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Li G, Manzoor MA, Ren X, Huang S, Wei Y, Zhang S, Sun Y, Cai Y, Zhang M, Song C. Functional analysis of two caffeoyl-coenzyme 3 a-o-methyltransferase involved in pear lignin metabolism. Gene 2024; 928:148810. [PMID: 39089530 DOI: 10.1016/j.gene.2024.148810] [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: 04/01/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Caffeoyl-coenzyme 3 A-O-methyltransferase (CCoAOMT) plays a crucial role in the lignin synthesis in many higher plants. In this study, nine PbCCoAOMT genes in total were identified from pear, and classified into six categories. We treated pear fruits with hormones abscisic acid (ABA) and methyl jasmonate (MeJA) and salicylic acid (SA) and observed differential expression levels of these genes. Through qRT-PCR, we also preliminarily identified candidate PbCCoAOMT gene, potentially involved in lignin synthesis in pear fruits. Additionally, the overexpression of PbCCoAOMT1/2 in Arabidopsis and pear fruits increased in lignin content. Enzymatic assays showed that recombinant PbCCoAOMT1/2 proteins have similar enzymatic activity in vitro. The Y1H (Yeast one-hybrid) and dual luciferase (dual-LUC) experiments demonstrated that PbMYB25 can bind to the AC elements in the promoter region of the PbCCoAOMT1 gene. Our findings suggested that the PbCCoAOMT1 and PbCCoAOMT2 genes may contribute to the synthesis of lignin and provide insights into the mechanism of lignin biosynthesis and stone cell development in pear fruits.
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Affiliation(s)
- Guohui Li
- Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Ren
- Anhui Agricultural University, Hefei 230036, China
| | - Shiping Huang
- Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Yuxin Wei
- Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Shuo Zhang
- Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Yanming Sun
- Anhui Agricultural University, Hefei 230036, China
| | - Yongping Cai
- Anhui Agricultural University, Hefei 230036, China
| | - Ming Zhang
- Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China.
| | - Cheng Song
- Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China.
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Sun T, Wu Q, Zang S, Zou W, Wang D, Wang W, Shen L, Zhang S, Su Y, Que Y. Molecular insights into OPR gene family in Saccharum identified a ScOPR2 gene could enhance plant disease resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 120:335-353. [PMID: 39167539 DOI: 10.1111/tpj.16990] [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: 06/07/2024] [Revised: 08/02/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
Abstract
12-Oxo-phytodienoic acid reductases (OPRs) perform vital functions in plants. However, few studies have been reported in sugarcane (Saccharum spp.), and it is of great significance to systematically investigates it in sugarcane. Here, 61 ShOPRs, 32 SsOPRs, and 36 SoOPRs were identified from R570 (Saccharum spp. hybrid cultivar R570), AP85-441 (Saccharum spontaneum), and LA-purple (Saccharum officinarum), respectively. These OPRs were phylogenetically classified into four groups, with close genes similar structures. During evolution, OPR gene family was mainly expanded via whole-genome duplications/segmental events and predominantly underwent purifying selection, while sugarcane OPR genes may function differently in response to various stresses. Further, ScOPR2, a tissue-specific OPR, which was localized in cytoplasm and cell membrane and actively response to salicylic acid (SA), methyl jasmonate, and smut pathogen (Sporisorium scitamineum) stresses, was cloned from sugarcane. In addition, both its transient overexpression and stable overexpression enhanced the resistance of transgenic plants to pathogen infection, most probably through activating pathogen-associated molecular pattern/pattern-recognition receptor-triggered immunity, producing reactive oxygen species, and initiating mitogen-activated protein kinase cascade. Subsequently, the transmission of SA and hypersensitive reaction were triggered, which stimulated the transcription of defense-related genes. These findings provide insights into the function of ScOPR2 gene for disease resistance.
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Affiliation(s)
- Tingting Sun
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, 572024, China
| | - Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, 572024, China
| | - Shoujian Zang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, 572024, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Wenhui Zou
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, 572024, China
| | - Dongjiao Wang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, 572024, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Wenzhi Wang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, 572024, China
| | - Linbo Shen
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, 572024, China
| | - Shuzhen Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, 572024, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Youxiong Que
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, 572024, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
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Zhang R, Chen X, Wang Y, Hu X, Zhu Q, Yang L, Zhou M. Genome-wide identification of hormone biosynthetic and metabolism genes in the 2OGD family of tobacco and JOX genes silencing enhances drought tolerance in plants. Int J Biol Macromol 2024:135731. [PMID: 39299420 DOI: 10.1016/j.ijbiomac.2024.135731] [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: 08/09/2024] [Revised: 09/10/2024] [Accepted: 09/14/2024] [Indexed: 09/22/2024]
Abstract
Phytohormones play crucial roles in regulation of plant growth and tolerance to abiotic stresses. The 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily responds to hormone biosynthesis and metabolism in plants. However, the Nt2OGD family in tobacco has not been fully explored. In this study, we identify 126 members of the Nt2OGD family, and 60 of them are involved in hormone biosynthesis and metabolism process (Nt2OGD-Hs), including 1-aminocyclopropane-1-carboxylic acid oxidases (ACO), dioxygenases for auxin oxidation (DAO), gibberellin (GA) 20-oxidases and 3-oxidases (GA20ox and GA3ox), carbon-19 and carbon-20 GA 2-oxidases (C19-GA2ox and C20-GA2ox), lateral branching oxidoreductases (LBO), jasmonate-induced oxygenases (JOX), downy mildew resistant 6, and DMR6-like oxygenases (DMR6/DLO). Gene duplication analysis suggests the segmental duplication and whole genome duplication (WGD) might be a potential mechanism for the expansion of this family. Expression analysis reveals that most of Nt2OGD-Hs show tissue-specific expression patterns, and some of them respond to environmental conditions. Of Nt2OGD-Hs, the expression of NtJOX3 and NtJOX5, which are involved in JA metabolism, exhibits remarkable changes during drought treatments. Silencing of NtJOX3 or NtJOX5 increases tobacco tolerance to drought stress. Furthermore, knocking out OsJOX3 and OsJOX4, respectively in rice, result in high tolerance to drought. Taken together, our work comprehensively identifies the Nt2OGD family in tobacco and provides new insights into roles of the JA pathway in drought tolerance in plants.
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Affiliation(s)
- Rui Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - XinYi Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaozhou Hu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - QingQuan Zhu
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, 223300, China
| | - Long Yang
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, 271018, China.
| | - Ming Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, 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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Cheng R, Zhao Z, Tang Y, Gu Y, Chen G, Sun Y, Wang X. Genome-wide survey of KT/HAK/KUP genes in the genus Citrullus and analysis of their involvement in K +-deficiency and drought stress responses in between C. lanatus and C. amarus. BMC Genomics 2024; 25:836. [PMID: 39237905 PMCID: PMC11378637 DOI: 10.1186/s12864-024-10712-5] [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: 06/15/2024] [Accepted: 08/14/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND The KT/HAK/KUP is the largest K+ transporter family in plants, playing crucial roles in K+ absorption, transport, and defense against environmental stress. Sweet watermelon is an economically significant horticultural crop belonging to the genus Citrullus, with a high demand for K+ during its growth process. However, a comprehensive analysis of the KT/HAK/KUP gene family in watermelon has not been reported. RESULTS 14 KT/HAK/KUP genes were identified in the genomes of each of seven Citrullus species. These KT/HAK/KUPs in watermelon were unevenly distributed across seven chromosomes. Segmental duplication is the primary driving force behind the expansion of the KT/HAK/KUP family, subjected to purifying selection during domestication (Ka/Ks < 1), and all KT/HAK/KUPs exhibit conserved motifs and could be phylogenetically classified into four groups. The promoters of KT/HAK/KUPs contain numerous cis-regulatory elements related to plant growth and development, phytohormone response, and stress response. Under K+ deficiency, the growth of watermelon seedlings was significantly inhibited, with cultivated watermelon experiencing greater impacts (canopy width, redox enzyme activity) compared to the wild type. All KT/HAK/KUPs in C. lanatus and C. amarus exhibit specific expression responses to K+-deficiency and drought stress by qRT-PCR. Notably, ClG42_07g0120700/CaPI482276_07g014010 were predominantly expressed in roots and were further induced by K+-deficiency and drought stress. Additionally, the K+ transport capacity of ClG42_07g0120700 under low K+ stress was confirmed by yeast functional complementation assay. CONCLUSIONS KT/HAK/KUP genes in watermelon were systematically identified and analyzed at the pangenome level and provide a foundation for understanding the classification and functions of the KT/HAK/KUPs in watermelon plants.
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Affiliation(s)
- Rui Cheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, 150006, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, 150006, China
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, Jiangsu, 223001, China
| | - Zhengxiang Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, 150006, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, 150006, China
| | - Yan Tang
- Huaiyin Institute of Technology, Huai'an, Jiangsu, 223003, China
| | - Yan Gu
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, Jiangsu, 223001, China
| | - Guodong Chen
- Huaiyin Institute of Technology, Huai'an, Jiangsu, 223003, China
| | - Yudong Sun
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, Jiangsu, 223001, China.
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, 150006, China.
