Integration of transcriptome and proteome analysis reveals the mechanism of freezing tolerance in winter rapeseed

Abstract

Winter rapeseed seedlings are susceptible to low temperature during overwintering in Northwest China, leading to reduced crops production. Freezing stress is one of the utmost environmental stresses in Northwest China from late autumn to early spring, which are eventful for overwinter survival rate of winter rapeseed. However, the molecular mechanism of freezing tolerance formation is still very backward in winter rapeseed. In this study, using a pair of freezing-sensitive and freezing-resistant cultivars NQF24 and NTS57, the exhaustive effects of freezing stress on freezing tolerance formation were evaluated by analyzing leaf at the levels of transcriptome, proteome, physiology and ultrastructure. There were 8497 differentially expressed genes (DEGs) and 418 differentially abundant proteins (DAPs) speci cally identi ed in leaf of NQF24 under freezing stress, while 7358 DEGs and 573 DAPs were speci cally identi ed in leaf of NTS57. Function enrichment analysis showed that most of the enriched DEGs and DAPs were associated with plant hormones signal transduction, fatty acid metabolism, ribosome, plant-pathogen interaction and secondary metabolites biosynthesis.Freezing tolerance is formed by enhanced signals transduction, increased the biosynthesis of protein and secondary metabolites, higher reactive oxygen species (ROS) scavenging, more osmolytes, lower lipid peroxidation, and stronger ultrastructure. These results can be taken as selection indicators in freezing tolerance breeding program in rapeseed.

DNA methylation affects freezing tolerance in winter rapeseed by mediating the expression of genes related to JA and CK pathways

“…Freezing stress can cause a set of physiological and morphological changes, leading to the accumulation of many protective substances in plants ( Gao et al, 2019 ). Freezing stress also results in membrane lipid peroxidation and cellular ultrastructure damage ( Deng et al, 2015 ; Shi et al, 2018 ), which was comparable with our previous researches ( Wei et al, 2021a ; Wei et al, 2021b ). In this study, under freezing stress, the 15NS plant showed obvious wilting, whereas no significant changes were found in the 16NS and 17NS plants, in compared with controls ( Figure 1A ), which implied that freezing stress was enhanced year by year.…”

“… Liu et al (2017) showed that the DNA methylation patterns were changed in rapeseed under freezing treatment by whole genome bisulfite sequencing (WGBS). Wei et al (2021b) identified some DMGs involved in freezing response in developing rapeseed leaves by integrated transcriptome and methylome analysis. However, these studies were mainly subjected to the screening of a broad range of epigenetically regulated genes, and the evolutionary mechanism of how DNA methylation regulates genes to enhance freezing resistance of winter rapeseed was still poorly understood.…”

Integrated methylome and transcriptome analysis unravel the cold tolerance mechanism in winter rapeseed(Brassica napus L.)

“…Over the past decade, our research group has successfully selected and bred rapeseed cultivars of B. napus that can overwinter safely in most of the northwestern areas from the 38° to the 42° north latitude, where the lowest temperature in winter is -26℃ [15,16]. Moreover, the cold tolerance characteristics of these rapeseed cultivars at the transcription, protein, physiological, biochemical, and subcellular levels were studied [15,21,22]. The strong coldresistant cultivar had stronger antioxidant enzyme activity and accumulation of cryoprotective molecules, associated with the metabolic pathways, including alpha-linolenic acid metabolism, plant hormone signal transduction, microbial metabolism in diverse environments, linoleic acid metabolism, phenylpropanoid biosynthesis, glutathione metabolism, flavonoid biosynthesis metabolism, and amino acid metabolism.…”

Integrative Omics Analysis of Three Oil Palm Varieties Reveals (Tanzania × Ekona) TE as a Cold-Resistant Variety in Response to Low-Temperature Stress

“…AP2-EREBP (APETALA2/ethylene-responsive element-binding protein) TFs are important and have played a crucial role in loquat fruitlet transcription profiling under freezing stress tolerance [ 41 ]. AP2/ERF TFs were also found in winter rapeseed transcriptome under freezing tolerance [ 43 ]. AP2-EREBP could be sub-classified into four sub-families, i.e., DREB/CBF, ERF, CBF, and RAP [ 44 ], whereas DREB/CBF TFs have demonstrated their indispensable role in low-temperature stress in the tea plant [ 45 ].…”

“…The protein that contained at least one unique peptide was set as necessary for the identified proteins. In order to control the rate of false-positives at the protein level, the false discovery rate (FDR) was set at less than 1%, with confidence intervals higher than 95% [ 43 ]. However, sequences of positively identified proteins were further carried out for BLAST searching of the UniProt database.…”