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Jiang M, Wang M, Zhang X, Zhang Z, Sha J, Wan J, Wei L, Wang R, Wang W, Wang W, Hu Z, Leng P, He X. Genome-wide identification of metal tolerance protein genes in Quercus dentata and their roles in response to various heavy metal stresses. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116942. [PMID: 39216217 DOI: 10.1016/j.ecoenv.2024.116942] [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: 04/11/2024] [Revised: 08/22/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
Metal tolerance protein (MTP) is a cation transporter that plays an important role in tolerance to heavy metal stress. However, thus far, there has been no genome-wide investigation of the MTP gene family in Quercus plants. Quercus dentata is one of the main constructive species of forest in northern China. It has strong tolerance to a variety of heavy metal stresses. In this study, 25 MTPs were identified from the Q. dentata genome and classified into three subfamilies and seven groups according to their sequence characteristics and phylogenetic relationships. Both tandem and segmental duplication events contributed to the expansion of the QdMTP gene family. Interestingly, all 10 tandem duplication events contributed to the expansion of the Mn-CDF subfamily. The expression of Mn-CDF subfamily members in different organs and tissues of Q. dentata was different, and they responded differently to manganese, iron, zinc and cadmium stress treatments. QdMTP10.7, a member of the Mn-CDF subfamily, enhanced yeast growth under manganese, zinc and iron stresses. The subcellular localization in tobacco leaf epidermis cells showed that QdMTP10.7 was located in vacuoles. These data generated from this study provide an important foundation to elucidate the biological roles of QdMTP genes related to heavy metal tolerance in Q. dentata.
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Affiliation(s)
- Meng Jiang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
| | - Meijia Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
| | - Xuejiao Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
| | - Zhen Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
| | - Jingjing Sha
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
| | - Junyi Wan
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
| | - Liyi Wei
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
| | - Rui Wang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China.
| | - Wenbo Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
| | - Wenhe Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
| | - Zenghui Hu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
| | - Pingsheng Leng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China.
| | - Xiangfeng He
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China.
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Shad MA, Wu S, Rao MJ, Luo X, Huang X, Wu Y, Zhou Y, Wang L, Ma C, Hu L. Evolution and Functional Dynamics of TCP Transcription Factor Gene Family in Passion Fruit ( Passiflora edulis). PLANTS (BASEL, SWITZERLAND) 2024; 13:2568. [PMID: 39339543 PMCID: PMC11435056 DOI: 10.3390/plants13182568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 09/02/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024]
Abstract
Passion fruit is a valued tropical fruit crop that faces environment-related growth strains. TCP genes are important for both growth modulation and stress prevention in plants. Herein, we systematically analyzed the TCP gene family in passion fruit, recognizing 30 members. Genes exhibiting closer phylogenetic relationships exhibited similar protein and gene structures. Gene members of the TCP family showed developmental-stage- or tissue-specific expression profiles during the passion fruit life cycle. Transcriptome data also demonstrated that many PeTCPs showed induced expression in response to hormonal treatments and cold, heat, and salt stress. Based on transcriptomics data, eight candidate genes were chosen for preferential gene expression confirmation under cold stress conditions. The qRT-PCR assays suggested PeTCP15/16/17/19/23 upregulation, while PeTCP1/11/25 downregulation after cold stress. Additionally, TCP19/20/29/30 exhibited in silico binding with cold-stress-related miRNA319s. GFP subcellular localization assays exhibited PeTCP19/1 were localized at the nucleus. This study will aid in the establishment of novel germplasm, as well as the further investigation of the roles of PeTCPs and their cold stress resistance characteristics.
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Affiliation(s)
- Munsif Ali Shad
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (M.A.S.); (L.W.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (S.W.); (X.L.)
| | - Songguo Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (S.W.); (X.L.)
| | - Muhammad Junaid Rao
- State Key Loboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China;
| | - Xiaoying Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (S.W.); (X.L.)
| | - Xiaojin Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (S.W.); (X.L.)
| | - Yuxin Wu
- College of Life Sciences and Technology, Huazhong University of Sciences and Technology, Wuhan 430074, China;
| | - Yuhong Zhou
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (M.A.S.); (L.W.)
| | - Lingqiang Wang
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (M.A.S.); (L.W.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (S.W.); (X.L.)
| | - Chongjian Ma
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (M.A.S.); (L.W.)
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (S.W.); (X.L.)
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Tian L, Wu L, Zhong XF, Ma LH, Du GY. Genome-Wide Characterization of ABC Transporter Genes and Expression Profiles in Red Macroalga Pyropia yezoensis Expose to Low-Temperature. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10355-3. [PMID: 39269589 DOI: 10.1007/s10126-024-10355-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 08/05/2024] [Indexed: 09/15/2024]
Abstract
Pyropia yezoensis is an important economic macroalga widely cultivated in the East Asia countries of China, Korea, and Japan. The ATP-binding cassette (ABC) transporter gene family is one of the largest transporter families in all forms of life involved in various biological processes. The characteristics of ABC transporter genes in P. yezoensis (PyABC) and their functions in stress resistance, however, remain largely unknown. In this study, PyABCs were identified and characterized their expression patterns under low-temperature stress. A total of 48 PyABCs transporters were identified and divided into eight subfamilies, which are mostly predicted as membrane-binding proteins. The cis-elements of phytohormone and low-temperature response were distinguished in promoter sequences of PyABCs. Transcriptome analysis showed that PyABCs are involved in response to low-temperature stress. Among them, 12 PyABCs were significantly up-regulated after 24 h of exposure to low temperature (2 °C). Further quantitative RT-PCR analysis corroborated the highest expression happened at 24 for detected genes of PyABCC8, PyABCF3, and PyABCI1, extraordinarily for PyABCF3, and followed by decreased expression at 48 h. The expression of PyABCI1 was generally low in all tested strains. Whereas, in a strain of P. yezoensis with lower tolerance to low temperature, the expression was observed higher in PyABCC1, PyABCC8, and remarkably high in PyABCF3. This study provided valuable information on ABC gene families in P. yezoensis and their functional characteristics, especially on low-temperature resistance, and would help to understand the adaptive mechanisms of P. yezoensis to adverse environments.
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Affiliation(s)
- Lin Tian
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Lan Wu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Xue-Feng Zhong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Li-Hong Ma
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Guo-Ying Du
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China.
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Zheng L, Tang L, Li J. Genome-wide identification of the GATA gene family in melon ( Cucumis melo) and analysis of their expression characteristics under biotic and abiotic stresses. FRONTIERS IN PLANT SCIENCE 2024; 15:1462924. [PMID: 39345983 PMCID: PMC11427367 DOI: 10.3389/fpls.2024.1462924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 08/19/2024] [Indexed: 10/01/2024]
Abstract
GATA transcription factors are an important class of transcription factors in plants, known for their roles in tissue development, signal transduction, and responses to biotic and abiotic stresses. To date, there have been no reports on the GATA gene family in melon (Cucumis melo). In this study, 24 CmGATA genes were identified from the melon genome. These family members exhibit significant differences in protein length, molecular weight, and theoretical isoelectric point and are primarily located in the nucleus. Based on the classification of Arabidopsis thaliana GATA members, the phylogenetic tree divided them into four groups: group I, group II, group III, and group IV, containing 10, 8, 4, and 2 genes, respectively. Notably, CmGATA genes within the same group have highly conserved protein motifs and similar exon-intron structures. The CmGATA family members are unevenly distributed across 10 chromosomes, with six pairs of segmentally duplicated genes and one pair of tandemly duplicated genes, suggesting that gene duplication may be the primary factor in the expansion of the CmGATA family. Melon shares 21, 4, 38, and 34 pairs of homologous genes with A. thaliana, Oryza sativa, Cucumis sativus, and Citrullus lanatus, respectively. The promoter regions are enriched with various cis-acting elements related to growth and development (eight types), hormone regulation (nine types), and stress responses (six types). Expression patterns indicate that different CmGATA family members are significantly expressed in seeds, roots, stems, leaves, tendrils, mesocarp, and epicarp, exhibiting distinct tissue-specific expression characteristics. Quantitative fluorescence analysis revealed that five genes, CmGATA3, CmGATA7, CmGATA16, CmGATA22, and CmGATA24, may be highly active under 48-h drought stress, while CmGATA1 and CmGATA22 may enhance melon resistance to heavy metal lead stress. Additionally, CmGATA22 and CmGATA24 are suggested to regulate melon resistance to Fusarium wilt infection. CmGATA22 appears to comprehensively regulate melon responses to both biotic and abiotic stresses. Lastly, potential protein interaction networks were predicted for the CmGATA family members, identifying CmGATA8 as a potential hub gene and predicting 2,230 target genes with enriched GO functions. This study preliminarily explores the expression characteristics of CmGATA genes under drought stress, heavy metal lead stress, and Fusarium wilt infection, providing a theoretical foundation for molecular mechanisms in melon improvement and stress resistance.
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Affiliation(s)
- Ling Zheng
- Department of Biology, Luoyang Normal University, Luoyang, Henan, China
| | - Lin Tang
- Department of Biology, Luoyang Normal University, Luoyang, Henan, China
| | - Jinbo Li
- Department of Biology, Luoyang Normal University, Luoyang, Henan, China
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55
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Abdoulaye AH, Yuhua C, Xiaoyan Z, Yiwei Y, Wang H, Yinhua C. Computational analysis and expression profiling of NAC transcription factor family involved in biotic stress response in Manihot esculenta. PLANT BIOLOGY (STUTTGART, GERMANY) 2024. [PMID: 39265049 DOI: 10.1111/plb.13715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/13/2024] [Indexed: 09/14/2024]
Abstract
The Nascent polypeptide-Associated Complex (NAC) family is among the largest plant-specific TF families and plays an important role in plant growth, development, and stress responses. NAC TFs have been extensively studied in plants such as rice and Arabidopsis; however, their characterization, functions, evolution, and expression patterns in Manihot esculenta (cassava) under environmental stress remain largely unexplored. Here, we used bioinformatic analyses and biotic stress responses to investigate the physicochemical properties, chromosome location, phylogeny, gene structure, expression patterns, and cis-elements in promoter regions of the NAC TFs in cassava. We identified 119 M. esculenta NAC (MeNAC) gene families, unevenly distributed on 16 chromosomes. We investigated expression patterns of all identified MeNAC TFs under Xanthomonas axonopodis pv. manihotis (Xam) infection, strain CHN11, at different time points. Only 20 MeNAC TFs showed expression of significant bacterial resistance. Six MeNACs (MeNAC7, 26, 63, 65, 77, and 113) were selected for functional analysis. qRT-PCR assays revealed that MeNAC7, 26, 63, 65, 77, and 113 were induced in response to XamCHN11 infection and may participate in the molecular interaction of cassava and bacterial blight. Interestingly, MeNAC26, MeNAC63, MeNAC65, and MeNAC113 responded to XamCHN11 infection at 3 h post-inoculation. Furthermore, we identified 13 stress-related cis-elements in promoter regions of the MeNAC genes that are involved in diverse environmental stress responses. Phylogenetic analysis revealed that MeNAC genes with similar structures and motif distributions were grouped. This study provides valuable insights into the evolution, diversity, and characterization of MeNAC TFs. It lays the groundwork for a better understanding of their biological roles and molecular mechanisms in cassava.
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Affiliation(s)
- A H Abdoulaye
- National Key Laboratory for Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou, China
| | - C Yuhua
- National Key Laboratory for Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou, China
| | - Z Xiaoyan
- National Key Laboratory for Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou, China
| | - Y Yiwei
- National Key Laboratory for Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou, China
| | - H Wang
- National Key Laboratory for Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou, China
| | - C Yinhua
- National Key Laboratory for Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou, China
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56
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Xue B, Liang Z, Liu Y, Li D, Cao P, Liu C. Comparative Analysis of Casparian Strip Membrane Domain Protein Family in Oryza sativa (L.) and Arabidopsis thaliana (L.). Int J Mol Sci 2024; 25:9858. [PMID: 39337349 PMCID: PMC11431883 DOI: 10.3390/ijms25189858] [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: 07/25/2024] [Revised: 08/20/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
The Casparian strip membrane domain proteins (CASPs) are pivotal for the formation of the Casparian strip (CS) in endodermal cells and play a crucial role in a plant's response to environmental stresses. However, existing research on the CASP gene family in rice and Arabidopsis lacks a comprehensive bioinformatics analysis and necessitates further exploration. In this study, we identified 41 OsCASP and 39 AtCASP genes, which were grouped into six distinct subgroups. Collinearity analysis underscored the pivotal roles of WGD and TD events in driving the evolution of CASPs, with WGDs being the dominant force. On the one hand, the analysis of cis-elements indicated that most OsCASP and AtCASP genes contain MYB binding motifs. On the other hand, RNA-seq revealed that the majority of OsCASP and AtCASP genes are highly expressed in roots, particularly in endodermal cells, where OsCASP_like11/9 and AtCASP_like1/31 demonstrated the most pronounced expression. These results suggest that OsCASP_like11/9 and AtCASP_like1/31 might be candidate genes involved in the formation of the endodermis CS. RT-qPCR results demonstrated that OsCASP_like2/3/13/17/21/30 may be candidate genes for the ion defect process. Collectively, this study offers a theoretical foundation for unraveling the biological functions of CASP genes in rice and Arabidopsis.
