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Wang Q, Wang Y, Zhang F, Han C, Wang Y, Ren M, Qi K, Xie Z, Zhang S, Tao S, Shiratake K. Genome-wide characterisation of HD-Zip transcription factors and functional analysis of PbHB24 during stone cell formation in Chinese white pear (Pyrus bretschneideri). BMC PLANT BIOLOGY 2024; 24:444. [PMID: 38778247 PMCID: PMC11112822 DOI: 10.1186/s12870-024-05138-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND The homodomain-leucine zipper (HD-Zip) is a conserved transcription factor family unique to plants that regulate multiple developmental processes including lignificaion. Stone cell content is a key determinant negatively affecting pear fruit quality, which causes a grainy texture of fruit flesh, because of the lignified cell walls. RESULTS In this study, a comprehensive bioinformatics analysis of HD-Zip genes in Chinese white pear (Pyrus bretschneideri) (PbHBs) was performed. Genome-wide identification of the PbHB gene family revealed 67 genes encoding PbHB proteins, which could be divided into four subgroups (I, II, III, and IV). For some members, similar intron/exon structural patterns support close evolutionary relationships within the same subgroup. The functions of each subgroup of the PbHB family were predicted through comparative analysis with the HB genes in Arabidopsis and other plants. Cis-element analysis indicated that PbHB genes might be involved in plant hormone signalling and external environmental responses, such as light, stress, and temperature. Furthermore, RNA-sequencing data and quantitative real-time PCR (RT-qPCR) verification revealed the regulatory roles of PbHB genes in pear stone cell formation. Further, co-expression network analysis revealed that the eight PbHB genes could be classified into different clusters of co-expression with lignin-related genes. Besides, the biological function of PbHB24 in promoting stone cell formation has been demonstrated by overexpression in fruitlets. CONCLUSIONS This study provided the comprehensive analysis of PbHBs and highlighted the importance of PbHB24 during stone cell development in pear fruits.
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Affiliation(s)
- Qi Wang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Horticultural Science, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Yueyang Wang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fanhang Zhang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chengyang Han
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanling Wang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mei Ren
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaijie Qi
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihua Xie
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoling Zhang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shutian Tao
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Katsuhiro Shiratake
- Laboratory of Horticultural Science, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.
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Lin H, Jiang X, Qian C, Zhang Y, Meng X, Liu N, Li L, Wang J, Ju Y. Genome-Wide Identification, Characterization, and Expression Analysis of the HD-Zip Gene Family in Lagerstroemia for Regulating Plant Height. Genes (Basel) 2024; 15:428. [PMID: 38674363 PMCID: PMC11049174 DOI: 10.3390/genes15040428] [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: 03/03/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
The Homeodomain leucine zipper (HD-Zip) family of transcription factors is crucial in helping plants adapt to environmental changes and promoting their growth and development. Despite research on the HD-Zip family in various plants, studies in Lagerstroemia (crape myrtle) have not been reported. This study aimed to address this gap by comprehensively analyzing the HD-Zip gene family in crape myrtle. This study identified 52 HD-Zip genes in the genome of Lagerstroemia indica, designated as LinHDZ1-LinHDZ52. These genes were distributed across 22 chromosomes and grouped into 4 clusters (HD-Zip I-IV) based on their phylogenetic relationships. Most gene structures and motifs within each cluster were conserved. Analysis of protein properties, gene structure, conserved motifs, and cis-acting regulatory elements revealed diverse roles of LinHDZs in various biological contexts. Examining the expression patterns of these 52 genes in 6 tissues (shoot apical meristem, tender shoot, and mature shoot) of non-dwarf and dwarf crape myrtles revealed that 2 LinHDZs (LinHDZ24 and LinHDZ14) and 2 LinHDZs (LinHDZ9 and LinHDZ35) were respectively upregulated in tender shoot of non-dwarf crape myrtles and tender and mature shoots of dwarf crape myrtles, which suggested the important roles of these genes in regulate the shoot development of Lagerstroemia. In addition, the expression levels of 2 LinHDZs (LinHDZ23 and LinHDZ34) were significantly upregulated in the shoot apical meristem of non-dwarf crape myrtle. These genes were identified as key candidates for regulating Lagerstroemia plant height. This study enhanced the understanding of the functions of HD-Zip family members in the growth and development processes of woody plants and provided a theoretical basis for further studies on the molecular mechanisms underlying Lagerstroemia plant height.
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Affiliation(s)
- Hang Lin
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Xinqiang Jiang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Cheng Qian
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Yue Zhang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Xin Meng
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Nairui Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Lulu Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
| | - Jingcai Wang
- East China Academy of Inventory and Planning of NFGA, Hangzhou 310019, China
| | - Yiqian Ju
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (H.L.); (X.J.); (C.Q.); (Y.Z.); (X.M.); (N.L.); (L.L.)
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Zhang B, Wang Z, Dai X, Gao J, Zhao J, Ma R, Chen Y, Sun Y, Ma H, Li S, Zhou C, Wang JP, Li W. A COMPASS histone H3K4 trimethyltransferase pentamer transactivates drought tolerance and growth/biomass production in Populus trichocarpa. THE NEW PHYTOLOGIST 2024; 241:1950-1972. [PMID: 38095236 DOI: 10.1111/nph.19481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Histone H3 lysine-4 trimethylation (H3K4me3) activating drought-responsive genes in plants for drought adaptation has long been established, but the underlying regulatory mechanisms are unknown. Here, using yeast two-hybrid, bimolecular fluorescence complementation, biochemical analyses, transient and CRISPR-mediated transgenesis in Populus trichocarpa, we unveiled in this adaptation a regulatory interplay between chromatin regulation and gene transactivation mediated by an epigenetic determinant, a PtrSDG2-1-PtrCOMPASS (complex proteins associated with Set1)-like H3K4me3 complex, PtrSDG2-1-PtrWDR5a-1-PtrRbBP5-1-PtrAsh2-2 (PtrSWRA). Under drought conditions, a transcription factor PtrAREB1-2 interacts with PtrSWRA, forming a PtrSWRA-PtrAREB1-2 pentamer, to recruit PtrSWRA to specific promoter elements of drought-tolerant genes, such as PtrHox2, PtrHox46, and PtrHox52, for depositing H3K4me3 to promote and maintain activated state of such genes for tolerance. CRISPR-edited defects in the pentamer impaired drought tolerance and elevated expression of PtrHox2, PtrHox46, or PtrHox52 improved the tolerance as well as growth in P. trichocarpa. Our findings revealed the identity of the underlying H3K4 trimethyltransferase and its interactive arrangement with the COMPASS for catalysis specificity and efficiency. Furthermore, our study uncovered how the H3K4 trimethyltransferase-COMPASS complex is recruited to the effector genes for elevating H3K4me3 marks for improved drought tolerance and growth/biomass production in plants.
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Affiliation(s)
- Baofeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhuwen Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinfeng Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Rong Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yanjie Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
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Wang Y, Wang H, Yu C, Yan X, Chu J, Jiang B, Zhu J. Comprehensive bioinformation analysis of homeodomain-leucine zipper gene family and expression pattern of HD-Zip I under abiotic stress in Salix suchowensis. BMC Genomics 2024; 25:182. [PMID: 38360569 PMCID: PMC10870566 DOI: 10.1186/s12864-024-10067-x] [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: 09/11/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Homeodomain-leucine zipper (HD-Zip) transcription factors are plant-specific and play important roles in plant defense against environmental stresses. Identification and functional studies have been carried out in model plants such as rice, Arabidopsis thaliana, and poplar, but comprehensive analysis on the HD-Zip family of Salix suchowensis have not been reported. RESULTS A total of 55 HD-Zip genes were identified in the willow genome, unevenly distributed on 18 chromosomes except for chromosome 19. And segmental duplication events containing SsHD-Zip were detected on all chromosomes except chromosomes 13 and 19. The SsHD-Zip were classified into 4 subfamilies subfamilies (I-IV) according to the evolutionary analysis, and members of each subfamily shared similar domain structure and gene structure. The combination of GO annotation and promoter analysis showed that SsHD-Zip genes responded to multiple abiotic stresses. Furthermore, the results of qPCR analysis showed that the SsHD-Zip I gene exhibited different degrees of expression under salt stress, PEG treatment and heat treatment. Moreover, there was a synergistic effect between SsHD-Zip I genes under stress conditions based on coregulatory networks analysis. CONCLUSIONS In this study, HD-Zip transcription factors were systematically identified and analyzed at the whole genome level. These results preliminarily clarified the structural characteristics and related functions of willow HD-Zip family members, and it was found that SsHox34, SsHox36 and SsHox51 genes were significantly involved in the response to various stresses. Together, these findings laid the foundation for further research on the resistance functions of willow HD-Zip genes.
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Affiliation(s)
- Yujiao Wang
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Hongjuan Wang
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Chun Yu
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Xiaoming Yan
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Jiasong Chu
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Benli Jiang
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China.
| | - Jiabao Zhu
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China.
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5
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Żyła N, Babula-Skowrońska D. Evolutionary Consequences of Functional and Regulatory Divergence of HD-Zip I Transcription Factors as a Source of Diversity in Protein Interaction Networks in Plants. J Mol Evol 2023; 91:581-597. [PMID: 37351602 PMCID: PMC10598176 DOI: 10.1007/s00239-023-10121-4] [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: 10/06/2022] [Accepted: 05/27/2023] [Indexed: 06/24/2023]
Abstract
The HD superfamily has been studied in detail for several decades. The plant-specific HD-Zip I subfamily attracts the most attention because of its involvement in plant development and stress responses. In this review, we provide a comprehensive insight into the evolutionary events responsible for the functional redundancy and diversification of the HD-Zip I genes in regulating various biological processes. We summarized the evolutionary history of the HD-Zip family, highlighting the important role of WGDs in its expansion and divergence of retained duplicates in the genome. To determine the relationship between the evolutionary origin and functional conservation of HD-Zip I in different species, we performed a phylogenetic analysis, compared their expression profiles in different tissues and under stress and traced the role of orthologs and paralogs in regulating developmental processes. We found that HD-Zip I from different species have similar gene structures with a highly conserved HD and Zip, bind to the same DNA sequences and are involved in similar biological processes. However, they exhibit a functional diversity, which is manifested in altered expression patterns. Some of them are involved in the regulation of species-specific leaf morphology and phenotypes. Here, we discuss the role of changes in functional domains involved in DNA binding and protein interaction of HD-Zip I and in cis-regulated regions of its target genes in promoting adaptive innovations through the formation of de novo regulatory systems. Understanding the role of the HD-Zip I subfamily in organism-environment interactions remains a challenge for evolutionary developmental biology (evo-devo).
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Affiliation(s)
- Natalia Żyła
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznan, Poland
| | - Danuta Babula-Skowrońska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznan, Poland.
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Bai Y, Zhou Y, Lei Q, Wang Y, Pu G, Liu Z, Chen X, Liu Q. Analysis of the HD-Zip I transcription factor family in Salvia miltiorrhiza and functional research of SmHD-Zip12 in tanshinone synthesis. PeerJ 2023; 11:e15510. [PMID: 37397009 PMCID: PMC10312201 DOI: 10.7717/peerj.15510] [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: 11/22/2022] [Accepted: 05/15/2023] [Indexed: 07/04/2023] Open
Abstract
Background The homeodomain-leucine zipper I (HD-Zip I) transcription factor is a plant-specific protein that plays an essential role in the abiotic stress response of plants. Research on the HD-Zip I family in Salvia miltiorrhiza is still lacking. Methods and Results In this study, a total of 25 SmHD-Zip I proteins were identified. Their characterizations, phylogenetic relationships, conserved motifs, gene structures, and cis-elements were analyzed comprehensively using bioinformatics methods. Expression profiling revealed that SmHD-Zip I genes exhibited distinctive tissue-specific patterns and divergent responses to ABA, PEG, and NaCl stresses. SmHD-Zip12 responded the most strongly to ABA, PEG, and NaCl, so it was used for transgenic experiments. The overexpression of SmHD-Zip12 significantly increased the content of cryptotanshinone, dihydrotanshinone I, tanshinone I, and tanshinone IIA by 2.89-fold, 1.85-fold, 2.14-fold, and 8.91-fold compared to the wild type, respectively. Moreover, in the tanshinone biosynthetic pathways, the overexpression of SmHD-Zip12 up-regulated the expression levels of SmAACT, SmDXS, SmIDS, SmGGPPS, SmCPS1, SmCPS2, SmCYP76AH1, SmCYP76AH3, and SmCYP76AK1 compared with the wild type. Conclusions This study provides information the possible functions of the HD-Zip I family and lays a theoretical foundation for clarifying the functional mechanism of the SmHD-Zip12 gene in regulating the synthesis of tanshinone in S. miltiorrhiza.
