Comprehensive genome-wide identification, characterization, and expression analysis of CCHC zinc finger gene family in wheat (Triticum aestivum L.)

Abstract Background: The CCHC zinc finger proteins (CCHC-ZFPs) are transcription factors that play versatile roles in plant growth, development, and responses to biotic/abiotic stress. However, little is known about the CCHC-ZF genes in bread wheat (Triticum aestivum), an important food crop. Results: In this study, 50 TaCCHC-ZF genes were identified and distributed unevenly on 21 wheat chromosomes. According to the phylogenetic features, the 50 TaCCHC-ZF genes were classified into eight groups with specific motifs and gene structures. 43 TaCCHC-ZF genes were identified as segmentally duplicated genes that formed 36 segmental duplication gene pairs. Additionally, the collinearity analyses between wheat and eight other representative plant species showed that wheat had closer phylogenetic relationships with monocots compared to dicots. A total of 636 cis-elements related to environmental stress and phytohormone responsiveness were identified in the promoter of TaCCHC-ZF genes. Moreover, GO enrichment results revealed that all 50 TaCCHC-ZF genes were annotated under metal ion binding and nucleic acid binding. 91 miRNA binding sites within the 34 TaCCHC-ZF genes were identified by miRNA targets analyses, indicating that the expression of TaCCHC-ZF genes could be regulated by the miRNAs. Based on published transcriptome data, 38 TaCCHC-ZF genes were identified as DEGs, and 15 TaCCHC-ZF genes among them were verified by qRT-PCR assays, which showed response to drought, heat, or simultaneous response of them. Conclusions: This study systematically explored the gene structures, evolutionary characteristics, and potential roles during environmental responses of TaCCHC-ZF genes, providing a foundation for further investigation and application of TaCCHC-ZF genes in the molecular breeding of T. aestivum. Keywords: Wheat, CCHC-ZFP genes, Structural analysis, Evolution, Abiotic stress, Expression patterns

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Comprehensive Genome-wide Identification, Characterization, and Expression Analysis of CCHC Zinc Finger Gene Family in Wheat (Triticum aestivum L.)

10.21203/rs.3.rs-900125/v2 ◽

2022 ◽

Author(s):

Aolong Sun ◽

Yongliang Li ◽

Xiaoxiao Zou ◽

Fenglin Chen ◽

Ruqiong Cai ◽

...

Keyword(s):

Triticum Aestivum ◽

Zinc Finger ◽

Metal Ion ◽

Triticum Aestivum L ◽

Nucleic Acid Binding ◽

Metal Ion Binding ◽

Genome Wide ◽

Gene Structures ◽

Environmental Responses ◽

Cchc Zinc Finger

Abstract Background: The CCHC zinc finger proteins (CCHC-ZFPs) are transcription factors that play versatile roles in plant growth, development, and responses to biotic/abiotic stress. However, little is known about the CCHC-ZF genes in bread wheat (Triticum aestivum), an important food crop.Results: In this study, 50 TaCCHC-ZF genes were identified and distributed unevenly on 21 wheat chromosomes. According to the phylogenetic features, the 50 TaCCHC-ZF genes were classified into eight groups with specific motifs and gene structures. 43 TaCCHC-ZF genes were identified as segmentally duplicated genes that formed 36 segmental duplication gene pairs. Additionally, the collinearity analyses between wheat and eight other representative plant species showed that wheat had closer phylogenetic relationships with monocots compared to dicots. A total of 636 cis-elements related to environmental stress and phytohormone responsiveness were identified in the promoter of TaCCHC-ZF genes. Moreover, GO enrichment results revealed that all 50 TaCCHC-ZF genes were annotated under metal ion binding and nucleic acid binding. 91 miRNA binding sites within the 34 TaCCHC-ZF genes were identified by miRNA targets analyses, indicating that the expression of TaCCHC-ZF genes could be regulated by the miRNAs. Based on published transcriptome data, 38 TaCCHC-ZF genes were identified as DEGs, and 15 TaCCHC-ZF genes among them were verified by qRT-PCR assays, which showed response to drought, heat, or simultaneous response of them.Conclusions: This study systematically explored the gene structures, evolutionary characteristics, and potential roles during environmental responses of TaCCHC-ZF genes, providing a foundation for further investigation and application of TaCCHC-ZF genes in the molecular breeding of T. aestivum.