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Affiliation(s)
- Baoping Xue
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
- Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zicong Liang
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
| | - Yue Liu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110866, China
| | - Dongyang Li
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
| | - Peng Cao
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Chang Liu
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
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Zhang J, Meng D, Li J, Bao Y, Yu P, Dou G, Guo J, Tang C, Lv J, Wang X, Wang X, Wu F, Shi Y. Analysis of the Rice Raffinose Synthase (OsRS) Gene Family and Haplotype Diversity. Int J Mol Sci 2024; 25:9815. [PMID: 39337301 PMCID: PMC11432550 DOI: 10.3390/ijms25189815] [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: 07/19/2024] [Revised: 09/03/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Based on the genome information of rice (Nipponbare), this study screened and identified six raffinose synthase (RS) genes and analyzed their physical and chemical properties, phylogenetic relationship, conserved domains, promoter cis-acting elements, and the function and genetic diversity of the gene-CDS-haplotype (gcHap). The results showed that these genes play key roles in abiotic stress response, such as OsRS5, whose expression in leaves changed significantly under high salt, drought, ABA, and MeJA treatments. In addition, the OsRS genes showed significant genetic variations in different rice populations. The main gcHaps of most OsRS loci had significant effects on key agronomic traits, and the frequency of these alleles varied significantly among different rice populations and subspecies. These findings provide direction for studying the RS gene family in other crops.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (J.Z.); (D.M.); (J.L.); (Y.B.); (P.Y.); (G.D.); (J.G.); (C.T.); (J.L.); (X.W.); (X.W.); (F.W.)
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58
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Bahadır S, Abdulla MF, Mostafa K, Kavas M, Hacıkamiloğlu S, Kurt O, Yıldırım K. Exploring the role of FAT genes in Solanaceae species through genome-wide analysis and genome editing. THE PLANT GENOME 2024:e20506. [PMID: 39253757 DOI: 10.1002/tpg2.20506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/08/2024] [Accepted: 08/04/2024] [Indexed: 09/11/2024]
Abstract
Plants produce numerous fatty acid derivatives, and some of these compounds have significant regulatory functions, such as governing effector-induced resistance, systemic resistance, and other defense pathways. This study systematically identified and characterized eight FAT genes (Acyl-acyl carrier protein thioesterases), four in the Solanum lycopersicum and four in the Solanum tuberosum genome. Phylogenetic analysis classified these genes into four distinct groups, exhibiting conserved domain structures across different plant species. Promoter analysis revealed various cis-acting elements, most of which are associated with stress responsiveness and growth and development. Micro-RNA (miRNA) analysis identified specific miRNAs, notably miRNA166, targeting different FAT genes in both species. Utilizing clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated knockout, mutant lines for SlFATB1 and SlFATB3 were successfully generated and exhibited diverse mutation types. Biochemical evaluation of selected mutant lines revealed significant changes in fatty acid composition, with linoleic and linolenic acid content variations. The study also explored the impact of FAT gene knockout on tomato leaf architecture through scanning electron microscopy, providing insights into potential morphological alterations. Knocking out of FAT genes resulted in a significant reduction in both trichome and stoma density. These findings contribute to a comprehensive understanding of FAT genes in Solanaceous species, encompassing genetic, functional, and phenotypic aspects.
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Affiliation(s)
- Sibel Bahadır
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
| | - Mohamed Farah Abdulla
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
| | - Karam Mostafa
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
- The Central Laboratory for Date Palm Research and Development, Agricultural Research Center (ARC), Giza, Egypt
| | - Musa Kavas
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
| | - Safa Hacıkamiloğlu
- Faculty of Agriculture, Department of Field Crops, Ondokuz Mayis University, Samsun, Turkey
| | - Orhan Kurt
- Faculty of Agriculture, Department of Field Crops, Ondokuz Mayis University, Samsun, Turkey
| | - Kubilay Yıldırım
- Faculty of Science, Department of Molecular Biology and Genetics, Ondokuz Mayis University, Samsun, Turkey
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59
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Zhang Y, Wang S, Zhang C, Qi M, Liu L, Yang L, Lian N. Genome-Wide Characterization of IQD Family Proteins in Apple and Functional Analysis of the Microtubule-Regulating Abilities of MdIQD17 and MdIQD28 under Cold Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:2532. [PMID: 39274016 PMCID: PMC11397337 DOI: 10.3390/plants13172532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 09/01/2024] [Accepted: 09/05/2024] [Indexed: 09/16/2024]
Abstract
Microtubules undergo dynamic remodeling in response to diverse abiotic stress in plants. The plant-specific IQ67 DOMAIN (IQD) family proteins serve as microtubule-associated proteins, playing multifaceted roles in plant development and response to abiotic stress. However, the biological function of IQD genes in apple remains unclear. In this study, we conducted a comprehensive analysis of the Malus domestica genome, identifying 42 IQD genes distributed across 17 chromosomes and categorized them into four subgroups. Promoter analysis revealed the presence of stress-responsive elements. Subsequent expression analysis highlighted the significant upregulation of MdIQD17 and MdIQD28 in response to cold treatments, prompting their selection for further functional investigation. Subcellular localization studies confirmed the association of MdIQD17 and MdIQD28 with microtubules. Crucially, confocal microscopy and quantification revealed diminished microtubule depolymerization in cells transiently overexpressing MdIQD17 and MdIQD28 compared to wild-type cells during cold conditions. In conclusion, this study provides a comprehensive analysis of IQD genes in apple, elucidating their molecular mechanism in response to cold stress.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shengjie Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Chaochao Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Meng Qi
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Luoqi Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lipeng Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Na Lian
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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60
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Tian Q, Yu T, Dong M, Hu Y, Chen X, Xue Y, Fang Y, Zhang J, Zhang X, Xue D. Identification and Characterization of Shaker Potassium Channel Gene Family and Response to Salt and Chilling Stress in Rice. Int J Mol Sci 2024; 25:9728. [PMID: 39273675 PMCID: PMC11395327 DOI: 10.3390/ijms25179728] [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: 07/24/2024] [Revised: 08/30/2024] [Accepted: 09/05/2024] [Indexed: 09/15/2024] Open
Abstract
Shaker potassium channel proteins are a class of voltage-gated ion channels responsible for K+ uptake and translocation, playing a crucial role in plant growth and salt tolerance. In this study, bioinformatic analysis was performed to identify the members within the Shaker gene family. Moreover, the expression patterns of rice Shaker(OsShaker) K+ channel genes were analyzed in different tissues and salt treatment by RT-qPCR. The results revealed that there were eight OsShaker K+ channel genes distributed on chromosomes 1, 2, 5, 6 and 7 in rice, and their promoters contained a variety of cis-regulatory elements, including hormone-responsive, light-responsive, and stress-responsive elements, etc. Most of the OsShaker K+ channel genes were expressed in all tissues of rice, but at different levels in different tissues. In addition, the expression of OsShaker K+ channel genes differed in the timing, organization and intensity of response to salt and chilling stress. In conclusion, our findings provide a reference for the understanding of OsShaker K+ channel genes, as well as their potential functions in response to salt and chilling stress in rice.
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Affiliation(s)
- Quanxiang Tian
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Tongyuan Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Mengyuan Dong
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yue Hu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xiaoguang Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuan Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
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Zi Y, Zhang Z, Zhao K, Yang X, Zhu L, Yin T, Chen C, Wen K, Li X, Zhang H, Liu X. Genome-wide identification of kiwifruit K + channel Shaker family members and their response to low-K + stress. BMC PLANT BIOLOGY 2024; 24:833. [PMID: 39243055 PMCID: PMC11378538 DOI: 10.1186/s12870-024-05555-x] [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: 10/24/2023] [Accepted: 08/29/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND 'Hongyang' kiwifruit (Actinidia chinensis cv 'Hongyang') is a high-quality variety of A. chinensis with the advantages of high yield, early ripening, and high stress tolerance. Studies have confirmed that the Shaker K+ genes family is involved in plant uptake and distribution of potassium (K+). RESULTS Twenty-eight Shaker genes were identified and analyzed from the 'Hongyang' kiwifruit (A. chinensis cv 'Hongyang') genome. Subcellular localization results showed that more than one-third of the AcShaker genes were on the cell membrane. Phylogenetic analysis indicated that the AcShaker genes were divided into six subfamilies (I-VI). Conservative model, gene structure, and structural domain analyses showed that AcShaker genes of the same subfamily have similar sequence features and structure. The promoter cis-elements of the AcShaker genes were classified into hormone-associated cis-elements and environmentally stress-associated cis-elements. The results of chromosomal localization and duplicated gene analysis demonstrated that AcShaker genes were distributed on 18 chromosomes, and segmental duplication was the prime mode of gene duplication in the AcShaker family. GO enrichment analysis manifested that the ion-conducting pathway of the AcShaker family plays a crucial role in regulating plant growth and development and adversity stress. Compared with the transcriptome data of the control group, all AcShaker genes were expressed under low-K+stress, and the expression differences of three genes (AcShaker15, AcShaker17, and AcShaker22) were highly significant. The qRT-PCR results showed a high correlation with the transcriptome data, which indicated that these three differentially expressed genes could regulate low-K+ stress and reduce K+ damage in kiwifruit plants, thus improving the resistance to low-K+ stress. Comparison between the salt stress and control transcriptomic data revealed that the expression of AcShaker11 and AcShaker18 genes was significantly different and lower under salt stress, indicating that both genes could be involved in salt stress resistance in kiwifruit. CONCLUSION The results showed that 28 AcShaker genes were identified and all expressed under low K+ stress, among which AcShaker22 was differentially and significantly upregulated. The AcShaker22 gene can be used as a candidate gene to cultivate new varieties of kiwifruit resistant to low K+ and provide a reference for exploring more properties and functions of the AcShaker genes.
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Affiliation(s)
- Yinqiang Zi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Zhiming Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Ke Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Xiuyao Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Ling Zhu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Chaoying Chen
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Ke Wen
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Xulin Li
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China.
| | - Xiaozhen Liu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China.
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Peng FC, Yuan M, Zhou L, Zheng BQ, Wang Y. Identification and Analysis of Aluminum-Activated Malate Transporter Gene Family Reveals Functional Diversification in Orchidaceae and the Expression Patterns of Dendrobium catenatum Aluminum-Activated Malate Transporters. Int J Mol Sci 2024; 25:9662. [PMID: 39273609 PMCID: PMC11394931 DOI: 10.3390/ijms25179662] [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: 08/21/2024] [Revised: 08/30/2024] [Accepted: 09/03/2024] [Indexed: 09/15/2024] Open
Abstract
Aluminum-activated malate transporter (ALMT) genes play an important role in aluminum ion (Al3+) tolerance, fruit acidity, and stomatal movement. Although decades of research have been carried out in many plants, there is little knowledge about the roles of ALMT in Orchidaceae. In this study, 34 ALMT genes were identified in the genomes of four orchid species. Specifically, ten ALMT genes were found in Dendrobium chrysotoxum and D. catenatum, and seven were found in Apostasia shenzhenica and Phalaenopsis equestris. These ALMT genes were further categorized into four clades (clades 1-4) based on phylogenetic relationships. Sequence alignment and conserved motif analysis revealed that most orchid ALMT proteins contain conserved regions (TM1, GABA binding motif, and WEP motif). We also discovered a unique motif (19) belonging to clade 1, which can serve as a specifically identified characteristic. Comparison with the gene structure of AtALMT genes (Arabidopsis thaliana) showed that the gene structure of ALMT was conserved across species, but the introns were longer in orchids. The promoters of orchid ALMT genes contain many light-responsive and hormone-responsive elements, suggesting that their expression may be regulated by light and phytohormones. Chromosomal localization and collinear analysis of D. chrysotoxum indicated that tandem duplication (TD) is the main reason for the difference in the number of ALMT genes in these orchids. D. catenatum was chosen for the RT-qPCR experiment, and the results showed that the DcaALMT gene expression pattern varied in different tissues. The expression of DcaALMT1-9 was significantly changed after ABA treatment. Combining the circadian CO2 uptake rate, titratable total acid, and RT-qPCR data analysis, most DcaALMT genes were highly expressed at night and around dawn. The result revealed that DcaALMT genes might be involved in photosynthate accumulation. The above study provides more comprehensive information for the ALMT gene family in Orchidaceae and a basis for subsequent functional analysis.
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Affiliation(s)
- Fu-Cheng Peng
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Meng Yuan
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lin Zhou
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Bao-Qiang Zheng
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yan Wang
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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Li G, Chen Z, Guo X, Tian D, Li C, Lin M, Hu C, Yan J. Genome-Wide Identification and Analysis of Maize DnaJ Family Genes in Response to Salt, Heat, and Cold at the Seedling Stage. PLANTS (BASEL, SWITZERLAND) 2024; 13:2488. [PMID: 39273972 PMCID: PMC11396969 DOI: 10.3390/plants13172488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/23/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024]
Abstract
DnaJ proteins, also known as HSP40s, play a key role in plant growth and development, and response to environmental stress. However, little comprehensive research has been conducted on the DnaJ gene family in maize. Here, we identify 91 ZmDnaJ genes from maize, which are likely distributed in the chloroplast, nucleus, and cytoplasm. Our analysis revealed that ZmDnaJs were classified into three types, with conserved protein motifs and gene structures within the same type, particularly among members of the same subfamily. Gene duplication events have likely contributed to the expansion of the ZmDnaJ family in maize. Analysis of cis-regulatory elements in ZmDnaJ promoters suggested involvement in stress responses, growth and development, and phytohormone sensitivity in maize. Specifically, four cis-acting regulatory elements associated with stress responses and phytohormone regulation indicated a role in adaptation. RNA-seq analysis showed constitutive expression of most ZmDnaJ genes, some specifically in pollen and endosperm. More importantly, certain genes also responded to salt, heat, and cold stresses, indicating potential interaction between stress regulatory networks. Furthermore, early responses to heat stress varied among five inbred lines, with upregulation of almost tested ZmDnaJ genes in B73 and B104 after 6 h, and fewer genes upregulated in QB1314, MD108, and Zheng58. After 72 h, most ZmDnaJ genes in the heat-sensitive inbred lines (B73 and B104) returned to normal levels, while many genes, including ZmDnaJ55, 79, 88, 90, and 91, remained upregulated in the heat-tolerant inbred lines (QB1314, MD108, and Zheng58) suggesting a synergistic function for prolonged protection against heat stress. In conclusion, our study provides a comprehensive analysis of the ZmDnaJ family in maize and demonstrates a correlation between heat stress tolerance and the regulation of gene expression within this family. These offer a theoretical basis for future functional validation of these genes.