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Affiliation(s)
- Yanhong Bai
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Ying Zhou
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Qiaoqi Lei
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yu Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Gaobin Pu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Zhenhua Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Xue Chen
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Qian Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- LiShizhen College of Traditional Chinese Medicine, Huanggang Normal University, Huanggang, Hubei, China
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Baek W, Bae Y, Lim CW, Lee SC. Pepper homeobox abscisic acid signalling-related transcription factor 1, CaHAT1, plays a positive role in drought response. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37128851 DOI: 10.1111/pce.14597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Abscisic acid (ABA) signalling triggers drought resistance mediated by SNF1-related kinase 2s (SnRK2s), which transmits stress signals through the phosphorylation of several downstream factors. However, these kinases and their downstream targets remain elusive in pepper plants. This study aimed to isolate interacting partners of CaSnRK2.6, a homologue of Arabidopsis SnRK2.6/OST1. Among the candidate proteins, we identified a homeodomain-leucine zipper (HD-Zip) class II protein and named it CaHAT1 (Capsicum annuum homeobox ABA signalling related- transcription factor 1). CaHAT1-silenced pepper and -overexpression (OE) transgenic Arabidopsis plants were generated to investigate the in vivo function of CaHAT1 in drought response. Following the application of drought stress, CaHAT1-silenced pepper plants exhibited drought-sensitive phenotypes with reduced ABA-mediated stomatal closure and lower expression of stress-responsive genes compared with control plants. In contrast, CaHAT1-OE transgenic Arabidopsis plants showed the opposite phenotypes, including increased drought resistance and ABA sensitivity. CaHAT1, particularly its N-terminal consensus sequences, was directly phosphorylated by CaSnRK2.6. Furthermore, CaSnRK2.6 kinase activity and CaSnRK2.6-mediated CaHAT1 phosphorylation levels were enhanced by treatment with ABA and drought stress. Taken together, our results indicated that CaHAT1, which is the target protein of CaSnRK2.6, is a positive regulator of drought stress response. This study advances our understanding of CaHAT1-CaSnRK2.6 mediated defence mechanisms in pepper plants against drought stress.
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Affiliation(s)
- Woonhee Baek
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
| | - Yeongil Bae
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
| | - Chae Woo Lim
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
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Genome-Wide Identification of Homeodomain Leucine Zipper (HD-ZIP) Transcription Factor, Expression Analysis, and Protein Interaction of HD-ZIP IV in Oil Palm Somatic Embryogenesis. Int J Mol Sci 2023; 24:ijms24055000. [PMID: 36902431 PMCID: PMC10002534 DOI: 10.3390/ijms24055000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Understanding the molecular mechanisms underlying somatic embryogenesis is essential for resolving the problems related to the long duration of the process and a low rate of somatic embryo induction in oil palm tissue culture. In this study, we conducted genome-wide identification of the oil palm homeodomain leucine zipper (EgHD-ZIP) family, which is one of the plant-specific transcription factors reported to be involved in embryogenesis. EgHD-ZIP proteins can be divided into four subfamilies, which have similarities in gene structure and protein-conserved motifs within a group. In silico expression analysis showed that the expression of EgHD-ZIP gene members in the EgHD-ZIP I and II families, as well as most members in the EgHD-ZIP IV family, were up-regulated during the zygotic and somatic embryo developmental stages. In contrast, the expression of EgHD-ZIP gene members in the EgHD-ZIP III family was down-regulated during zygotic embryo development. Moreover, the expression of EgHD-ZIP IV genes was validated in the oil palm callus and at the somatic embryo stages (globular, torpedo, and cotyledon). The results revealed that EgHD-ZIP IV genes were up-regulated at the late stages of somatic embryogenesis (torpedo and cotyledon). While BABY BOOM (BBM) gene was up-regulated at the early stage of somatic embryogenesis (globular). In addition, the Yeast-two hybrid assay revealed the direct binding between all members of the oil palm HD-ZIP IV subfamily (EgROC2, EgROC3, EgROC5, EgROC8, and EgBBM). Our findings suggested that the EgHD-ZIP IV subfamily and EgBBM work together to regulate somatic embryogenesis in oil palms. This process is important because it is widely used in plant biotechnology to produce large quantities of genetically identical plants, which can be used for oil palm tissue culture improvement.
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9
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Wang Z, Wu X, Zhang B, Xiao Y, Guo J, Liu J, Chen Q, Peng F. Genome-wide identification, bioinformatics and expression analysis of HD-Zip gene family in peach. BMC PLANT BIOLOGY 2023; 23:122. [PMID: 36864374 PMCID: PMC9979464 DOI: 10.1186/s12870-023-04061-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND HD-Zips (Homeodomain-Leucine Zippers) are a class of plant-specific transcription factors that play multiple roles in plant growth and development. Although some functions of HD-Zip transcription factor have been reported in several plants, it has not been comprehensively studied in peach, especially during adventitious root formation of peach cuttings. RESULTS In this study, 23 HD-Zip genes distributed on 6 chromosomes were identified from the peach (Prunus persica) genome, and named PpHDZ01-23 according to their positions on the chromosomes. These 23 PpHDZ transcription factors all contained a homeomorphism box domain and a leucine zipper domain, were divided into 4 subfamilies(I-IV) according to the evolutionary analysis, and their promoters contained many different cis-acting elements. Spatio-temporal expression pattern showed that these genes were expressed in many tissues with different levels, and they had distinct expression pattern during adventitious root formation and development. CONCLUSION Our results showed the roles of PpHDZs on root formation, which is helpful to better understand the classification and function of peach HD-Zip genes.
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Affiliation(s)
- Zhe Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Xuelian Wu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Binbin Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Yuansong Xiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Jian Guo
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Jin Liu
- Agricultural Technical Service Center of Yiyuan County, 256100, Zibo, China
| | - Qiuju Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China.
- Agricultural Technical Service Center of Yiyuan County, 256100, Zibo, China.
| | - Futian Peng
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China.
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Zhang X, Chen Z, Wang C, Zhou X, Tang N, Zhang W, Xu F, Yang Z, Luo C, Liao Y, Ye J. Genome-wide identification of HD-ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum. THE PLANT GENOME 2023; 16:e20295. [PMID: 36606521 DOI: 10.1002/tpg2.20295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/11/2022] [Indexed: 05/10/2023]
Abstract
Zanthoxylum armatum is an important cash crop for medicinal and food purposes in Asia. However, its stems and leaves are covered with a large number of prickles, which cause many problems in the production process. The homeodomain leucine zipper (HD-ZIP) gene family is a class of transcription factors unique to plants that play an important role in biological processes such as morphogenesis, signal transduction, and secondary metabolite synthesis. However, little is known about HD-ZIP gene information that may be involved in prickle development of Z. armatum. Here, we identified 76 ZaHDZ genes from the Z. armatum genome and classified them into four subfamilies (I-IV) based on phylogenetic analysis, a classification further supported by gene structure and conserved motif analysis. Seventy-six ZaHDZ genes were unevenly distributed on chromosomes. Evolutionary analysis revealed that the expansion of ZaHDZ genes mainly were due to whole-genome duplication (WGD) or segmental duplication, and they experienced strong purifying selection pressure in the process of evolution. A total of 47 cis-elements were identified in the promoter region of ZaHDZ genes. Quantitative real-time polymerase chain reaction analysis was performed on subfamily IV ZaHDZ gene expression levels in five tissues and under four hormone treatments. Finally, ZaHDZ16 was predicted to be the candidate gene most likely to be involved in prickle development of Z. armatum. These results contribute to a better understanding of the characteristics of HD-ZIP gene family and lay a foundation for further study on the function of genes related to prickle development of Z. armatum.
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Affiliation(s)
- Xiaoxi Zhang
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Zexiong Chen
- Research Institute for Special Plants, Chongqing Univ. of Arts and Sciences, Chongqing, 402160, China
| | - Caini Wang
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Xian Zhou
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Ning Tang
- Research Institute for Special Plants, Chongqing Univ. of Arts and Sciences, Chongqing, 402160, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
- Spice Crops Research Institute, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Zhiwu Yang
- Sichuan Academy of Forestry, Chengdu, Sichuan, 610081, China
| | - Chengrong Luo
- Sichuan Academy of Forestry, Chengdu, Sichuan, 610081, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
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11
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Zhu Y, Peng S, Zhao L, Feng W, Dong C. Genome-wide identification and characterization of the HD-Zip gene family and expression analysis in response to stress in Rehmannia glutinosa Libosch. PLANT SIGNALING & BEHAVIOR 2022; 17:2096787. [PMID: 35899840 PMCID: PMC9336491 DOI: 10.1080/15592324.2022.2096787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The HD-Zip family of transcription factors is unique to the plant kingdom, and play roles in modulation of plant growth and response to environmental stresses. R. glutinosa is an important Chinese medicinal material. Its yield and quality are susceptible to various stresses. The HD-Zip transcription factors is unique to the plant, and roles in modulation of plant growth and response to environmental stresses. However, there is no relevant research on the HD-ZIP of R. glutinosa. In this study, 92 HD-Zip transcription factors were identified in R. glutinosa, and denominated as RgHDZ1-RgHDZ92. Members of RgHDZ were classified into four groups (HD-ZipI-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, and each group contains 38, 18, 17, and 19 members, respectively. Expression analyses of RgHDZ genes based on transcriptome data showed that the expression of these genes could be induced by the endophytic fungus of R. glutinosa. Additionally, we showed that RgHDZ genes were differentially expressed in response to drought, waterlogging, temperature, and salinity treatments. This study provides important information for different expression patterns of stress-responsive HD-Zip and may contribute to the better understanding of the different responses of plants to biotic and abiotic stresses, and provide a molecular basis for the cultivation of resistant varieties of R. glutinosa.
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Affiliation(s)
- Yunhao Zhu
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R.China, Zhengzhou, Henan, China
| | - Shuping Peng
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Le Zhao
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R.China, Zhengzhou, Henan, China
| | - Weisheng Feng
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Chengming Dong
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R.China, Zhengzhou, Henan, China
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12
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Wang Y, Fan J, Wu X, Guan L, Li C, Gu T, Li Y, Ding J. Genome-Wide Characterization and Expression Profiling of HD-Zip Genes in ABA-Mediated Processes in Fragaria vesca. PLANTS (BASEL, SWITZERLAND) 2022; 11:3367. [PMID: 36501406 PMCID: PMC9737017 DOI: 10.3390/plants11233367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Members of homeodomain-leucine zipper (HD-Zip) transcription factors can play their roles by modulating abscisic acid (ABA) signaling in Arabidopsis. So far, our knowledge of the functions of HD-Zips in woodland strawberries (Fragaria vesca), a model plant for studying ABA-mediated fruit ripening, is limited. Here, we identified a total of 31 HD-Zip genes (FveHDZ1-31) in F. vesca, and classified them into four subfamilies (I to IV). Promoter analyses show that the ABA-responsive element, ABRE, is prevalent in the promoters of subfamily I and II FveHDZs. RT-qPCR results demonstrate that 10 of the 14 investigated FveHDZs were consistently >1.5-fold up-regulated or down-regulated in expression in response to exogenous ABA, dehydration, and ABA-induced senescence in leaves. Five of the six consistently up-regulated genes are from subfamily I and II. Thereinto, FveHDZ4, and 20 also exhibited significantly enhanced expression along with increased ABA content during fruit ripening. In yeast one-hybrid assays, FveHDZ4 proteins could bind the promoter of an ABA signaling gene FvePP2C6. Collectively, our results strongly support that the FveHDZs, particularly those from subfamilies I and II, are involved in the ABA-mediated processes in F. vesca, providing a basis for further functional characterization of the HD-Zips in strawberry and other plants.
