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Comparative Transcriptome Analysis of CCCH Family in Roles of Flower Opening and Abiotic Stress in Osmanthus fragrans. Int J Mol Sci 2022; 23:ijms232315363. [PMID: 36499688 PMCID: PMC9735588 DOI: 10.3390/ijms232315363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
CCCH is a zinc finger family with a typical CCCH-type motif which performs a variety of roles in plant growth and development and responses to environmental stressors. However, the information about this family has not been reported for Osmanthus fragrans. In this study, a total of 66 CCCH predicted genes were identified from the O. fragrans genome, the majority of which had multiple CCCH motifs. The 66 OfCCCHs were found to be unevenly distributed on 21 chromosomes and were clustered into nine groups based on their phylogenetic analysis. In each group, the gene structure and domain makeup were comparatively conserved. The expression profiles of the OfCCCH genes were examined in various tissues, the flower-opening processes, and under various abiotic stresses using transcriptome sequencing and qRT-PCR (quantitative real-time PCR). The results demonstrated the widespread expression of OfCCCHs in various tissues, the differential expression of 22 OfCCCHs during flower-opening stages, and the identification of 4, 5, and 13 OfCCCHs after ABA, salt, and drought stress treatment, respectively. Furthermore, characterization of the representative OfCCCHs (OfCCCH8, 23, 27, and 36) revealed that they were all localized in the nucleus and that the majority of them had transcriptional activation in the yeast system. Our research offers the first thorough examination of the OfCCCH family and lays the groundwork for future investigations regarding the functions of CCCH genes in O. fragrans.
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Pi B, Pan J, Xiao M, Hu X, Zhang L, Chen M, Liu B, Ruan Y, Huang Y. Systematic analysis of CCCH zinc finger family in Brassica napus showed that BnRR-TZFs are involved in stress resistance. BMC PLANT BIOLOGY 2021; 21:555. [PMID: 34814855 PMCID: PMC8609832 DOI: 10.1186/s12870-021-03340-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/10/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND CCCH zinc finger family is one of the largest transcription factor families related to multiple biotic and abiotic stresses. Brassica napus L., an allotetraploid oilseed crop formed by natural hybridization between two diploid progenitors, Brassica rapa and Brassica oleracea. A systematic identification of rapeseed CCCH family genes is missing and their functional characterization is still in infancy. RESULTS In this study, 155 CCCH genes, 81 from its parent B. rapa and 74 from B. oleracea, were identified and divided into 15 subfamilies in B. napus. Organization and syntenic analysis explained the distribution and collinearity relationship of CCCH genes, the selection pressure and evolution of duplication gene pairs in B. napus genome. 44 diploid duplication gene pairs and 4 triple duplication gene groups were found in B. napus of CCCH family and the segmental duplication is attributed to most CCCH gene duplication events in B. napus. Nine types of CCCH motifs exist in B. napus CCCH family members, and motif C-X7/8-C-X5-C-X3-H is the most common and a new conserved CCH motif (C-X5-C-X3-H) has been identified. In addition, abundant stress-related cis-elements exist in promoters of 27 subfamily IX (RR-TZF) genes and their expression profiles indicated that RR-TZF genes could be involved in responses to hormone and abiotic stress. CONCLUSIONS The results provided a foundation to understand the basic characterization and genes evolution of CCCH gene family in B. napus, and provided potential targets for genetic engineering in Brassicaceae crops in pursuit of stress-tolerant traits.
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Affiliation(s)
- Boyi Pi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Jiao Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Mu Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Xinchang Hu
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Lei Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Min Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Boyu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Ying Ruan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Yong Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China.
