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Wang D, Qiu Z, Xu T, Yao S, Chen M, Li Q, Agassin RH, Ji K. Transcriptomic Identification of Potential C2H2 Zinc Finger Protein Transcription Factors in Pinus massoniana in Response to Biotic and Abiotic Stresses. Int J Mol Sci 2024; 25:8361. [PMID: 39125930 PMCID: PMC11312842 DOI: 10.3390/ijms25158361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Biotic and abiotic stresses have already seriously restricted the growth and development of Pinus massoniana, thereby influencing the quality and yield of its wood and turpentine. Recent studies have shown that C2H2 zinc finger protein transcription factors play an important role in biotic and abiotic stress response. However, the members and expression patterns of C2H2 TFs in response to stresses in P. massoniana have not been performed. In this paper, 57 C2H2 zinc finger proteins of P. massoniana were identified and divided into five subgroups according to a phylogenetic analysis. In addition, six Q-type PmC2H2-ZFPs containing the plant-specific motif 'QALGGH' were selected for further study under different stresses. The findings demonstrated that PmC2H2-ZFPs exhibit responsiveness towards various abiotic stresses, including drought, NaCl, ABA, PEG, H2O2, etc., as well as biotic stress caused by the pine wood nematode. In addition, PmC2H2-4 and PmC2H2-20 were nuclear localization proteins, and PmC2H2-20 was a transcriptional activator. PmC2H2-20 was selected as a potential transcriptional regulator in response to various stresses in P. massoniana. These findings laid a foundation for further study on the role of PmC2H2-ZFPs in stress tolerance.
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Affiliation(s)
- Dengbao Wang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zimo Qiu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Tao Xu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Sheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Meijing Chen
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qianzi Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Romaric Hippolyte Agassin
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Liu H, Liu Y, Liu F, Zeng L, Xu Y, Jin Q, Wang Y. Genome-wide identification of the Q-type C2H2 zinc finger protein gene family and expression analysis under abiotic stress in lotus (Nelumbo nucifera G.). BMC Genomics 2024; 25:648. [PMID: 38943098 PMCID: PMC11214253 DOI: 10.1186/s12864-024-10546-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Lotus (Nelumbo nucifera G.) is an important aquatic plant with high ornamental, economic, cultural and ecological values, but abiotic stresses seriously affect its growth and distribution. Q-type C2H2 zinc finger proteins (ZFPs) play an important role in plant growth development and environmental stress responses. Although the Q-type C2H2 gene family has been identified in some plants, limited reports has been carried out it in lotus. RESULTS In this study, we identified 45 Q-type NnZFP members in lotus. Based on the phylogenetic tree, these Q-type NnZFP gene family members were divided into 4 groups, including C1-1i, C1-2i, C1-3i and C1-4i. Promoter cis-acting elements analysis indicated that most Q-type NnZFP gene family members in lotus were associated with response to abiotic stresses. Through collinearity analyses, no tandem duplication gene pairs and 14 segmental duplication gene pairs were identified, which showed that duplication events might play a key role in the expansion of the Q-type NnZFP gene family. The synteny results suggested that 54 and 28 Q-type NnZFP genes were orthologous to Arabidopsis and rice, respectively. The expression patterns of these Q-type NnZFP genes revealed that 30 Q-type NnZFP genes were expressed in at least one lotus tissue. Nn5g30550 showed relatively higher expression levels in all tested tissues. 12 genes were randomly selected with at least one gene from each phylogenetic clade, and the expression of these selected genes were confirmed by qRT-PCR (quantitative real-time polymerase chain reaction). The results indicated that Q-type NnZFP genes were extensively involved in cadmium, drought, salt and cold stresses responses. Among them, 11 genes responded to at least three different stress treatments, especially Nn2g12894, which induced by all four treatments. CONCLUSIONS These results could increase our understanding of the characterization of the Q-type NnZFP gene family and provide relevant information for further functional analysis of Q-type NnZFP genes in plant development, and abiotic stress tolerance in lotus.