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Affiliation(s)
- Gang Li
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Ziqiang Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Xinrui Guo
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Dagang Tian
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Chenchen Li
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Min Lin
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Changquan Hu
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Jingwan Yan
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
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Zou LH, Zhu B, Chen Y, Lu Y, Ramkrishnan M, Xu C, Zhou X, Ding Y, Cho J, Zhou M. Genetic and epigenetic reprogramming in response to internal and external cues by induced transposon mobilization in Moso bamboo. THE NEW PHYTOLOGIST 2024. [PMID: 39238152 DOI: 10.1111/nph.20107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 08/21/2024] [Indexed: 09/07/2024]
Abstract
Long terminal repeat retroelements (LTR-REs) have profound effects on DNA methylation and gene regulation. Despite the vast abundance of LTR-REs in the genome of Moso bamboo (Phyllostachys edulis), an industrial crop in underdeveloped countries, their precise implication of the LTR-RE mobility in stress response and development remains unknown. We investigated the RNA and DNA products of LTR-REs in Moso bamboo under various developmental stages and stressful conditions. Surprisingly, our analyses identified thousands of active LTR-REs, particularly those located near genes involved in stress response and developmental regulation. These genes adjacent to active LTR-REs exhibited an increased expression under stress and are associated with reduced DNA methylation that is likely affected by the induced LTR-REs. Moreover, the analyses of simultaneous mapping of insertions and DNA methylation showed that the LTR-REs effectively alter the epigenetic status of the genomic regions where they inserted, and concomitantly their transcriptional competence which might impact the stress resilience and growth of the host. Our work unveils the unusually strong LTR-RE mobility in Moso bamboo and its close association with (epi)genetic changes, which supports the co-evolution of the parasitic DNAs and host genome in attaining stress tolerance and developmental robustness.
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Affiliation(s)
- Long-Hai Zou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Bailiang Zhu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yaxin Chen
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yaping Lu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Muthusamy Ramkrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Chao Xu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Xiaohong Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yiqian Ding
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Jungnam Cho
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
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Yang H, Liu B, Ding H, Liu Z, Li X, He T, Wu Y, Zhang Y, Wang C, Leng L, Chen S, Song C. Genome-wide analysis of the ERF Family in Stephania japonica provides insights into the regulatory role in Cepharanthine biosynthesis. FRONTIERS IN PLANT SCIENCE 2024; 15:1433015. [PMID: 39297007 PMCID: PMC11408324 DOI: 10.3389/fpls.2024.1433015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/15/2024] [Indexed: 09/21/2024]
Abstract
Introduction Cepharanthine (CEP), a bisbenzylisoquinoline alkaloid (bisBIA) extracted from Stephania japonica, has received significant attention for its anti-coronavirus properties. While ethylene response factors (ERFs) have been reported to regulate the biosynthesis of various alkaloids, their role in regulating CEP biosynthesis remains unexplored. Methods Genome-wide analysis of the ERF genes was performed with bioinformatics technology, and the expression patterns of different tissues, were analyzed by transcriptome sequencing analysis and real-time quantitative PCR verification. The nuclear-localized ERF gene cluster was shown to directly bind to the promoters of several CEP-associated genes, as demonstrated by yeast one-hybrid assays and subcellular localization assays. Results In this work, 59 SjERF genes were identified in the S. japonica genome and further categorized into ten subfamilies. Notably, a SjERF gene cluster containing three SjERF genes was found on chromosome 2. Yeast one-hybrid assays confirmed that the SjERF gene cluster can directly bind to the promoters of several CEP-associated genes, suggesting their crucial role in CEP metabolism. The SjERFs cluster-YFP fusion proteins were observed exclusively in the nuclei of Nicotiana benthamiana leaves. Tissue expression profiling revealed that 13 SjERFs exhibit high expression levels in the root, and the qRT-PCR results of six SjERFs were consistent with the RNA-Seq data. Furthermore, a co-expression network analysis demonstrated that 24 SjERFs were highly positively correlated with the contents of various alkaloids and expression levels of CEP biosynthetic genes. Conclusion This study provides the first systematic identification and analysis of ERF transcription factors in the S.japonica genome, laying the foundation for the future functional research of SjERFs transcription factors.
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Affiliation(s)
- Hanting Yang
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Baimei Liu
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Haiyan Ding
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhaoyu Liu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaodong Li
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Tianxing He
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ya Wu
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuxuan Zhang
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Can Wang
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liang Leng
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shilin Chen
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chi Song
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Chaudhary J, Gangwar H, Jaiswal V, Gupta PK. Identification and characterization of sulphotransferase (SOT) genes for tolerance against drought and heat in wheat and six related species. Mol Biol Rep 2024; 51:956. [PMID: 39230759 DOI: 10.1007/s11033-024-09899-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 08/27/2024] [Indexed: 09/05/2024]
Abstract
BACKGROUND Sulphotransferase (SOT) enzyme (encoded by a conserved family of SOT genes) is involved in sulphonation of a variety of compounds, through transfer of a sulphuryl moiety from 3'phosphoadenosine- 5'phosphosulphate (PAPS) to a variety of secondary metabolites. The PAPS itself is derived from 3'adenosine-5'phosphosulphate (APS) that is formed after uptake of sulphate ions from the soil. The process provides tolerance against abiotic stresses like drought and heat in plants. Therefore, a knowledge of SOT genes in any crop may help in designing molecular breeding methods for improvement of tolerance for drought and heat. METHODS Sequences of rice SOT genes and SOT domain (PF00685) of corresponding proteins were both used for identification of SOT genes in wheat and six related species (T. urartu, Ae. tauschii, T. turgidum, Z. mays, B. distachyon and Hordeum vulgare), although detailed analysis was conducted only in wheat. The wheat genes were mapped on individual chromosomes and also subjected to synteny and collinearity analysis. The proteins encoded by these genes were examined for the presence of a complete SOT domain using 'Conserved Domain Database' (CDD) search tool at NCBI. RESULTS In wheat, 107 TaSOT genes, ranging in length from 969 bp to 7636 bp, were identified and mapped onto individual chromosomes. SSRs (simple sequence repeats), microRNAs, long non-coding RNAs (lncRNAs) and their target sites were also identified in wheat SOT genes. SOT proteins were also studied in detail. An expression assay of TaSOT genes via wheat RNA-seq data suggested engagement of these genes in growth, development and responses to various hormones and biotic/abiotic stresses. CONCLUSIONS The results of the present study should help in further functional characterization of SOT genes in wheat and other related crops.
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Affiliation(s)
- Jyoti Chaudhary
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Himanshi Gangwar
- Council of Scientific & Industrial Research-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vandana Jaiswal
- Council of Scientific & Industrial Research-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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Duan L, Hou Z, Zhang W, Liang S, Huangfu M, Zhang J, Yang T, Dong J, Che D. Genome-wide analysis of the WOX gene family and function exploration of RhWOX331 in rose ( R. 'The Fairy'). FRONTIERS IN PLANT SCIENCE 2024; 15:1461322. [PMID: 39290741 PMCID: PMC11405225 DOI: 10.3389/fpls.2024.1461322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 08/13/2024] [Indexed: 09/19/2024]
Abstract
WOXs are a class of plant-specific transcription factors that play key roles in plant growth and stress responses. However, the mechanism by which WOXs influence adventitious root development in Rosa hybrida remains unclear. In this study, RcWOX gene family in rose was identified and phylogenetically analyzed using bioinformatics analysis. A total of 381 RcWOX gene members were localized on seven chromosomes except of nine members. The main cis-acting elements involved in hormonal, light, developmental, and abiotic stress responses were identified in the promoters of RcWOX genes, suggesting their regulation by these signals. Nine RhWOX genes had significant different expression during rooting process of rose. RhWOX331, RhWOX308, RhWOX318 were positive with the formation of rose roots. RhWOX331 was positively involved in the formation of adventitious root primordia, which gene coding a transcription factor localized in the nucleus. The HOX conserved domain in the protein contributed to the self-activating activity of RhWOX331. We obtained genetically modified Arabidopsis to validate the function of RhWOX331. Overexpression of RhWOX331 gene alleviated the inhibition of root length of A. thaliana primary roots by high concentration of IBA and NPA, and significantly increased the number of lateral roots on the primary roots, as well as the height of A. thaliana plants. Additionally, RhWOX331 promoted adventitious root formation in A. thaliana and mitigated hormonal inhibition by exogenous 6-BA, NPA, and GA3. The RhWOX331 promoter contained cis-acting elements such as ABRE, Box 4 and CGTCA-motif et.al. GUS activity analysis showed that the gene acted at the cotyledon attachment site. Taken together, these studies identified a significant expansion of the RcWOX gene family, inferred roles of certain branch members in adventitious root formation, elucidated the function of RhWOX331 in adventitious root initiation, and laid the foundation for further research on the function of WOX gene family in roses.
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Affiliation(s)
- Lian Duan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Zhihui Hou
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Wuhua Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Shuang Liang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Minge Huangfu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Jinzhu Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Tao Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Jie Dong
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Daidi Che
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
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Liu X, Guo N, Li S, Duan M, Wang G, Zong M, Han S, Wu Z, Liu F, Zhang J. Characterization of the Bax Inhibitor-1 Family in Cauliflower and Functional Analysis of BobBIL4. Int J Mol Sci 2024; 25:9562. [PMID: 39273509 PMCID: PMC11395134 DOI: 10.3390/ijms25179562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/22/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
The Bax inhibitor-1 (BI-1) gene family, which is important for plant growth, development, and stress tolerance, remains largely unexplored in cauliflower. In this study, we identified and characterized cauliflower BI-1 family genes. Based on aligned homologous sequences and collinearity with Arabidopsis genes, we identified nine cauliflower BI-1 genes, which encode proteins that varied in length, molecular weight, isoelectric point, and predicted subcellular localization, including the Golgi apparatus, plasma membrane, and various compartments within the chloroplast. Phylogenetic analyses detected evolutionary conservation and divergence among these genes. Ten structural motifs were identified, with Motif 5 found to be crucial for inhibiting apoptosis. According to the cis-regulatory elements in their promoters, these genes likely influence hormone signaling and stress responses. Expression profiles among tissues highlighted the functional diversity of these genes, with particularly high expression levels observed in the silique and root. Focusing on BobBIL4, we investigated its role in brassinosteroid (BR)-mediated root development and salt stress tolerance. BobBIL4 expression levels increased in response to BR and salt treatments. The functional characterization of this gene in Arabidopsis revealed that it enhances root growth and salinity tolerance. These findings provide insights into BI-1 gene functions in cauliflower while also highlighting the potential utility of BobBIL4 for improving crop stress resistance.
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Affiliation(s)
- Xin Liu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Ning Guo
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Shasha Li
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Mengmeng Duan
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Guixiang Wang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Mei Zong
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Shuo Han
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Zihan Wu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Fan Liu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
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Martínez-Navarro SM, de Iceta Soler X, Martínez-Martínez M, Olazábal-Morán M, Santos-Moriano P, Gómez S. Structural and Phylogenetic In Silico Characterization of Vitis vinifera PRR Protein as Potential Target for Plasmopara viticola Infection. Int J Mol Sci 2024; 25:9553. [PMID: 39273500 PMCID: PMC11395273 DOI: 10.3390/ijms25179553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024] Open
Abstract
Fungi infection, especially derived from Plasmopara viticola, causes severe grapevine economic losses worldwide. Despite the availability of chemical treatments, looking for eco-friendly ways to control Vitis vinifera infection is gaining much more attention. When a plant is infected, multiple disease-control molecular mechanisms are activated. PRRs (Pattern Recognition Receptors) and particularly RLKs (receptor-like kinases) take part in the first barrier of the immune system, and, as a consequence, the kinase signaling cascade is activated, resulting in an immune response. In this context, discovering new lectin-RLK (LecRLK) membrane-bounded proteins has emerged as a promising strategy. The genome-wide localization of potential LecRLKs involved in disease defense was reported in two grapevine varieties of great economic impact: Chardonnay and Pinot Noir. A total of 23 potential amino acid sequences were identified, exhibiting high-sequence homology and evolution related to tandem events. Based on the domain architecture, a carbohydrate specificity ligand assay was conducted with docking, revealing two sequences as candidates for specific Vitis vinifera-Plasmopara viticola host-pathogen interaction. This study confers a starting point for designing new effective antifungal treatments directed at LecRLK targets in Vitis vinifera.