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Junmiao Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Xinjie Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Ling Guan
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Chun Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Tingting Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Jing Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
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Transcriptome-Wide Identification of CCCH-Type Zinc Finger Proteins Family in Pinus massoniana and RR-TZF Proteins in Stress Response. Genes (Basel) 2022; 13:genes13091639. [PMID: 36140811 PMCID: PMC9498899 DOI: 10.3390/genes13091639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
CCCH-type zinc finger proteins play an important role in multiple biotic and abiotic stresses. More and more reports about CCCH functions in plant development and stress responses have appeared over the past few years, focusing especially on tandem CCCH zinc finger proteins (TZFs). However, this has not been reported in Pinaceae. In this study, we identified 46 CCCH proteins, including 6 plant TZF members in Pinus massoniana, and performed bioinformatic analysis. According to RT-PCR analysis, we revealed the expression patterns of five RR-TZF genes under different abiotic stresses and hormone treatments. Meanwhile, tissue-specific expression analysis suggested that all genes were mainly expressed in needles. Additionally, RR-TZF genes showed transcriptional activation activity in yeast. The results in this study will be beneficial in improving the stress resistance of P. massoniana and facilitating further studies on the biological and molecular functions of CCCH zinc finger proteins.
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Expression Profiling and MicroRNA Regulatory Networks of Homeobox Family Genes in Sugarcane Saccharum spontaneum L. Int J Mol Sci 2022; 23:ijms23158724. [PMID: 35955858 PMCID: PMC9369071 DOI: 10.3390/ijms23158724] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 01/13/2023] Open
Abstract
Homeobox (HB) genes play important roles in plant growth and development processes, particularly in the formation of lateral organs. Thus, they could influence leaf morphogenesis and biomass formation in plants. However, little is known about HBs in sugarcane, a crucial sugar crop, due to its complex genetic background. Here, 302 allelic sequences for 104 HBs were identified and divided into 13 subfamilies in sugarcane Saccharum spontaneum. Comparative genomics revealed that whole-genome duplication (WGD)/segmental duplication significantly promoted the expansion of the HB family in S. spontaneum, with SsHB26, SsHB63, SsHB64, SsHB65, SsHB67, SsHB95, and SsHB96 being retained from the evolutionary event before the divergence of dicots and monocots. Based on the analysis of transcriptome and degradome data, we speculated that SsHB15 and SsHB97 might play important roles in regulating sugarcane leaf morphogenesis, with miR166 and SsAGO10 being involved in the regulation of SsHB15 expression. Moreover, subcellular localization and transcriptional activity detection assays demonstrated that these two genes, SsHB15 and SsHB97, were functional transcription factors. This study demonstrated the evolutionary relationship and potential functions of SsHB genes and will enable the further investigation of the functional characterization and the regulatory mechanisms of SsHBs.
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15
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Tu Z, Yu L, Wen S, Zhai X, Li W, Li H. Identification and analysis of HD-Zip genes involved in the leaf development of Liriodendron chinense using multidimensional analysis. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:874-886. [PMID: 35491433 DOI: 10.1111/plb.13431] [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: 01/30/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Homeodomain-leucine zipper (HD-Zip) proteins are plant-specific transcription factors that play important roles in different biological processes, especially leaf development. However, no studies to date have identified the HD-Zip genes in Liriodendron chinense nor characterized their functions. We identified the HD-Zip genes in L. chinense by analysing the phylogeny, chromosome location, structure, conserved motif, cis-regulatory elements, synteny, post-transcriptional regulation and expression patterns of these genes during leaf development. A total of 36 LcHD-Zip genes were identified and divided into four subfamilies (HD-Zip I to IV). Synteny analysis revealed that segmental duplication was the main force driving the expansion of LcHD-Zip genes. These 36 LcHD-Zip genes exhibited 11 different expression patterns. Pattern 1, 2, 3, 4, 6, 7, 8 and 9 genes may play important roles in leaf development, such as leaf initiation, leaf polarity establishment, leaf shape development, phytohormone-mediated leaf growth and leaf epidermal structure formation. Four HD-Zip III genes were targeted by microRNAs (miRNAs), and the miR165/166a-HD-Zip regulatory module formed regulated leaf initiation and leaf polarity establishment. Overall, LcHD-Zip genes play key roles in leaf development of L. chinense. This work provides a foundation for the functional verification of HD-Zip genes identified in this study.
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Affiliation(s)
- Z Tu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - L Yu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - S Wen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - X Zhai
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - W Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - H Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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16
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Yang Q, Xiang W, Li Z, Nian Y, Fu X, Zhou G, Li L, Zhang J, Huang G, Han X, Xu L, Bai X, Liu L, Wu D. Genome-Wide Characterization and Expression Analysis of HD-ZIP Gene Family in Dendrobium officinale. Front Genet 2022; 13:797014. [PMID: 35368655 PMCID: PMC8971680 DOI: 10.3389/fgene.2022.797014] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022] Open
Abstract
The homeodomain-leucine zipper (HD-ZIP) gene family, as one of the plant-specific transcription factor families, plays an important role in regulating plant growth and development as well as in response to diverse stresses. Although it has been extensively characterized in many plants, the HD-ZIP family is not well-studied in Dendrobium officinale, a valuable ornamental and traditional Chinese medicinal herb. In this study, 37 HD-ZIP genes were identified in Dendrobium officinale (Dohdzs) through the in silico genome search method, and they were classified into four subfamilies based on phylogenetic analysis. Exon–intron structure and conserved protein domain analyses further supported the prediction with the same group sharing similar gene and protein structures. Furthermore, their expression patterns were investigated in nine various tissues and under cold stress based on RNA-seq datasets to obtain the tissue-specific and cold-responsive candidates. Finally, Dohdz5, Dohdz9, and Dohdz12 were selected to validate their expression through qRT-PCR analysis, and they displayed significantly differential expression under sudden chilling stress, suggesting they might be the key candidates underlying cold stress response. These findings will contribute to better understanding of the regulatory roles of the HD-ZIP family playing in cold stress and also will provide the vital targets for further functional studies of HD-ZIP genes in D. officinale.
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Affiliation(s)
- Qianyu Yang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Weibo Xiang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing, China
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing, China
| | - Zhihui Li
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Yuxin Nian
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xiaoyun Fu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Guangzhu Zhou
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Linbao Li
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing, China
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing, China
| | - Jun Zhang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing, China
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing, China
| | - Guiyun Huang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing, China
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing, China
| | - Xiao Han
- Natural Resources Affairs Service Center of Dalian, Dalian, China
| | - Lu Xu
- College of Horticulture, Hunan Agricultural University, Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha, China
| | - Xiao Bai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Lei Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Lei Liu, ; Di Wu,
| | - Di Wu
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing, China
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing, China
- *Correspondence: Lei Liu, ; Di Wu,
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17
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Mehmood M, Khan MJ, Khan MJ, Akhtar N, Mughal F, Shah STA, Hyder MZ, Farrakh S, Sadiq I. Systematic analysis of HD-ZIP transcription factors in sesame genome and gene expression profiling of SiHD-ZIP class I entailing drought stress responses at early seedling stage. Mol Biol Rep 2022; 49:2059-2071. [PMID: 34993726 DOI: 10.1007/s11033-021-07024-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Sesame is an ancient oilseed crop, known for its high oil content and quality. Its sensitivity to drought at early seedling stage is one of the limiting factors affecting its world-wide growth and productivity. Among plant specific transcription factors, the association of HD-ZIPs with sesame drought responses at early seedling stage is not well-established yet and is very important to develop our molecular understanding on sesame drought tolerance. METHODS AND RESULTS In this study, total 61 sesame HD-ZIP proteins were identified, based on their protein sequence homology with Arabidopsis and protein domain(s) architecture prediction, followed by their phylogenetic, conserved domain(s) motifs and gene structure analyses to classify them into four classes (HD-ZIP Class I-IV). HD-ZIP Class I was also subdivided into four subgroups: α (SiHZ25, SiHZ43, SiHZ9 and SiHZ16), β1 (SiHZ10, SiHZ30, SiHZ32 and SiHZ26), β2 (SiHZ42 and SiHZ45) and γ (SiHZ17, SiHZ7 and SiHZ35) by a comparative phylogenetic analysis of sesame with Arabidopsis and maize. Afterwards, twenty-one days old sesame seedlings were exposed to drought stress by withholding water for 7 days (when soil moisture content reduced to ~16%) and gene expression of HD-ZIP Class I (13 members) was performed in well- watered (control) and drought stressed seedlings. The gene expression analysis showed that the expressions of SiHZ7 (6.8 fold) and SiHZ35 (2.6 fold) from γ subgroup were significantly high in drought seedlings. CONCLUSIONS This study is useful in demonstrating the role of SiHD-ZIP Class I in sesame drought responses at early seedling stage and to develop its novel drought tolerant varieties.
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Affiliation(s)
- Maryam Mehmood
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Muhammad Jadoon Khan
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Nadeem Akhtar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Fizza Mughal
- Illinois Informatics Institute, University of Illinois, Urbana-Champaign, USA
| | - Syed Tahir Abbas Shah
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | | | - Sumaira Farrakh
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan.
| | - Irfan Sadiq
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan.
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18
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Genome-Wide Characterization and Expression Analysis of the HD-ZIP Gene Family in Response to Salt Stress in Pepper. Int J Genomics 2021; 2021:8105124. [PMID: 33604369 PMCID: PMC7869415 DOI: 10.1155/2021/8105124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/18/2020] [Accepted: 12/10/2020] [Indexed: 11/17/2022] Open
Abstract
HD-ZIP is a unique type of transcription factor in plants, which are closely linked to the regulation of plant growth and development, the response to abiotic stress, and disease resistance. However, there is little known about the HD-ZIP gene family of pepper. In this study, 40 HD-ZIP family members were analyzed in the pepper genome. The analysis indicated that the introns number of Ca-HD-ZIP varied from 1 to 17; the number of amino acids was between 119 and 841; the theoretical isoelectric point was between 4.54 and 9.85; the molecular weight was between 14.04 and 92.56; most of them were unstable proteins. The phylogenetic tree divided CaHD-ZIP into 4 subfamilies; 40 CaHD-ZIP genes were located on different chromosomes, and all of them contained the motif 1; two pairs of CaHD-ZIP parallel genes of six paralogism genes were fragment duplications which occurred in 58.28~88.24 million years ago. There were multiple pressure-related action elements upstream of the start codon of the HD-Z-IP family. Protein interaction network proved to be coexpression phenomenon between ATML1 (CaH-DZ22, CaHDZ32) and At4g048909 (CaHDZ12, CaHDZ31), and three regions of them were highly homology. The expression level of CaHD-ZIP gene was different with tissues and developmental stages, which suggested that CaHD-ZIP may be involved in biological functions during pepper progress. In addition, Pepper HD-ZIP I and II genes played a major role in salt stress. CaHDZ03, CaHDZ 10, CaHDZ17, CaHDZ25, CaHDZ34, and CaHDZ35 were significantly induced in response to salt stress. Notably, the expression of CaHDZ07, CaHDZ17, CaHDZ26, and CaHDZ30, homologs of Arabidopsis AtHB12 and AtHB7 genes, was significantly upregulated by salt stresses. CaHDZ03 possesses two closely linked ABA action elements, and its expression level increased significantly at 4 h under salt stress. qRT-P-CR and transcription analysis showed that the expression of CaHDZ03 and CaHDZ10 was upregulated under short-term salt stress, but CaHDZ10 was downregulated with long-term salt stress, which provided a theoretical basis for research the function of Ca-HDZIP in response to abiotic stress.
