Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice
Abstract Background: Wild rice ( Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance for many abiotic stresses including cold stress, but little is known about the mechanism underlying its resistance to cold. Low temperature is one of the most prevalent factors that limit rice productivity and geographical distribution.Results: This study aimed to elucidate the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29128 and 30131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in cold-tolerant genotypes than in cold-sensitive genotypes at four stages under cold stress. Gene ontology enrichment analyses indicated more upregulated genes than downregulated ones in cold-tolerant genotypes based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity. To confirm the RNA Sequencing (RNA-seq) data, Quantitative real time polymerase chain reaction (qRT-PCR) was performed on seven randomly selected DEGs. These genes showed similar expression patterns corresponding with the RNA-Seq method. We also explored a gene for cold tolerance LTG5 , encoding a UDP-glucosyltransferase. The overexpression of LTG5 gene conferred cold tolerance to indica rice.Conclusion: Overall, our results suggested that gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crop plants.