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Affiliation(s)
- Sofía M Martínez-Navarro
- Innovative Seed Lab (ISL), Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Villaviciosa de Odón, Spain
| | - Xavier de Iceta Soler
- Innovative Seed Lab (ISL), Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Villaviciosa de Odón, Spain
| | - Mónica Martínez-Martínez
- Innovative Seed Lab (ISL), Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Villaviciosa de Odón, Spain
| | - Manuel Olazábal-Morán
- Innovative Seed Lab (ISL), Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Villaviciosa de Odón, Spain
| | - Paloma Santos-Moriano
- Innovative Seed Lab (ISL), Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Villaviciosa de Odón, Spain
| | - Sara Gómez
- Innovative Seed Lab (ISL), Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Villaviciosa de Odón, Spain
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Bai X, Qiao P, Liu H, Shang Y, Guo J, Dai K. Genome-wide identification of the E-class gene family in wheat: evolution, expression, and interaction. FRONTIERS IN PLANT SCIENCE 2024; 15:1419437. [PMID: 39290745 PMCID: PMC11405201 DOI: 10.3389/fpls.2024.1419437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/14/2024] [Indexed: 09/19/2024]
Abstract
Introduction Wheat (Triticum aestivum L.) is among themost important crop worldwide. Given a growing population and changing climate, enhancing wheat yield is of great importance. Yield is closely associated with flower and spike development, and E-class genes play important roles in the flower and kernel development of plants. Currently, the absence of systematic analysis on the E gene family hinders our comprehension of their roles in plant growth and development. Methods Identify E-class genes based on homologous sequence searches. Analyze the identified E-class genes through a series of gene family analyses. Determine the expression levels of wheat E-class genes by searching public databases. Validate the functions of these genes by transforming them into Arabidopsis. Finally, determine the interactions between the genes through yeast two-hybrid experiments. Results Fifteen E-class genes (TaEs) were identified in common wheat. Nine E-class genes were detected in five ancestral/closely related species, including one in Aegilops tauschii (AtE), one in T. Urartu (TuEs), two in T. turgidum (TtEs), two in T. dicoccoides (TdEs), and three in T. spelta (TsEs). The 24 E-class genes were classified into three subgroups using a phylogenetic approach. All genes were highly expressed in spikes, and most were only highly expressed at the floret meristem stage. The effects of TaSEP5-A on flowering and growth cycles were confirmed in homologous mutants and transgenic Arabidopsis thaliana. The E-class genes were able to regulate the growth cycle of Arabidopsis. Finally, we confirmed the interactions between TaSEP5-A and other wheat E-class genes based on yeast two-hybrid assays. Discussion Our findings provide information regarding the E-class genes in wheat and will potentially promote the application of these genes in wheat improvement.
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Affiliation(s)
- Xionghui Bai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
| | - Pengfei Qiao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
| | - Hanxiao Liu
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
| | - Yuping Shang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
| | - Jie Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
| | - Keli Dai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
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Liu Q, Wang B, Xu W, Yuan Y, Yu J, Cui G. Genome-wide investigation of the PIF gene family in alfalfa (Medicago sativa L.) expression profiles during development and stress. BMC Genom Data 2024; 25:79. [PMID: 39223486 PMCID: PMC11370104 DOI: 10.1186/s12863-024-01264-4] [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: 06/20/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Phytochrome-interacting factors (PIFs) plays an important role in plants as hubs for intracellular signaling regulation. The PIF gene family has been identified and characterized in many plants, but alfalfa (Medicago sativa L.), an important perennial high-quality legume forage, has not been reported on the PIF gene family. RESULTS In this study, we presented the identification and characterization of five MsPIF genes in alfalfa (Medicago sativa L.). Phylogenetic analysis indicated that PIFs from alfalfa and other four plant species could be divided into three groups supported by similar motif analysis. The collinearity analysis of the MsPIF gene family showed the presence of two gene pairs, and the collinearity analysis with AtPIFs showed three gene pairs, indicating that the evolutionary process of this family is relatively conservative. Analysis of cis-acting elements in promoter regions of MsPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. Gene expression analyses demonstrated that MsPIFs were primarily expressed in the leaves and were induced by various abiotic stresses. CONCLUSION This study conducted genome-wide identification, evolution, synteny analysis, and expression analysis of the PIFs in alfalfa. Our study lays a foundation for the study of the biological functions of the PIF gene family and provides a useful reference for improving abiotic stress resistance in alfalfa.
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Affiliation(s)
- Qianning Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Baiji Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Wen Xu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yuying Yuan
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jinqiu Yu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.
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Kababji AM, Butt H, Mahfouz M. Synthetic directed evolution for targeted engineering of plant traits. FRONTIERS IN PLANT SCIENCE 2024; 15:1449579. [PMID: 39286837 PMCID: PMC11402689 DOI: 10.3389/fpls.2024.1449579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 08/12/2024] [Indexed: 09/19/2024]
Abstract
Improving crop traits requires genetic diversity, which allows breeders to select advantageous alleles of key genes. In species or loci that lack sufficient genetic diversity, synthetic directed evolution (SDE) can supplement natural variation, thus expanding the possibilities for trait engineering. In this review, we explore recent advances and applications of SDE for crop improvement, highlighting potential targets (coding sequences and cis-regulatory elements) and computational tools to enhance crop resilience and performance across diverse environments. Recent advancements in SDE approaches have streamlined the generation of variants and the selection processes; by leveraging these advanced technologies and principles, we can minimize concerns about host fitness and unintended effects, thus opening promising avenues for effectively enhancing crop traits.
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Affiliation(s)
- Ahad Moussa Kababji
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Shah OU, Peng J, Zhou L, Khan WU, Shanshan Z, Zhuyu P, Liu P, Khan LU. Comparative omics-based characterization, phylogeny and melatonin-mediated expression analyses of GDSL genes in pitaya ( Selenicereus undatus L.) against multifactorial abiotic stresses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1493-1515. [PMID: 39310703 PMCID: PMC11413313 DOI: 10.1007/s12298-024-01506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 08/12/2024] [Accepted: 08/19/2024] [Indexed: 09/25/2024]
Abstract
The GDSL gene family plays diverse roles in plant growth and development. Despite its significance, the functions of the GDSL in the pitaya plant are still unknown. Pitaya (Selenicereus undatus L.) also called Hylocereus undatus (Hu), belongs to the family Cactaceae and is an important tropical plant that contains high dietary fibers and antioxidants. In the present investigation, we screened 91 HuGDSL genes in the pitaya genome by conducting a comprehensive computational analysis. The phylogenetic tree categorized HuGDSL genes into 9 distinct clades in combination with four other species. Further, 29 duplicate events were identified of which 12 were tandem, and 17 were segmental. The synteny analysis revealed that segmental duplication was more prominent than tandem duplication among these genes. The majority of duplicated gene pairs (95%) indicate their Ka/Ks ratios ranging from 0.1 to 0.3, which shows that maximum HuGDSL genes were under purifying selection pressure. The cis-acting element in the promotor region contains phytohormones such as auxin, gibberellin, jasmonic acid, and abscisic acid abundantly. Finally, the HuGDSL gene expression pattern under single and multiple stresses was analyzed via; RNA-seq. We select ten stress-responsive HuGDSL genes for RT-qPCR validation. After careful investigation, we identified five HuGDSL candidate genes (HuGDSL-1/3/55/59, and HuGDSL-78) based on RNA-seq, and RT-qPCR data that showed enhanced expression in stress and melatonin-applied seedlings. This study represents valuable insights into maintaining pitaya growth and development by preparing stress-resilient pitaya genotypes through modern biotechnological techniques. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01506-w.
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Affiliation(s)
- Obaid Ullah Shah
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry Hainan University, Sanya, 572025 Hainan China
| | - Jiantao Peng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry Hainan University, Sanya, 572025 Hainan China
| | - Lingling Zhou
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry Hainan University, Sanya, 572025 Hainan China
| | - Wasi Ullah Khan
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry Hainan University, Sanya, 572025 Hainan China
| | - Zhang Shanshan
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry Hainan University, Sanya, 572025 Hainan China
| | - Pan Zhuyu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry Hainan University, Sanya, 572025 Hainan China
| | - Pingwu Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry Hainan University, Sanya, 572025 Hainan China
| | - Latif Ullah Khan
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry Hainan University, Sanya, 572025 Hainan China
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Liu Q, Zeng W, Qi L, Li X, Zhou Y, Gao F. The module consisting of transcription factor WRKY14 and thaumatin-like protein TLP25 is involved in winter adaptation in Ammopiptanthus mongolicus. PHYSIOLOGIA PLANTARUM 2024; 176:e14560. [PMID: 39344373 DOI: 10.1111/ppl.14560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/20/2024] [Accepted: 09/23/2024] [Indexed: 10/01/2024]
Abstract
Thaumatin-like proteins (TLPs) are conserved proteins involved in the defense and stress responses of plants. Previous studies showed that several TLPs were accumulated in leaf apoplast in Ammopiptanthus mongolicus in winter, indicating that TLPs might be related to the adaptation to winter climate in A. mongolicus. To investigate the roles of TLPs in winter adaptation, we first analyzed the expression pattern of TLP genes in A. mongolicus and then focused on the biological function and regulation pathway of AmTLP25 gene. Several TLP genes, including AmTLP25, were upregulated during winter and in response to both cold and osmotic stress. Overexpression of the AmTLP25 gene led to an increased tolerance of transgenic Arabidopsis to freezing and osmotic stress. Furthermore, the elevated AmWRKY14 transcription factor during winter activated AmTLP25 gene expression by specifically binding to its promoter. It is speculated that the AmWRKY14 - AmTLP25 module contributes to the adaptation to temperate winter climate in A. mongolicus. Our research advances the current understanding of the biological function and regulatory pathway of TLP genes and provides valuable information for understanding the molecular mechanism of temperate evergreen broad-leaved plants adapting to winter climate.
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Affiliation(s)
- Qi Liu
- Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Weiying Zeng
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Lanting Qi
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Xuting Li
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Yijun Zhou
- Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Fei Gao
- Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
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Song LY, Xu CQ, Zhang LD, Li J, Jiang LW, Ma DN, Guo ZJ, Wang Q, Wang XX, Zheng HL. Trehalose along with ABA promotes the salt tolerance of Avicennia marina by regulating Na + transport. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2349-2362. [PMID: 38981025 DOI: 10.1111/tpj.16921] [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: 03/12/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024]
Abstract
Mangroves grow in tropical/subtropical intertidal habitats with extremely high salt tolerance. Trehalose and trehalose-6-phosphate (T6P) have an alleviating function against abiotic stress. However, the roles of trehalose in the salt tolerance of salt-secreting mangrove Avicennia marina is not documented. Here, we found that trehalose was significantly accumulated in A. marina under salt treatment. Furthermore, exogenous trehalose can enhance salt tolerance by promoting the Na+ efflux from leaf salt gland and root to reduce the Na+ content in root and leaf. Subsequently, eighteen trehalose-6-phosphate synthase (AmTPS) and 11 trehalose-6-phosphate phosphatase (AmTPP) genes were identified from A. marina genome. Abscisic acid (ABA) responsive elements were predicted in AmTPS and AmTPP promoters by cis-acting elements analysis. We further identified AmTPS9A, as an important positive regulator, that increased the salt tolerance of AmTPS9A-overexpressing Arabidopsis thaliana by altering the expressions of ion transport genes and mediating Na+ efflux from the roots of transgenic A. thaliana under NaCl treatments. In addition, we also found that ABA could promote the accumulation of trehalose, and the application of exogenous trehalose significantly promoted the biosynthesis of ABA in both roots and leaves of A. marina. Ultimately, we confirmed that AmABF2 directly binds to the AmTPS9A promoter in vitro and in vivo. Taken together, we speculated that there was a positive feedback loop between trehalose and ABA in regulating the salt tolerance of A. marina. These findings provide new understanding to the salt tolerance of A. marina in adapting to high saline environment at trehalose and ABA aspects.
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Affiliation(s)
- Ling-Yu Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
| | - Chao-Qun Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
| | - Lu-Dan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
- Houji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan, Shanxi, 030000, People's Republic of China
| | - Jing Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
| | - Li-Wei Jiang
- College of Horticulture, Henan Agricultural University, Zhengzhou, Henan, 450046, People's Republic of China
| | - Dong-Na Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Ze-Jun Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
| | - Qian Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
| | - Xiu-Xiu Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
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Rahman JF, Hoque H, Jubayer AA, Jewel NA, Hasan MN, Chowdhury AT, Prodhan SH. Alfin-like (AL) transcription factor family in Oryza sativa L.: Genome-wide analysis and expression profiling under different stresses. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 43:e00845. [PMID: 38962072 PMCID: PMC11217604 DOI: 10.1016/j.btre.2024.e00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/24/2024] [Accepted: 05/29/2024] [Indexed: 07/05/2024]
Abstract
Oryza sativa L. is the world's most essential and economically important food crop. Climate change and ecological imbalances make rice plants vulnerable to abiotic and biotic stresses, threatening global food security. The Alfin-like (AL) transcription factor family plays a crucial role in plant development and stress responses. This study comprehensively analyzed this gene family and their expression profiles in rice, revealing nine AL genes, classifying them into three distinct groups based on phylogenetic analysis and identifying four segmental duplication events. RNA-seq data analysis revealed high expression levels of OsALs in different tissues, growth stages, and their responsiveness to stresses. RT-qPCR data showed significant expression of OsALs in different abiotic stresses. Identification of potential cis-regulatory elements in promoter regions has also unveiled their involvement. Tertiary structures of the proteins were predicted. These findings would lay the groundwork for future research to reveal their molecular mechanism in stress tolerance and plant development.