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Gao Y, Liu H, Zhang K, Li F, Wu M, Xiang Y. A moso bamboo transcription factor, Phehdz1, positively regulates the drought stress response of transgenic rice. PLANT CELL REPORTS 2021; 40:187-204. [PMID: 33098450 DOI: 10.1007/s00299-020-02625-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/08/2020] [Indexed: 05/16/2023]
Abstract
78 HD-Zip family genes in Phyllostachys edulis were analyzed. Overexpression of Phehdz1 can improve the drought tolerance of transgenic rice and affect its secondary metabolism. Many studies suggested homeodomain-leucine zipper (HD-Zip) transcription factors are important regulators of plant growth and development, signal transduction, and responses to environmental stresses. In this study, 78 moso bamboo (Phyllostachys edulis) HD-Zip genes were investigated and classified into four subfamilies (HD-Zip I-IV). Additionally, Phehdz1 (HD-Zip I gene) was isolated and confirmed to be highly expressed in the roots. A quantitative real-time PCR analysis indicated Phehdz1 expression was significantly induced by drought, high salinity, and abscisic acid (ABA). A transient expression assay proved that Phehdz1 was localized in the nucleus of tobacco cells. Moreover, it could bind to the core region encoded by the H-box sequence (CAATAATTG) in yeast. In response to mannitol treatments, the Phehdz1-overexpressing transgenic rice had a higher germination rate and longer shoots than the wild-type controls. Moreover, Phehdz1-overexpressing rice plants had a higher survival rate as well as higher relative water and proline contents, but a lower malondialdehyde content, than the WT plants after a 30% polyethylene glycol 6000 treatment. Accordingly, the overexpression of Phehdz1 enhances the drought tolerance of transgenic rice. Many of the differentially expressed genes identified by a transcriptome analysis are involved in MAPK signal transduction and the biosynthesis of secondary metabolites. Thus, the overexpression of Phehdz1 enhances the drought stress tolerance of transgenic rice, while also potentially modulating the expression of metabolism-related genes.
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Affiliation(s)
- Yameng Gao
- National Engineering Laboratory of Crop Stress Resistance Breeding, College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Huanlong Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Kaimei Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Fei Li
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Yan Xiang
- National Engineering Laboratory of Crop Stress Resistance Breeding, College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
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20
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Wei M, Liu Q, Wang Z, Yang J, Li W, Chen Y, Lu H, Nie J, Liu B, Lv K, Mao X, Chen S, Sanders J, Wei H, Li C. PuHox52-mediated hierarchical multilayered gene regulatory network promotes adventitious root formation in Populus ussuriensis. THE NEW PHYTOLOGIST 2020; 228:1369-1385. [PMID: 32589766 DOI: 10.1111/nph.16778] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/15/2020] [Indexed: 05/25/2023]
Abstract
Adventitious root (AR) formation is critically important in vegetative propagation through cuttings in some plants, especially woody species. However, the underlying molecular mechanisms remain elusive. Here, we report the identification of a poplar homeobox gene, PuHox52, which was induced rapidly (within 15 min) at the basal ends of stems upon cutting and played a key regulatory role in adventitious rooting. We demonstrated that overexpression of PuHox52 significantly increased the number of ARs while suppression of PuHox52 had the opposite effect. A multilayered hierarchical gene regulatory network (ML-hGRN) mediated by PuHox52 was reverse-engineered and demonstrated to govern AR formation. PuHox52 regulated AR formation through upregulation of nine hub regulators, including a jasmonate signaling pathway gene, PuMYC2, and an auxin signaling pathway gene, PuAGL12. We also identified coherent type 4 feed-forward loops within this ML-hGRN; PuHox52 repressed PuHDA9, which encodes a histone deacetylase, and led to an increase in acetylation and presumably expression of three hub regulators, PuWRKY51, PuLBD21 and PuIAA7. Our results indicate that the ML-hGRN mediated by PuHox52 governs AR formation at the basal ends of stem cuttings from poplar trees.
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Affiliation(s)
- Ming Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Quangang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhanchao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jingli Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Wenlong Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yingxi Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Han Lu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinfu Nie
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230000, China
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510000, China
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Kaiwen Lv
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xuliang Mao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jennifer Sanders
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
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21
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Yang YY, Shan W, Kuang JF, Chen JY, Lu WJ. Four HD-ZIPs are involved in banana fruit ripening by activating the transcription of ethylene biosynthetic and cell wall-modifying genes. PLANT CELL REPORTS 2020; 39:351-362. [PMID: 31784771 DOI: 10.1007/s00299-019-02495-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/20/2019] [Indexed: 05/20/2023]
Abstract
Four MaHDZs are possibly involved in banana fruit ripening by activating the transcription of genes related to ethylene biosynthesis and cell wall degradation, such as MaACO5, MaEXP2, MaEXPA10, MaPG4 and MaPL4. The homeodomain-leucine zipper (HD-ZIP) proteins represent plant-specific transcription factors, which contribute to various plant physiological processes. However, little information is available regarding the association of HD-ZIPs with banana fruit ripening. In this study, we identified a total of 96 HD-ZIP genes in banana genome, which were divided into four different groups consisting of 35, 31, 9 and 21 members in the I, II, III and IV subfamilies, respectively. The expression patterns of MaHDZ genes during fruit ripening showed that MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 were significantly up-regulated in the ripening stage and thus suggested to be potential regulators of banana fruit ripening. Furthermore, MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 were found to localize exclusively in the nucleus and exhibit transcriptional activation capacities. Importantly, MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 stimulated the transcription of several ripening-related genes including MaACO5 related to ethylene biosynthesis, MaEXP2, MaEXPA10, MaPG4 and MaPL4 were associated with cell wall degradation, through directly binding to their promoters. Taken together, our findings expand the functions of HD-ZIP transcription factors and identify four MaHDZs likely involved in regulating banana fruit ripening by activating the expression of genes related to ethylene biosynthesis and cell wall modification, which may have potential application in banana molecular breeding.
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Affiliation(s)
- Ying-Ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest, Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest, Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest, Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest, Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest, Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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22
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Li S, Chen N, Li F, Mei F, Wang Z, Cheng X, Kang Z, Mao H. Characterization of wheat homeodomain-leucine zipper family genes and functional analysis of TaHDZ5-6A in drought tolerance in transgenic Arabidopsis. BMC PLANT BIOLOGY 2020; 20:50. [PMID: 32005165 PMCID: PMC6993422 DOI: 10.1186/s12870-020-2252-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/14/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Many studies in Arabidopsis and rice have demonstrated that HD-Zip transcription factors play important roles in plant development and responses to abiotic stresses. Although common wheat (Triticum aestivum L.) is one of the most widely cultivated and consumed food crops in the world, the function of the HD-Zip proteins in wheat is still largely unknown. RESULTS To explore the potential biological functions of HD-Zip genes in wheat, we performed a bioinformatics and gene expression analysis of the HD-Zip family. We identified 113 HD-Zip members from wheat and classified them into four subfamilies (I-IV) based on phylogenic analysis against proteins from Arabidopsis, rice, and maize. Most HD-Zip genes are represented by two to three homeoalleles in wheat, which are named as TaHDZX_ZA, TaHDZX_ZB, or TaHDZX_ZD, where X denotes the gene number and Z the wheat chromosome on which it is located. TaHDZs in the same subfamily have similar protein motifs and intron/exon structures. The expression profiles of TaHDZ genes were analysed in different tissues, at different stages of vegetative growth, during seed development, and under drought stress. We found that most TaHDZ genes, especially those in subfamilies I and II, were induced by drought stress, suggesting the potential importance of subfamily I and II TaHDZ members in the responses to abiotic stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaHDZ5-6A displayed enhanced drought tolerance, lower water loss rates, higher survival rates, and higher proline content under drought conditions. Additionally, the transcriptome analysis identified a number of differentially expressed genes between 35S::TaHDZ5-6A transgenic and wild-type plants, many of which are involved in stress response. CONCLUSIONS Our results will facilitate further functional analysis of wheat HD-Zip genes, and also indicate that TaHDZ5-6A may participate in regulating the plant response to drought stress. Our experiments show that TaHDZ5-6A holds great potential for genetic improvement of abiotic stress tolerance in crops.
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Affiliation(s)
- Shumin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Nan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhongxue Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinxiu Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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23
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Li L, Zheng T, Zhuo X, Li S, Qiu L, Wang J, Cheng T, Zhang Q. Genome-wide identification, characterization and expression analysis of the HD-Zip gene family in the stem development of the woody plant Prunus mume. PeerJ 2019; 7:e7499. [PMID: 31410318 PMCID: PMC6689393 DOI: 10.7717/peerj.7499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/16/2019] [Indexed: 02/04/2023] Open
Abstract
The homeodomain-leucine zipper (HD-Zip) gene family, a group of plant-specific transcriptional factors (TFs), participates in regulating growth, development, and environmental responses. However, the characteristics and biological functions of HD-Zip genes in Prunus mume, which blooms in late winter or early spring, have not been reported. In this study, 32 HD-Zip genes, named PmHB1-PmHB32 based on their chromosomal positions, were identified in the genome of P. mume. These genes are distributed among seven chromosomes and are phylogenetically clustered into four major groups. Gene structure and motif composition were mostly conserved in each group. The Ka/Ks ratios showed that purifying selection has played a leading role in the long-term evolution of the genes, which maintained the function of this family. MicroRNA target site prediction indicated that the genes of the HD-Zip III subfamily may be regulated by miR165/166. Expression pattern analysis showed that the 32 genes were differentially expressed across five different tissues (leaf, flower bud, stem, fruit, and root) and at different stages of stem and leaf-bud development, suggesting that 10 of the genes may play important roles in stem development. Protein-protein interaction predictions showed that the subfamily III genes may regulate vascular development and shoot apical meristem (SAM) maintenance. Promoter analysis showed that the HD-Zip III genes might be involved in responses to light, hormones, and abiotic stressors and stem development. Taken together, our results provide an overview of the HD-Zip family in P. mume and lay the foundation for the molecular breeding of woody ornamental plants.
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Affiliation(s)
- Lulu Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Xiaokang Zhuo
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Suzhen Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Like Qiu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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24
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Li Y, Xiong H, Cuo D, Wu X, Duan R. Genome-wide characterization and expression profiling of the relation of the HD-Zip gene family to abiotic stress in barley (Hordeum vulgare L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:250-258. [PMID: 31195255 DOI: 10.1016/j.plaphy.2019.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 05/16/2023]
Abstract
The homeodomain-leucine zipper (HD-Zip) gene family plays an important role in plant growth and environmental responses. At present, research on the HD-Zip gene family of barley is incomplete. In this study, 32 HD-Zip genes (HvHD-Zip 1-32) were identified from the barley genome and were subsequently divided into four subfamilies according to conserved structure and motif analysis. Whole genome replication events in barley and Arabidopsis, rice, and wheat HD-Zip gene families were analyzed, yielding 3, 14 and 25 gene pairs, respectively, but no segmental or tandem duplication events were identified in the barley HD-Zip gene family. Subsequently, quantitative real-time PCR (qRT-PCR) analysis revealed that the HvHD-Zip gene is sensitive to drought stress and that members of the HD-Zip I and HD-Zip IV subfamilies are generally more sensitive to abiotic stresses. Our results suggest a relationship between barley resistance and the potential key HvHD-Zip gene, which lay the foundation for further functional studies.
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Affiliation(s)
- Yuan Li
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China
| | - Huiyan Xiong
- College of Agriculture and Animal Husbandry, Qinghai University, Qinghai, 810016, China
| | - Duojie Cuo
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China
| | - Xiongxiong Wu
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China
| | - Ruijun Duan
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China; Qinghai Provincial Key Laboratory of Hulless Barley Genetics and Breeding, Qinghai University, Qinghai, 810016, China.