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, 150006, 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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Zhou H, Wang Y, Wang X, Cheng R, Zhang H, Yang L. Genome-wide characterization of DELLA gene family in blueberry (Vaccinium darrowii) and their expression profiles in development and response to abiotic stress. BMC Genomics 2024; 25:815. [PMID: 39210263 PMCID: PMC11360860 DOI: 10.1186/s12864-024-10721-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The DELLA proteins, a class of GA signaling repressors, belong to the GRAS family of plant-specific nuclear proteins. Members of DELLA gene family encode transcriptional regulators with diverse functions in plant development and abiotic stress responses. To date, DELLAs have been identified in various plant species, such as Arabidopsis thaliana, Malus domestica, Populus trichocarpa, and other land plants. Most information of DELLA family genes was obtained from A. thaliana, whereas little is known about the DELLA gene family in blueberry. RESULTS In this study, we identified three DELLA genes in blueberry (Vaccinium darrowii, VdDELLA) and provided a complete overview of VdDELLA gene family, describing chromosome localization, protein properties, conserved domain, motif organization, and phylogenetic analysis. Three VdDELLA members, containing two highly conserved DELLA domain and GRAS domain, were distributed across three chromosomes. Additionally, cis-acting elements analysis indicated that VdDELLA genes might play a critical role in blueberry developmental processes, hormone, and stress responses. Expression analysis using quantitative real-time PCR (qRT-PCR) revealed that all of three VdDELLA genes were differentially expressed across various tissues. VdDELLA2 was the most highly expressed VdDELLA in all denoted tissues, with a highest expression in mature fruits. In addition, all of the three VdDELLA genes actively responded to diverse abiotic stresses. Based on qRT-PCR analysis, VdDELLA2 might act as a key regulator in V. darrowii in response to salt stress, whereas VdDELLA1 and VdDELLA2 might play an essential role in cold stress response. Under drought stress, all of three VdDELLA genes were involved in mediating drought response. Furthermore, their transiently co-localization with nuclear markers in A. thaliana protoplasts demonstrated their transcriptional regulator roles. CONCLUSIONS In this study, three VdDELLA genes were identified in V. darrowii genome. Three VdDELLA genes were closely related to the C. moschata DELLA genes, S. lycopersicum DELLA genes, and M. domestica DELLA genes, respectively, indicating their similar biological functions. Expression analysis indicated that VdDELLA genes were highly efficient in blueberry fruit development. Expression patterns under different stress conditions revealed the differentially expressed VdDELLA genes responding to salt, drought, and cold stress. Overall, these results enrich our understanding of evolutionary relationship and potential functions of VdDELLA genes, which provide valuable information for further studies on genetic improvement of the plant yield and plant resistance.
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Affiliation(s)
- Houjun Zhou
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China.
- Bestplant (Shandong) Stem Cell Engineering Co., Ltd, 300 Changjiang Road, Yantai, 264001, China.
| | - Yanwen Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China
| | - Xinyu Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China
| | - Rui Cheng
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China
| | - Hongxia Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China
- Bestplant (Shandong) Stem Cell Engineering Co., Ltd, 300 Changjiang Road, Yantai, 264001, China
| | - Lei Yang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China.
- Bestplant (Shandong) Stem Cell Engineering Co., Ltd, 300 Changjiang Road, Yantai, 264001, China.
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8
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Amjad M, Wang Y, Han S, Haider MZ, Sami A, Batool A, Shafiq M, Ali Q, Dong J, Sabir IA, Manzoor MA. Genome wide identification of phenylalanine ammonia-lyase (PAL) gene family in Cucumis sativus (cucumber) against abiotic stress. BMC Genom Data 2024; 25:76. [PMID: 39187758 PMCID: PMC11348668 DOI: 10.1186/s12863-024-01259-1] [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: 06/21/2024] [Accepted: 08/12/2024] [Indexed: 08/28/2024] Open
Abstract
Phenylalanine ammonia lyase (PAL) is a widely studied enzyme in plant biology due to its role in connecting primary metabolism to secondary phenylpropanoid metabolism, significantly influencing plant growth, development, and stress response. Although PAL genes have been extensively studied in various plant species but their exploration in cucumber has been limited. This study successfully identified 11 CsPAL genes in Cucumis sativus (cucumber). These CsPAL genes were categorized based on their conserved sequences revealing patterns through MEME analysis and multiple sequence alignment. Interestingly, cis-elements related to stress were found in the promoter regions of CsPAL genes, indicating their involvement in responding to abiotic stress. Furthermore, these gene's promoters contained components associated with light, development and hormone responsiveness. This suggests that they may have roles in hormone developmental processes. MicroRNAs were identified as a key regulators for the CsPAL genes, playing a crucial role in modulating their expression. This discovery underscores the complex regulatory network involved in the plant's response to various stress conditions. The influence of these microRNAs further highlights the complicated mechanisms that plants use to manage stress. Gene expression patterns were analyzed using RNA-seq data. The significant upregulation of CsPAL9 during HT3h (heat stress for 3 h) and the heightened upregulation of both CsPAL9 and CsPAL7 under HT6h (heat stress for 6 h) in the transcriptome study suggest a potential role for these genes in cucumber's tolerance to heat stress. This comprehensive investigation aims to enhance our understanding of the PAL gene family's versatility, offering valuable insights for advancements in cucumber genetics.
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Affiliation(s)
- Muskan Amjad
- School of Public Policy & Management, China University of Mining and Technology, Xuzhou, China
- Department of Botany, Government Graduate College Township, Lahore, Pakistan
| | - Yuexia Wang
- School of Public Policy & Management, China University of Mining and Technology, Xuzhou, China
- School of Biological Sciences and Technology, Liupanshui Normal University, Liupanshui, 553004, China
| | - Shiming Han
- School of Public Policy & Management, China University of Mining and Technology, Xuzhou, China.
- School of Biological Sciences and Technology, Liupanshui Normal University, Liupanshui, 553004, China.
| | - Muhammad Zeshan Haider
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan.
| | - Adnan Sami
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan.
| | - Alia Batool
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan
| | - Muhammad Shafiq
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan.
| | - Jihong Dong
- School of Public Policy & Management, China University of Mining and Technology, Xuzhou, China
| | - Irfan Ali Sabir
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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Masura SS, Shaharuddin NA, Masani MYA, Chan KL, Low ETL, Chan PL, Rahmah ARS, Amiruddin N, Abdullah MP, Azzeme AM, Parveez GKA, Rasid OA. Functional analysis of root-preferential oil palm metallothionein promoter in tobacco. Transgenic Res 2024:10.1007/s11248-024-00396-8. [PMID: 39120800 DOI: 10.1007/s11248-024-00396-8] [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: 04/15/2024] [Accepted: 07/04/2024] [Indexed: 08/10/2024]
Abstract
Root-specific or preferential promoters are essential to genetically modify plants with beneficial root traits. We have characterised the promoter from an oil palm metallothionein gene (EgMT) and performed a serial 5' deletion analysis to identify the region(s) essential for transgenes expression in roots. Stable functional characterisation of tobacco transgenic lines using the T1 generation showed that a deletion construct, designated as RSP-2D (1107 bp), directed strong GUS expression at all stages of root development, particularly in mature roots. Other constructs, RSP-2A (2481 bp) and RSP-2C (1639 bp), drove GUS expression in roots with an intensity lower than RSP-2D. The promoter activity was also detectable in seed pods and immature seeds, albeit at lower levels than CaMV35S. The promoter activity may also be induced by wounding as intact GUS staining was observed at the flower- and leaf-cutting sites of T1 samples carrying either RSP-2C or RSP-2D constructs. The promoter sequence contains cis-acting elements that may act as negative regulators and be responsible for root specificity. The results further indicated that the 5' UTR and ATATT sequences are essential for strong promoter activity. This study highlights the potential of RSP-2D promoter as a tool for modifying root traits through genetic engineering.
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Affiliation(s)
- Subhi Siti Masura
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
- Centre for Foundation Studies in Science of Universiti Putra Malaysia (ASPutra), Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Mat Yunus Abdul Masani
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Pek-Lan Chan
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Abdul Rahman Siti Rahmah
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Nadzirah Amiruddin
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Mohd Puad Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Azzreena Mohamad Azzeme
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | | | - Omar Abd Rasid
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia.
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10
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Khan ZA, Gupta K, Dasgupta I. Transient expression analysis of promoters of okra enation leaf curl virus in Nicotiana benthamiana, cotton and okra plants. Virus Genes 2024; 60:412-422. [PMID: 38727968 DOI: 10.1007/s11262-024-02074-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 04/22/2024] [Indexed: 07/13/2024]
Abstract
Viral promoters can be used to drive heterologous gene expression in transgenic plants. As part of our quest to look for new promoters, we have explored, for the first time, the promoters of okra enation leaf curl virus (OELCuV), a begomovirus infecting okra (Abelmoschus esculentus). The Rep and CP promoters of OELCuV fused with the gfp reporter gene, were expressed transiently in the natural host okra and the laboratory host cotton and Nicotiana benthamiana. The expression levels of the promoters were quantified through confocal laser scanning microscopy and GFP assay in N. benthamiana and okra. The results indicated that the Rep promoter was more active than the CP promoter, whose activity was similar to that of CaMV 35S promoter. Additionally, the Rep and CP promoters showed increase of expression, probably due to transactivation, when assayed following inoculation of OELCuV and betasatellite DNAs in cotton plants. A moderate increase in promoter activity in N. benthamiana was also seen, when assayed following the inoculation of the heterologous begomovirus Sri Lankan cassava mosaic virus.