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Affiliation(s)
- Jeba Faizah Rahman
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Hammadul Hoque
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Abdullah -Al- Jubayer
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Nurnabi Azad Jewel
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md. Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Aniqua Tasnim Chowdhury
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Shamsul H. Prodhan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
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Qi J, Luo Y, Lu S, Liu H, Huang H, Qiu Y, Zhou X, Ma C. Multi-omics integration analysis reveals the molecular mechanisms of drought adaptation in homologous tetraploid alfalfa(Medicago sativa 'Xinjiang-Daye'). PHYSIOLOGIA PLANTARUM 2024; 176:e14476. [PMID: 39262125 DOI: 10.1111/ppl.14476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/27/2024] [Accepted: 07/08/2024] [Indexed: 09/13/2024]
Abstract
Drought stress is a predominant abiotic factor leading to decreased alfalfa yield. Genomic ploidy differences contribute to varying adaptation mechanisms of different alfalfa cultivars to drought conditions. This study employed a multi-omics approach to characterize the molecular basis of drought tolerance in a tetraploid variant of alfalfa (Medicago sativa, Xinjiang-Daye). Under drought treatment, a total of 4446 genes, 859 proteins, and 524 metabolites showed significant differences in abundance. Integrative analysis of the multi-omics data revealed that regulatory modules involved in flavonoid biosynthesis, plant hormone signalling transduction, linoleic acid metabolism, and amino acid biosynthesis play crucial roles in alfalfa adaptation to drought stress. The severity of drought led to the substantial accumulation of flavonoids, plant hormones, free fatty acids, amino acids, and their derivatives in the leaves. Genes such as PAL, 4CL, CHI, CHS, PP2C, ARF_3, and AHP_4 play pivotal regulatory roles in flavonoid biosynthesis and hormone signalling pathways. Differential expression of the LOX gene emerged as a key factor in the elevated levels of free fatty acids. Upregulation of P5CS_1 and GOT1/2 contributed significantly to the accumulation of Pro and Phe contents. ERF19 emerged as a principal positive regulator governing the synthesis of the aforementioned compounds. Furthermore, observations suggest that Xinjiang-Daye alfalfa may exhibit widespread post-transcriptional regulatory mechanisms in adapting to drought stress. The study findings unveil the critical mechanisms by which Xinjiang-Daye alfalfa adapts to drought stress, offering novel insights for the improvement of alfalfa germplasm resources.
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Affiliation(s)
- Jianwei Qi
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Yongzhong Luo
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Songsong Lu
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Hui Liu
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Haixia Huang
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Yingde Qiu
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Xiaotong Zhou
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Chao Ma
- College of Forestry, Gansu Agricultural University, Lanzhou, China
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Ma F, Song S, Li C, Huang D, Wu B, Xing W, Huang H, Tan Y, Xu Y. Passion fruit HD-ZIP genes: Characterization, expression variance, and overexpression PeHB31 enhanced drought tolerance via lignin pathway. Int J Biol Macromol 2024; 276:133603. [PMID: 38969043 DOI: 10.1016/j.ijbiomac.2024.133603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/26/2024] [Accepted: 06/30/2024] [Indexed: 07/07/2024]
Abstract
The HD-ZIP (homeodomain-leucine zipper) genes hold significant importance in transcriptional regulation, especially in plant development and responses to abiotic stresses. However, a comprehensive study targeting HD-ZIP family members in passion fruit has been absent. In our current research, 34 HD-ZIP family members (PeHBs) were identified by bioinformatics analysis. Transcriptome analysis revealed that PeHBs exhibited distinct expression patterns when subjected to the four different abiotic stresses, and significant differential expression of PeHBs was also found among the three developmental stages of the fruit and between the purple and yellow genotype passion fruit leaves. An integrated metabolome and transcriptome analysis further revealed that the HD-ZIP III class gene PeHB31 (homologous to ATHB8), was co-upexpressed with lignans in yellow fruit P. edulis (commonly used as a resistance rootstock) when compared to purple fruit P. edulis. The transformation of Arabidopsis and yeast with the PeHB31 gene showed an enhancement in their capacity to withstand drought conditions. Notably, the transgenic Arabidopsis plants exhibited an increase in lignin content within the vascular tissues of their stems. This research lays the groundwork for future studies on the control mechanisms of lignin biosynthesis by HD-ZIP genes (especially HD-ZIP classes III and I) involved in drought tolerance.
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Affiliation(s)
- Funing Ma
- Tropical Crops Genetic Resources Institute, CATAS, National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Germplasm Repository of Passiflora, CATAS, Hainan 571101, China; Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou 571101, China
| | - Shun Song
- Tropical Crops Genetic Resources Institute, CATAS, National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Germplasm Repository of Passiflora, CATAS, Hainan 571101, China; Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou 571101, China; Hainan Seed Industry Laboratory, Sanya 572024, China.
| | - Chuanlin Li
- Sanya Institute of Technology, Sanya 572099, China
| | - Dongmei Huang
- Tropical Crops Genetic Resources Institute, CATAS, National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Germplasm Repository of Passiflora, CATAS, Hainan 571101, China; Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou 571101, China
| | - Bin Wu
- Tropical Crops Genetic Resources Institute, CATAS, National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Germplasm Repository of Passiflora, CATAS, Hainan 571101, China; Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou 571101, China
| | - Wenting Xing
- Tropical Crops Genetic Resources Institute, CATAS, National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Germplasm Repository of Passiflora, CATAS, Hainan 571101, China; Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou 571101, China
| | - Haijie Huang
- Tropical Crops Genetic Resources Institute, CATAS, National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Germplasm Repository of Passiflora, CATAS, Hainan 571101, China; Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou 571101, China
| | - Yuxin Tan
- Tropical Crops Genetic Resources Institute, CATAS, National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Germplasm Repository of Passiflora, CATAS, Hainan 571101, China; Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou 571101, China
| | - Yi Xu
- Tropical Crops Genetic Resources Institute, CATAS, National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Germplasm Repository of Passiflora, CATAS, Hainan 571101, China; Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou 571101, China; Hainan Seed Industry Laboratory, Sanya 572024, China.
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Geng K, Zhan Z, Xue X, Hou C, Li D, Wang Z. Genome‑wide identification of the SWEET gene family in grape ( Vitis vinifera L.) and expression analysis of VvSWEET14a in response to water stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1565-1579. [PMID: 39310704 PMCID: PMC11413283 DOI: 10.1007/s12298-024-01501-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 07/12/2024] [Accepted: 08/06/2024] [Indexed: 09/25/2024]
Abstract
Sugars are considered primary metabolites that determine the flavor and quality of grape berries, also playing a crucial role in the plants to resist stress. Sugars Will Eventually be Exported Transporters (SWEETs) gene family has been previously reported to be involved in the growth and development of grape, while the changes in transcriptional levels under water stress remain unclear. In this study, sixteen grape SWEETs members were identified and annotated based on their homologous genes in Arabidopsis and tomato, they were classified into four clades (Clades I to IV) with VvSWEETs by phylogenetic analysis. The highly conserved motifs and gene structures of VvSWEETs indicate that they are closely evolutionary conservation. Chromosomal localization and synteny analysis found that VvSWEETs were unevenly distributed on 11 chromosomes, and the VvSWEET5a, VvSWEET5b, VvSWEET14b and VvSWEET14c existed a relatively recent evolutionary relationship. Promoter cis-acting elements showed that the clade III has more ABRE motif, especially the VvSWEET14a. The regulation of VvSWEETs is mainly influenced by the Dof and MYB families, which are associated with grape ripening, while VvSWEET14a is closely related to the bHLH, MYB, NAC, and bZIP families. RT-qPCR data and subcellular localization show that VvSWEET14a was highly induced under early water stress and is located in the vacuole membrane. The instantaneous transformation assay identified that this gene could promote to transport hexose in the vacuole to maintain normal osmotic pressure. In summary, our study provides a basis for further research on SWEET genes function and regulatory mechanism in the future, and lays the foundation for stress resistance breeding of Vitis vinifera. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01501-1.
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Affiliation(s)
- Kangqi Geng
- School of Life Sciences, Ningxia University, Yinchuan, 750021 Ningxia People’s Republic of China
| | - Zhennan Zhan
- School of Life Sciences, Ningxia University, Yinchuan, 750021 Ningxia People’s Republic of China
| | - Xiaobin Xue
- Agriculture of College, Ningxia University, Yinchuan, 750021 Ningxia People’s Republic of China
| | - Chenyang Hou
- Agriculture of College, Ningxia University, Yinchuan, 750021 Ningxia People’s Republic of China
| | - Dongmei Li
- Agriculture of College, Ningxia University, Yinchuan, 750021 Ningxia People’s Republic of China
| | - Zhenping Wang
- School of Life Sciences, Ningxia University, Yinchuan, 750021 Ningxia People’s Republic of China
- Agriculture of College, Ningxia University, Yinchuan, 750021 Ningxia People’s Republic of China
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80
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Hui W, Wu H, Zheng H, Wang K, Yang T, Fan J, Wu J, Wang J, Al Mutairi AA, Yang H, Yang C, Cui B, Loake GJ, Gong W. Genome-wide characterization of RR gene family members in Zanthoxylum armatum and the subsequent functional characterization of the C-type RR. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108943. [PMID: 39032447 DOI: 10.1016/j.plaphy.2024.108943] [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: 12/27/2023] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Response Regulators (RRs) are crucial regulators in plant development and stress responses, comprising A-type, B-type, C-type, and pseudo-RR subfamilies. However, previous studies have often focused on specific subfamilies, which restricts our understanding of the complete RR gene family. In this study, we conducted a comprehensive analysis of 63 RR members from Zanthoxylum armatum, using phylogenetic relationships, motif composition, cis-acting elements, gene duplication and collinearity analyses. Segmental repeats among ZaRR genes enhanced the various environmental adaptabilities of Z. armatum, and the B-type ZaRR exhibited significant collinearity with the RRs in P. trichocarpa and C. sinensis. Cis-element analysis indicated ZaRRs play a significant role in abiotic stress and phytohormone pathways, particularly in light, drought, cold, abscisic acid (ABA) and salicylic acid (SA) responses. Abundant Ethylene Response Factor (ERF) and reproduction-associated binding sites in ZaRR promoters suggested their roles in stress and reproductive processes. A-type ZaRRs were implicated in plant vegetative and reproductive growth, whereas B-type ZaRRs contributed to both growth and stress responses. C-type ZaRRs were associated with plant reproductive growth, whereas pseudo-RRs may function in plant stress responses, such as water logging, cold, and response to ethylene (ETH), SA, and jasmonic acid (JA). Ectopic expression of ZaRR24, a C-type RR, inhibits growth, induces early flowering, and shortens fruit length in Arabidopsis. ZaRR24 overexpression also affected the expression of A- and B-type RRs, as well as floral meristem and organ identity genes. These findings establish a solid and comprehensive foundation for RR gene research in Z. armatum, and provide a platform for investigating signal transduction in other woody plants.
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Affiliation(s)
- Wenkai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Han Wu
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hao Zheng
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiangtao Fan
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaojiao Wu
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingyan Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Ahmed A Al Mutairi
- Biology Department, College of Science, Jouf University, Sakaka, 41412, Saudi Arabia
| | - Hua Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chunlin Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Beimi Cui
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Wei Gong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
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81
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Ahmad A, Sajjad M, Sadau SB, Elasad M, Sun L, Quan Y, Wu A, Boying L, Wei F, Wu H, Chen P, Fu X, Ma L, Wang H, Wei H, Yu S. GhJUB1_3-At positively regulate drought and salt stress tolerance under control of GhHB7, GhRAP2-3 and GhRAV1 in Cotton. PHYSIOLOGIA PLANTARUM 2024; 176:e14497. [PMID: 39223909 DOI: 10.1111/ppl.14497] [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: 03/28/2024] [Revised: 06/12/2024] [Accepted: 06/25/2024] [Indexed: 09/04/2024]
Abstract
Climate change severely affects crop production. Cotton is one of the primary fiber crops in the world and its production is susceptible to various environmental stresses, especially drought and salinity. Development of stress tolerant genotypes is the only way to escape from these environmental constraints. We identified sixteen homologs of the Arabidopsis JUB1 gene in cotton. Expression of GhJUB1_3-At was significantly induced in the temporal expression analysis of GhJUB1 genes in the roots of drought tolerant (H177) and susceptible (S9612) cotton genotypes under drought. The silencing of the GhJUB1_3-At gene alone and together with its paralogue GhJUB1_3-Dt reduced the drought tolerance in cotton plants. The transgenic lines exhibited tolerance to the drought and salt stress as compared to the wildtype (WT). The chlorophyll and relative water contents of wildtype decreased under drought as compared to the transgenic lines. The transgenic lines showed decreased H2O2 and increased proline levels under drought and salt stress, as compared to the WT, indicating that the transgenic lines have drought and salt stress tolerance. The expression analysis of the transgenic lines and WT revealed that GAI was upregulated in the transgenic lines in normal conditions as compared to the WT. Under drought and salt treatment, RAB18 and RD29A were strongly upregulated in the transgenic lines as compared to the WT. Conclusively, GhJUB1_3-At is not an auto activator and it is regulated by the crosstalk of GhHB7, GhRAP2-3 and GhRAV1. GhRAV1, a negative regulator of abiotic stress tolerance and positive regulator of leaf senescence, suppresses the expression of GhJUB1_3-At under severe circumstances leading to plant death.
