QTL mapping of photosynthetic-related traits in rice under salt and alkali stresses

Salt-alkali stress causes serious abiotic damage during the growth stage of rice. Photosynthetic characteristics and their related physiological traits affect the growth and development of rice under stressed conditions. In this study, using a recombinant inbred line (RIL) population derived from a cross between Dongnong 425 and Changbai 10 (CB10), quantitative trait loci (QTLs) for seven photosynthetic-related traits, including net photosynthetic rate (Pn), transpiration rate, stomatal conductance, intercellular CO2 concentration, chlorophyll content (Cc), canopy temperature and leaf area (La), were identified in control, salt and alkali stress conditions at the grain filling stage of rice over two years. In total, 23 QTLs were detected by using the CIM module of Windows QTL Cartographer 2.5 software, and 19 out of the 23 QTLs were salt-alkali stress-related. qPn3-2, qTr8, qCc3, qCc12 and qLa12 were specifically expressed in salt or alkali stress conditions. qTr6 expression was detected under both salt and alkali stresses for two consecutive years, suggesting it may have a key role in salt-alkali tolerance breeding. OsGLYII-2, which is a salt tolerant gene located in the mapping interval of major QTLs qPn3-2 and qCc3, was sequenced to verify the additive effect orientation of the two QTLs. The sequenced result showed that the OsGLYII-2 allele of extremely salt-tolerant RIL lines was consistent with that of the tolerant parent CB10 and showed that the positive alleles of qPn3-2 and qCc3 originated from CB10. The information obtained in this study may be useful for understanding the genetic basis of salt-alkali tolerance; it also provides an important base for the fine mapping and map-based cloning of the QTLs for photosynthetic-related traits under salt-alkali stress.