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Affiliation(s)
- Zainul A Khan
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Kanika Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Khisti M, Avuthu T, Yogendra K, Kumar Valluri V, Kudapa H, Reddy PS, Tyagi W. Genome-wide identification and expression profiling of growth‑regulating factor (GRF) and GRF‑interacting factor (GIF) gene families in chickpea and pigeonpea. Sci Rep 2024; 14:17178. [PMID: 39060385 PMCID: PMC11282205 DOI: 10.1038/s41598-024-68033-2] [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: 01/19/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The growth-regulating factor (GRF) and GRF-interacting factor (GIF) families encode plant-specific transcription factors and play vital roles in plant development and stress response processes. Although GRF and GIF genes have been identified in various plant species, there have been no reports of the analysis and identification of the GRF and GIF transcription factor families in chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan). The present study identified seven CaGRFs, eleven CcGRFs, four CaGIFs, and four CcGIFs. The identified proteins were grouped into eight and three clades for GRFs and GIFs, respectively based on their phylogenetic relationships. A comprehensive in-silico analysis was performed to determine chromosomal location, sub-cellular localization, and types of regulatory elements present in the putative promoter region. Synteny analysis revealed that GRF and GIF genes showed diploid-polyploid topology in pigeonpea, but not in chickpea. Tissue-specific expression data at the vegetative and reproductive stages of the plant showed that GRFs and GIFs were strongly expressed in tissues like embryos, pods, and seeds, indicating that GRFs and GIFs play vital roles in plant growth and development. This research characterized GRF and GIF families and hints at their primary roles in the chickpea and pigeonpea growth and developmental process. Our findings provide potential gene resources and vital information on GRF and GIF gene families in chickpea and pigeonpea, which will help further understand the regulatory role of these gene families in plant growth and development.
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Affiliation(s)
- Mitesh Khisti
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Tejaswi Avuthu
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Kalenahalli Yogendra
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Vinod Kumar Valluri
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Himabindu Kudapa
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Palakolanu Sudhakar Reddy
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Wricha Tyagi
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India.
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12
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Yang J, Xiao S, Lu L, Wang H, Jiang Y. Genomic and molecular characterization of a cyprinid herpesvirus 2 YC-01 strain isolated from gibel carp. Heliyon 2024; 10:e32811. [PMID: 39035518 PMCID: PMC11259805 DOI: 10.1016/j.heliyon.2024.e32811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/27/2024] [Accepted: 06/10/2024] [Indexed: 07/23/2024] Open
Abstract
Cyprinid herpesvirus 2 (CyHV-2) is the pathogen of herpesviral hematopoietic necrosis (HVHN), causing the severe economic losses in farmed gibel carp (Carassius gibelio). Further exploration of the genome structure and potential molecular pathogenesis of CyHV-2 through complete genome sequencing, comparative genomics, and molecular characterization is required. Herein, the genome of a CyHV-2 YC-01 strain isolated from diseased gibel carp collected in Yancheng, Jiangsu Province, China was sequenced, then we analyzed the genomic structure, genetic properties, and molecular characterization. First, the complete YC-01 genome comprises 275,367 bp without terminal repeat (TR) regions, with 151 potential open reading frames (ORFs). Second, compared with other representative published strains of the genus Cyvirus, several evident variations are found in YC-01, particularly the orientation and position of ORF25 and ORF25B. ORF107 and ORF156 are considered as potential molecular genetic markers for YC-01. ORF55 (encoding thymidine kinase) might be used to distinguish YC-01 and ST-J1 from other CyHV-2 isolates. Third, phylogenetically, YC-01 clusters with the members of the genus Cyvirus (together with the other six CyHV-2 isolates). Fourth, 43 putative proteins are predicted to be functional and are mainly divided into five categories. Several conserved motifs are found in nucleotide, amino acid, and promoter sequences including cis-acting elements identification of YC-01. Finally, the potential virulence factors and linear B cell epitopes of CyHV-2 are predicted to supply possibilities for designing novel vaccines rationally. Our results provide insights for further understanding genomic structure, genetic evolution, and potential molecular mechanisms of CyHV-2.
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Affiliation(s)
- Jia Yang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, 201306, China
| | - Simin Xiao
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, 201306, China
| | - Liqun Lu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Hao Wang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Yousheng Jiang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China
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13
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Zhao F, Chen JX, Xu H, Han Y, Zhou M, Wang G, Ma LQ, Chen Y. Arsenite Antiporter PvACR3 Driven by Its Native Promoter Increases Leaf Arsenic Accumulation in Tobacco. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11534-11541. [PMID: 38865317 DOI: 10.1021/acs.est.4c00977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Pteris vittata is the first-reported arsenic (As) hyperaccumulator, which has been applied to phytoremediation of As-contaminated soil. PvACR3, a key arsenite (AsIII) antiporter, plays an important role in As hyperaccumulation in P. vittata. However, its functions in plants are not fully understood. In this study, the PvACR3 gene was heterologously expressed in tobacco, driven by its native promoter (ProPvACR3). After growing at 5 μM AsIII or 10 μM AsV in hydroponics for 1-5 days, PvACR3-expression enhanced the As levels in leaves by 66.4-113 and 51.8-101%, without impacting the As contents in the roots or stems. When cultivated in As-contaminated soil, PvACR3-expressed transgenic plants accumulated 47.9-85.5% greater As in the leaves than wild-type plants. In addition, PvACR3-expression increased the As resistance in transgenic tobacco, showing that enhanced leaf As levels are not detrimental to its overall As tolerance. PvACR3 was mainly expressed in tobacco leaf veins and was likely to unload AsIII from the vein xylem vessels to the mesophyll cells, thus elevating the leaf As levels. This work demonstrates that heterologously expressing PvACR3 under its native promoter specifically enhances leaf As accumulation in tobacco, which helps to reveal the As-hyperaccumulation mechanism in P. vittata and to enhance the As accumulation in plant leaves for phytoremediation.
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Affiliation(s)
- Fei Zhao
- School of Environment, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, Nanjing 210023, China
| | - Jun-Xiu Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Hua Xu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yu Han
- School of Environment, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, Nanjing 210023, China
| | - Mingxi Zhou
- School of Environment, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, Nanjing 210023, China
| | - Guoxiang Wang
- School of Environment, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, Nanjing 210023, China
| | - Lena Q Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanshan Chen
- School of Environment, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, Nanjing 210023, China
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14
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Wang Q, Lei X, Wang Y, Di P, Meng X, Peng W, Rong J, Wang Y. Genome-wide identification of the LEA gene family in Panax ginseng: Evidence for the role of PgLEA2-50 in plant abiotic stress response. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108742. [PMID: 38772166 DOI: 10.1016/j.plaphy.2024.108742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/21/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024]
Abstract
Ginseng frequently encounters environmental stress during its growth and development. Late Embryogenesis Abundant (LEA) proteins play a crucial role in combating adversity stress, particularly against abiotic challenges In this study, 107 LEA genes from ginseng, spanning eight subfamilies, were identified, demonstrating significant evolutionary conservation, with the LEA2 subfamily being most prominent. Gene duplication events, primarily segmental duplications, have played a major role in the expansion of the LEA gene family, which has undergone strong purifying selection. PgLEAs were unevenly distributed across 22 chromosomes, with each subfamily featuring unique structural domains and conserved motifs. PgLEAs were expressed in various tissues, exhibiting distinct variations in abundance and tissue specificity. Numerous regulatory cis-elements, related to abiotic stress and hormones, were identified in the promoter region. Additionally, PgLEAs were regulated by a diverse array of abiotic stress-related transcription factors. A total of 35 PgLEAs were differentially expressed following treatments with ABA, GA, and IAA. Twenty-three PgLEAs showed significant but varied responses to drought, extreme temperatures, and salinity stress. The transformation of tobacco with the key gene PgLEA2-50 enhanced osmoregulation and antioxidant levels in transgenic lines, improving their resistance to abiotic stress. This study offers insights into functional gene analysis, focusing on LEA proteins, and establishes a foundational framework for research on ginseng's resilience to abiotic stress.
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Affiliation(s)
- Qi Wang
- Jilin Agricultural University, Changchun, Jilin, China
| | - Xiujuan Lei
- Jilin Agricultural University, Changchun, Jilin, China
| | - Yihan Wang
- Jilin Agricultural University, Changchun, Jilin, China
| | - Peng Di
- Jilin Agricultural University, Changchun, Jilin, China
| | - Xiangru Meng
- Jilin Agricultural University, Changchun, Jilin, China
| | - Wenyue Peng
- Jilin Agricultural University, Changchun, Jilin, China
| | - Junbo Rong
- Jilin Agricultural University, Changchun, Jilin, China
| | - Yingping Wang
- Jilin Agricultural University, Changchun, Jilin, China.
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15
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Zhao D, Guan P, Wei L, Gao J, Guo L, Tian D, Li Q, Guo Z, Cui H, Li Y, Guo J. Comprehensive identification and expression analysis of FAR1/FHY3 genes under drought stress in maize ( Zea mays L.). PeerJ 2024; 12:e17684. [PMID: 38952979 PMCID: PMC11216215 DOI: 10.7717/peerj.17684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024] Open
Abstract
Background FAR1/FHY3 transcription factors are derived from transposase, which play important roles in light signal transduction, growth and development, and response to stress by regulating downstream gene expression. Although many FAR1/FHY3 members have been identified in various species, the FAR1/FHY3 genes in maize are not well characterized and their function in drought are unknown. Method The FAR1/FHY3 family in the maize genome was identified using PlantTFDB, Pfam, Smart, and NCBI-CDD websites. In order to investigate the evolution and functions of FAR1 genes in maize, the information of protein sequences, chromosome localization, subcellular localization, conserved motifs, evolutionary relationships and tissue expression patterns were analyzed by bioinformatics, and the expression patterns under drought stress were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Results A total of 24 ZmFAR members in maize genome, which can be divided into five subfamilies, with large differences in protein and gene structures among subfamilies. The promoter regions of ZmFARs contain abundant abiotic stress-responsive and hormone-respovensive cis-elements. Among them, drought-responsive cis-elements are quite abundant. ZmFARs were expressed in all tissues detected, but the expression level varies widely. The expression of ZmFARs were mostly down-regulated in primary roots, seminal roots, lateral roots, and mesocotyls under water deficit. Most ZmFARs were down-regulated in root after PEG-simulated drought stress. Conclusions We performed a genome-wide and systematic identification of FAR1/FHY3 genes in maize. And most ZmFARs were down-regulated in root after drought stress. These results indicate that FAR1/FHY3 transcription factors have important roles in drought stress response, which can lay a foundation for further analysis of the functions of ZmFARs in response to drought stress.