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Affiliation(s)
- Adeel Ahmad
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- Central Cotton Research Institute, Pakistan Central Cotton Committee, Multan, Pakistan
| | - Muhammad Sajjad
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Salisu Bello Sadau
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | | | - Lu Sun
- Handan Academy of Agricultural Sciences, Handan, Hebei, China
| | - Yuewei Quan
- Handan Academy of Agricultural Sciences, Handan, Hebei, China
| | - Aimin Wu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Lian Boying
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Fei Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Hongmei Wu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Pengyun Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Xiaokang Fu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Liang Ma
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Hantao Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Hengling Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Shuxun Yu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization /Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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82
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Guo P, Liu A, Qi Y, Wang X, Fan X, Guo X, Yu C, Tian C. Genome-wide identification of cold shock proteins (CSPs) in sweet cherry (Prunus avium L.) and exploring the differential responses of PavCSP1 and PavCSP3 to low temperature and salt stress. Genes Genomics 2024; 46:1023-1036. [PMID: 38997611 DOI: 10.1007/s13258-024-01542-6] [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: 04/11/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND Cold shock proteins (CSPs) are ubiquitous nucleic acid-binding proteins involved in growth, development, and stress response across various organisms. While extensively studied in many species, their regulatory roles in sweet cherry (Prunus avium L.) remain unclear. OBJECTIVE To identify and analyze CSP genes (PavCSPs) in sweet cherry genome, and explore the differential responses of PavCSP1 and PavCSP3 to low temperature and salt stress. METHODS Three methods were employed to identify and characterize CSP in sweet cherry genomes. To explore the potential functions and evolutionary relationships of sweet cherry CSP proteins, sequence alignment and phylogenetic tree incorporating genes from five species were conducted and constructed, respectively. To investigate the responses to abiotic stresses, cis-acting elements analysis and gene expression patterns to low-temperature and salt stress were examined. Moreover, transgenic yeasts overexpressing PavCSP1 or PavCSP3 were generated and their growth under stress conditions were observed. RESULTS In this study, three CSP genes (PavCSPs) were identified and comprehensively analyzed. The quantitative real-time PCR revealed diverse expression patterns, with PavCSP1-3 demonstrating a particular activity in the upper stem and all members were responsive to low-temperature and salt stress. Further investigation demonstrated that transgenic yeasts overexpressing PavCSP1 or PavCSP3 exhibited improved growth states following high-salt and low-temperature stress. CONCLUSION These findings elucidated the responses of PavCSP1 and PavCSP3 to salt and low-temperature stresses, laying the groundwork for further functional studies of PavCSPs in response to abiotic stresses.
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Affiliation(s)
- Pan Guo
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
- Yantai Academy of Agricultural Sciences, Yantai, Shandong, 265500, China
| | - Ao Liu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
- Yantai Academy of Agricultural Sciences, Yantai, Shandong, 265500, China
| | - Yueting Qi
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
| | - Xueting Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
| | - Xiaole Fan
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
| | - Xiaotong Guo
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
| | - Chunyan Yu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China.
| | - Changping Tian
- Yantai Academy of Agricultural Sciences, Yantai, Shandong, 265500, China.
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Fang Y, Wang L, Liu K, Wu H, Zheng Y, Duan Y, Feng S, Wang Y. Genome-wide investigation of HD-ZIP gene family and functional characterization of BnaHDZ149 and BnaHDZ22 in salt and drought response in Brassica napus L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112130. [PMID: 38795751 DOI: 10.1016/j.plantsci.2024.112130] [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: 04/01/2024] [Revised: 05/08/2024] [Accepted: 05/18/2024] [Indexed: 05/28/2024]
Abstract
HD-ZIP proteins comprise a plant-specific transcription factor family, which play pivotal roles in plant development and adaptation to ever-changing environment. Although HD-ZIP family members have been identified in some plant species, so far our knowledge about HD-ZIP genes in rapeseed is still limited. In this study, 178 Brassica napus HD-ZIP (BnaHDZ) family members were identified in the rapeseed genome. The phylogenetic relationship, chromosomal locations, intron-exon structures, motif composition, and expression patterns of the BnaHDZ members were analyzed. The BnaHDZ family can be phylogenetically divided into four categories (Ⅰ, Ⅱ, Ⅲ and Ⅳ). Genome-wide transcriptome analysis revealed that most of the HD-ZIP I members respond to at least one abiotic stress. Two closely homologous stress-responsive HD-ZIP Ⅰ genes, BnaHDZ22 and BnaHDZ149, were identified to be involved in drought and salt responses, and selected for further functional characterization. Overexpressing BnaHDZ149 in rapeseed increased salt sensitivity of the transgenic plants, whereas overexpressing BnaHDZ22 increased sensitivity of the transgenic plants to polyethylene glycol (PEG)-simulated drought stress. This research provides not only a comprehensive landscape of BnaHDZ genes, but also a theoretical basis for elucidating the molecular mechanism of the abiotic stress responses of the HD-ZIP family in rapeseed.
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Affiliation(s)
- Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Lu Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Kuan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Han Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yuqian Zheng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yujing Duan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shanshan Feng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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84
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Wang Q, Tian S, Zhang X, Zhang Y, Wang Y, Xie S. Insights into the tolerant function of VWA proteins in terms of expression analysis and RGLG5-VWA crystal structure. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108864. [PMID: 38943876 DOI: 10.1016/j.plaphy.2024.108864] [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: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024]
Abstract
The VWA domain commonly functions as a crucial component of multiprotein complexes, facilitating protein-protein interactions. However, limited studies have focused on the systemic study of VWA proteins in plants. Here, we identified 28 VWA protein genes in Arabidopsis thaliana, categorized into three clades, with one tandem duplication event and four paralogous genes within collinearity blocks. Then, we determined their expression patterns under abiotic stresses by transcriptomic analysis. All five RGLG genes were found to be responsive to at least one kind of abiotic stress, and RGLG5 was identified as a multiple stress-responsive gene, coding an E3 ubiquitin ligase with a VWA domain and a C-terminal RING domain. Subsequently, we explored tolerant function of RGLG5 by determining the crystal structure of its VWA domain. The structural comparison revealed the allosteric regulation mechanism of RGLG5-VWA, wherein the deflection of α7 led to displacement of key residue binding metal ion within MIDAS motif. Our findings provide full-scale knowledge on VWA proteins, and insights into tolerant function of RGLG5-VWA in terms of crystal structure.
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Affiliation(s)
- Qin Wang
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China.
| | - Shicheng Tian
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China
| | | | - Yutong Zhang
- College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuran Wang
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China
| | - Shuyang Xie
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China.
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Jiang M, Zhang H, Song Y, Chen J, Bai J, Tang J, Wang Q, Fotopoulos V, Zhu QH, Yang R, Li R. Transcription factor OsbZIP10 modulates rice grain quality by regulating OsGIF1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2181-2198. [PMID: 38981001 DOI: 10.1111/tpj.16911] [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: 01/15/2024] [Revised: 06/01/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024]
Abstract
Understanding and optimizing the process of grain filling helps the quest to maximize rice (Oryza sativa L.) seed yield and quality, yet the intricate mechanisms at play remain fragmented. Transcription factors (TFs) are major players in the gene networks underlying the grain filling process. Here, we employed grain incomplete filling (OsGIF1)/cell wall invertase 2, a key gene involved in grain filling, to explore its upstream TFs and identified a bZIP family TF, OsbZIP10, to be a transcriptional activator of OsGIF1. Rice grains of the knockouts of OsbZIP10 showed increased white-core rates but lower amylose content (AC), leading to better eating and cooking qualities in all genetic backgrounds investigated, though the impact of mutations in OsbZIP10 on grain weight depended on genetic background. Multi-omics analyses suggested that, in addition to OsGIF1, multiple genes involved in different biological processes contributing to grain filling were targeted by OsbZIP10, including OsAGPS1, a gene encoding the ADP-Glc pyrophosphorylase (AGPase) small subunit, and genes contributing to homeostasis of reactive oxygen species. Distinct genetic make-up was observed in OsbZIP10 between japonica and indica rice varieties, with the majority varieties of each subspecies belonging to two different haplotypes that were closely associated with AC. Overexpressing the haplotype linked to high-AC in the low-AC genetic background increased AC. Overall, this study sheds crucial light on the significance of the OsbZIP10-OsGIF1 module in the determination of rice grain quality, offering a potential avenue for genetic engineering of rice to produce seeds with tailored attributes.
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Affiliation(s)
- Meng Jiang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, 572000, People's Republic of China
| | - Huali Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Yue Song
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, 572000, People's Republic of China
| | - Jiale Chen
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, 572000, People's Republic of China
| | - Jianjiang Bai
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Jianhao Tang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Qing Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Wuxi Hupper Bioseed Technology Institute Ltd., Wuxi, 214000, Jiangsu, People's Republic of China
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, 3603, Cyprus
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, 2601, Australian Capital Territory, Australia
| | - Ruifang Yang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Ruiqing Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
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86
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Mou SJ, Angon PB. Genome-wide characterization and expression profiling of FARL (FHY3/FAR1) family genes in Zea mays. J Genet Eng Biotechnol 2024; 22:100401. [PMID: 39179323 PMCID: PMC11342881 DOI: 10.1016/j.jgeb.2024.100401] [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: 06/09/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
A significant role of the plant is played by the transcription factor FARL, which is light signal transduction as well as plant growth and development. Despite being transposases, FARL has developed a variety of dominant biological actions in evolution and speciation. On the other hand, little is known about the Zea mays FARL protein family. This study identifies and characterizes fifteen ZmFARL genes genome-wide, and RNA sequencing data was used to profile their expression. 105 FARL proteins from five plant species were classified into five groups based on sequence alignment and phylogeny. The ZmFARL genes' exon-intron and motif distribution were conserved based on their evolutionary group. The fifteen ZmFARL genes were distributed over seven of the ten Z. mays chromosomes, although no duplication was discovered. Cis-element analysis reveals that ZmFARL genes play a variety of activities, including tissue-specific, stress- and hormone-responsive expressions. Furthermore, the results of the RNA sequencing used to profile expression showed that the genes ZmFARL2 and ZmFARL5 were much more expressed than other genes in various tissues, particularly in leaf characteristics. The identification of likely genes involved in cellular activity in Z. mays and related species will be aided by the characterization of the FARL genes.
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Affiliation(s)
- Sharah Jabeen Mou
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Prodipto Bishnu Angon
- Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
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87
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Michael R, Ranjan A, Gautam S, Trivedi PK. HY5 and PIF antagonistically regulate HMGR expression and sterol biosynthesis in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112168. [PMID: 38914157 DOI: 10.1016/j.plantsci.2024.112168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/08/2024] [Accepted: 06/18/2024] [Indexed: 06/26/2024]
Abstract
Secondary metabolites play multiple crucial roles in plants by modulating various regulatory networks. The biosynthesis of these compounds is unique to each species and is intricately controlled by a range of developmental and environmental factors. While light's role in certain secondary metabolites is evident, its impact on sterol biosynthesis remains unclear. Previous studies indicate that ELONGATED HYPOCOTYL5 (HY5), a bZIP transcription factor, is pivotal in skotomorphogenesis to photomorphogenesis transition. Additionally, PHYTOCHROME INTERACTING FACTORs (PIFs), bHLH transcription factors, act as negative regulators. To unveil the light-dependent regulation of the mevalonic acid (MVA) pathway, a precursor for sterol biosynthesis, mutants of light signaling components, specifically hy5-215 and the pifq quadruple mutant (pif 1,3,4, and 5), were analyzed in Arabidopsis thaliana. Gene expression analysis in wild-type and mutants implicates HY5 and PIFs in regulating sterol biosynthesis genes. DNA-protein interaction analysis confirms their interaction with key genes like AtHMGR2 in the rate-limiting pathway. Results strongly suggest HY5 and PIFs' pivotal role in light-dependent MVA pathway regulation, including the sterol biosynthetic branch, in Arabidopsis, highlighting a diverse array of light signaling components finely tuning crucial growth pathways.
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Affiliation(s)
- Rahul Michael
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR, Ghaziabad 201002, India
| | - Avriti Ranjan
- Academy of Scientific and Innovative Research (AcSIR), CSIR, Ghaziabad 201002, India; Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Picnic Spot Road, Lucknow 226015, India
| | - Swati Gautam
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR, Ghaziabad 201002, India
| | - Prabodh Kumar Trivedi
- Academy of Scientific and Innovative Research (AcSIR), CSIR, Ghaziabad 201002, India; Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Picnic Spot Road, Lucknow 226015, India.
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88
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Zhou Y, Wang M, Liu Y, Li Z, Hu Z, Zhang M, Yang J. An HD-Zip III transcription factor, BjPHVa, negatively regulates non-glandular trichome formation in Brassica juncea. PHYSIOLOGIA PLANTARUM 2024; 176:e14553. [PMID: 39377147 DOI: 10.1111/ppl.14553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 09/17/2024] [Indexed: 10/09/2024]
Abstract
Trichomes are specialized structures derived from epidermal cells. Non-glandular trichomes primarily protect plants from herbivores and intense ultraviolet radiation by acting as a physical barrier. Recent research has highlighted the importance of homeodomain leucine zipper (HD-Zip) IV transcription factors (TFs) in promoting trichome development. In this study, an HD-Zip III TF called PHAVOLUTA (BjPHVa) was identified as a negative regulator of non-glandular trichome initiation in Brassica juncea. Genome editing of BjPHVa resulted in a significant increase in trichome number in B. juncea. Co-expression networks revealed a strong association between trichome development and the HD-Zip family, which was supported by transcriptomic analysis findings. An R2R3-MYB TF, BjGL1a, a key regulator of trichome development, was found to be associated with BjPHVa-regulated trichome development. Knockdown of BjGL1a expression resulted in reduced trichome number in B. juncea. BjPHVa was observed to interact directly with BjGL1a while binding to the BjGL1a promoter, resulting in the inhibition of BjGL1a transcription. These results provide new insights into the identification of regulators involved in trichome development and offer new opportunities to enhance resistance to predicted stresses through genome editing targeting PHVa within Brassicaceae.