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Genome-wide identification, characterization, and expression patterns analysis of the SBP-box gene family in wheat (Triticum aestivum L.)

Scientific Reports ◽

10.1038/s41598-020-74417-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ying Li ◽

Qilu Song ◽

Yamin Zhang ◽

Zheng Li ◽

Jialin Guo ◽

...

Keyword(s):

Triticum Aestivum ◽

Abiotic Stress ◽

Stress Responses ◽

Tandem Duplication ◽

Expression Profiles ◽

Expression Patterns ◽

Triticum Aestivum L ◽

Genome Wide ◽

Related Development ◽

Gene Structures

Abstract SQUAMOSA promoter-binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play roles in plant growth and development. The characteristics of SBP-box genes in rice (Oryza sativa) and Arabidopsis have been reported, but their potential roles in wheat (Triticum aestivum) are not fully understood. In this study, 48 SBP-box genes (TaSBPs) were identified; they were located in all wheat chromosomes except for 4B and 4D. Six TaSBPs were identified as tandem duplication genes that formed three tandem duplication pairs, while 22 were segmentally duplicated genes that formed 16 segmental duplication pairs. Subcellular localization prediction showed TaSBPs were located in nucleus. Among the 48 TaSBPs, 24 were predicted to be putative targets of TamiR156. Phylogenetic analysis showed that TaSBPs, AtSBPs, and OsSBPs that shared similar functions were clustered into the same subgroups. The phylogenetic relationships between the TaSBPs were supported by the identification of highly conserved motifs and gene structures. Four types of cis-elements––transcription-related, development-related, hormone-related, and abiotic stress-related elements––were found in the TaSBP promoters. Expression profiles indicated most TaSBPs participate in flower development and abiotic stress responses. This study establishes a foundation for further investigation of TaSBP genes and provides novel insights into their biological functions.

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Identification of MdDof genes in apple and analysis of their response to biotic or abiotic stress

Functional Plant Biology ◽

10.1071/fp17288 ◽

2018 ◽

Vol 45 (5) ◽

pp. 528 ◽

Cited By ~ 1

Author(s):

Qing Yang ◽

Qiuju Chen ◽

Yuandi Zhu ◽

Tianzhong Li

Keyword(s):

Abiotic Stress ◽

Zinc Finger ◽

Flower Development ◽

Higher Plants ◽

Expression Patterns ◽

Fruit Trees ◽

Biological Processes ◽

Protein Motifs ◽

Gene Structures ◽

Dof Transcription Factors

As a classic plant-specific transcription factor family – the Dof domain proteins – are involved in a variety of biological processes in organisms ranging from unicellular Chlamydomonas to higher plants. However, there are limited reports of MdDof (Malus domestica Borkh. DNA-binding One Zinc Finger) domain proteins in fruit trees, especially in apple. In this study we identified 54 putative Dof transcription factors in the apple genome. We analysed the gene structures, protein motifs, and chromosome locations of each of the MdDof genes. Next, we characterised all 54 MdDofs their expression patterns under different abiotic and biotic stress conditions. It was found that MdDof6,26 not only played an important role in the biotic/abiotic stress but may also be involved in many molecular functions. Further, both in flower development and pollen tube growth it was found that the relative expression of MdDof24 increased rapidly, also with gene ontology analysis it was indicated that MdDof24 was involved in the chemical reaction and flower development pathways. Taken together, our results provide useful clues as to the function of MdDof genes in apple and serve as a reference for studies of Dof zinc finger genes in other plants.