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Affiliation(s)
- Huan Liu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, Jiangsu Province, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, People's Republic of China
| | - Yidan Liu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, Jiangsu Province, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, People's Republic of China
| | - Fangyu Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lihong Zeng
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, Jiangsu Province, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, People's Republic of China
| | - Yingchun Xu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, Jiangsu Province, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, People's Republic of China
| | - Qijiang Jin
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, Jiangsu Province, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, People's Republic of China
| | - Yanjie Wang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, Jiangsu Province, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, People's Republic of China.
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Luo Y, Li Y, Yin X, Deng W, Liao J, Pan Y, Jiang B, Yang H, Ding K, Jia Y. Transcriptomics analyses reveal the key genes involved in stamen petaloid formation in Alcea rosea L. BMC PLANT BIOLOGY 2024; 24:551. [PMID: 38877392 PMCID: PMC11177533 DOI: 10.1186/s12870-024-05263-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
Abstract
Alcea rosea L. is a traditional flower with a long cultivation history. It is extensively cultivated in China and is widely planted in green belt parks or used as cut flowers and potted ornamental because of its rich colors and flower shapes. Double-petal A. rosea flowers have a higher aesthetic value compared to single-petal flowers, a phenomenon determined by stamen petaloid. However, the underlying molecular mechanism of this phenomenon is still very unclear. In this study, an RNA-based comparative transcriptomic analysis was performed between the normal petal and stamen petaloid petal of A. rosea. A total of 3,212 differential expressed genes (DEGs), including 2,620 up-regulated DEGs and 592 down-regulated DEGs, were identified from 206,188 unigenes. Numerous DEGs associated with stamen petaloid were identified through GO and KEGG enrichment analysis. Notably, there were 63 DEGs involved in the plant hormone synthesis and signal transduction, including auxin, cytokinin, gibberellin, abscisic acid, ethylene, brassinosteroid, jasmonic acid, and salicylic acid signaling pathway and 56 key transcription factors (TFs), such as MADS-box, bHLH, GRAS, and HSF. The identification of these DEGs provides an important clue for studying the regulation pathway and mechanism of stamen petaloid formation in A. rosea and provides valuable information for molecular plant breeding.
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Affiliation(s)
- Yuanzhi Luo
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yifeng Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiancai Yin
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wanqing Deng
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jianwei Liao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanzhi Pan
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Beibei Jiang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongchen Yang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Keying Ding
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yin Jia
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China.
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Liu K, Hou Q, Yu R, Deng H, Shen L, Wang Q, Wen X. Genome-wide analysis of C2H2 zinc finger family and their response to abiotic stresses in apple. Gene 2024; 904:148164. [PMID: 38224923 DOI: 10.1016/j.gene.2024.148164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/26/2023] [Accepted: 01/11/2024] [Indexed: 01/17/2024]
Abstract
C2H2-type zinc finger proteins are one of the most widely studied families in plants and play important roles in abiotic stress responses. In the present study, the physicochemical properties, chromosomal locations, evolutionary relationships, and gene structures of 54 C2H2 zinc finger protein (ZFP) family members were analyzed in apple. The MdC2H2-ZFP genes were phylogenetically clustered into seven subfamilies distributed in different densities on 16 chromosomes. The RNA-seq data from various tissues revealed that MdC2H2-ZFPs differentially expressed among root, stem, leaf, flower, and fruits. Quantitative analysis of its expression characteristics showed that the MdC2H2-ZFP genes were rapidly induced as exposure to abiotic stresses such as drought, salt and low temperature etc. Under drought stress, the expression of eight members was significantly up-regulated, and the highest was obtained from MdC2H2-17; as exposure to salt stress, nine MdC2H2-ZFPs was obviously up-regulated, with the highest expression of MdC2H2-13; and under low temperature stress, the expression of seven members was highly up-regulated, and MdC2H2-13 also demonstrated the highest expression which is same as the case under salt stress. Therefore, some members of MdC2H2-ZFP gene family considerably involve in the multiple abiotic stress responses, which may better understand the function of this family and facilitate the breeding of apple for stress tolerance.
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Affiliation(s)
- Ke Liu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Qiandong Hou
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Runrun Yu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Hong Deng
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Luonan Shen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Institute for Forest Resources & Environment of Guizhou/ College of Forestry, Guizhou University, Guiyang 550025, China
| | - Qian Wang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China.