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Affiliation(s)
- Yulan Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Mingyun Wang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Yutong Liu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Zhangping Li
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Zhejiang Provincial Key Laboratory of Vegetable Germplasm Innovation and Quality Breeding, Hangzhou, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Zhejiang Provincial Key Laboratory of Vegetable Germplasm Innovation and Quality Breeding, Hangzhou, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Zhejiang Provincial Key Laboratory of Vegetable Germplasm Innovation and Quality Breeding, Hangzhou, China
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89
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Zhou T, Chang F, Li X, Yang W, Huang X, Yan J, Wu Q, Wen F, Pei J, Ma Y, Xu B. Role of auxin and gibberellin under low light in enhancing saffron corm starch degradation during sprouting. Int J Biol Macromol 2024; 279:135234. [PMID: 39218189 DOI: 10.1016/j.ijbiomac.2024.135234] [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: 06/03/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
The mechanisms by which low light accelerates starch macromolecules degradation by auxin and gibberellin (GA) in geophytes during sprouting remain largely unknown. This study investigated these mechanisms in saffron, grown under low light (50 μmol m-2 s-1) and optimal light (200 μmol m-2 s-1) during the sprouting phase. Low light reduced starch concentration in corms by 34.0 % and increased significantly sucrose levels in corms, leaves, and leaf sheaths by 19.2 %, 9.8 %, and 134.5 %, respectively. This was associated with a 33.3 % increase in GA3 level and enhanced auxin signaling. Leaves synthesized IAA under low light, which was transported to the corms to promote GA synthesis, facilitating starch degradation through a 228.7 % increase in amylase activity. Exogenous applications of GA and IAA, as well as the use of their synthesis or transport inhibitors, confirmed the synergistic role of these phytohormones in starch metabolism. The unigenes associated with GA biosynthesis and auxin signaling were upregulated under low light, highlighting the IAA-GA module role in starch degradation. Moreover, increased respiration rate and invertase activity, crucial for ATP biosynthesis and the tricarboxylic acid cycle, were consistent with the upregulation of related unigenes, suggesting that auxin signaling accelerates starch degradation by promoting energy metabolism. Upregulated of auxin signaling (CsSAUR32) and starch metabolism (CsSnRK1) genes under low light suggests that auxin directly regulate starch degradation in saffron corms. This study elucidates that low light modulates auxin and GA interactions to accelerate starch degradation in saffron corms during sprouting, offering insights for optimizing agricultural practices under suboptimal light conditions.
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Affiliation(s)
- Tao Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Fei Chang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Xin Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Weijing Yang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Xulong Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Jie Yan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Qinghua Wu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Feiyan Wen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China.
| | - Yuntong Ma
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China.
| | - Binjie Xu
- Innovative institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China.
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90
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Zhao Y, Wang T, Wan S, Tong Y, Wei Y, Li P, Hu N, Liu Y, Chen H, Pan X, Zhang B, Peng R, Hu S. Genome-wide identification and functional analysis of the SiCIN gene family in foxtail millet (Setaria italica L.). Gene 2024; 921:148499. [PMID: 38718970 DOI: 10.1016/j.gene.2024.148499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Cell wall invertase (CIN) is a vital member of plant invertase (INV) and plays a key role in the breakdown of sucrose. This enzyme facilitates the hydrolysis of sucrose into glucose and fructose, which is crucial for various aspects of plant growth and development. However, the function of CIN genes in foxtail millet (Setaria italica) is less studied. In this research, we used the blast-p of NCBI and TBtools for bidirectional comparison, and a total of 13 CIN genes (named SiCINs) were identified from foxtail millet by using Arabidopsis and rice CIN sequences as reference sequences. The phylogenetic tree analysis revealed that the CIN genes can be categorized into three subfamilies: group 1, group 2, and group 3. Furthermore, upon conducting chromosomal localization analysis, it was observed that the 13 SiCINs were distributed unevenly across five chromosomes. Cis-acting elements of SiCIN genes can be classified into three categories: plant growth and development, stress response, and hormone response. The largest number of cis-acting elements were those related to light response (G-box) and the cis-acting elements related to seed-specific regulation (RY-element). qRT-PCR analysis further confirmed that the expression of SiCIN7 and SiCIN8 in the grain was higher than that in any other tissues. The overexpression of SiCIN7 in Arabidopsis improved the grain size and thousand-grain weight, suggesting that SiCIN7 could positively regulate grain development. Our findings will help to further understand the grain-filling mechanism of SiCIN and elucidate the biological mechanism underlying the grain development of SiCIN.
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Affiliation(s)
- Yongqing Zhao
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China
| | - Tao Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Sumei Wan
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China
| | - Yan Tong
- Anyang Academy of Agriculture Sciences, Anyang 455000, Henan, China
| | - Yangyang Wei
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Pengtao Li
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Nan Hu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Yuling Liu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Hongqi Chen
- Anyang Academy of Agriculture Sciences, Anyang 455000, Henan, China
| | - Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC 27858, United States
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, United States.
| | - Renhai Peng
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China.
| | - Shoulin Hu
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China.
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91
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Qu Y, Wang J, Gao T, Qu C, Mo X, Zhang X. Systematic analysis of bZIP gene family in Suaeda australis reveal their roles under salt stress. BMC PLANT BIOLOGY 2024; 24:816. [PMID: 39210264 PMCID: PMC11363414 DOI: 10.1186/s12870-024-05535-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Suaeda australis is one of typical halophyte owing to high levels of salt tolerance. In addition, the bZIP gene family assumes pivotal functions in response to salt stress. However, there are little reports available regarding the bZIP gene family in S. australis. RESULTS In this study, we successfully screened 44 bZIP genes within S. australis genome. Subsequently, we conducted an extensive analysis, encompassing investigations into chromosome location, gene structure, phylogenetic relationship, promoter region, conserved motif, and gene expression profile. The 44 bZIP genes were categorized into 12 distinct groups, exhibiting an uneven distribution among the 9 chromosomes of S. australis chromosomes, but one member (Sau23745) was mapped on unanchored scaffolds. Examination of cis-regulatory elements revealed that bZIP promoters were closely related to anaerobic induction, transcription start, and light responsiveness. Comparative transcriptome analysis between ST1 and ST2 samples identified 2,434 DEGs, which were significantly enriched in some primary biological pathways related to salt response-regulating signaling based on GO and KEGG enrichment analysis. Expression patterns analyses clearly discovered the role of several differently expressed SabZIPs, including Sau08107, Sau08911, Sau11415, Sau16575, and Sau19276, which showed higher expression levels in higher salt concentration than low concentration and a response to salt stress. These expression patterns were corroborated through RT-qPCR analysis. The six differentially expressed SabZIP genes, all localized in the nucleus, exhibited positive regulation involved in the salt stress response. SabZIP14, SabZIP26, and SabZIP36 proteins could bind to the promoter region of downstream salt stress-related genes and activate their expressions. CONCLUSIONS Our findings offer valuable insights into the evolutionary trajectory of the bZIP gene family in S. australis and shed light on their roles in responding to salt stress. In addition to fundamental genomic information, these results would serve as a foundational framework for future investigations into the regulation of salt stress responses in S. australis.
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Affiliation(s)
- Yinquan Qu
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Ji Wang
- School of Teacher Education, Nanjing Xiaozhuang University, Nanjing, 211171, Jiangsu, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Caihui Qu
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Xiaoyun Mo
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Xiumei Zhang
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China.
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92
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Cheng W, Xu J, Mu C, Jiang J, Cheng Z, Gao J. Conservation and Divergence of PEPC Gene Family in Different Ploidy Bamboos. PLANTS (BASEL, SWITZERLAND) 2024; 13:2426. [PMID: 39273910 PMCID: PMC11397392 DOI: 10.3390/plants13172426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/23/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024]
Abstract
Phosphoenolpyruvate carboxylase (PEPC), as a necessary enzyme for higher plants to participate in photosynthesis, plays a key role in photosynthetic carbon metabolism and the stress response. However, the molecular biology of the PEPC family of Bambusoideae has been poorly studied, and the function of its members in the growth and development of Bambusoideae is still unclear. Here, we identified a total of 62 PEPC family members in bamboo. All the PEPC genes in the bamboo subfamily were divided into twelve groups, each group typically containing significantly fewer PEPC members in Olyra latifolia than in Phyllostachys edulis, Dendrocalamus latiflorus and Dendrocalamus brandisii. The results of an intraspecific and interspecies collinearity analysis showed that fragment replication and whole genome replication were the main driving forces of bamboo PEPC members. Furthermore, the Ka/Ks values of collinear genes showed that bamboo PEPC experienced purification selection. In addition, the promoter region of PEPC genes contains cis-acting elements related to light response, plant hormone response and response to stress. An analysis of the expression levels of the PEPC family in different developmental stages and tissues of bamboo shoots has shown that PhePEPC7, PhePEPC9 and PhePEPC10 were highly expressed in the leaves of non-flowering plants and culms. Furthermore, PhePEPC6 was significantly upregulated in leaves after GA treatment. Further research has shown that PhePEPC6 was mainly localized in the cell membrane. This provides a solid bioinformatics foundation for further understanding the biological functions of the bamboo PEPC family.
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Affiliation(s)
- Wenlong Cheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
| | - Junlei Xu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
| | - Changhong Mu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
| | - Jutang Jiang
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
| | - Zhanchao Cheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
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93
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Wu C, Zhang J, Chen M, Liu J, Tang Y. Characterization of a Nicotiana tabacum phytochelatin synthase 1 and its response to cadmium stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1418762. [PMID: 39280946 PMCID: PMC11393743 DOI: 10.3389/fpls.2024.1418762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 08/12/2024] [Indexed: 09/18/2024]
Abstract
Phytochelatin synthase (PCS) is a critical enzyme involved in heavy metal detoxification in organisms. In this study, we aim to comprehensively investigate the molecular and functional characteristics of the PCS1 gene from Nicotiana tabacum by examining its enzymatic activity, tissue-specific expression pattern, Cd-induced expression, as well as the impact on Cd tolerance and accumulation. The results demonstrated that the amino acid sequence of NtPCS1 shared a high similarity in its N-terminal region with PCS from other species. The enzymatic activity of NtPCS1 was found to be enhanced in the order Ag2+ > Cd2+ > Cu2+ > Pb2+ > Hg2+ > Fe2+ > Zn2+. In addition, RT-PCR data indicated that NtPCS1 gene is constitutively expressed, with the highest expression observed in flowers, and that its transcript levels are up-regulated by CdCl2. When tobacco overexpressing NtPCS1 (PCS1 lines) were grown under CdCl2 stress, they produced more phytochelatins (PCs) than WT plants, but this did not result in increased Cd accumulation. However, in a root growth assay, the PCS1 lines exhibited hypersensitivity to Cd. The overexpression of NtPCS1 itself does not appear to be the primary cause of this heightened sensitivity to Cd, as the Arabidopsis thaliana Atpcs1 mutant overexpressing NtPCS1 actually exhibited enhanced tolerance to Cd. Furthermore, the addition of exogenous glutathione (GSH) progressively reduced the Cd hypersensitivity of the PCS1 lines, with the hypersensitivity even being completely eliminated. Surprisingly, the application of exogenous GSH led to a remarkably enhanced Cd accumulation in the PCS1 lines. This study enriches our understanding of the molecular function of the NtPCS1 gene and suggests a promising avenue for Cd tolerance through the heterologous expression of PCS genes in different species.
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Affiliation(s)
- Chanjuan Wu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Jie Zhang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Mei Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Jikai Liu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Yunlai Tang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
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94
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Peracchi LM, Brew-Appiah RAT, Garland-Campbell K, Roalson EH, Sanguinet KA. Genome-wide characterization and expression analysis of the CINNAMYL ALCOHOL DEHYDROGENASE gene family in Triticum aestivum. BMC Genomics 2024; 25:816. [PMID: 39210247 PMCID: PMC11363449 DOI: 10.1186/s12864-024-10648-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND CINNAMYL ALCOHOL DEHYDROGENASE (CAD) catalyzes the NADPH-dependent reduction of cinnamaldehydes into cinnamyl alcohols and is a key enzyme found at the final step of the monolignol pathway. Cinnamyl alcohols and their conjugates are subsequently polymerized in the secondary cell wall to form lignin. CAD genes are typically encoded by multi-gene families and thus traditionally organized into general classifications of functional relevance. RESULTS In silico analysis of the hexaploid Triticum aestivum genome revealed 47 high confidence TaCAD copies, of which three were determined to be the most significant isoforms (class I) considered bone fide CADs. Class I CADs were expressed throughout development both in RNAseq data sets as well as via qRT-PCR analysis. Of the 37 class II TaCADs identified, two groups were observed to be significantly co-expressed with class I TaCADs in developing tissue and under chitin elicitation in RNAseq data sets. These co-expressed class II TaCADs were also found to be phylogenetically unrelated to a separate clade of class II TaCADs previously reported to be an influential resistance factor to pathogenic fungal infection. Lastly, two groups were phylogenetically identified as class III TaCADs, which possess distinct conserved gene structures. However, the lack of data supporting their catalytic activity for cinnamaldehydes and their bereft transcriptional presence in lignifying tissues challenges their designation and function as CADs. CONCLUSIONS Taken together, our comprehensive transcriptomic analyses suggest that TaCAD genes contribute to overlapping but nonredundant functions during T. aestivum growth and development across a wide variety of agroecosystems and provide tolerance to various stressors.
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Affiliation(s)
- Luigi M Peracchi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Group, Washington State University, Pullman, WA, 99164, USA
| | - Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Kimberly Garland-Campbell
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Group, Washington State University, Pullman, WA, 99164, USA
- USDA-ARS Wheat Health, Genetics and Quality Research, Pullman, WA, 99164, USA
| | - Eric H Roalson
- Molecular Plant Sciences Graduate Group, Washington State University, Pullman, WA, 99164, USA
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
- Molecular Plant Sciences Graduate Group, Washington State University, Pullman, WA, 99164, USA.