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25
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Tang Y, Wang J, Bao X, Liang M, Lou H, Zhao J, Sun M, Liang J, Jin L, Li G, Qiu Y, Liu K. Genome-wide identification and expression profile of HD-ZIP genes in physic nut and functional analysis of the JcHDZ16 gene in transgenic rice. BMC PLANT BIOLOGY 2019; 19:298. [PMID: 31286900 PMCID: PMC6615155 DOI: 10.1186/s12870-019-1920-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 07/03/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Homeodomain-leucine zipper (HD-ZIP) transcription factors play important roles in the growth, development and stress responses of plants, including (presumably) physic nut (Jatropha curcas), which has high drought and salinity tolerance. However, although physic nut's genome has been released, there is little knowledge of the functions, expression profiles and evolutionary histories of the species' HD-ZIP genes. RESULTS In this study, 32 HD-ZIP genes were identified in the physic nut genome (JcHDZs) and divided into four groups (I-IV) based on phylogenetic analysis with homologs from rice, maize and Arabidopsis. The analysis also showed that most of the JcHDZ genes were closer to members from Arabidopsis than to members from rice and maize. Of the 32 JcHDZ genes, most showed differential expression patterns among four tissues (root, stem cortex, leaf, and seed). Expression profile analysis based on RNA-seq data indicated that 15 of the JcHDZ genes respond to at least one abiotic stressor (drought and/or salinity) in leaves at least at one time point. Transient expression of a JcHDZ16-YFP fusion protein in Arabidopsis protoplasts cells showed that JcHDZ16 is localized in the nucleus. In addition, rice seedlings transgenically expressing JcHDZ16 had lower proline contents and activities of antioxidant enzymes (catalase and superoxide dismutase) together with higher relative electrolyte leakage and malondialdehyde contents under salt stress conditions (indicating higher sensitivity) than wild-type plants. The transgenic seedlings also showed increased sensitivity to exogenous ABA, and increases in the transcriptional abundance of several salt stress-responsive genes were impaired in their responses to salt stress. Further data on JcHDZ16-overexpressing plants subjected to salt stress treatment verified the putative role of JcHDZ genes in salt stress responses. CONCLUSION Our results may provide foundations for further investigation of functions of JcHDZ genes in responses to abiotic stress, and promote application of JcHDZ genes in physic nut breeding.
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Affiliation(s)
- Yuehui Tang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan China
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Zhoukou, Henan China
| | - Jian Wang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan China
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Zhoukou, Henan China
| | - Xinxin Bao
- School of Journalism and Communication, Zhoukou Normal University, Zhoukou, Henan China
| | - Mengyu Liang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan China
| | - Huimin Lou
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan China
| | - Junwei Zhao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan China
| | - Mengting Sun
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan China
| | - Jing Liang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan China
| | - Lisha Jin
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan China
| | - Guangling Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan China
| | - Yahui Qiu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan China
| | - Kun Liu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan China
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Zhoukou, Henan China
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26
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Saeidi K, Zare N, Baghizadeh A, Asghari-Zakaria R. Phaseolus vulgaris genome possesses CAMTA genes, and phavuCAMTA1 contributes to the drought tolerance. J Genet 2019. [PMID: 30945676 DOI: 10.1007/s11118-011-9244-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Calmodulin-binding transcription activators (CAMTAs) are a family of transcription factors that play an important role in plants' response to the various biotic and abiotic stresses. The common bean (Phaseolus vulgaris L.) is one of the most important crops in the world and plays a pivotal role in sustainable agriculture. To date, the composition of CAMTA genes in genomes of Phaseolus species and their role in resistance to drought stress are not known. In this study, five PhavuCAMTA genes were characterized in common bean genome through bioinformatics analysis, the morphological and biochemical response of 23 Ph.vulgaris genotypes to different levels of drought stress were evaluated and the expression patterns of PhCAMTA1 in the leaf tissues of sensitive and tolerant genotypes were analysed. Gene structure, protein domain organization and phylogenetic analyses showed that the CAMTAs of Phaseolus were structurally similar and clustered into three groups as other plant CAMTAs. Genotypes showeda differential response to drought stress. Thus, the plant height, number of nodes and flower, total chlorophyll and total protein content, and activity of antioxidant enzymes (ascorbate peroxidase and catalase) in plants significantly influenced by genotype and drought stress interaction. Moreover, the resistant and susceptible genotypes were identified according to three-dimensional plots and the expression patterns of PhavuCAMTA1 gene were studied using real-time quantitative polymerase chain reaction. The results of the present study serve as the basis for future functional studies on the Phaseolus CAMTA family.
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Affiliation(s)
- Kobra Saeidi
- Agronomy and Plant Breeding Department, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil 5619911367, Iran. ,
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27
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Li R, Ge H, Dai Y, Yuan L, Liu X, Sun Q, Wang X. Genomewide analysis of homeobox gene family in apple (Malus domestica Borkh.) and their response to abiotic stress. J Genet 2019. [DOI: 10.1007/s12041-018-1049-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Sessa G, Carabelli M, Possenti M, Morelli G, Ruberti I. Multiple Links between HD-Zip Proteins and Hormone Networks. Int J Mol Sci 2018; 19:ijms19124047. [PMID: 30558150 PMCID: PMC6320839 DOI: 10.3390/ijms19124047] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/06/2018] [Accepted: 12/12/2018] [Indexed: 01/01/2023] Open
Abstract
HD-Zip proteins are unique to plants, and contain a homeodomain closely linked to a leucine zipper motif, which are involved in dimerization and DNA binding. Based on homology in the HD-Zip domain, gene structure and the presence of additional motifs, HD-Zips are divided into four families, HD-Zip I–IV. Phylogenetic analysis of HD-Zip genes using transcriptomic and genomic datasets from a wide range of plant species indicate that the HD-Zip protein class was already present in green algae. Later, HD-Zips experienced multiple duplication events that promoted neo- and sub-functionalizations. HD-Zip proteins are known to control key developmental and environmental responses, and a growing body of evidence indicates a strict link between members of the HD-Zip II and III families and the auxin machineries. Interactions of HD-Zip proteins with other hormones such as brassinolide and cytokinin have also been described. More recent data indicate that members of different HD-Zip families are directly involved in the regulation of abscisic acid (ABA) homeostasis and signaling. Considering the fundamental role of specific HD-Zip proteins in the control of key developmental pathways and in the cross-talk between auxin and cytokinin, a relevant role of these factors in adjusting plant growth and development to changing environment is emerging.
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Affiliation(s)
- Giovanna Sessa
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
| | - Monica Carabelli
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
| | - Marco Possenti
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Via Ardeatina 546, 00178 Rome, Italy.
| | - Giorgio Morelli
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Via Ardeatina 546, 00178 Rome, Italy.
| | - Ida Ruberti
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
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Genome-Wide Investigation and Expression Profiling of HD-Zip Transcription Factors in Foxtail Millet ( Setaria italica L.). BIOMED RESEARCH INTERNATIONAL 2018; 2018:8457614. [PMID: 29862293 PMCID: PMC5976958 DOI: 10.1155/2018/8457614] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 02/15/2018] [Accepted: 03/07/2018] [Indexed: 02/06/2023]
Abstract
HD-Zip proteins represent the major transcription factors in higher plants, playing essential roles in plant development and stress responses. Foxtail millet is a crop to investigate the systems biology of millet and biofuel grasses and the HD-Zip gene family has not been studied in foxtail millet. For further investigation of the expression profile of the HD-Zip gene family in foxtail millet, a comprehensive genome-wide expression analysis was conducted in this study. We found 47 protein-encoding genes in foxtail millet using BLAST search tools; the putative proteins were classified into four subfamilies, namely, subfamilies I, II, III, and IV. Gene structure and motif analysis indicate that the genes in one subfamily were conserved. Promotor analysis showed that HD-Zip gene was involved in abiotic stress. Duplication analysis revealed that 8 (~17%) hdz genes were tandemly duplicated and 28 (58%) were segmentally duplicated; purifying duplication plays important roles in gene expansion. Microsynteny analysis revealed the maximum relationship in foxtail millet-sorghum and foxtail millet-rice. Expression profiling upon the abiotic stresses of drought and high salinity and the biotic stress of ABA revealed that some genes regulated responses to drought and salinity stresses via an ABA-dependent process, especially sihdz29 and sihdz45. Our study provides new insight into evolutionary and functional analyses of HD-Zip genes involved in environmental stress responses in foxtail millet.
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Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Wheat (Triticum aestivum L.). Genes (Basel) 2018; 9:genes9020070. [PMID: 29389910 PMCID: PMC5852566 DOI: 10.3390/genes9020070] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/23/2018] [Accepted: 01/26/2018] [Indexed: 11/16/2022] Open
Abstract
The homeodomain-leucine zipper (HD-Zip) gene family, as plant-specific transcription factors, plays an important role in plant development and growth as well as in the response to diverse stresses. Although HD-Zip genes have been extensively studied in many plants, they had not yet been studied in wheat, especially those involved in response to abiotic stresses. In this study, 46 wheat HD-Zip genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into four groups, numbered 4, 5, 17 and 20 respectively. In total, only three genes with A, B and D homoeologous copies were identified. Furthermore, the gene interaction networks found that the TaHDZ genes played a critical role in the regulatory pathway of organ development and osmotic stress. Finally, the expression profiles of the wheat HD-Zips in different tissues and under various abiotic stresses were investigated using the available RNA sequencing (RNA-Seq) data and then validated by quantitative real-time polymerase chain reaction (qRT-PCR) to obtain the tissue-specific and stress-responsive candidates. This study systematically identifies the HD-Zip gene family in wheat at the genome-wide level, providing important candidates for further functional analysis and contributing to the better understanding of the molecular basis of development and stress tolerance in wheat.
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Mou S, Liu Z, Gao F, Yang S, Su M, Shen L, Wu Y, He S. CaHDZ27, a Homeodomain-Leucine Zipper I Protein, Positively Regulates the Resistance to Ralstonia solanacearum Infection in Pepper. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:960-973. [PMID: 28840788 DOI: 10.1094/mpmi-06-17-0130-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Homeodomain-leucine zipper class I (HD-Zip I) transcription factors have been functionally characterized in plant responses to abiotic stresses, but their roles in plant immunity are poorly understood. Here, a HD-Zip I gene, CaHZ27, was isolated from pepper (Capsicum annum) and characterized for its role in pepper immunity. Quantitative real-time polymerase chain reaction showed that CaHDZ27 was transcriptionally induced by Ralstonia solanacearum inoculation and exogenous application of methyl jasmonate, salicylic acid, or ethephon. The CaHDZ27-green fluorescent protein fused protein was targeted exclusively to the nucleus. Chromatin immunoprecipitation demonstrated that CaHDZ27 bound to the 9-bp pseudopalindromic element (CAATAATTG) and triggered β-glucuronidase expression in a CAATAATTG-dependent manner. Virus-induced gene silencing of CaHDZ27 significantly attenuated the resistance of pepper plants against R. solanacearum and downregulated defense-related marker genes, including CaHIR1, CaACO1, CaPR1, CaPR4, CaPO2, and CaBPR1. By contrast, transient overexpression of CaHDZ27 triggered strong cell death mediated by the hypersensitive response and upregulated the tested immunity-associated marker genes. Ectopic CaHDZ27 expression in tobacco enhances its resistance against R. solanacearum. These results collectively suggest that CaHDZ27 functions as a positive regulator in pepper resistance against R. solanacearum. Bimolecular fluorescence complementation and coimmunoprecipitation assays indicate that CaHDZ27 monomers bind with each other, and this binding is enhanced significantly by R. solanacearum inoculation. We speculate that homodimerization of CaHZ27 might play a role in pepper response to R. solanacearum, further direct evidence is required to confirm it.