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China.
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Duan SF, Zhao Y, Yu JC, Xiang GS, Xiao L, Cui R, Hu QQ, Baldwin TC, Lu YC, Liang YL. Genome-wide identification and expression analysis of the C2H2-zinc finger transcription factor gene family and screening of candidate genes involved in floral development in Coptis teeta Wall. (Ranunculaceae). Front Genet 2024; 15:1349673. [PMID: 38317660 PMCID: PMC10839097 DOI: 10.3389/fgene.2024.1349673] [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: 12/05/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Background: C2H2-zinc finger transcription factors comprise one of the largest and most diverse gene superfamilies and are involved in the transcriptional regulation of flowering. Although a large number of C2H2 zinc-finger proteins (C2H2-ZFPs) have been well characterized in a number of model plant species, little is known about their expression and function in Coptis teeta. C. teeta displays two floral phenotypes (herkogamy phenotypes). It has been proposed that the C2H2-zinc finger transcription factor family may play a crucial role in the formation of floral development and herkogamy observed in C. teeta. As such, we performed a genome-wide analysis of the C2H2-ZFP gene family in C. teeta. Results: The complexity and diversity of C. teeta C2H2 zinc finger proteins were established by evaluation of their physicochemical properties, phylogenetic relationships, exon-intron structure, and conserved motifs. Chromosome localization showed that 95 members of the C2H2 zinc-finger genes were unevenly distributed across the nine chromosomes of C. teeta, and that these genes were replicated in tandem and segmentally and had undergone purifying selection. Analysis of cis-acting regulatory elements revealed a possible involvement of C2H2 zinc-finger proteins in the regulation of phytohormones. Transcriptome data was then used to compare the expression levels of these genes during the growth and development of the two floral phenotypes (F-type and M-type). These data demonstrate that in groups A and B, the expression levels of 23 genes were higher in F-type flowers, while 15 genes showed higher expressions in M-type flowers. qRT-PCR analysis further revealed that the relative expression was highly consistent with the transcriptome data. Conclusion: These data provide a solid basis for further in-depth studies of the C2H2 zinc finger transcription factor gene family in this species and provide preliminary information on which to base further research into the role of the C2H2 ZFPs gene family in floral development in C. teeta.
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Affiliation(s)
- Shao-Feng Duan
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Gemplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yan Zhao
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Gemplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ji-Chen Yu
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Gemplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Gui-Sheng Xiang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Gemplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Lin Xiao
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Gemplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Rui Cui
- Yunnan Land and Resources Vocational College, Kunming, Yunnan, China
| | - Qian-Qian Hu
- Zhongshan Zhongzhi Pharmaceutical Group Co., Ltd., Zhongshan, Guangdong, China
| | - Timothy Charles Baldwin
- Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, United Kingdom
| | - Ying-Chun Lu
- Yunnan Agricultural University College of Education and Vocational Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yan-Li Liang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Gemplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
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Li M, Dong X, Long G, Zhang Z, Han C, Wang Y. Genome-Wide Analysis of Q-Type C2H2 ZFP Genes in Response to Biotic and Abiotic Stresses in Sugar Beet. BIOLOGY 2023; 12:1309. [PMID: 37887019 PMCID: PMC10604892 DOI: 10.3390/biology12101309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023]
Abstract
A plant's Q-type C2H2-type ZFP plays key roles in plant growth and development and responses to biotic and abiotic stresses. Sugar beet (Beta vulgaris L.) is an important crop for sugar production. Salt stress and viral infection significantly reduce the root yield and sugar content of sugar beet. However, there is a lack of comprehensive genome-wide analyses of Q-type C2H2 ZFPs and their expression patterns in sugar beet under stress. In this study, 35 sugar beet Q-type C2H2 ZFPs (BvZFPs) containing at least one conserved "QALGGH" motif were identified via bioinformatics techniques using TBtools software. According to their evolutionary relationship, the BvZFPs were classified into five subclasses. Within each subclass, the physicochemical properties and motif compositions showed strong similarities. A Ka/Ks analysis indicated that the BvZFPs were conserved during evolution. Promoter cis-element analysis revealed that most BvZFPs are associated with elements related to phytohormone, biotic or abiotic stress, and plant development. The expression data showed that the BvZFPs in sugar beet are predominantly expressed in the root. In addition, BvZFPs are involved in the response to abiotic and biotic stresses, including salt stress and viral infection. Overall, these results will extend our understanding of the Q-type C2H2 gene family and provide valuable information for the biological breeding of sugar beet against abiotic and biotic stresses in the future.