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Genome-Wide Identification and Expression Profile of OSCA Gene Family Members in Triticum aestivum L.

International Journal of Molecular Sciences ◽

10.3390/ijms23010469 ◽

2021 ◽

Vol 23 (1) ◽

pp. 469

Author(s):

Kai Tong ◽

Xinyang Wu ◽

Long He ◽

Shiyou Qiu ◽

Shuang Liu ◽

...

Keyword(s):

Triticum Aestivum ◽

Gene Family ◽

Expression Profiles ◽

Stomatal Closure ◽

Expression Patterns ◽

Family Members ◽

Triticum Aestivum L ◽

Free Calcium ◽

Cis Acting ◽

Gene Structures

Hyperosmolality and various other stimuli can trigger an increase in cytoplasmic-free calcium concentration ([Ca2+]cyt). Members of the Arabidopsis thaliana (L.) reduced hyperosmolality-gated calcium-permeable channels (OSCA) gene family are reported to be involved in sensing extracellular changes to trigger hyperosmolality-induced [Ca2+]cyt increases and controlling stomatal closure during immune signaling. Wheat (Triticum aestivum L.) is a very important food crop, but there are few studies of its OSCA gene family members. In this study, 42 OSCA members were identified in the wheat genome, and phylogenetic analysis can divide them into four clades. The members of each clade have similar gene structures, conserved motifs, and domains. TaOSCA genes were predicted to be regulated by cis-acting elements such as STRE, MBS, DRE1, ABRE, etc. Quantitative PCR results showed that they have different expression patterns in different tissues. The expression profiles of 15 selected TaOSCAs were examined after PEG (polyethylene glycol), NaCl, and ABA (abscisic acid) treatment. All 15 TaOSCA members responded to PEG treatment, while TaOSCA12/-39 responded simultaneously to PEG and ABA. This study informs research into the biological function and evolution of TaOSCA and lays the foundation for the breeding and genetic improvement of wheat.

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Genome-wide identification and expression analysis of ADP-ribosylation factors associated with biotic and abiotic stress in wheat (Triticum aestivum L.)

PeerJ ◽

10.7717/peerj.10963 ◽

2021 ◽

Vol 9 ◽

pp. e10963 ◽

Cited By ~ 1

Author(s):

Yaqian Li ◽

Jinghan Song ◽

Guang Zhu ◽

Zehao Hou ◽

Lin Wang ◽

...

Keyword(s):

Triticum Aestivum ◽

Abiotic Stress ◽

Intracellular Transport ◽

Expression Patterns ◽

Functional Characterization ◽

Triticum Aestivum L ◽

Pcr Analysis ◽

Biotic And Abiotic Stress ◽

Specific Expression ◽

Wheat Varieties

The ARF gene family plays important roles in intracellular transport in eukaryotes and is involved in conferring tolerance to biotic and abiotic stresses in plants. To explore the role of these genes in the development of wheat (Triticum aestivum L.), 74 wheat ARF genes (TaARFs; including 18 alternate transcripts) were identified and clustered into seven sub-groups. Phylogenetic analysis revealed that TaARFA1 sub-group genes were strongly conserved. Numerous cis-elements functionally associated with the stress response and hormones were identified in the TaARFA1 sub-group, implying that these TaARFs are induced in response to abiotic and biotic stresses in wheat. According to available transcriptome data and qRT-PCR analysis, the TaARFA1 genes displayed tissue-specific expression patterns and were regulated by biotic stress (powdery mildew and stripe rust) and abiotic stress (cold, heat, ABA, drought and NaCl). Protein interaction network analysis further indicated that TaARFA1 proteins may interact with protein phosphatase 2C (PP2C), which is a key protein in the ABA signaling pathway. This comprehensive analysis will be useful for further functional characterization of TaARF genes and the development of high-quality wheat varieties.

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