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.
Rice quality is one of the important indicators of rice breeding, including milling quality, appearance, cooking and eating quality and nutritional quality. Guangxi is one of the origins of cultivated rice, and great progress has been made in the genetic improvement of rice quality by utilizing abundant rice germplasm resources. In this study, 1570 rice varieties approved in Guangxi from 1983 to 2021 were used to analyze the changes of 16 traits. We found that the appearance quality and cooking and eating quality of Guangxi rice were significantly improved, especially the hybrid rice varieties. By conducting genome-wide association analysis and variant allele frequency analysis from 38 representative varieties, we found that ALK, BG2, GL3.1, GL7/GW7, GPA3, GS3, OsMKKK10, Wx, An-1, BG1, CLG1, GS5, GW8 and RGG2 may be closely related to the genetic improvement of rice quality traits in Guangxi, among which 11 genes are related to rice grain shape. The functional variation sites of seven important quality genes, including ALK, Wx, and GS3, were analyzed by the penta-primer amplification refractory mutation system (PARMS). The data showed that Gui569, Gui117, Gui721, Gui726, RYousi, RSimiao, and RBasi exhibited multiple elite alleles. In this study, we analyzed the phenotypic changes and molecular basis of varieties in Guangxi over the past 40 years. These results will provide theoretical guidance for the genetic improvement of rice quality and the cultivation of new varieties, which is of great significance for improving rice quality.
Background: Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. Results: This study elucidated 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 29 128 and 30 131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis(WGCNA)revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. Conclusion: Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.
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