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Affiliation(s)
- Dongbo Zhao
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Peiyan Guan
- College of Life Science, Dezhou University, Dezhou, Shandong, China
| | - Longxue Wei
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Jiansheng Gao
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Lianghai Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Dianbin Tian
- Pingyuan County Rural Revitalization Service Center, Pingyuan, Shandong, China
| | - Qingfang Li
- Linyi County Agricultural and Rural Bureau, Linyi, Shandong, China
| | - Zhihui Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Huini Cui
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Yongjun Li
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Jianjun Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
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16
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Lei C, Dang Z, Zhu M, Zhang M, Wang H, Chen Y, Zhang H. Identification of the ERF gene family of Mangifera indica and the defense response of MiERF4 to Xanthomonas campestris pv. mangiferaeindicae. Gene 2024; 912:148382. [PMID: 38493974 DOI: 10.1016/j.gene.2024.148382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/03/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
An important regulatory role for ethylene-responsive transcription factors (ERFs) is in plant growth and development, stress response, and hormone signaling. However, AP2/ERF family genes in mango have not been systematically studied. In this study, a total of 113 AP2/ERF family genes were identified from the mango genome and phylogenetically classified into five subfamilies: AP2 (28 genes), DREB (42 genes), ERF (33 genes), RAV (6 genes), and Soloist (4 genes). Of these, the ERF family, in conjunction with Arabidopsis and rice, forms a phylogenetic tree divided into seven groups, five of which have MiERF members. Analysis of gene structure and cis-elements showed that each MiERF gene contains only one AP2 structural domain, and that MiERF genes contain a large number of cis-elements associated with hormone signaling and stress response. Collinearity tests revealed a high degree of homology between MiERFs and CsERFs. Tissue-specific and stress-responsive expression profiling revealed that MiERF genes are primarily involved in the regulation of reproductive growth and are differentially and positively expressed in response to external hormones and pathogenic bacteria. Physiological results from a gain-of-function analysis of MiERF4 transiently overexpressed in tobacco and mango showed that transient expression of MiERF4 resulted in decreased colony count and callose deposition, as well as varying degrees of response to hormonal signals such as ETH, JA, and SA. Thus, MiERF4 may be involved in the JA/ETH signaling pathway to enhance plant defense against pathogenic bacteria. This study provides a basis for further research on the function and regulation of MiERF genes and lays a foundation for the selection of disease-resistant genes in mango.
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Affiliation(s)
- Chen Lei
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China; Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhiguo Dang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Min Zhu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
| | - Mengting Zhang
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Huiliang Wang
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yeyuan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China.
| | - He Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China; Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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17
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Li H, Zou T, Chen S, Zhong M. Genome-wide identification, characterization and expression analysis of the DUF668 gene family in tomato. PeerJ 2024; 12:e17537. [PMID: 38912042 PMCID: PMC11192028 DOI: 10.7717/peerj.17537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/19/2024] [Indexed: 06/25/2024] Open
Abstract
The domain of unknown function 668 (DUF668) is a gene family that may play a key role in plant growth and development as well as in responding to adversity coercion stresses. However, the DUF668 gene family has not yet been well identified and characterized in tomato. In this study, a total of nine putative SlDUF668 genes were identified in tomato, distributed on six chromosomes. Phylogenetic analyses revealed that SlDUF668 proteins were classified into two major groups. Members within the same group largely displayed analogous gene structure and conserved motif compositions. Several cis-elements were exhibited in the upstream sequences of the SlDUF668 genes, including elements implicated in plant growth and development processes, abiotic stress and hormone responses. Further, the study assessed the expression patterns of the SlDUF668 gene family in various tomato tissues, five plant hormones treatments, three abiotic stresses using qRT-PCR. The SlDUF668 genes expressed ubiquitously in various tissues, and five genes (SlDUF668-04, SlDUF668-06, SlDUF668-07, SlDUF668-08 and SlDUF668-09) showed tissue specificity. And SlDUF668 genes responded to abiotic stresses such as salt, drought and cold to varying degrees. Overall, our study provided a base for the tomato DUF668 gene family and laid a foundation for further understanding the functional characteristics of DUF668 genes in tomato plants.
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Affiliation(s)
- Hui Li
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
| | - Tingrui Zou
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
| | - Shuisen Chen
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
| | - Ming Zhong
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
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Dakal TC, Dhabhai B, Pant A, Moar K, Chaudhary K, Yadav V, Ranga V, Sharma NK, Kumar A, Maurya PK, Maciaczyk J, Schmidt‐Wolf IGH, Sharma A. Oncogenes and tumor suppressor genes: functions and roles in cancers. MedComm (Beijing) 2024; 5:e582. [PMID: 38827026 PMCID: PMC11141506 DOI: 10.1002/mco2.582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/21/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Cancer, being the most formidable ailment, has had a profound impact on the human health. The disease is primarily associated with genetic mutations that impact oncogenes and tumor suppressor genes (TSGs). Recently, growing evidence have shown that X-linked TSGs have specific role in cancer progression and metastasis as well. Interestingly, our genome harbors around substantial portion of genes that function as tumor suppressors, and the X chromosome alone harbors a considerable number of TSGs. The scenario becomes even more compelling as X-linked TSGs are adaptive to key epigenetic processes such as X chromosome inactivation. Therefore, delineating the new paradigm related to X-linked TSGs, for instance, their crosstalk with autosome and involvement in cancer initiation, progression, and metastasis becomes utmost importance. Considering this, herein, we present a comprehensive discussion of X-linked TSG dysregulation in various cancers as a consequence of genetic variations and epigenetic alterations. In addition, the dynamic role of X-linked TSGs in sex chromosome-autosome crosstalk in cancer genome remodeling is being explored thoroughly. Besides, the functional roles of ncRNAs, role of X-linked TSG in immunomodulation and in gender-based cancer disparities has also been highlighted. Overall, the focal idea of the present article is to recapitulate the findings on X-linked TSG regulation in the cancer landscape and to redefine their role toward improving cancer treatment strategies.
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Affiliation(s)
- Tikam Chand Dakal
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Bhanupriya Dhabhai
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Anuja Pant
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kareena Moar
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kanika Chaudhary
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vikas Yadav
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vipin Ranga
- Dearptment of Agricultural BiotechnologyDBT‐NECAB, Assam Agricultural UniversityJorhatAssamIndia
| | | | - Abhishek Kumar
- Manipal Academy of Higher EducationManipalKarnatakaIndia
- Institute of Bioinformatics, International Technology ParkBangaloreIndia
| | - Pawan Kumar Maurya
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Jarek Maciaczyk
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
| | - Ingo G. H. Schmidt‐Wolf
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
| | - Amit Sharma
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
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19
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Ye P, Che X, Liu Y, Zeng M, Guo W, Long Y, Liu T, Wang Z. Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine ( Pinus taeda L.). PeerJ 2024; 12:e17388. [PMID: 38799072 PMCID: PMC11122039 DOI: 10.7717/peerj.17388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.
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Affiliation(s)
- Peiqi Ye
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Xiaoliang Che
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Yang Liu
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Ming Zeng
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Wenbing Guo
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Yongbin Long
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Tianyi Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhe Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
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20
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Ma Y, Jie H, Zhao L, He P, Lv X, Xu Y, Zhang Y, Xing H, Jie Y. BnXTH1 regulates cadmium tolerance by modulating vacuolar compartmentalization and the cadmium binding capacity of cell walls in ramie (Boehmeria nivea). JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134172. [PMID: 38569340 DOI: 10.1016/j.jhazmat.2024.134172] [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: 09/17/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024]
Abstract
Xyloglucan endotransglucosylase/hydrolases (XTH) are cell wall-modifying enzymes important in plant response to abiotic stress. However, the role of XTH in cadmium (Cd) tolerance in ramie remains largely unknown. Here, we identified and cloned BnXTH1, a member of the XTH family, in response to Cd stress in ramie. The BnXTH1 promoter (BnXTH1p) demonstrated that MeJA induces the response of BnXTH1p to Cd stress. Moreover, overexpressing BnXTH1 in Boehmeria nivea increased Cd tolerance by significantly increasing the Cd content in the cell wall and decreasing Cd inside ramie cells. Cadmium stress induced BnXTH1-expression and consequently increased xyloglucan endotransglucosylase (XET) activity, leading to high xyloglucan contents and increased hemicellulose contents in ramie. The elevated hemicellulose content increased Cd chelation onto the cell walls and reduced the level of intracellular Cd. Interestingly, overexpressing BnXTH1 significantly increased the content of Cd in vacuoles of ramie and vacuolar compartmentalization genes. Altogether, these results evidence that Cd stress induced MeJA accumulation in ramie, thus, activating BnXTH1 expression and increasing the content of xyloglucan to enhance the hemicellulose binding capacity and increase Cd chelation onto cell walls. BnXTH1 also enhances the vacuolar Cd compartmentalization and reduces the level of Cd entering the organelles and soluble solution.