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Han G, Qiao Z, Li Y, Wang C, Wang B. The Roles of CCCH Zinc-Finger Proteins in Plant Abiotic Stress Tolerance. Int J Mol Sci 2021; 22:ijms22158327. [PMID: 34361093 PMCID: PMC8347928 DOI: 10.3390/ijms22158327] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 01/07/2023] Open
Abstract
Zinc-finger proteins, a superfamily of proteins with a typical structural domain that coordinates a zinc ion and binds nucleic acids, participate in the regulation of growth, development, and stress adaptation in plants. Most zinc fingers are C2H2-type or CCCC-type, named after the configuration of cysteine (C) and histidine (H); the less-common CCCH zinc-finger proteins are important in the regulation of plant stress responses. In this review, we introduce the domain structures, classification, and subcellular localization of CCCH zinc-finger proteins in plants and discuss their functions in transcriptional and post-transcriptional regulation via interactions with DNA, RNA, and other proteins. We describe the functions of CCCH zinc-finger proteins in plant development and tolerance to abiotic stresses such as salt, drought, flooding, cold temperatures and oxidative stress. Finally, we summarize the signal transduction pathways and regulatory networks of CCCH zinc-finger proteins in their responses to abiotic stress. CCCH zinc-finger proteins regulate the adaptation of plants to abiotic stress in various ways, but the specific molecular mechanisms need to be further explored, along with other mechanisms such as cytoplasm-to-nucleus shuttling and post-transcriptional regulation. Unraveling the molecular mechanisms by which CCCH zinc-finger proteins improve stress tolerance will facilitate the breeding and genetic engineering of crops with improved traits.
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Affiliation(s)
- Guoliang Han
- Correspondence: (G.H.); (B.W.); Tel./Fax: +86-531-8618-0197 (B.W.)
| | | | | | | | - Baoshan Wang
- Correspondence: (G.H.); (B.W.); Tel./Fax: +86-531-8618-0197 (B.W.)
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Medina CA, Hawkins C, Liu XP, Peel M, Yu LX. Genome-Wide Association and Prediction of Traits Related to Salt Tolerance in Autotetraploid Alfalfa ( Medicago sativa L.). Int J Mol Sci 2020; 21:ijms21093361. [PMID: 32397526 PMCID: PMC7247575 DOI: 10.3390/ijms21093361%20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 05/28/2023] Open
Abstract
Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.
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Affiliation(s)
- Cesar Augusto Medina
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
| | - Charles Hawkins
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
- Current address: Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Xiang-Ping Liu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
- Current address: College of Animal Science & Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163316, Heilongjiang, China
| | - Michael Peel
- United States Department of Agriculture-Agricultural Research Service, Forage and Range Research Lab, Logan, UT 84322, USA;
| | - Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
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Medina CA, Hawkins C, Liu XP, Peel M, Yu LX. Genome-Wide Association and Prediction of Traits Related to Salt Tolerance in Autotetraploid Alfalfa ( Medicago sativa L.). Int J Mol Sci 2020; 21:E3361. [PMID: 32397526 PMCID: PMC7247575 DOI: 10.3390/ijms21093361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.
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Affiliation(s)
- Cesar Augusto Medina
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
| | - Charles Hawkins
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
- Current address: Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Xiang-Ping Liu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
- Current address: College of Animal Science & Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163316, Heilongjiang, China
| | - Michael Peel
- United States Department of Agriculture-Agricultural Research Service, Forage and Range Research Lab, Logan, UT 84322, USA;
| | - Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA; (C.A.M.); (C.H.); (X.-P.L.)
