QTL analysis of rice photosynthesis-related traits under the cold stress across multi-environments

Abstract

Cold stress is one of the major abiotic stress factors influencing photosynthesis in rice. In the present study, a linkage analysis and genome-wide association study (GWAS) of photosynthesis-related traits (PRT) at the grain filling stage of rice, including net photosynthetic rate (Pn), stomatal conductance (Sc), transpiration rate (Tr), and intercellular CO2 concentration (Ci), were performed under cold stress using a recombinant inbred line population and single-nucleotide polymorphism (SNP) re-sequencing data of 295 japonica varieties. Twenty-nine additive QTLs (A-QTLs) were detected, and 17 out of the 29 QTLs were cold stress-related. qPn7-1, qTr1, qTr7-1, qTr7-2, qCi7-1 and qSc7-1 were specifically expressed under the cold stress and control conditions in different years, with one major pleiotropic QTL interval (RM1306–RM70) detected. In addition, additive × environment interaction QTLs revealed that qPn7-1, qTr1, qTr7-1, qCi7-1, qSc7-1, and qSc8-1 were influenced mainly by genetic factors, suggesting they could be exploited in cold tolerance breeding activities. Ten SNPs were associated significantly with PRT under cold-water stress based on GWAS, and three out the ten were included in the major QTL interval of RM1306–RM70, verifying the QTLs detected in multiple environments by linkage analysis. According to the major QTL genotypes linked to PRT, phenotypically superior RIL47 could be considered for genetic improvement of PRT under cold water stress. The results could facilitate the fine mapping of QTLs related to Pn, Tr, Ci, and Sc under the cold stress condition through the marker-assisted selection approaches.