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Affiliation(s)
- Yushen Ma
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; Hunan Academy of Forestry, Changsha 410004, Hunan, China
| | - Hongdong Jie
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Long Zhao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Pengliang He
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xueying Lv
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Yan Xu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Ying Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Hucheng Xing
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Changsha 410128, China
| | - Yucheng Jie
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Changsha 410128, China.
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21
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Chen Y, Li M, Yan M, Chen Y, Saeed M, Ni Z, Fang Z, Chen H. Bacillus subtilis: current and future modification strategies as a protein secreting factory. World J Microbiol Biotechnol 2024; 40:195. [PMID: 38722426 DOI: 10.1007/s11274-024-03997-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Bacillus subtilis is regarded as a promising microbial expression system in bioengineering due to its high stress resistance, nontoxic, low codon preference and grow fast. The strain has a relatively efficient expression system, as it has at least three protein secretion pathways and abundant molecular chaperones, which guarantee its expression ability and compatibility. Currently, many proteins are expressed in Bacillus subtilis, and their application prospects are broad. Although Bacillus subtilis has great advantages compared with other prokaryotes related to protein expression and secretion, it still faces deficiencies, such as low wild-type expression, low product activity, and easy gene loss, which limit its large-scale application. Over the years, many researchers have achieved abundant results in the modification of Bacillus subtilis expression systems, especially the optimization of promoters, expression vectors, signal peptides, transport pathways and molecular chaperones. An optimal vector with a suitable promoter strength and other regulatory elements could increase protein synthesis and secretion, increasing industrial profits. This review highlights the research status of optimization strategies related to the expression system of Bacillus subtilis. Moreover, research progress on its application as a food-grade expression system is also presented, along with some future modification and application directions.
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Affiliation(s)
- Yanzhen Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Miaomiao Li
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Mingchen Yan
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yong Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Muhammad Saeed
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zhong Ni
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zhen Fang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Huayou Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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22
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Mishra LS, Cook SD, Kushwah S, Isaksson H, Straub IR, Abele M, Mishra S, Ludwig C, Libby E, Funk C. Overexpression of the plastidial pseudo-protease AtFtsHi3 enhances drought tolerance while sustaining plant growth. PHYSIOLOGIA PLANTARUM 2024; 176:e14370. [PMID: 38818570 DOI: 10.1111/ppl.14370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024]
Abstract
With climate change, droughts are expected to be more frequent and severe, severely impacting plant biomass and quality. Here, we show that overexpressing the Arabidopsis gene AtFtsHi3 (FtsHi3OE) enhances drought-tolerant phenotypes without compromising plant growth. AtFtsHi3 encodes a chloroplast envelope pseudo-protease; knock-down mutants (ftshi3-1) are found to be drought tolerant but exhibit stunted growth. Altered AtFtsHi3 expression therefore leads to drought tolerance, while only diminished expression of this gene leads to growth retardation. To understand the underlying mechanisms of the enhanced drought tolerance, we compared the proteomes of ftshi3-1 and pFtsHi3-FtsHi3OE (pFtsHi3-OE) to wild-type plants under well-watered and drought conditions. Drought-related processes like osmotic stress, water transport, and abscisic acid response were enriched in pFtsHi3-OE and ftshi3-1 mutants following their enhanced drought response compared to wild-type. The knock-down mutant ftshi3-1 showed an increased abundance of HSP90, HSP93, and TIC110 proteins, hinting at a potential downstream role of AtFtsHi3 in chloroplast pre-protein import. Mathematical modeling was performed to understand how variation in the transcript abundance of AtFtsHi3 can, on the one hand, lead to drought tolerance in both overexpression and knock-down lines, yet, on the other hand, affect plant growth so differently. The results led us to hypothesize that AtFtsHi3 may form complexes with at least two other protease subunits, either as homo- or heteromeric structures. Enriched amounts of AtFtsH7/9, AtFtsH11, AtFtsH12, and AtFtsHi4 in ftshi3-1 suggest a possible compensation mechanism for these proteases in the hexamer.
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Affiliation(s)
| | - Sam D Cook
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Hanna Isaksson
- Department of Mathematics and Mathematical Statistics, Integrated Science Lab (Icelab), Umeå University, Umeå, Sweden
- IceLab, Umeå University, Umeå, Sweden
| | - Isabella R Straub
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Miriam Abele
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Sanatkumar Mishra
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Eric Libby
- Department of Mathematics and Mathematical Statistics, Integrated Science Lab (Icelab), Umeå University, Umeå, Sweden
- IceLab, Umeå University, Umeå, Sweden
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23
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Zhang D, Zhao X, Huang Y, Zhang MM, He X, Yin W, Lan S, Liu ZJ, Ma L. Genome-wide characterization and expression profiling of the HD-ZIP gene family in Acoraceae under salinity and cold stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1372580. [PMID: 38736444 PMCID: PMC11082295 DOI: 10.3389/fpls.2024.1372580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/11/2024] [Indexed: 05/14/2024]
Abstract
The Homeodomain-Leucine Zipper (HD-ZIP) transcription factors play a pivotal role in governing various aspects of plant growth, development, and responses to abiotic stress. Despite the well-established importance of HD-ZIPs in many plants, their functions in Acoraceae, the basal lineage of monocots, remain largely unexplored. Using recently published whole-genome data, we identified 137 putative HD-ZIPs in two Acoraceae species, Acorus gramineus and Acorus calamus. These HD-ZIP genes were further classified into four subfamilies (I, II, III, IV) based on phylogenetic and conserved motif analyses, showcasing notable variations in exon-intron patterns among different subfamilies. Two microRNAs, miR165/166, were found to specifically target HD-ZIP III genes with highly conserved binding sites. Most cis-acting elements identified in the promoter regions of Acoraceae HD-ZIPs are involved in modulating light and phytohormone responsiveness. Furthermore, our study revealed an independent duplication event in Ac. calamus and a one-to-multiple correspondence between HD-ZIP genes of Ac. calamus and Ac. gramineus. Expression profiles obtained from qRT-PCR demonstrated that HD-ZIP I genes are strongly induced by salinity stress, while HD-ZIP II members have contrasting stress responses in two species. HD-ZIP III and IV genes show greater sensitivity in stress-bearing roots. Taken together, these findings contribute valuable insights into the roles of HD-ZIP genes in stress adaptation and plant resilience in basal monocots, illuminating their multifaceted roles in plant growth, development, and response to abiotic stress.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuewei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meng-Meng Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin He
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilun Yin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liang Ma
- School of Pharmacy, Fujian Health Vocational and Technical College, Fuzhou, China
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24
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Awan MJA, Farooq MA, Naqvi RZ, Karamat U, Bukhari SAR, Waqas MAB, Mahmood MA, Buzdar MI, Rasheed A, Amin I, Saeed NA, Mansoor S. Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat cultivars and hybrids at different growth stages. Mol Biol Rep 2024; 51:537. [PMID: 38642174 DOI: 10.1007/s11033-024-09454-0] [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: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Hexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity and resulted in duplication and neofunctionalization of major agronomic genes. The genetic architecture of polyploid wheat not only confers adaptive plasticity but also offers huge genetic diversity. However, the contribution of different gene copies (homeologs) encoded from different subgenomes (A, B, D) at different growth stages remained unexplored. METHODS In this study, hybrid of elite cultivars of wheat were developed via reciprocal crosses (cytoplasm swapping) and phenotypically evaluated. We assessed differential expression profiles of yield-related negative regulators in these cultivars and their F1 hybrids and identified various cis-regulatory signatures by employing bioinformatics tools. Furthermore, the preferential expression patterns of the syntenic triads encoded from A, B, and D subgenomes were assessed to decipher their functional redundancy at six different growth stages. RESULTS Hybrid progenies showed better heterosis such as up to 17% increase in the average number of grains and up to 50% increase in average thousand grains weight as compared to mid-parents. Based on the expression profiling, our results indicated significant dynamic transcriptional expression patterns, portraying the different homeolog-dominance at the same stage in the different cultivars and their hybrids. Albeit belonging to same syntenic triads, a dynamic trend was observed in the regulatory signatures of these genes that might be influencing their expression profiles. CONCLUSION These findings can substantially contribute and provide insights for the selective introduction of better cultivars into traditional and hybrid breeding programs which can be harnessed for the improvement of future wheat.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Awais Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Umer Karamat
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sayyad Ali Raza Bukhari
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Abu Bakar Waqas
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Ismail Buzdar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS) & CIMMYT-China office, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Nasir A Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan.
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
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25
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Sobrino-Mengual G, Alvarez D, Twyman RM, Gerrish C, Fraser PD, Capell T, Christou P. Activation of the native PHYTOENE SYNTHASE 1 promoter by modifying near-miss cis-acting elements induces carotenoid biosynthesis in embryogenic rice callus. PLANT CELL REPORTS 2024; 43:118. [PMID: 38632121 PMCID: PMC11024007 DOI: 10.1007/s00299-024-03199-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
KEY MESSAGE Modification of silent latent endosperm-enabled promoters (SLEEPERs) allows the ectopic activation of non-expressed metabolic genes in rice callus Metabolic engineering in plants typically involves transgene expression or the mutation of endogenous genes. An alternative is promoter modification, where small changes in the promoter sequence allow genes to be switched on or off in particular tissues. To activate silent genes in rice endosperm, we screened native promoters for near-miss cis-acting elements that can be converted to endosperm-active regulatory motifs. We chose rice PHYTOENE SYNTHASE 1 (PSY1), encoding the enzyme responsible for the first committed step in the carotenoid biosynthesis pathway, because it is not expressed in rice endosperm. We identified six motifs within a 120-bp region, upstream of the transcriptional start site, which differed from endosperm-active elements by up to four nucleotides. We mutated four motifs to match functional elements in the endosperm-active BCH2 promoter, and this promoter was able to drive GFP expression in callus and in seeds of regenerated plants. The 4 M promoter was not sufficient to drive PSY1 expression, so we mutated the remaining two elements and used the resulting 6 M promoter to drive PSY1 expression in combination with a PDS transgene. This resulted in deep orange callus tissue indicating the accumulation of carotenoids, which was subsequently confirmed by targeted metabolomics analysis. PSY1 expression driven by the uncorrected or 4 M variants of the promoter plus a PDS transgene produced callus that lacked carotenoids. These results confirm that the adjustment of promoter elements can facilitate the ectopic activation of endogenous plant promoters in rice callus and endosperm and most likely in other tissues and plant species.