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Affiliation(s)
- Shaoliang Mou
- 1 National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
- 2 College of Life Science, Fujian Agriculture and Forestry University
| | - Zhiqin Liu
- 1 National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
- 3 College of Crop Science, Fujian Agriculture and Forestry University; and
| | - Feng Gao
- 1 National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
- 2 College of Life Science, Fujian Agriculture and Forestry University
| | - Sheng Yang
- 1 National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
- 3 College of Crop Science, Fujian Agriculture and Forestry University; and
| | - Meixia Su
- 2 College of Life Science, Fujian Agriculture and Forestry University
| | - Lei Shen
- 1 National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
- 3 College of Crop Science, Fujian Agriculture and Forestry University; and
| | - Yang Wu
- 4 College of Life Science, Jinggang Shan University, Ji'an, Jiangxi 343000, PR China
| | - Shuilin He
- 1 National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
- 3 College of Crop Science, Fujian Agriculture and Forestry University; and
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Li N, Meng H, Xing H, Liang L, Zhao X, Luo K. Genome-wide analysis of MATE transporters and molecular characterization of aluminum resistance in Populus. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5669-5683. [PMID: 29099944 PMCID: PMC5853298 DOI: 10.1093/jxb/erx370] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 09/28/2017] [Indexed: 05/21/2023]
Abstract
Ionic aluminum (Al) in acidic soils, comprising approximately 50% of arable land globally, is highly toxic to most plant species. Populus grow naturally in acidic soils and tolerate high concentrations of Al. Multidrug and toxic compound extrusion (MATE) family genes in plants are involved in responses to Al tolerance. To date, however, the functional roles of the MATE genes in Populus remain unclear. In the present study, 71 putative MATE transporters were predicted in the genome of Populus trichocarpa. The chromosome distribution, phylogenetic relationships, and expression level analysis revealed that four candidate MATE genes belonging to subgroup IIIc might contribute to high Al tolerance in poplar. Further, the expression levels of two subgroup IIIc members, PtrMATE1 and PtrMATE2, were induced by Al stress. Transient expression in onion epidermal cells showed that PtrMATE1 was localized to the plasma membrane. Overexpression of PtrMATE1 increased Al-induced secretion of citrate from the root apex of transgenic plants. Al-induced inhibition of root growths were alleviated in both PtrMATE1 overexpression lines in Populus and in Arabidopsis compared with wild-type plants. In addition, PtrMATE1 expression was induced at 12 h after exposure to Al stress whereas PtrMATE2 expression was induced at 24 h, indicating that these proteins coordinately function in response to Al stress in poplar. Taken together, these results provide important insights into the molecular mechanisms involved in Al tolerance in poplar.
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Affiliation(s)
- Nannan Li
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
- College of Resources and Environment, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Hongjun Meng
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
| | - Haitao Xing
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
| | - Lan Liang
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
| | - Xin Zhao
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
| | - Keming Luo
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
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Xu Z, Gao L, Tang M, Qu C, Huang J, Wang Q, Yang C, Liu G, Yang C. Genome-wide identification and expression profile analysis of CCH gene family in Populus. PeerJ 2017; 5:e3962. [PMID: 29085758 PMCID: PMC5661435 DOI: 10.7717/peerj.3962] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/05/2017] [Indexed: 11/20/2022] Open
Abstract
Copper plays key roles in plant physiological activities. To maintain copper cellular homeostasis, copper chaperones have important functions in binding and transporting copper to target proteins. Detailed characterization and function analysis of a copper chaperone, CCH, is presently limited to Arabidopsis. This study reports the identification of 21 genes encoding putative CCH proteins in Populus trichocarpa. Besides sharing the conserved metal-binding motif MXCXXC and forming a βαββαβ secondary structure at the N-terminal, all the PtCCHs possessed the plant-exclusive extended C-terminal. Based on their gene structure, conserved motifs, and phylogenetic analysis, the PtCCHs were divided into three subgroups. Our analysis indicated that whole-genome duplication and tandem duplication events likely contributed to expansion of the CCH gene family in Populus. Tissue-specific data from PlantGenIE revealed that PtCCH genes had broad expression patterns in different tissues. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that PnCCH genes of P. simonii × P. nigra also had different tissue-specific expression traits, as well as different inducible-expression patterns in response to copper stresses (excessive and deficiency). In summary, our study of CCH genes in the Populus genome provides a comprehensive analysis of this gene family, and lays an important foundation for further investigation of their roles in copper homeostasis of poplar.
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Affiliation(s)
- Zhiru Xu
- College of Life Science, Northeast Forestry University, HarBin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China
| | - Liying Gao
- College of Life Science, Northeast Forestry University, HarBin, China
| | - Mengquan Tang
- College of Life Science, Northeast Forestry University, HarBin, China
| | - Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China
- School of Forestry, Northeast Forestry University, HarBin, China
| | - Jiahuan Huang
- College of Life Science, Northeast Forestry University, HarBin, China
| | - Qi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China
- School of Forestry, Northeast Forestry University, HarBin, China
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China
- School of Forestry, Northeast Forestry University, HarBin, China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China
- School of Forestry, Northeast Forestry University, HarBin, China
| | - Chengjun Yang
- School of Forestry, Northeast Forestry University, HarBin, China
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Li Z, Zhang C, Guo Y, Niu W, Wang Y, Xu Y. Evolution and expression analysis reveal the potential role of the HD-Zip gene family in regulation of embryo abortion in grapes (Vitis vinifera L.). BMC Genomics 2017; 18:744. [PMID: 28934927 PMCID: PMC5609062 DOI: 10.1186/s12864-017-4110-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well as in various vegetative organs. RESULTS A genome-wide survey for HD-Zip transcription factors in Vitis was conducted based on the 12 X grape genome (V. vinifera L.). A total of 33 members were identified and classified into four subfamilies (I-IV) based on phylogeny analysis with Arabidopsis, rice and maize. VvHDZs in the same subfamily have similar protein motifs and intron/exon structures. An evaluation of duplication events suggests several HD-Zip genes arose before the divergence of the grape and Arabidopsis lineages. The 33 members of HD-Zip were differentially expressed in ovules of the stenospermic grape, Thompson Seedless and of the seeded grape, Pinot noir. Most have higher expressions during ovule abortion in Thompson Seedless. In addition, transcripts of the HD-Zip family were also detected in somatic embryogenesis of Thompson Seedless and in different vegetative organs of Thompson Seedless at varying levels. Additionally, VvHDZ28 is located in the nucleus and had transcriptional activity consistent with the typical features of the HD-Zip family. Our results provide a foundation for future grape HD-Zip gene function research. CONCLUSIONS The identification and expression profiles of the HD-Zip transcription factors in grape, reveal their diverse roles during ovule abortion and organ development. Our results lay a foundation for functional analysis of grape HDZ genes.
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Affiliation(s)
- Zhiqian Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
| | - Chen Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
| | - Yurui Guo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
| | - Weili Niu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
| | - Yuejin Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
| | - Yan Xu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
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Ding Z, Fu L, Yan Y, Tie W, Xia Z, Wang W, Peng M, Hu W, Zhang J. Genome-wide characterization and expression profiling of HD-Zip gene family related to abiotic stress in cassava. PLoS One 2017; 12:e0173043. [PMID: 28249019 PMCID: PMC5332091 DOI: 10.1371/journal.pone.0173043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/14/2017] [Indexed: 11/18/2022] Open
Abstract
Homeodomain-leucine zipper (HD-Zip) gene family plays important roles in various abiotic stresses and hormone signaling in plants. However, no information is currently available regarding this family in cassava (Manihot esculenta), an important drought-tolerant crop in tropical and sub-tropical areas. Here, 57 HD-Zip genes (MeHDZ01-57) were identified in the cassava genome, and they were classified into four subfamilies based on phylogenetic analysis, which was further supported by their gene structure and conserved motif characteristics. Of which five gene pairs were involved in segmental duplication but none for tandem duplication, suggesting that segmental duplication was the main cause for the expansion of MeHDZ gene family in cassava. Global expression profiles revealed that MeHDZ genes were constitutively expressed, or not expressed, or tissue-specific expressed in examined tissues in both cultivated and wild subspecies. Transcriptomic analysis of three genotypes showed that most of MeHDZ genes responded differently to drought and polyethylene glycol treatments. Subsequently, quantitative RT-PCR analysis revealed comprehensive responses of twelve selected MeHDZ genes to various stimuli including cold, salt, and ABA treatments. These findings will increase our understanding of HD-Zip gene family involved in abiotic stresses and signaling transduction, and will provide a solid base for further functional characterization of MeHDZ genes in cassava.
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Affiliation(s)
- Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- * E-mail: (ZD); (WH); (JZ)
| | - Lili Fu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Zhiqiang Xia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Wenquan Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- * E-mail: (ZD); (WH); (JZ)
| | - Jiaming Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- * E-mail: (ZD); (WH); (JZ)
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Chen E, Zhang X, Yang Z, Wang X, Yang Z, Zhang C, Wu Z, Kong D, Liu Z, Zhao G, Butt HI, Zhang X, Li F. Genome-wide analysis of the HD-ZIP IV transcription factor family in Gossypium arboreum and GaHDG11 involved in osmotic tolerance in transgenic Arabidopsis. Mol Genet Genomics 2017; 292:593-609. [PMID: 28251315 DOI: 10.1007/s00438-017-1293-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 01/24/2017] [Indexed: 12/29/2022]
Abstract
HD-ZIP IV proteins belong to the homeodomain-leucine zipper (HD-ZIP) transcription factor family and are involved in trichome development and drought stress in plants. Although some functions of the HD-ZIP IV group are well understood in Arabidopsis, little is known about their function in cotton. In this study, HD-ZIP genes were identified from three Gossypium species (G. arboreum, G. raimondii and G. hirsutum) and clustered into four families (HD-ZIP I, II, III and IV) to separate HD-ZIP IV from the other three families. Systematic analyses of phylogeny, gene structure, conserved domains, and expression profiles in different plant tissues and the expression patterns under osmotic stress in leaves were further conducted in G. arboreum. More importantly, ectopic overexpression of GaHDG11, a representative of the HD-ZIP IV family, confers enhanced osmotic tolerance in transgenic Arabidopsis plants, possibly due to elongated primary root length, lower water loss rates, high osmoprotectant proline levels, significant levels of antioxidants CAT, and/or SOD enzyme activity with reduced levels of MDA. Taken together, these observations may lay the foundation for future functional analysis of cotton HD-ZIP IV genes to unravel their biological roles in cotton.
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Affiliation(s)
- Eryong Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Huazhong Agricultural University, Wuhan, 430070, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaoen Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Xiaoqian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chaojun Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhixia Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Depei Kong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhao Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ge Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hamama Islam Butt
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | | | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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Wang H, Zhao S, Gao Y, Yang J. Characterization of Dof Transcription Factors and Their Responses to Osmotic Stress in Poplar (Populus trichocarpa). PLoS One 2017; 12:e0170210. [PMID: 28095469 PMCID: PMC5241002 DOI: 10.1371/journal.pone.0170210] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/02/2017] [Indexed: 11/26/2022] Open
Abstract
The DNA-binding One Zinc Finger (Dof) genes are ubiquitous in many plant species and are especial transcription regulators that participate in plant growth, development and various procedures, including biotic and abiotic stress reactions. In this study, we identified 41 PtrDof members from Populus trichocarpa genomes and classified them into four groups. The conserved motifs and gene structures of some PtrDof genes belonging to the same subgroup were almost the same. The 41 PtrDof genes were dispersed on 18 of the 19 Populus chromosomes. Many key stress- or phytohormone-related cis-elements were discovered in the PtrDof gene promoter regions. Consequently, we undertook expression profiling of the PtrDof genes in leaves and roots in response to osmotic stress and abscisic acid. A total of seven genes (PtrDof14, 16, 25, 27, 28, 37 and 39) in the Populus Dof gene family were consistently upregulated at point in all time in the leaves and roots under osmotic and abscisic acid (ABA) stress. We observed that 12 PtrDof genes could be targeted by 15 miRNAs. Moreover, we mapped the cleavage site in PtrDof30 using the 5’RLM-RACE. The results showed that PtrDofs may have a role in resistance to abiotic stress in Populus trichocarpa.
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Affiliation(s)
- Han Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shicheng Zhao
- School of Pharmacy, Harbin University of Commerce, Harbin, China
| | - Yuchi Gao
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Jingli Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China
- * E-mail:
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Yao W, Zhang X, Zhou B, Zhao K, Li R, Jiang T. Expression Pattern of ERF Gene Family under Multiple Abiotic Stresses in Populus simonii × P. nigra. FRONTIERS IN PLANT SCIENCE 2017; 8:181. [PMID: 28265277 PMCID: PMC5316532 DOI: 10.3389/fpls.2017.00181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/30/2017] [Indexed: 05/05/2023]
Abstract
Identification of gene expression patterns of key genes across multiple abiotic stresses is critical for mechanistic understanding of stress resistance in plant. In the present study, we identified differentially expressed genes (DEGs) in di-haploid Populus simonii × P. nigra under respective stresses of NaCl, KCl, CdCl2, and PEG. On the basis of RNA-Seq, we detected 247 DEGs that are shared by the four stresses in wild type poplar, and mRNA abundance of the DEGs were validated in transgenic poplar overexpressing ERF76 gene by RNA-Seq and RT-qPCR. Results from gene ontology analysis indicated that these genes are enriched in significant pathways, such as phenylpropanoid biosynthesis, phenylalanine metabolism, starch and sucrose metabolism, and plant hormone signal transduction. Ethylene response factor (ERF) gene family plays significant role in plant abiotic stress responses. We also investigated expression pattern of ERF gene family under the four stresses. The ERFs and DEGs share similar expression pattern across the four stresses. The transgenic poplar is superior to WT in morphologic, physiological and biochemical traits, which demonstrated the ERF76 gene plays a significant role in stress resistance. These studies will give a rise in understanding the stress response mechanisms in poplar.