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Affiliation(s)
| | | | | | | | | | - Ying Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (M.L.); (X.D.); (G.L.); (Z.Z.); (C.H.)
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Shao L, Li L, Huang X, Fu Y, Yang D, Li C, Yang J. Identification of C2H2 zinc finger genes through genome-wide association study and functional analyses of LkZFPs in response to stresses in Larix kaempferi. BMC PLANT BIOLOGY 2023; 23:298. [PMID: 37268918 DOI: 10.1186/s12870-023-04298-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/19/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND C2H2 zinc finger proteins (C2H2-ZFPs), one of the largest transcription factors, play a variety of roles in plant development and growth as well as stress response. While, the evolutionary history and expression profile of the C2H2-ZFP genes in Larix kaempferi (LkZFPs) have not been reported so far. RESULTS In this study, the whole genome of the LkZFPs was identified and characterized, including physicochemical properties, phylogenetic relationships, conservative motifs, the promoter cis-elements and Gene Ontology (GO) annotation. We identified 47 LkZFPs and divided them into four subfamilies based on phylogenetic analysis and conserved motifs. Subcellular localization prediction showed that most of the LkZFPs were located in the nucleus. Promoter cis-element analysis suggested that the LkZFPs may be involved in the regulation of stress responses. Moreover, Real-time quantitative PCR (RT-qPCR) results showed that Q-type LkZFP genes were involved in the response to abiotic stress, such as salt, drought and hormone stresses. Subcellular localization results showed that LkZFP7 and LkZFP37 were located in the nucleus, LkZFP32 was located in both cytoplasm and nucleus. CONCLUSION The identification and functional analysis of LkZFPs suggested that some LkZFP genes might play important roles in coping with both biological and abiotic stresses. These results could further increase understanding of the function of the LkZFPs, and provide some research direction and theoretical support.
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Affiliation(s)
- Liying Shao
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Lu Li
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Xun Huang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yanrui Fu
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Da Yang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Chenghao Li
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Jingli Yang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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Puentes-Romero AC, González SA, González-Villanueva E, Figueroa CR, Ruiz-Lara S. AtZAT4, a C 2H 2-Type Zinc Finger Transcription Factor from Arabidopsis thaliana, Is Involved in Pollen and Seed Development. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11151974. [PMID: 35956451 PMCID: PMC9370812 DOI: 10.3390/plants11151974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/16/2022] [Accepted: 07/27/2022] [Indexed: 06/01/2023]
Abstract
Pollen plays an essential role in plant fertility by delivering the male gametes to the embryo sac before double fertilization. In several plant species, including Arabidopsis, C2H2-type zinc-finger transcription factors (TFs) have been involved in different stages of pollen development and maturation. ZINC FINGER of Arabidopsis thaliana 4 (AtZAT4) is homologous to such TFs and subcellular localization analysis has revealed that AtZAT4 is located in the nucleus. Moreover, analysis of AtZAT4 expression revealed strong levels of it in flowers and siliques, suggesting a role of the encoded protein in the regulation of genes that are associated with reproductive development. We characterized a T-DNA insertional heterozygous mutant Atzat4 (+/−). The relative gene expression analysis of Atzat4 (+/−) showed significant transcript reductions in flowers and siliques. Furthermore, the Atzat4 (+/−) phenotypic characterization revealed defects in the male germline, showing a reduction in pollen tube germination and elongation. Atzat4 (+/−) presented reduced fertility, characterized by a smaller silique size compared to the wild type (WT), and a lower number of seeds per silique. Additionally, seeds displayed lower viability and germination. Altogether, our data suggest a role for AtZAT4 in fertilization and seed viability, through the regulation of gene expression associated with reproductive development.