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Affiliation(s)
- Guillermo Sobrino-Mengual
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Derry Alvarez
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, BioActives Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Christopher Gerrish
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Teresa Capell
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain.
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26
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Zhang F, Yu Q, Huang Y, Luo Y, Qin J, Chen L, Li E, Wang X. Study on the osmotic response and function of myo-inositol oxygenase in euryhaline fish nile tilapia ( Oreochromis niloticus). Am J Physiol Cell Physiol 2024; 326:C1054-C1066. [PMID: 38344798 DOI: 10.1152/ajpcell.00513.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 03/13/2024]
Abstract
To understand the role of myo-inositol oxygenase (miox) in the osmotic regulation of Nile tilapia, its expression was analyzed in various tissues. The results showed that the expression of miox gene was highest in the kidney, followed by the liver, and was significantly upregulated in the kidney and liver under 1 h hyperosmotic stress. The relative luminescence efficiency of the miox gene transcription starting site (-4,617 to +312 bp) under hyperosmotic stress was measured. Two fragments (-1,640/-1,619 and -620/-599) could induce the luminescence activity. Moreover, the -1,640/-1,619 and -620/-599 responded to hyperosmotic stress and high-glucose stimulation by base mutation, suggesting that osmotic and carbohydrate response elements may exist in this region. Finally, the salinity tolerance of Nile tilapia was significantly reduced after the knocking down of miox gene. The accumulation of myo-inositol was affected, and the expression of enzymes in glucose metabolism was significantly reduced after the miox gene was knocked down. Furthermore, hyperosmotic stress can cause oxidative stress, and MIOX may help maintain the cell redox balance under hyperosmotic stress. In summary, MIOX is essential in osmotic regulation to enhance the salinity tolerance of Nile tilapia by affecting myo-inositol accumulation, glucose metabolism, and antioxidant performance.NEW & NOTEWORTHY Myo-inositol oxygenase (MIOX) is the rate-limiting enzyme that catalyzes the first step of MI metabolism and determines MI content in aquatic animals. To understand the role of miox in the osmotic regulation of Nile tilapia, we analyzed its expression in different tissues and its function under hyperosmotic stress. This study showed that miox is essential in osmotic regulation to enhance the salinity tolerance of Nile tilapia by affecting myo-inositol accumulation, glucose metabolism, and antioxidant performance.
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Affiliation(s)
- Fan Zhang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Qiuran Yu
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Yuxing Huang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Yuan Luo
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Jianguang Qin
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Liqiao Chen
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Erchao Li
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Xiaodan Wang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
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Huang G, Hu Y, Li F, Zuo X, Wang X, Li F, Li R. Genome-wide characterization of heavy metal-associated isoprenylated plant protein gene family from Citrus sinensis in response to huanglongbing. FRONTIERS IN PLANT SCIENCE 2024; 15:1369883. [PMID: 38601304 PMCID: PMC11004388 DOI: 10.3389/fpls.2024.1369883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024]
Abstract
Introduction Heavy metal-associated isoprenylated plant proteins (HIPPs) play vital roles in maintaining heavy metal balance and responding to both biotic and abiotic stresses in vascular plants. However, the role of HIPPs in the response to Huanglongbing (HLB), a harmful disease of citrus caused by the phloem-colonizing bacterium Candidatus Liberibacter asiaticus (CLas), has not been examined. Methods and results In this study, a total of 26 HIPP genes were identified in Citrus sinensis, and they were grouped into 5 clades. The CsHIPP genes are distributed on 8 chromosomes and exhibited considerable synteny with HIPPs found in Arabidopsis thaliana. Additionally, we analyzed the gene structure, conserved motifs and domains of the CsHIPPs. Various cis-acting elements related to plant hormones and stress responses were identified in the promoters of CsHIPPs. Public transcriptome data and RT-qPCR analysis showed that the expression level of CsHIPP03 was significantly reduced in samples infected by CLas and Xanthomonas citri ssp. citri (Xcc). Furthermore, silencing the homologous gene of CsHIPP03 in Nicotiana benthamiana increased the disease resistance of plants to bacteria. Discussion Our results provide a basis for functional studies of HIPP gene family in C. sinensis, highlighting their functions in bacterial resistance, and improve our understanding to the susceptibility mechanism of HLB.
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Affiliation(s)
- Guiyan Huang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yanan Hu
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Fuxuan Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Xiru Zuo
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Xinyou Wang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Fengyao Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Ruimin Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, China
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Guo H, Tan J, Jiao Y, Huang B, Ma R, Ramakrishnan M, Qi G, Zhang Z. Genome-wide identification and expression analysis of the HAK/KUP/KT gene family in Moso bamboo. FRONTIERS IN PLANT SCIENCE 2024; 15:1331710. [PMID: 38595761 PMCID: PMC11002169 DOI: 10.3389/fpls.2024.1331710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/04/2024] [Indexed: 04/11/2024]
Abstract
The K+ uptake permease/high-affinity K+/K+ transporter (KUP/HAK/KT) family is the most prominent group of potassium (K+) transporters, playing a key role in K+ uptake, transport, plant growth and development, and stress tolerance. However, the presence and functions of the KUP/HAK/KT family in Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau), the fastest-growing plant, have not been studied. In this study, we identified 41 KUP/HAK/KT genes (PeHAKs) distributed across 18 chromosomal scaffolds of the Moso bamboo genome. PeHAK is a typical membrane protein with a conserved structural domain and motifs. Phylogenetic tree analysis classified PeHAKs into four distinct clusters, while collinearity analysis revealed gene duplications resulting from purifying selection, including both tandem and segmental duplications. Enrichment analysis of promoter cis-acting elements suggested their plausible role in abiotic stress response and hormone induction. Transcriptomic data and STEM analyses indicated that PeHAKs were involved in tissue and organ development, rapid growth, and responded to different abiotic stress conditions. Subcellular localization analysis demonstrated that PeHAKs are predominantly expressed at the cell membrane. In-situ PCR experiments confirmed that PeHAK was mainly expressed in the lateral root primordia. Furthermore, the involvement of PeHAKs in potassium ion transport was confirmed by studying the potassium ion transport properties of a yeast mutant. Additionally, through homology modeling, we revealed the structural properties of HAK as a transmembrane protein associated with potassium ion transport. This research provides a solid basis for understanding the classification, characterization, and functional analysis of the PeHAK family in Moso bamboo.
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Affiliation(s)
- Hui Guo
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Jiaqi Tan
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Yang Jiao
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Bing Huang
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Ruifang Ma
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Muthusamy Ramakrishnan
- 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, China
| | - Guoning Qi
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zhijun Zhang
- Bamboo Industry Institute, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
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Nie M, Li L, He C, Lu J, Guo H, Li X, Jiang M, Zhan R, Sun W, Yin J, Wu Q. Genome-wide identification, subcellular localization, and expression analysis of the phosphatidyl ethanolamine-binding protein family reveals the candidates involved in flowering and yield regulation of Tartary buckwheat ( Fagopyrum tataricum). PeerJ 2024; 12:e17183. [PMID: 38560476 PMCID: PMC10979741 DOI: 10.7717/peerj.17183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Background PEBP (phosphatidyl ethanolamine-binding protein) is widely found in eukaryotes including plants, animals and microorganisms. In plants, the PEBP family plays vital roles in regulating flowering time and morphogenesis and is highly associated to agronomic traits and yields of crops, which has been identified and characterized in many plant species but not well studied in Tartary buckwheat (Fagopyrum tataricum Gaertn.), an important coarse food grain with medicinal value. Methods Genome-wide analysis of FtPEBP gene family members in Tartary buckwheat was performed using bioinformatic tools. Subcellular localization analysis was performed by confocal microscopy. The expression levels of these genes in leaf and inflorescence samples were analyzed using qRT-PCR. Results Fourteen Fagopyrum tataricum PEBP (FtPEBP) genes were identified and divided into three sub-clades according to their phylogenetic relationships. Subcellular localization analysis of the FtPEBP proteins in tobacco leaves indicated that FT- and TFL-GFP fusion proteins were localized in both the nucleus and cytoplasm. Gene structure analysis showed that most FtPEBP genes contain four exons and three introns. FtPEBP genes are unevenly distributed in Tartary buckwheat chromosomes. Three tandem repeats were found among FtFT5/FtFT6, FtMFT1/FtMFT2 and FtTFL4/FtTFL5. Five orthologous gene pairs were detected between F. tataricum and F. esculentum. Seven light-responsive, nine hormone-related and four stress-responsive elements were detected in FtPEBPs promoters. We used real-time PCR to investigate the expression levels of FtPEBPs among two flowering-type cultivars at floral transition time. We found FtFT1/FtFT3 were highly expressed in leaf and young inflorescence of early-flowering type, whereas they were expressed at very low levels in late-flowering type cultivars. Thus, we deduced that FtFT1/FtFT3 may be positive regulators for flowering and yield of Tartary buckwheat. These results lay an important foundation for further studies on the functions of FtPEBP genes which may be utilized for yield improvement.