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Pi B, He X, Ruan Y, Jang JC, Huang Y. Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa. BMC PLANT BIOLOGY 2018; 18:373. [PMID: 30587139 PMCID: PMC6307296 DOI: 10.1186/s12870-018-1608-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/17/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Ubiquitous CCCH nucleic acid-binding motif is found in a wide-variety of organisms. CCCH genes are involved in plant developmental processes and biotic and abiotic stress responses. Brassica rapa is a vital economic crop and classical model plant of polyploidy evolution, but the functions of CCCH genes in B. rapa are unclear. RESULTS In this study, 103 CCCH genes in B. rapa were identified. A comparative analysis of the chromosomal position, gene structure, domain organization and duplication event between B. rapa and Arabidopsis thaliana were performed. Results showed that CCCH genes could be divided into 18 subfamilies, and segmental duplication might mainly contribute to this family expansion. C-X7/8-C-X5-C3-H was the most commonly found motif, but some novel CCCH motifs were also found, along with some loses of typical CCCH motifs widespread in other plant species. The multifarious gene structures and domain organizations implicated functional diversity of CCCH genes in B. rapa. Evidence also suggested functional redundancy in at least one subfamily due to high conservation between members. Finally, the expression profiles of subfamily-IX genes indicated that they are likely involved in various stress responses. CONCLUSION This study provides the first genome-wide characterization of the CCCH genes in B. rapa. The results suggest that B. rapa CCCH genes are likely functionally divergent, but mostly involved in plant development and stress response. These results are expected to facilitate future functional characterization of this potential RNA-binding protein family in Brassica crops.
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Affiliation(s)
- Boyi Pi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Xinghui He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Ying Ruan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Jyan-Chyun Jang
- Department of Horticulture and Crop Science, Molecular Genetics, and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - Yong Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
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Gupta B, Sengupta A, Gupta K. Commentary: Conservation of AtTZF1, AtTZF2, and AtTZF3 homolog gene regulation by salt stress in evolutionarily distant plant species. FRONTIERS IN PLANT SCIENCE 2016; 7:254. [PMID: 26941776 PMCID: PMC4765391 DOI: 10.3389/fpls.2016.00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 02/15/2016] [Indexed: 06/05/2023]
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Zang D, Li H, Xu H, Zhang W, Zhang Y, Shi X, Wang Y. An Arabidopsis Zinc Finger Protein Increases Abiotic Stress Tolerance by Regulating Sodium and Potassium Homeostasis, Reactive Oxygen Species Scavenging and Osmotic Potential. FRONTIERS IN PLANT SCIENCE 2016; 7:1272. [PMID: 27605931 PMCID: PMC4995212 DOI: 10.3389/fpls.2016.01272] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/10/2016] [Indexed: 05/18/2023]
Abstract
Plant zinc finger proteins (ZFPs) comprise a large protein family and they are mainly involved in abiotic stress tolerance. Although Arabidopsis RING/FYVE/PHD ZFP At5g62460 (AtRZFP) is found to bind to zinc, whether it is involved in abiotic stress tolerance is still unknown. In the present study, we characterized the roles of AtRZFP in response to abiotic stresses. The expression of AtRZFP was induced significantly by salt and osmotic stress. AtRZFP positively mediates tolerance to salt and osmotic stress. Additionally, compared with wild-type Arabidopsis plants, plants overexpressing AtRZFP showed reduced reactive oxygen species (ROSs) accumulation, enhanced superoxide dismutase and peroxidase activity, increased soluble sugars and proline contents, reduced K(+) loss, decreased Na(+) accumulation, stomatal aperture and the water loss rate. Conversely, AtRZFP knockout plants displayed the opposite physiological changes when exposed to salt or osmotic stress conditions. These data suggested that AtRZFP enhances salt and osmotic tolerance through a series of physiological processes, including enhanced ROSs scavenging, maintaining Na(+) and K(+) homeostasis, controlling the stomatal aperture to reduce the water loss rate, and accumulating soluble sugars and proline to adjust the osmotic potential.
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Affiliation(s)
- Dandan Zang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, HarbinChina
| | - Hongyan Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, HarbinChina
| | - Hongyun Xu
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, HarbinChina
| | - Wenhui Zhang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, HarbinChina
| | - Yiming Zhang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, HarbinChina
| | - Xinxin Shi
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, HarbinChina
| | - Yucheng Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, HarbinChina
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, XinjiangChina
- *Correspondence: Yucheng Wang,
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