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Genome-wide identification of CCT genes in wheat (Triticum aestivum L.) and their expression analysis during vernalization.

ABSTRACT: Numerous CCT genes are known to regulate various biological processes, such as circadian rhythm regulation, flowering, light signaling, plant development, and stress resistance. The CCT gene family has been characterized in many plants but remains unknown in the major cereal wheat (Triticum aestivum L.). Extended exposure to low temperature (vernalization) is necessary for winter wheat to flower successfully. VERNALIZATION2 (VRN2), a specific CCT-containing gene, has been proved to be strongly associated with vernalization in winter wheat. Mutation of all VRN2 copies in three subgenomes results in the eliminated demands of low temperature in flowering. However, no other CCT genes have been reported to be associated with vernalization to date. The present study screened CCT genes in the whole wheat genome, and preliminarily identified the vernalization related CCT genes through expression analysis. 127 CCT genes were identified in three subgenomes of common wheat through a hidden Markov model-based method. Based on multiple alignment, these genes were grouped into 40 gene clusters, including the duplicated gene clusters TaCMF6 and TaCMF8, each tandemly arranged near the telomere. The phylogenetic analysis classified these genes into eight groups. The transcriptome analysis using leaf tissues collected before, during, and after vernalization revealed 49 upregulated and 31 downregulated CCT genes during vernalization, further validated by quantitative real-time PCR. Among the differentially expressed and well-investigated CCT gene clusters analyzed in this study, TaCMF11, TaCO18, TaPRR95, TaCMF6, and TaCO16 were induced during vernalization but decreased immediately after vernalization, while TaCO1, TaCO15, TaCO2, TaCMF8, and TaPPD1 were stably suppressed during and after vernalization. These data imply that some vernalization related CCT genes other than VRN2 may exist in wheat. This study improves our understanding of CCT genes and provides a foundation for further research on CCT genes related to vernalization in wheat.

SUBMITTER: Zhang H

PROVIDER: S-EPMC8730456 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundVernalization, as a vital process in the life cycle of winter cereal, has important effects on floral organ formation and flowering time. Many morphological changes together with molecular changes occur during the vernalization period. Here, we used transcriptome sequencing to analyze the transcriptomic changes in wheat leaves before, during and after vernalization using the winter wheat cultivar 'Shiluan02-1'.ResultsA total of 16,370 differentially expressed genes were obtained across different vernalization periods. Gene Ontology enrichment analysis revealed that photoperiodism, photoprotection, photosynthesis, lipid transport and biosynthetic process, and chlorophyll metabolic process were closely related to vernalization. In addition, AP2/ERF, C2H2, bHLH, WRKY, MYB, MYB-related, and NAC transcription factors were significantly enriched during vernalization, and the transcription factor expression patterns suggested the intricate regulation of transcription factor modules in plant vernalization pathways. Analysis of gene expression patterns of the MADS-box transcription factor genes showed different expression patterns during vernalization phases, among which VERNALIZATION1 (VRN1) genes were found to gradually increase during vernalization periods from V0 to V35, while decline in the V42 phase, then increase after vernalization. The Tavrt-2 gene cooperated with Tavrn1 to regulate flowering induced by vernalization, and its expression level was rapidly increased by vernalization but declined in the V42 phase and then increased after vernalization. Some genes from the ICE-CBF-COR pathway were also identified, and additional analysis indicated that some key genes related to phytohormone biosynthesis and signal transduction were enriched during the vernalization period, such as gibberellic acid, ethylene, abscisic acid and jasmonic acid biosynthesis and signaling pathway genes.ConclusionsOur study provides valuable molecular information for future studies on wheat vernalization regulation and also serves as an excellent reference for future wheat breeding.

Project description:Cytokinins (CKs) are involved in determining the final grain yield in wheat. Multiple gene families are responsible for the controlled production of CKs in plants, including isopentenyl transferases for de novo synthesis, zeatin O-glucosyltransferases for reversible inactivation, β-glucosidases for reactivation, and CK oxidases/dehydrogenases for permanent degradation. Identifying and characterizing the genes of these families is an important step in furthering our understanding of CK metabolism. Using bioinformatics tools, we identified four new TaIPT, four new TaZOG, and 25 new TaGLU genes in common wheat. All of the genes harbored the characteristic conserved domains of their respective gene families. We renamed TaCKX genes on the basis of their true orthologs in rice and maize to remove inconsistencies in the nomenclature. Phylogenetic analysis revealed the early divergence of monocots from dicots, and the gene duplication event after speciation was obvious. Abscisic acid-, auxin-, salicylic acid-, sulfur-, drought- and light-responsive cis-regulatory elements were common to most of the genes under investigation. Expression profiling of CK metabolic gene families was carried out at the seedlings stage in AA genome donor of common wheat. Exogenous application of phytohormones (6-benzylaminopurine, salicylic acid, indole-3-acetic acid, gibberellic acid, and abscisic acid) for 3 h significantly upregulated the transcript levels of all four gene families, suggesting that plants tend to maintain CK stability. A 6-benzylaminopurine-specific maximum fold-change was observed for TuCKX1 and TuCKX3 in root and shoot tissues, respectively; however, the highest expression level was observed in the TuGLU gene family, indicating that the reactivation of the dormant CK isoform is the quickest way to counter external stress. The identification of new CK metabolic genes provides the foundation for their in-depth functional characterization and for elucidating their association with grain yield.

Project description:Plant protein phosphatase 2Cs (PP2Cs) play crucial roles in phytohormone signaling, developmental processes, and both biotic and abiotic stress responses. However, little research has been conducted on the PP2C gene family in hexaploid wheat (Triticum aestivum L.), which is an important cereal crop. In this study, a genome-wide investigation of TaPP2C gene family was performed. A total of 257 homoeologs of 95 TaPP2C genes were identified, of which 80% of genes had all the three homoeologs across A, B, and D subgenomes. Domain analysis indicated that all the TaPP2C homoeologs harbored the type 2C phosphatase domains. Based on the phylogenetic analysis, TaPP2Cs were divided into 13 groups (A-M) and 4 single branches, which corresponded to the results of gene structure and protein motif analyses. Results of chromosomal location and synteny relationship analysis of TaPP2C homoeologs revealed that known chromosome translocation events and pericentromeric inversions were responsible for the formation of TaPP2C gene family. Expression patterns of TaPP2C homoeologs in various tissues and under diverse stress conditions were analyzed using publicly available RNA-seq data. The results suggested that TaPP2C genes regulate wheat developmental processes and stress responses. Homoeologous expression patterns of TaPP2C triad homoeologs from A, B, and D subgenomes, revealed expression bias within triads under the normal condition, and variability in expression under different stress treatments. Quantitative real-time PCR (qRT-PCR) analysis of eight TaPP2C genes in group A revealed that they were all up-regulated after abscisic acid treatment. Some genes in group A also responded to other phytohormones such as methyl jasmonate and gibberellin. Yeast two-hybrid assays showed that group A TaPP2Cs also interacted with TaSnRK2.1 and TaSnRK2.2 from subclass II, besides with subclass III TaSnRK2s. TaPP2C135 in group A was transformed into Arabidopsis and germination assay revealed that ectopic expression of TaPP2C135 in Arabidopsis enhanced its tolerance to ABA. Overall, these results enhance our understanding of the function of TaPP2Cs in wheat, and provide novel insights into the roles of group A TaPP2Cs. This information will be useful for in-depth functional analysis of TaPP2Cs in future studies and for wheat breeding.

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Genome-wide identification of CCT genes in wheat (Triticum aestivum L.) and their expression analysis during vernalization.

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