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Affiliation(s)
- Mengping Nie
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Li Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Cailin He
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Jing Lu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Huihui Guo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Xiao'an Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Mi Jiang
- Key Laboratory of Wheat Crop Research in Ganzi Academy of Agricultural Sciences, Ganzi Academy of Agricultural Sciences, Ganzi, Sichuan, China
| | - Ruiling Zhan
- Key Laboratory of Wheat Crop Research in Ganzi Academy of Agricultural Sciences, Ganzi Academy of Agricultural Sciences, Ganzi, Sichuan, China
| | - Wenjun Sun
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
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Jiao Y, Tan J, Guo H, Huang B, Ying Y, Ramakrishnan M, Zhang Z. Genome-wide analysis of the KNOX gene family in Moso bamboo: insights into their role in promoting the rapid shoot growth. BMC PLANT BIOLOGY 2024; 24:213. [PMID: 38528453 DOI: 10.1186/s12870-024-04883-2] [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: 10/17/2023] [Accepted: 03/04/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND KNOTTED1-like homeobox (KNOX) genes, plant-specific homologous box transcription factors (TFs), play a central role in regulating plant growth, development, organ formation, and response to biotic and abiotic stresses. However, a comprehensive genome-wide identification of the KNOX genes in Moso bamboo (Phyllostachys edulis), the fastest growing plant, has not yet been conducted, and the specific biological functions of this family remain unknown. RESULTS The expression profiles of 24 KNOX genes, divided into two subfamilies, were determined by integrating Moso bamboo genome and its transcriptional data. The KNOX gene promoters were found to contain several light and stress-related cis-acting elements. Synteny analysis revealed stronger similarity with rice KNOX genes than with Arabidopsis KNOX genes. Additionally, several conserved structural domains and motifs were identified in the KNOX proteins. The expansion of the KNOX gene family was primarily regulated by tandem duplications. Furthermore, the KNOX genes were responsive to naphthaleneacetic acid (NAA) and gibberellin (GA) hormones, exhibiting distinct temporal expression patterns in four different organs of Moso bamboo. Short Time-series Expression Miner (STEM) analysis and quantitative real-time PCR (qRT-PCR) assays demonstrated that PeKNOX genes may play a role in promoting rapid shoot growth. Additionally, Gene Ontology (GO) and Protein-Protein Interaction (PPI) network enrichment analyses revealed several functional annotations for PeKNOXs. By regulating downstream target genes, PeKNOXs are involved in the synthesis of AUX /IAA, ultimately affecting cell division and elongation. CONCLUSIONS In the present study, we identified and characterized a total of 24 KNOX genes in Moso bamboo and investigated their physiological properties and conserved structural domains. To understand their functional roles, we conducted an analysis of gene expression profiles using STEM and RNA-seq data. This analysis successfully revealed regulatory networks of the KNOX genes, involving both upstream and downstream genes. Furthermore, the KNOX genes are involved in the AUX/IAA metabolic pathway, which accelerates shoot growth by influencing downstream target genes. These results provide a theoretical foundation for studying the molecular mechanisms underlying the rapid growth and establish the groundwork for future research into the functions and transcriptional regulatory networks of the KNOX gene family.
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Affiliation(s)
- Yang Jiao
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Jiaqi Tan
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Hui Guo
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Bin Huang
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Yeqing Ying
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Muthusamy Ramakrishnan
- 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, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Zhijun Zhang
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
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Yan Y, Yan Z, Zhao G. Genome-wide identification of WRKY transcription factor family members in Miscanthus sinensis (Miscanthus sinensis Anderss). Sci Rep 2024; 14:5522. [PMID: 38448638 PMCID: PMC10918066 DOI: 10.1038/s41598-024-55849-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/28/2024] [Indexed: 03/08/2024] Open
Abstract
Miscanthus is an emerging sustainable bioenergy crop whose growing environment is subject to many abiotic and biological stresses. WRKY transcription factors play an important role in stress response and growth of biotic and abiotic. To clarify the distribution and expression of the WRKY genes in Miscanthus, it is necessary to classify and phylogenetically analyze the WRKY genes in Miscanthus. The v7.1 genome assembly of Miscanthus was analyzed by constructing an evolutionary tree. In Miscanthus, there are 179 WRKY genes were identified. The 179 MsWRKYs were classified into three groups with conserved gene structure and motif composition. The tissue expression profile of the WRKY genes showed that MsWRKY genes played an essential role in all growth stages of plants. At the early stage of plant development, the MsWRKY gene is mainly expressed in the rhizome of plants. In the middle stage, it is mainly expressed in the leaf. At the end stage, mainly in the stem. According to the results, it showed significant differences in the expression of the MsWRKY in different stages of Miscanthus sinensis. The results of the study contribute to a better understanding of the role of the MsWRKY gene in the growth and development of Miscanthus.
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Affiliation(s)
- Yongkang Yan
- Faculty of Science, the University of Hong Kong, Hong Kong, China.
| | - Zhanyou Yan
- Shijiazhuang Tiedao University, Shijiazhuang, China
| | - Guofang Zhao
- Hebei Vocational University of Industry and Technology, Shijiazhuang, China
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Wen Y, Zhao Z, Cheng L, Zhou S, An M, Zhao J, Dong S, Yuan X, Yin M. Genome-wide identification and expression profiling of the ABI5 gene family in foxtail millet (Setaria italica). BMC PLANT BIOLOGY 2024; 24:164. [PMID: 38431546 PMCID: PMC10908088 DOI: 10.1186/s12870-024-04865-4] [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: 12/17/2023] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND ABA Insensitive 5 (ABI5) is a basic leucine zipper transcription factor that crucially influences plant growth, development, and stress response. However, there is minimal research on the ABI5 family in foxtail millet. RESULTS In this study, 16 ABI5 genes were identified in foxtail millet, and their sequence composition, gene structures, cis-acting elements, chromosome positions, and gene replication events were analyzed. To more thoroughly evaluate the developmental mechanisms of the SiABI5 family during evolution, we selected three dicotyledons (S. lycopersicum, A. thaliana, F. tataricum) and three (Z. mays, O. sativa, S. bicolor) specific representative monocotyledons associated with foxtail millet for comparative homology mapping. The results showed that foxtail millet ABI5 genes had the best homology with maize. A promoter sequence analysis showed that the SiABI5s contain numerous cis-acting elements related to hormone and stress responses, indicating that the regulation of SiABI5 expression was complex. The expression responses of 16 genes in different tissues, seed germination, and ear development were analyzed. A total of six representative genes were targeted from five subfamilies to characterize their gene expression responses to four different abiotic stresses. Overexpression of SiABI5.12 confers tolerance to osmotic stress in transgenic Arabidopsis thaliana, which demonstrated the function of SiABI5 responded to abiotic stress. CONCLUSIONS In summary, our research results comprehensively characterized the SiABI5 family and can provide a valuable reference for demonstrating the role of SiABI5s in regulating abiotic stress responses in foxtail millet.
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Affiliation(s)
- Yinyuan Wen
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Zeya Zhao
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Liuna Cheng
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Shixue Zhou
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Mengyao An
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Juan Zhao
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Shuqi Dong
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiangyang Yuan
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China.
| | - Meiqiang Yin
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China.
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Deng H, Hou Q, Wen Z, Yu R, Cao X, Shang C, Cai X, Qiao G. Chinese cherry CpMYB44-CpSPDS2 module regulates spermidine content and florescence in tobacco. PHYSIOLOGIA PLANTARUM 2024; 176:e14300. [PMID: 38629194 DOI: 10.1111/ppl.14300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/10/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
The flower bud differentiation plays a crucial role in cherry yield and quality. In a preliminary study, we revealed the promotion of spermidine (Spd) in bud differentiation and quality. However, the molecular mechanism underlying Spd regulating cherry bud differentiation remains unclear. To address this research gap, we cloned CpSPDS2, a gene that encodes Spd synthase and is highly expressed in whole flowers and pistils of the Chinese cherry (cv. 'Manaohong'). Furthermore, an overexpression vector with this gene was constructed to transform tobacco plants. The findings demonstrated that transgenic lines exhibited higher Spd content, an earlier flowering time by 6 d, and more lateral buds and flowers than wild-type lines. Additionally, yeast one-hybrid assays and two-luciferase experiments confirmed that the R2R3-MYB transcription factor (CpMYB44) directly binds to and activates the CpSPDS2 promoter transcription. It is indicated that CpMYB44 promotes Spd accumulation via regulating CpSPDS2 expression, thus accelerating the flower growth. This research provides a basis for resolving the molecular mechanism of CpSPDS2 involved in cherry bud differentiation.