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95
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Han T, Khan MA, Wang Y, Tan W, Li C, Ai P, Zhao W, Li Z, Wang Z. Identification of SDG gene family members and exploration of flowering related genes in different cultivars of chrysanthemums and their wild ancestors. BMC PLANT BIOLOGY 2024; 24:813. [PMID: 39210253 PMCID: PMC11360836 DOI: 10.1186/s12870-024-05465-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
The SET domain genes (SDGs) are significant contributors to various aspects of plant growth and development, mainly includes flowering, pollen development, root growth, regulation of the biological clock and branching patterns. To clarify the biological functions of the chrysanthemum SDG family, the SDG family members of four chrysanthemum cultivars and three related wild species were identified; their physical and chemical properties, protein domains and conserved motifs were predicted and analyzed. The results showed that 59, 67, 67, 102, 106, 114, and 123 SDGs were identified from Chrysanthemum nankingense, Chrysanthemum lavandulifolium, Chrysanthemum seticuspe, Chrysanthemum × morifolium cv. 'Hechengxinghuo', 'Zhongshanzigui', 'Quanxiangshuichang' and 'Jinbeidahong', respectively. The SDGs were divided into 5-7 subfamilies by cluster analysis; different conserved motifs were observed in particular families. The SDGs of C. lavandulifolium and C. seticuspe were distributed unevenly on 9 chromosomes. SDG promoters of different species include growth and development, photo-response, stress response and hormone responsive elements, among them, the cis-acting elements related to MeJA response had the largest proportion. The expression of chrysanthemum SDG genes was observed for most variable selected genes which has close association with important Arabidopsis thaliana genes related to flowering regulation. The qPCR results showed that the expression trend of SDG genes varied in different tissues at different growth stages with high expression in the flowering period. The ClSDG29 showed higher expression in the flower and bud tissues, which indicate that ClSDG29 might be associated with flowering regulation in chrysanthemum. In summary, the results of this study can provide a basis for subsequent research on chrysanthemum flowering time regulation.
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Affiliation(s)
- Ting Han
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Muhammad Ayoub Khan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Yiming Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Wenchao Tan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Chenran Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Penghui Ai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Wenqian Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Zhongai Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Zicheng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China.
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96
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Wang Q, Zhou L, Yuan M, Peng F, Zhu X, Wang Y. Genome-Wide Identification of NAC Gene Family Members of Tree Peony ( Paeonia suffruticosa Andrews) and Their Expression under Heat and Waterlogging Stress. Int J Mol Sci 2024; 25:9312. [PMID: 39273263 PMCID: PMC11395581 DOI: 10.3390/ijms25179312] [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: 07/16/2024] [Revised: 08/14/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
An important family of transcription factors (TFs) in plants known as NAC (NAM, ATAF1/2, and CUC2) is crucial for the responses of plants to environmental stressors. In this study, we mined the NAC TF family members of tree peony (Paeonia suffruticosa Andrews) from genome-wide data and analyzed their response to heat and waterlogging stresses in conjunction with transcriptome data. Based on tree peony's genomic information, a total of 48 PsNAC genes were discovered. Based on how similar their protein sequences were, these PsNAC genes were divided into 14 branches. While the gene structures and conserved protein motifs of the PsNAC genes within each branch were largely the same, the cis-acting elements in the promoter region varied significantly. Transcriptome data revealed the presence of five PsNAC genes (PsNAC06, PsNAC23, PsNAC38, PsNAC41, PsNAC47) and one PsNAC gene (PsNAC37) in response to heat and waterlogging stresses, respectively. qRT-PCR analysis reconfirmed the response of these five PsNAC genes to heat stress and one PsNAC gene to waterlogging stress. This study lays a foundation for the study of the functions and regulatory mechanisms of NAC TFs in tree peony. Meanwhile, the NAC TFs of tree peony in response to heat and waterlogging stress were excavated, which is of great significance for the selection and breeding of new tree peony varieties with strong heat and waterlogging tolerance.
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Affiliation(s)
- Qun Wang
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lin Zhou
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Meng Yuan
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Fucheng Peng
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Xiangtao Zhu
- College of Jiyang, Zhejiang A&F University, Zhuji 311800, China
| | - Yan Wang
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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97
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Zhu X, Li W, Zhang N, Duan H, Jin H, Chen Z, Chen S, Zhou J, Wang Q, Tang J, Majeed Y, Zhang Y, Si H. Identification of autophagy-related genes ATG18 subfamily genes in potato ( Solanum tuberosum L.) and the role of StATG18a gene in heat stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1439972. [PMID: 39263419 PMCID: PMC11387889 DOI: 10.3389/fpls.2024.1439972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/16/2024] [Indexed: 09/13/2024]
Abstract
Autophagy is a highly conserved process in eukaryotes that is used to recycle the cellular components from the cytoplasm. It plays a crucial function in responding to both biotic and abiotic stress, as well as in the growth and development of plants. Autophagy-related genes (ATG) and their functions have been identified in numerous crop species. However, their specific tasks in potatoes (Solanum tuberosum L.), are still not well understood. This work is the first to identify and characterize the potato StATG18 subfamily gene at the whole-genome level, resulting in a total of 6 potential StATG18 subfamily genes. We analyzed the phylogenetic relationships, chromosome distribution and gene replication, conserved motifs and gene structure, interspecific collinearity relationship, and cis-regulatory elements of the ATG18 subfamily members using bioinformatics approaches. Furthermore, the quantitative real-time polymerase chain reaction (qRT-PCR) analysis suggested that StATG18 subfamily genes exhibit differential expression in various tissues and organs of potato plants. When exposed to heat stress, their expression pattern was observed in the root, stem, and leaf. Based on a higher expression profile, the StATG18a gene was further analyzed under heat stress in potatoes. The subcellular localization analysis of StATG18a revealed its presence in both the cytoplasm and nucleus. In addition, StATG18a altered the growth indicators, physiological characteristics, and photosynthesis of potato plants under heat stresses. In conclusion, this work offers a thorough assessment of StATG18 subfamily genes and provides essential recommendations for additional functional investigation of autophagy-associated genes in potato plants. Moreover, these results also contribute to our understanding of the potential mechanism and functional validation of the StATG18a gene's persistent tolerance to heat stress in potato plants.
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Affiliation(s)
- Xi Zhu
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs/Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
- National Key Laboratory for Tropical Crop Breeding, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Wei Li
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs/Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Huimin Duan
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs/Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Hui Jin
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs/Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Zhuo Chen
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs/Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Shu Chen
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs/Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Jiannan Zhou
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs/Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Qihua Wang
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs/Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Jinghua Tang
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs/Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Yasir Majeed
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yu Zhang
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs/Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
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98
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Yuan Y, Fan Y, Huang L, Lu H, Tan B, Ramirez C, Xia C, Niu X, Chen S, Gao M, Zhang C, Liu Y, Xiao F. The SINA1-BSD1 Module Regulates Vegetative Growth Involving Gibberellin Biosynthesis in Tomato. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400995. [PMID: 39190572 DOI: 10.1002/advs.202400995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 07/10/2024] [Indexed: 08/29/2024]
Abstract
In plants, vegetative growth is controlled by synergistic and/or antagonistic effects of many regulatory factors. Here, the authors demonstrate that the ubiquitin ligase seven in absentia1 (SINA1) mammalian BTF2-like transcription factors, Drosophila synapse-associated proteins, and yeast DOS2-like proteins (BSD1) function as a regulatory module to control vegetative growth in tomato via regulation of the production of plant growth hormone gibberellin (GA). SINA1 negatively regulates the protein level of BSD1 through ubiquitin-proteasome-mediated degradation, and the transgenic tomato over-expressing SINA1 (SINA1-OX) resembles the dwarfism phenotype of the BSD1-knockout (BSD1-KO) tomato plant. BSD1 directly activates expression of the BSD1-regulated gene 1 (BRG1) via binding to a novel core BBS (standing for BSD1 binding site) binding motif in the BRG1 promoter. Knockout of BRG1 (BRG1-KO) in tomato also results in a dwarfism phenotype, suggesting BRG1 plays a positive role in vegetative growth as BSD1 does. Significantly, GA contents are attenuated in transgenic SINA1-OX, BSD1-KO, and BRG1-KO plants exhibiting dwarfism phenotype and exogenous application of bioactive GA3 restores their vegetative growth. Moreover, BRG1 is required for the expression of multiple GA biosynthesis genes and BSD1 activates three GA biosynthesis genes promoting GA production. Thus, this study suggests that the SINA1-BSD1 module controls vegetative growth via direct and indirect regulation of GA biosynthesis in tomato.
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Affiliation(s)
- Yulin Yuan
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Youhong Fan
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Li Huang
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Han Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco‑Chongming, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Bowen Tan
- Department of Biology, University of Mississippi, Oxford, MS, 38677, USA
| | - Chloe Ramirez
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Chao Xia
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangli Niu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS, 38677, USA
| | - Mingjun Gao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco‑Chongming, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Cankui Zhang
- Department of Agronomy, Purdue Center for Plant Biology, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, IN, 47907, USA
| | - Yongsheng Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Fangming Xiao
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
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99
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Feng Z, Li Y, Zhang S, Song J, Xiang H, Huang J, Fan H, Liu L. DoSPX1 and DoMYB37 regulate the expression of DoCSLA6 in Dendrobium officinale during phosphorus starvation. BMC PLANT BIOLOGY 2024; 24:803. [PMID: 39183325 PMCID: PMC11346060 DOI: 10.1186/s12870-024-05512-8] [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: 06/19/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND Dendrobium officinale Kimura et Migo (D. officinale) is parasitic on rocks or plants with very few mineral elements that can be absorbed directly, so its growth and development are affected by nutritional deficiencies. Previous studies found that phosphorus deficiency promotes polysaccharides accumulation in D. officinale, the expression of DoCSLA6 (glucomannan synthase gene) was positively correlated with polysaccharide synthesis. However, the molecular mechanism by which the low phosphorus environment affects polysaccharide accumulation remains unclear. RESULTS We found that DoSPX1 can reduce phosphate accumulation in plants and promote the expression of PSIs genes, thereby enhancing plant tolerance to low phosphorus environments.Y1H and EMSA experimental show that DoMYB37 can bind the promoter of DoCSLA6. DoSPX1 interact with DoMYB37 transiently overexpressed DoSPX1 and DoMYB37 in D. officinale protocorm-like bodies, decreased the Pi content, while increased the expression of DoCSLA6. CONCLUSIONS The signaling pathway of DoSPX1-DoMYB37-DoCSLA6 was revealed. This provides a theoretical basis for the accumulation of polysaccharide content in D. officinale under phosphorus starvation.
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Affiliation(s)
- ZhiYuan Feng
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - YaWen Li
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - SiXue Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - Jingjing Song
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - HaoXin Xiang
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - JunRu Huang
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - HongHong Fan
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China.
- Integrated Experimental Station in Dabie Mountains, Anhui Agricultural University, Lu'an, China.
| | - Lin Liu
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China.
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100
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Chen X, Niu M, Wu X, Peng Y, Zheng R, Cheng M, Zhao K, Zhou Y, Peng D. BBX Genes of Cymbidium ensifolium Exhibited Intense Response to Blue Light in Meristem Induction through Artificial Control. PLANTS (BASEL, SWITZERLAND) 2024; 13:2375. [PMID: 39273858 PMCID: PMC11396916 DOI: 10.3390/plants13172375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/18/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024]
Abstract
Cymbidium ensifolium, a prominent orchid species, is both highly valued for its ornamental qualities and commercially cultivated. However, the species has a considerable challenge in its breeding efforts due to the lengthy period of 7-8 years required for it to transition from seed germination to flowering. BBXs are multifunctional proteins that modulate the actions of critical regulators including HY5 and COP1 in response to blue light, ultimately impacting photomorphogenic processes. In this study, BBX proteins, known for their essential roles in regulating developmental processes under various light conditions, were chosen as the main subject of investigation. The outcome reveals the presence of 19 BBX genes in their genome. The genes are classified into four separate clades and dispersed among 12 out of the 20 chromosomes. Located in the nuclear, physicochemical properties of proteins, analysis of the promoter region reveals the existence of almost 800 cis-acting elements, highlighting the complex regulatory mechanisms that control the expression of the CeBBXs in various organs, as well as their response to light and hormone inputs. Moreover, the examination of differential expression under blue light therapy reveals their involvement in photomorphogenic reactions. The expression of CeBBXs exhibits substantial alterations as the duration of exposure to blue light increases. These findings contribute to a deeper understanding of the roles that BBX genes serve in C. ensifolium, providing a basis for future studies on the functions and regulatory mechanisms of BBX members in the context of floral initiation and development within this species.
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Affiliation(s)
- Xiuming Chen
- Cross-Strait Floriculture Industry Science and Technology Innovation Hub, Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Muqi Niu
- Cross-Strait Floriculture Industry Science and Technology Innovation Hub, Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaopei Wu
- Cross-Strait Floriculture Industry Science and Technology Innovation Hub, Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yukun Peng
- Cross-Strait Floriculture Industry Science and Technology Innovation Hub, Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ruiyue Zheng
- Cross-Strait Floriculture Industry Science and Technology Innovation Hub, Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengya Cheng
- Cross-Strait Floriculture Industry Science and Technology Innovation Hub, Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kai Zhao
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Yuzhen Zhou
- Cross-Strait Floriculture Industry Science and Technology Innovation Hub, Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Donghui Peng
- Cross-Strait Floriculture Industry Science and Technology Innovation Hub, Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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