varieties reveals the positive correlation between the seedlings salt tolerance and photosynthetic efficiency

Background Photosynthetic efficiency might be a key factor determining plant resistance to abiotic stresses. Plants can sense when growing conditions are not favorable and trigger an internal response at an early stage before showing external symptoms. When a high amount of salt enters the plant cell, the membrane system and function of thylakoids in chloroplasts could be destroyed and affect photosynthetic performance if the salt concentration is not regulated to optimal values. Oryza species have salt-tolerant and salt-sensitive genotypes; however, very few studies have investigated the genetic architecture responsible for photosynthetic efficiency under salinity stress in cultivated rice. Results We used an imaging-based chlorophyll fluorometer to monitor eight rice varieties that showed different salt tolerance levels for four consecutive days under control and salt conditions. An analysis of the changes in chlorophyll fluorescence parameters clearly showed the maximum quantum efficiency of PSII in sensitive varieties was significantly reduced after NaCl treatment when compared to tolerant varieties. A panel of 232 diverse rice accessions was then analyzed for chlorophyll fluorescence under salt conditions, the results showed that chlorophyll fluorescence parameters such as F-0 and NPQ were higher in Japonica subspecies, phi PSII of Indica varieties was higher than that in other subgroups, which suggested that the variation in photosynthetic efficiency was extensively regulated under salt treatment in diverse cultivated rice. Two significant regions on chromosome 5 were identified to associate with the fraction of open PSII centers (qL) and the minimum chlorophyll fluorescence (F-0). These regions harbored genes related to senescence, chloroplast biogenesis and response to salt stress are of interest for future functional characterization to determine their roles in regulating photosynthesis. Conclusions Rice plant is very sensitive to salinity stress, especially at young seedling stage. Our work identified the distribution pattern of chlorophyll fluorescence parameters in seedlings leaf and their correlations with salt tolerance level in a diverse gene pool. We also revealed the complexity of the genetic architecture regulating rice seedling photosynthetic performance under salinity stress, the germplasm analyzed in this study and the associated genetic information could be utilized in rice breeding program.