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Affiliation(s)
- Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
- Northeast Institute of Geography and Agroecology, Chinese Academy of SciencesHarbin, China
| | - Xuemei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
| | - Kai Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
| | - Renhua Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
- *Correspondence: Tingbo Jiang,
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Yu Y, Wang N, Hu R, Xiang F. Genome-wide identification of soybean WRKY transcription factors in response to salt stress. SPRINGERPLUS 2016; 5:920. [PMID: 27386364 PMCID: PMC4927560 DOI: 10.1186/s40064-016-2647-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/22/2016] [Indexed: 01/23/2023]
Abstract
Members of the large family of WRKY transcription factors are involved in a wide range of developmental and physiological processes, most particularly in the plant response to biotic and abiotic stress. Here, an analysis of the soybean genome sequence allowed the identification of the full complement of 188 soybean WRKY genes. Phylogenetic analysis revealed that soybean WRKY genes were classified into three major groups (I, II, III), with the second group further categorized into five subgroups (IIa-IIe). The soybean WRKYs from each group shared similar gene structures and motif compositions. The location of the GmWRKYs was dispersed over all 20 soybean chromosomes. The whole genome duplication appeared to have contributed significantly to the expansion of the family. Expression analysis by RNA-seq indicated that in soybean root, 66 of the genes responded rapidly and transiently to the imposition of salt stress, all but one being up-regulated. While in aerial part, 49 GmWRKYs responded, all but two being down-regulated. RT-qPCR analysis showed that in the whole soybean plant, 66 GmWRKYs exhibited distinct expression patterns in response to salt stress, of which 12 showed no significant change, 35 were decreased, while 19 were induced. The data present here provide critical clues for further functional studies of WRKY gene in soybean salt tolerance.
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Affiliation(s)
- Yanchong Yu
- />The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100 Shandong China
- />Shandong Key Laboratory of Plant Biotechnology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109 Shandong China
| | - Nan Wang
- />The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100 Shandong China
| | - Ruibo Hu
- />Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road No. 189, Qingdao, 266101 Shandong China
| | - Fengning Xiang
- />The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100 Shandong China
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Song A, Li P, Xin J, Chen S, Zhao K, Wu D, Fan Q, Gao T, Chen F, Guan Z. Transcriptome-Wide Survey and Expression Profile Analysis of Putative Chrysanthemum HD-Zip I and II Genes. Genes (Basel) 2016; 7:genes7050019. [PMID: 27196930 PMCID: PMC4880839 DOI: 10.3390/genes7050019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/05/2016] [Accepted: 05/03/2016] [Indexed: 12/30/2022] Open
Abstract
The homeodomain-leucine zipper (HD-Zip) transcription factor family is a key transcription factor family and unique to the plant kingdom. It consists of a homeodomain and a leucine zipper that serve in combination as a dimerization motif. The family can be classified into four subfamilies, and these subfamilies participate in the development of hormones and mediation of hormone action and are involved in plant responses to environmental conditions. However, limited information on this gene family is available for the important chrysanthemum ornamental species (Chrysanthemum morifolium). Here, we characterized 17 chrysanthemum HD-Zip genes based on transcriptome sequences. Phylogenetic analyses revealed that 17 CmHB genes were distributed in the HD-Zip subfamilies I and II and identified two pairs of putative orthologous proteins in Arabidopsis and chrysanthemum and four pairs of paralogous proteins in chrysanthemum. The software MEME was used to identify 7 putative motifs with E values less than 1e-3 in the chrysanthemum HD-Zip factors, and they can be clearly classified into two groups based on the composition of the motifs. A bioinformatics analysis predicted that 8 CmHB genes could be targeted by 10 miRNA families, and the expression of these 17 genes in response to phytohormone treatments and abiotic stresses was characterized. The results presented here will promote research on the various functions of the HD-Zip gene family members in plant hormones and stress responses.
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Affiliation(s)
- Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Peiling Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jingjing Xin
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kunkun Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dan Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qingqing Fan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tianwei Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Mao H, Yu L, Li Z, Liu H, Han R. Molecular evolution and gene expression differences within the HD-Zip transcription factor family of Zea mays L. Genetica 2016; 144:243-57. [PMID: 26979310 DOI: 10.1007/s10709-016-9896-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/13/2016] [Indexed: 01/18/2023]
Abstract
Homeodomain-leucine zipper (HD-Zip) transcription factors regulate developmental processes and stress responses in plants, and they vary widely in gene number and family structure. In this study, 55 predicted maize HD-Zip genes were systematically analyzed with respect to their phylogenetic relationships, molecular evolution, and gene expression in order to understand the functional diversification within the family. Phylogenetic analysis of HD-Zip proteins from Zea mays, Oryza sativa, Arabidopsis thaliana, Vitis vinifera, and Physcomitrella patens showed that they group into four classes. We inferred that the copy numbers of classes I and III genes were relatively conserved in all five species. The 55 maize HD-Zip genes are distributed randomly on the ten chromosomes, with 15 segmental duplication and 4 tandem duplication events, suggesting that segmental duplications were the major contributors in the expansion of the maize HD-Zip gene family. Expression analysis of the 55 maize HD-Zip genes in different tissues and drought conditions revealed differences in the expression levels and patterns between the four classes. Promoter analysis revealed that a number of stress response-, hormone response-, light response-, and development-related cis-acting elements were present in their promoters. Our results provide novel insights into the molecular evolution and gene expression within the HD-Zip gene family in maize, and provide a solid foundation for future functional study of the HD-Zip genes in maize.
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Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Lijuan Yu
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Zhanjie Li
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Hui Liu
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Ran Han
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
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Harris JC, Sornaraj P, Taylor M, Bazanova N, Baumann U, Lovell B, Langridge P, Lopato S, Hrmova M. Molecular interactions of the γ-clade homeodomain-leucine zipper class I transcription factors during the wheat response to water deficit. PLANT MOLECULAR BIOLOGY 2016; 90:435-52. [PMID: 26803501 DOI: 10.1007/s11103-015-0427-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/25/2015] [Indexed: 05/09/2023]
Abstract
The γ-clade of class I homeodomain-leucine zipper (HD-Zip I) transcription factors (TFs) constitute members which play a role in adapting plant growth to conditions of water deficit. Given the importance of wheat (Triticum aestivum L.) as a global food crop and the impact of water deficit upon grain yield, we focused on functional aspects of wheat drought responsive HD-Zip I TFs. While the wheat γ-clade HD-Zip I TFs share significant sequence similarities with homologous genes from other plants, the clade-specific features in transcriptional response to abiotic stress were detected. We demonstrate that wheat TaHDZipI-3, TaHDZipI-4, and TaHDZipI-5 genes respond differentially to a variety of abiotic stresses, and that proteins encoded by these genes exhibit pronounced differences in oligomerisation, strength of DNA binding, and trans-activation of an artificial promoter. Three-dimensional molecular modelling of the protein-DNA interface was conducted to address the ambiguity at the central nucleotide in the pseudo-palindromic cis-element CAATNATTG that is recognised by all three HD-Zip I proteins. The co-expression of these genes in the same plant tissues together with the ability of HD-Zip I TFs of the γ-clade to hetero-dimerise suggests a role in the regulatory mechanisms of HD-Zip I dependent transcription. Our findings highlight the complexity of TF networks involved in plant responses to water deficit. A better understanding of the molecular complexity at the protein level during crop responses to drought will enable adoption of efficient strategies for production of cereal plants with enhanced drought tolerance.
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Affiliation(s)
- John C Harris
- From the Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- South Australian Research and Development Institute, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Pradeep Sornaraj
- From the Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Mathew Taylor
- From the Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Natalia Bazanova
- From the Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Ute Baumann
- From the Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Ben Lovell
- From the Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Peter Langridge
- From the Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Sergiy Lopato
- From the Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Maria Hrmova
- From the Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
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Li D, Xu X, Hu X, Liu Q, Wang Z, Zhang H, Wang H, Wei M, Wang H, Liu H, Li C. Genome-Wide Analysis and Heavy Metal-Induced Expression Profiling of the HMA Gene Family in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE 2015; 6:1149. [PMID: 26779188 DOI: 10.1007/s11104-018-3637-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 12/03/2015] [Indexed: 05/25/2023]
Abstract
The heavy metal ATPase (HMA) family plays an important role in transition metal transport in plants. However, this gene family has not been extensively studied in Populus trichocarpa. We identified 17 HMA genes in P. trichocarpa (PtHMAs), of which PtHMA1-PtHMA4 belonged to the zinc (Zn)/cobalt (Co)/cadmium (Cd)/lead (Pb) subgroup, and PtHMA5-PtHMA8 were members of the copper (Cu)/silver (Ag) subgroup. Most of the genes were localized to chromosomes I and III. Gene structure, gene chromosomal location, and synteny analyses of PtHMAs indicated that tandem and segmental duplications likely contributed to the expansion and evolution of the PtHMAs. Most of the HMA genes contained abiotic stress-related cis-elements. Tissue-specific expression of PtHMA genes showed that PtHMA1 and PtHMA4 had relatively high expression levels in the leaves, whereas Cu/Ag subgroup (PtHMA5.1- PtHMA8) genes were upregulated in the roots. High concentrations of Cu, Ag, Zn, Cd, Co, Pb, and Mn differentially regulated the expression of PtHMAs in various tissues. The preliminary results of the present study generated basic information on the HMA family of Populus that may serve as foundation for future functional studies.
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Affiliation(s)
- Dandan Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin, China
| | - Xuemei Xu
- Library of Northeast Forestry University Harbin, China
| | - Xiaoqing Hu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin, China
| | - Quangang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin, China
| | - Zhanchao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin, China
| | - Haizhen Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin, China
| | - Han Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin, China
| | - Ming Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin, China
| | - Hanzeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin, China
| | - Haimei Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin, China
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin, China
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Chen Z, Gao K, Su X, Rao P, An X. Genome-Wide Identification of the Invertase Gene Family in Populus. PLoS One 2015; 10:e0138540. [PMID: 26393355 PMCID: PMC4579127 DOI: 10.1371/journal.pone.0138540] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 08/31/2015] [Indexed: 11/18/2022] Open
Abstract
Invertase plays a crucial role in carbohydrate partitioning and plant development as it catalyses the irreversible hydrolysis of sucrose into glucose and fructose. The invertase family in plants is composed of two sub-families: acid invertases, which are targeted to the cell wall and vacuole; and neutral/alkaline invertases, which function in the cytosol. In this study, 5 cell wall invertase genes (PtCWINV1-5), 3 vacuolar invertase genes (PtVINV1-3) and 16 neutral/alkaline invertase genes (PtNINV1-16) were identified in the Populus genome and found to be distributed on 14 chromosomes. A comprehensive analysis of poplar invertase genes was performed, including structures, chromosome location, phylogeny, evolutionary pattern and expression profiles. Phylogenetic analysis indicated that the two sub-families were both divided into two clades. Segmental duplication is contributed to neutral/alkaline sub-family expansion. Furthermore, the Populus invertase genes displayed differential expression in roots, stems, leaves, leaf buds and in response to salt/cold stress and pathogen infection. In addition, the analysis of enzyme activity and sugar content revealed that invertase genes play key roles in the sucrose metabolism of various tissues and organs in poplar. This work lays the foundation for future functional analysis of the invertase genes in Populus and other woody perennials.
