An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

Abstract

Background Rice (Oryza sativa L.) is one of the most widely grown food crops, and its yield and quality are particularly important for a warm-saturated diet. Cold stress restricts rice growth, development, and yield; however, the specific mechanism of cold tolerance in rice remains unknown. Results The analysis of leaf physiological and photosynthetic characteristics showed that the two rice varieties were significantly affected by cold stress, but the cold-tolerant variety KY131 had more stable physiological characteristics, maintaining relatively good photosynthetic capacity. To better explore the transcriptional regulation mechanism and biological basis of rice response to cold stress, a comprehensive analysis of the rice transcriptome and lipidome under low temperature and control temperature conditions was carried out. The transcriptomic analysis revealed that lipid metabolism, including membrane lipid and fatty acid metabolism, may be an important factor in rice cold tolerance, and 397 lipid metabolism related genes have been identified. Lipidomics data confirmed the importance of membrane lipid remodeling and fatty acid unsaturation for rice adaptation to cold stress. This indicates that the changes in the fluidity and integrity of the photosynthetic membrane under cold stress lead to the reduction of photosynthetic capacity, which could be relieved by increased levels of monogalactosyldiacylglycerol that mainly caused by markedly increased expression of levels of 1,2-diacylglycerol 3-beta-galactosyltransferase (MGD). The upregulation of phosphatidate phosphatase (PAP2) inhibited the excessive accumulation of phosphatidate (PA) to produce more phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG), thereby preventing of membrane phase transition under cold stress. In addition, fatty acid β-oxidation is worth further study in rice cold tolerance. Finally, we constructed a metabolic model for the regulatory mechanism of cold tolerance in rice, in which the advanced lipid metabolism system plays a central role. Conclusions Lipidome analysis showed that membrane lipid composition and unsaturation were significantly affected, especially phospholipids and galactolipids. Our study provides new information to further understand the response of rice to cold stress.

Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions

“…GO enrichment analysis indicated that the 1,018 targets that were negatively correlated with parameters of air temperature included a significantly higher proportion of genes related to ‘fatty acid beta-oxidation’ ( Table 5 ). This result appears to be consistent with those of previous reports of peanut ( Arachis hypogaea L.) [ 68 ] and rice ( Oryza sativa L.) [ 69 ], which exhibited up-regulation of genes related to fatty acid beta-oxidation under cold stress. Up-regulated expression of multiple beta-oxidation genes during germination was also reported in Tung tree ( Vernicia fordii , Hemsl.)…”

Transcriptome Analysis Revealed the Dynamic and Rapid Transcriptional Reprogramming Involved in Cold Stress and Related Core Genes in the Rice Seedling Stage

“…Cold stress as a major environmental factor severely limits the growth and development, as well as the improvement of yield and quality, in rice. According to the degree of cold stress, the plant undergoes corresponding changes at the phenotypic, physiological, and molecular levels to respond to the low temperature, including photosynthetic rate, redox homeostasis, hormone signal transduction, transcriptional regulation, and posttranslational modification [4,7]. In this study, we integrated the transcriptomic analysis and genome data to reveal the rapid and dramatic transcriptional reprogramming process in the early stage of cold treatment and predict the cold sensitivity-related candidate genes.…”

“…Rice (Oryza sativa L.) is one of the major cereal crops in the world and plays a key role in global food security [1]. Cold damage as a kind of natural disaster is often encountered during the whole growth and development of rice, and limits its growth, geographical distribution, yield, and quality [2][3][4]. Especially for rice seedlings, low temperature causes damage to leaves and roots, a withered state, and even death [5].…”

Alterations of phenotype, physiology, and functional substances reveal the chilling-tolerant mechanism in two common Olea Europaea cultivars

“…Numerous studies have reported that unsaturated fatty acids are closely associated with chilling responses. Under low-temperature conditions, cold-tolerant varieties have higher membrane lipid unsaturation and unsaturated fatty acid content, enabling the plant to maintain a certain degree of stability and fluidity of the membrane system ( Liu et al., 2022 ). For instance, 3-day cold or dark treatment significantly induces eicosapentaenoic acid biosynthesis ( Chua et al., 2020 ).…”