Computational genomics insights into cold acclimation in wheat

Abstract

Development of cold acclimation in crops involves transcriptomic reprograming, metabolic shift, and physiological changes. Cold responses in transcriptome and lipid metabolism has been examined in separate studies for various crops. In this study, integrated computational approaches was employed to investigate the transcriptomics and lipidomics data associated with cold acclimation and vernalization in four wheat genotypes of distinct cold tolerance. Differential expression was investigated between cold treated and control samples and between the winter-habit and spring-habit wheat genotypes. Collectively, 12,676 differentially expressed genes (DEGs) were identified. Principal component analysis of these DEGs indicated that the first, second, and third principal components (PC1, PC2, and PC3) explained the variance in cold treatment, vernalization and cold hardiness, respectively. Differential expression feature extraction (DEFE) analysis revealed that the winter-habit wheat genotype Norstar had high number of unique DEGs (1884 up and 672 down) and 63 winter-habit genes, which were clearly distinctive from the 64 spring-habit genes based on PC1, PC2 and PC3. Correlation analysis revealed 64 cold hardy genes and 39 anti-hardy genes. Cold acclimation encompasses a wide spectrum of biological processes and the involved genes work cohesively as revealed through network propagation and collective association strength of local subnetworks. Integration of transcriptomics and lipidomics data revealed that the winter-habit genes, such as COR413-TM1, CIPKs and MYB20, together with the phosphatidylglycerol lipids, PG(34:3) and PG(36:6), played a pivotal role in cold acclimation and coordinated cohesively associated subnetworks to confer cold tolerance.

The Triticeae CBF Gene Cluster—To Frost Resistance and Beyond

“…Moreover, three MTA identified at a lower significance level matched CBF genes at FR-2R, namely CBFIIId-19, CBFIVa-2.2, and CBFIIIa-6.2. What is more interesting is that ICE1 showed 97% sequence identity to orthologous TaICE41 of hexaploidy wheat, and CBFIIId-19 and CBFIVa-2.2 are putatively orthologous to hexaploid wheat genes reported to be induced by vernalization [199,204] (see above). For ICE1 protein, amino acid variation within the DNA-binding bHLH region and/or start of the zipper region resulted in traits such as WFS and low temperature tolerance.…”

“…Recent studies expanded the investigation of ICE-CBF-COR interconnection with other environmental stimuli with high-throughput functional analysis [78,195,[203][204][205][206]. Guo et al [78] carried out RNAseq and qPCR analysis in wheat tissues under different stress conditions, observing the expression of 53 genes belonging to the ICE-CBF-COR signaling cascade that revealed tissue-specific expression patterns of the ICE, CBF, and COR genes under different stress conditions.…”

Deacclimation and reacclimation processes in winter wheat: novel perspectives from time-series transcriptome analysis

“…The CBF TFs, in turn, upregulate the COR group of proteins, which carry out various protective functions – for example, COR14b protects the photosynthetic apparatus after freezing damage ( Rapacz et al., 2008 ), while COR dehydrins play a cryoprotective role during frost-induced desiccation ( Kosová et al., 2011 ). Therefore, numerous transcriptomic and bioinformatic studies have reported increased expression of the ICE-CBF-COR pathway genes in wheat under cold stress ( Li et al., 2018 ; Guo et al., 2019 ; Aleliūnas et al., 2020 ; Pan et al., 2022 ).…”