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Affiliation(s)
- Zhong Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Kai Gao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaoxing Su
- Beijing Berry Genomics Company Limited, Beijing, China
| | - Pian Rao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xinmin An
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Polle A, Chen S. On the salty side of life: molecular, physiological and anatomical adaptation and acclimation of trees to extreme habitats. PLANT, CELL & ENVIRONMENT 2015; 38:1794-816. [PMID: 25159181 DOI: 10.1111/pce.12440] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 08/11/2014] [Accepted: 08/17/2014] [Indexed: 05/04/2023]
Abstract
Saline and sodic soils that cannot be used for agriculture occur worldwide. Cultivating stress-tolerant trees to obtain biomass from salinized areas has been suggested. Various tree species of economic importance for fruit, fibre and timber production exhibit high salinity tolerance. Little is known about the mechanisms enabling tree crops to cope with high salinity for extended periods. Here, the molecular, physiological and anatomical adjustments underlying salt tolerance in glycophytic and halophytic model tree species, such as Populus euphratica in terrestrial habitats, and mangrove species along coastlines are reviewed. Key mechanisms that have been identified as mediating salt tolerance are discussed at scales from the genetic to the morphological level, including leaf succulence and structural adjustments of wood anatomy. The genetic and transcriptomic bases for physiological salt acclimation are salt sensing and signalling networks that activate target genes; the target genes keep reactive oxygen species under control, maintain the ion balance and restore water status. Evolutionary adaptation includes gene duplication in these pathways. Strategies for and limitations to tree improvement, particularly transgenic approaches for increasing salt tolerance by transforming trees with single and multiple candidate genes, are discussed.
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Affiliation(s)
- Andrea Polle
- Forstbotanik und Baumphysiologie, Büsgen-Institut, Georg-August Universität Göttingen, Göttingen, 37077, Germany
| | - Shaoliang Chen
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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46
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Liu Q, Wang Z, Xu X, Zhang H, Li C. Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa). PLoS One 2015; 10:e0134753. [PMID: 26237514 PMCID: PMC4523194 DOI: 10.1371/journal.pone.0134753] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/13/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND C2H2 zinc-finger (C2H2-ZF) proteins are a large gene family in plants that participate in various aspects of normal plant growth and development, as well as in biotic and abiotic stress responses. To date, no overall analysis incorporating evolutionary history and expression profiling of the C2H2-ZF gene family in model tree species poplar (Populus trichocarpa) has been reported. PRINCIPAL FINDINGS Here, we identified 109 full-length C2H2-ZF genes in P. trichocarpa, and classified them into four groups, based on phylogenetic analysis. The 109 C2H2-ZF genes were distributed unequally on 19 P. trichocarpa linkage groups (LGs), with 39 segmental duplication events, indicating that segmental duplication has been important in the expansion of the C2H2-ZF gene family. Promoter cis-element analysis indicated that most of the C2H2-ZF genes contain phytohormone or abiotic stress-related cis-elements. The expression patterns of C2H2-ZF genes, based on heatmap analysis, suggested that C2H2-ZF genes are involved in tissue and organ development, especially root and floral development. Expression analysis based on quantitative real-time reverse transcription polymerase chain reaction indicated that C2H2-ZF genes are significantly involved in drought, heat and salt response, possibly via different mechanisms. CONCLUSIONS This study provides a thorough overview of the P. trichocarpa C2H2-ZF gene family and presents a new perspective on the evolution of this gene family. In particular, some C2H2-ZF genes may be involved in environmental stress tolerance regulation. PtrZFP2, 19 and 95 showed high expression levels in leaves and/or roots under environmental stresses. Additionally, this study provided a solid foundation for studying the biological roles of C2H2-ZF genes in Populus growth and development. These results form the basis for further investigation of the roles of these candidate genes and for future genetic engineering and gene functional studies in Populus.
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Affiliation(s)
- Quangang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Zhanchao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Xuemei Xu
- Library of Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Haizhen Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
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Ge XX, Liu Z, Wu XM, Chai LJ, Guo WW. Genome-wide identification, classification and analysis of HD-ZIP gene family in citrus, and its potential roles in somatic embryogenesis regulation. Gene 2015; 574:61-8. [PMID: 26232336 DOI: 10.1016/j.gene.2015.07.079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 01/13/2023]
Abstract
The homeodomain-leucine zipper (HD-Zip) transcription factors, which belong to a class of Homeobox proteins, has been reported to be involved in different biological processes of plants, including growth and development, photomorphogenesis, flowering, fruit ripening and adaptation responses to environmental stresses. In this study, 27 HD-Zip genes (CsHBs) were identified in Citrus. Based on the phylogenetic analysis and characteristics of individual gene or protein, the HD-Zip gene family in Citrus can be classified into 4 subfamilies, i.e. HD-Zip I, HD-Zip II, HD-Zip III, and HD-Zip IV containing 16, 2, 4, and 5 members respectively. The digital expression patterns of 27 HD-Zip genes were analyzed in the callus, flower, leaf and fruit of Citrus sinensis. The qRT-PCR and RT-PCR analyses of six selected HD-Zip genes were performed in six citrus cultivars with different embryogenic competence and in the embryo induction stages, which revealed that these genes were differentially expressed and might be involved in citrus somatic embryogenesis (SE). The results exhibited that the expression of CsHB1 was up-regulated in somatic embryo induction process, and its expression was higher in citrus cultivars with high embryogenic capacity than in cultivars recalcitrant to form somatic embryos. Moreover, a microsatellite site of three nucleotide repeats was found in CsHB1 gene among eighteen citrus genotypes, indicating the possible association of CsHB1 gene to the capacity of callus induction.
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Affiliation(s)
- Xiao-Xia Ge
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan 430415, China.
| | - Zheng Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Li-Jun Chai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China.
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Shen Z, Yao J, Sun J, Chang L, Wang S, Ding M, Qian Z, Zhang H, Zhao N, Sa G, Hou P, Lang T, Wang F, Zhao R, Shen X, Chen S. Populus euphratica HSF binds the promoter of WRKY1 to enhance salt tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:89-100. [PMID: 25900569 DOI: 10.1016/j.plantsci.2015.03.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 02/02/2015] [Accepted: 03/06/2015] [Indexed: 05/04/2023]
Abstract
Poplar species increase expressions of transcription factors to deal with salt environments. We assessed the salt-induced transcriptional responses of heat-shock transcription factor (HSF) and WRKY1 in Populus euphratica, and their roles in salt tolerance. High NaCl (200mM) induced PeHSF and PeWRKY1 expressions in P. euphratica, with a rapid rise in roots than in leaves. Moreover, the salt-elicited PeHSF reached its peak level 6h earlier than PeWRKY1 in leaves. PeWRKY1 was down-regulated in salinized P. euphratica when PeHSF was silenced by tobacco rattle virus-based gene silencing. Subcellular assays in onion epidermal cells and Arabidopsis protoplasts revealed that PeHSF and PeWRKY1 were restricted to the nucleus. Transgenic tobacco plants overexpressing PeWRKY1 showed improved salt tolerance in terms of survival rate, root growth, photosynthesis, and ion fluxes. We further isolated an 1182-bp promoter fragment upstream of the translational start of PeWRKY1 from P. euphratica. Promoter sequence analysis revealed that PeWRKY1 harbours four tandem repeats of heat shock element (HSE) in the upstream regulatory region. Yeast one-hybrid assay showed that PeHSF directly binds the cis-acting HSE. To determine whether the HSE cluster was important for salt-induced PeWRKY1 expression, the promoter-reporter construct PeWRKY1-pro::GUS was transferred to tobacco plants. β-glucuronidase activities increased in root, leaf, and stem tissues under salt stress. Therefore, we conclude that salinity increased PeHSF transcription in P. euphratica, and that PeHSF binds the cis-acting HSE of the PeWRKY1 promoter, thus activating PeWRKY1 expression.
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Affiliation(s)
- Zedan Shen
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Jun Yao
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Jian Sun
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, PR China
| | - Liwei Chang
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Shaojie Wang
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Mingquan Ding
- College of Agricultural and Food Science, Zhejiang Agricultural and Forestry University, Hangzhou, Zhejiang 311300, PR China
| | - Zeyong Qian
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Huilong Zhang
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Nan Zhao
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Gang Sa
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Peichen Hou
- National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, PR China
| | - Tao Lang
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Feifei Wang
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Rui Zhao
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Xin Shen
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China
| | - Shaoliang Chen
- College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing 100083, PR China.
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Chen Z, Chen X, Yan H, Li W, Li Y, Cai R, Xiang Y. The Lipoxygenase Gene Family in Poplar: Identification, Classification, and Expression in Response to MeJA Treatment. PLoS One 2015; 10:e0125526. [PMID: 25928711 PMCID: PMC4415952 DOI: 10.1371/journal.pone.0125526] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/13/2015] [Indexed: 11/23/2022] Open
Abstract
Background Lipoxygenases (LOXs) are important dioxygenases in cellular organisms. LOXs contribute to plant developmental processes and environmental responses. However, a systematic and comprehensive analysis has not been focused on the LOX gene family in poplar. Therefore, in the present study, we performed a comprehensive analysis of the LOX gene family in poplar. Results Using bioinformatics methods, we identified a total of 20 LOX genes. These LOX genes were clustered into two subfamilies. The gene structure and motif composition of each subfamily were relatively conserved. These genes are distributed unevenly across nine chromosomes. The PtLOX gene family appears to have expanded due to high tandem and low segmental duplication events. Microarray analysis showed that a number of PtLOX genes have different expression pattern across disparate tissues and under various stress treatments. Quantitative real-time PCR (qRT-PCR) analysis was further performed to confirm the responses to MeJA treatment of the 20 poplar LOX genes. The results show that the PtLOX genes are regulated by MeJA (Methyl jasmonate) treatment. Conclusions This study provides a systematic analysis of LOX genes in poplar. The gene family analysis reported here will be useful for conducting future functional genomics studies to uncover the roles of LOX genes in poplar growth and development.
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Affiliation(s)
- Zhu Chen
- Laboratory of Modern Biotechnology, Anhui Agricultural University, Hefei, China
| | - Xue Chen
- Laboratory of Modern Biotechnology, Anhui Agricultural University, Hefei, China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, Anhui Agricultural University, Hefei, China
| | - Weiwei Li
- Laboratory of Modern Biotechnology, Anhui Agricultural University, Hefei, China
| | - Yuan Li
- Laboratory of Modern Biotechnology, Anhui Agricultural University, Hefei, China
| | - Ronghao Cai
- Key Laboratory of Biomass Improvement and Conversion, Anhui Agriculture University, Hefei, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, Anhui Agricultural University, Hefei, China
- Key Laboratory of Biomass Improvement and Conversion, Anhui Agriculture University, Hefei, China
- * E-mail:
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Zhang J, Liu B, Li J, Zhang L, Wang Y, Zheng H, Lu M, Chen J. Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses. BMC Genomics 2015; 16:181. [PMID: 25887520 PMCID: PMC4373061 DOI: 10.1186/s12864-015-1398-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 02/24/2015] [Indexed: 11/21/2022] Open
Abstract
Background Heat shock proteins (Hsps) are molecular chaperones that are involved in many normal cellular processes and stress responses, and heat shock factors (Hsfs) are the transcriptional activators of Hsps. Hsfs and Hsps are widely coordinated in various biological processes. Although the roles of Hsfs and Hsps in stress responses have been well characterized in Arabidopsis, their roles in perennial woody species undergoing various environmental stresses remain unclear. Results Here, a comprehensive identification and analysis of Hsf and Hsp families in poplars is presented. In Populus trichocarpa, we identified 42 paralogous pairs, 66.7% resulting from a whole genome duplication. The gene structure and motif composition are relatively conserved in each subfamily. Microarray and quantitative real-time RT-PCR analyses showed that most of the Populus Hsf and Hsp genes are differentially expressed upon exposure to various stresses. A coexpression network between Populus Hsf and Hsp genes was generated based on their expression. Coordinated relationships were validated by transient overexpression and subsequent qPCR analyses. Conclusions The comprehensive analysis indicates that different sets of PtHsps are downstream of particular PtHsfs and provides a basis for functional studies aimed at revealing the roles of these families in poplar development and stress responses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1398-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| | - Bobin Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China. .,College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
| | - Jianbo Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Li Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Yan Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Huanquan Zheng
- Department of Biology, McGill University, 1205 Dr Penfield Avenue, Montreal, Quebec, H3A 1B1, Canada.
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| | - Jun Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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