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Affiliation(s)
- A. Carolina Puentes-Romero
- Laboratorio de Genómica Funcional, Institute of Biological Sciences, Universidad de Talca, Talca 3460000, Chile; (A.C.P.-R.); (S.A.G.); (E.G.-V.)
- Millenium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8340755, Chile;
| | - Sebastián A. González
- Laboratorio de Genómica Funcional, Institute of Biological Sciences, Universidad de Talca, Talca 3460000, Chile; (A.C.P.-R.); (S.A.G.); (E.G.-V.)
| | - Enrique González-Villanueva
- Laboratorio de Genómica Funcional, Institute of Biological Sciences, Universidad de Talca, Talca 3460000, Chile; (A.C.P.-R.); (S.A.G.); (E.G.-V.)
| | - Carlos R. Figueroa
- Millenium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8340755, Chile;
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Universidad de Talca, Talca 3460000, Chile
| | - Simón Ruiz-Lara
- Laboratorio de Genómica Funcional, Institute of Biological Sciences, Universidad de Talca, Talca 3460000, Chile; (A.C.P.-R.); (S.A.G.); (E.G.-V.)
- Millenium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8340755, Chile;
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Shyamli PS, Pradhan S, Panda M, Parida A. De novo Whole-Genome Assembly of Moringa oleifera Helps Identify Genes Regulating Drought Stress Tolerance. FRONTIERS IN PLANT SCIENCE 2021; 12:766999. [PMID: 34970282 PMCID: PMC8712769 DOI: 10.3389/fpls.2021.766999] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
Abiotic stresses, especially drought stress, are responsible for heavy losses in productivity, which in turn poses an imminent threat for future food security. Understanding plants' response to abiotic stress at the molecular level is crucially important for mitigating the impacts of climate change. Moringa oleifera is an important multipurpose plant with medicinal and nutritional properties and with an ability to grow in low water conditions, which makes the species an ideal candidate to study the regulatory mechanisms that modulate drought tolerance and its possible use in agroforestry system. In the present communication, we report whole-genome sequencing (WGS) of this species and assemble about 90% of the genome of M. oleifera var. Bhagya into 915 contigs with a N50 value of 4.7 Mb and predicted 32,062 putative protein-coding genes. After annotating the genome, we have chosen to study the heat shock transcription factor (HSF) family of genes to analyze their role in drought tolerance in M. oleifera. We predicted a total of 21 HSFs in the M. oleifera genome and carried out phylogenetic analyses, motif identification, analysis of gene duplication events, and differential expression of the HSF-coding genes in M. oleifera. Our analysis reveals that members of the HSF family have an important role in the plant's response to abiotic stress and are viable candidates for further characterization.
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Affiliation(s)
- P Sushree Shyamli
- Institute of Life Sciences, An Autonomous Institute Under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, India
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Seema Pradhan
- Institute of Life Sciences, An Autonomous Institute Under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, India
| | - Mitrabinda Panda
- Institute of Life Sciences, An Autonomous Institute Under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, India
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Ajay Parida
- Institute of Life Sciences, An Autonomous Institute Under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, India
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Genetic Interactions of Awnness Genes in Barley. Genes (Basel) 2021; 12:genes12040606. [PMID: 33924025 PMCID: PMC8073869 DOI: 10.3390/genes12040606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/08/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
Awns are extending structures from lemmas in grasses and are very active in photosynthesis, contributing directly to the filling of the developing grain. Barley (Hordeum vulgare L.) awns are highly diverse in shape and length and are known to be controlled by multiple awn-related genes. The genetic effects of these genes on awn diversity and development in barley are multiplexed and include complementary effect, cumulative effect, duplicate effect, recessive epistasis, dominant epistasis, and inhibiting effect, each giving a unique modified Mendelian ratio of segregation. The complexity of gene interactions contributes to the awn diversity in barley. Excessive gene interactions create a challenging task for genetic mapping and specific strategies have to be developed for mapping genes with specific interactive effects. Awn gene interactions can occur at different levels of gene expression, from the transcription factor-mediated gene transcription to the regulation of enzymes and metabolic pathways. A better understanding of gene interactions will greatly facilitate deciphering the genetic mechanisms underlying barley awn diversity and development.
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