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Affiliation(s)
- Hong Deng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Laboratory of Agricultural Bioengineering, Institute of Agro-bioengineering /College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China
| | - Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Laboratory of Agricultural Bioengineering, Institute of Agro-bioengineering /College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China
| | - Zhuang Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Laboratory of Agricultural Bioengineering, Institute of Agro-bioengineering /College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China
| | - Runrun Yu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Laboratory of Agricultural Bioengineering, Institute of Agro-bioengineering /College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China
| | - Xuejiao Cao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Laboratory of Agricultural Bioengineering, Institute of Agro-bioengineering /College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China
| | - Chunqiong Shang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Laboratory of Agricultural Bioengineering, Institute of Agro-bioengineering /College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China
| | - Xiaowei Cai
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Laboratory of Agricultural Bioengineering, Institute of Agro-bioengineering /College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Laboratory of Agricultural Bioengineering, Institute of Agro-bioengineering /College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China
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Guo F, Meng X, Hong H, Liu S, Yu J, Huang C, Dong T, Geng H, Li Z, Zhu M. Systematic identification and expression analysis of bHLH gene family reveal their relevance to abiotic stress response and anthocyanin biosynthesis in sweetpotato. BMC PLANT BIOLOGY 2024; 24:156. [PMID: 38424529 PMCID: PMC10905920 DOI: 10.1186/s12870-024-04788-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND bHLH transcription factors play significant roles in regulating plant growth and development, stress response, and anthocyanin biosynthesis. Sweetpotato is a pivotal food and industry crop, but little information is available on sweetpotato bHLH genes. RESULTS Herein, 227 putative IbbHLH genes were defined on sweetpotato chromosomes, and fragment duplications were identified as the dominant driving force for IbbHLH expansion. These IbbHLHs were divided into 26 subfamilies through phylogenetic analysis, as supported by further analysis of exon-intron structure and conserved motif composition. The syntenic analysis between IbbHLHs and their orthologs from other plants depicted evolutionary relationships of IbbHLHs. Based on the transcriptome data under salt stress, the expression of 12 IbbHLHs was screened for validation by qRT-PCR, and differential and significant transcriptions under abiotic stress were detected. Moreover, IbbHLH123 and IbbHLH215, which were remarkably upregulated by stress treatments, had obvious transactivation activity in yeasts. Protein interaction detections and yeast two-hybrid assays suggested an intricate interaction correlation between IbbHLHs. Besides, transcriptome screening revealed that multiple IbbHLHs may be closely related to anthocyanin biosynthesis based on the phenotype (purple vs. white tissues), which was confirmed by subsequent qRT-PCR analysis. CONCLUSIONS These results shed light on the promising functions of sweetpotato IbbHLHs in abiotic stress response and anthocyanin biosynthesis.
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Affiliation(s)
- Fen Guo
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Xiaoqing Meng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Haiting Hong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Siyuan Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Jing Yu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Can Huang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Huixue Geng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China.
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Liu J, Wei L, Wu Y, Wang Z, Wang H, Xiao J, Wang X, Sun L. Characterization of sucrose nonfermenting-1-related protein kinase 2 (SnRK2) gene family in Haynaldia villosa demonstrated SnRK2.9-V enhances drought and salt stress tolerance of common wheat. BMC Genomics 2024; 25:209. [PMID: 38408894 PMCID: PMC10895793 DOI: 10.1186/s12864-024-10114-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND The sucrose nonfermenting-1-related protein kinase 2 (SnRK2) plays a crucial role in responses to diverse biotic/abiotic stresses. Currently, there are reports on these genes in Haynaldia villosa, a diploid wild relative of wheat. RESULTS To understand the evolution of SnRK2-V family genes and their roles in various stress conditions, we performed genome-wide identification of the SnRK2-V gene family in H. villosa. Ten SnRK2-V genes were identified and characterized for their structures, functions and spatial expressions. Analysis of gene exon/intron structure further revealed the presence of evolutionary paths and replication events of SnRK2-V gene family in the H. villosa. In addition, the features of gene structure, the chromosomal location, subcellular localization of the gene family were investigated and the phylogenetic relationship were determined using computational approaches. Analysis of cis-regulatory elements of SnRK2-V gene members revealed their close correlation with different phytohormone signals. The expression profiling revealed that ten SnRK2-V genes expressed at least one tissue (leave, stem, root, or grain), or in response to at least one of the biotic (stripe rust or powdery mildew) or abiotic (drought or salt) stresses. Moreover, SnRK2.9-V was up-regulated in H. villosa under the drought and salt stress and overexpressing of SnRK2.9-V in wheat enhanced drought and salt tolerances via enhancing the genes expression of antioxidant enzymes, revealing a potential value of SnRK2.9-V in wheat improvement for salt tolerance. CONCLUSION Our present study provides a basic genome-wide overview of SnRK2-V genes in H. villosa and demonstrates the potential use of SnRK2.9-V in enhancing the drought and salt tolerances in common wheat.
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Affiliation(s)
- Jia Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
- Jinhua Academy, Zhejiang Chinese Medical University, Jinhua, 321000, China
| | - Luyang Wei
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Yirong Wu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Zongkuan Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Haiyan Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Jin Xiao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Xiue Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.
| | - Li Sun
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.
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Baruah IK, Shao J, Ali SS, Schmidt ME, Meinhardt LW, Bailey BA, Cohen SP. Cacao pod transcriptome profiling of seven genotypes identifies features associated with post-penetration resistance to Phytophthora palmivora. Sci Rep 2024; 14:4175. [PMID: 38378988 PMCID: PMC10879190 DOI: 10.1038/s41598-024-54355-8] [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: 05/18/2023] [Accepted: 02/12/2024] [Indexed: 02/22/2024] Open
Abstract
The oomycete Phytophthora palmivora infects the fruit of cacao trees (Theobroma cacao) causing black pod rot and reducing yields. Cacao genotypes vary in their resistance levels to P. palmivora, yet our understanding of how cacao fruit respond to the pathogen at the molecular level during disease establishment is limited. To address this issue, disease development and RNA-Seq studies were conducted on pods of seven cacao genotypes (ICS1, WFT, Gu133, Spa9, CCN51, Sca6 and Pound7) to better understand their reactions to the post-penetration stage of P. palmivora infection. The pod tissue-P. palmivora pathogen assay resulted in the genotypes being classified as susceptible (ICS1, WFT, Gu133 and Spa9) or resistant (CCN51, Sca6 and Pound7). The number of differentially expressed genes (DEGs) ranged from 1625 to 6957 depending on genotype. A custom gene correlation approach identified 34 correlation groups. De novo motif analysis was conducted on upstream promoter sequences of differentially expressed genes, identifying 76 novel motifs, 31 of which were over-represented in the upstream sequences of correlation groups and associated with gene ontology terms related to oxidative stress response, defense against fungal pathogens, general metabolism and cell function. Genes in one correlation group (Group 6) were strongly induced in all genotypes and enriched in genes annotated with defense-responsive terms. Expression pattern profiling revealed that genes in Group 6 were induced to higher levels in the resistant genotypes. An additional analysis allowed the identification of 17 candidate cis-regulatory modules likely to be involved in cacao defense against P. palmivora. This study is a comprehensive exploration of the cacao pod transcriptional response to P. palmivora spread after infection. We identified cacao genes, promoter motifs, and promoter motif combinations associated with post-penetration resistance to P. palmivora in cacao pods and provide this information as a resource to support future and ongoing efforts to breed P. palmivora-resistant cacao.
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Affiliation(s)
- Indrani K Baruah
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Jonathan Shao
- Statistics and Bioinformatics Group-Northeast Area, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Shahin S Ali
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, 20705, USA
- ATCC (American Type Culture Collection), Gaithersburg, MD, 20877, USA
| | - Martha E Schmidt
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Stephen P Cohen
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, 20705, USA.
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Xiong R, Peng Z, Zhou H, Xue G, He A, Yao X, Weng W, Wu W, Ma C, Bai Q, Ruan J. Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.). BMC PLANT BIOLOGY 2024; 24:113. [PMID: 38365619 PMCID: PMC10870581 DOI: 10.1186/s12870-024-04774-6] [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: 10/24/2023] [Accepted: 01/29/2024] [Indexed: 02/18/2024]
Abstract
BACKGROUND The WRKY gene family is one of the largest families of transcription factors in higher plants, and WRKY transcription factors play important roles in plant growth and development as well as in response to abiotic stresses; however, the WRKY gene family in pea has not been systematically reported. RESULTS In this study, 89 pea WRKY genes were identified and named according to the random distribution of PsWRKY genes on seven chromosomes. The gene family was found to have nine pairs of tandem duplicates and 19 pairs of segment duplicates. Phylogenetic analyses of the PsWRKY and 60 Arabidopsis WRKY proteins were performed to determine their homology, and the PsWRKYs were classified into seven subfamilies. Analysis of the physicochemical properties, motif composition, and gene structure of pea WRKYs revealed significant differences in the physicochemical properties within the PsWRKY family; however, their gene structure and protein-conserved motifs were highly conserved among the subfamilies. To further investigate the evolutionary relationships of the PsWRKY family, we constructed comparative syntenic maps of pea with representative monocotyledonous and dicotyledonous plants and found that it was most recently homologous to the dicotyledonous WRKY gene families. Cis-acting element analysis of PsWRKY genes revealed that this gene family can respond to hormones, such as abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin (GA), methyl jasmonate (MeJA), and salicylic acid (SA). Further analysis of the expression of 14 PsWRKY genes from different subfamilies in different tissues and fruit developmental stages, as well as under five different hormone treatments, revealed differences in their expression patterns in the different tissues and fruit developmental stages, as well as under hormone treatments, suggesting that PsWRKY genes may have different physiological functions and respond to hormones. CONCLUSIONS In this study, we systematically identified WRKY genes in pea for the first time and further investigated their physicochemical properties, evolution, and expression patterns, providing a theoretical basis for future studies on the functional characterization of pea WRKY genes during plant growth and development.
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Affiliation(s)
- Ruiqi Xiong
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Zhonghua Peng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Hui Zhou
- Sichuan Province Seed Station, Chengdu, Sichuan, 610041, China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Xin Yao
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Wenfeng Weng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Weijiao Wu
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Chao Ma
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Qing Bai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China.
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He X, He Y, Dong Y, Gao Y, Sun X, Chen W, Xu X, Su C, Lv Y, Ren B, Yin H, Zeng J, Ma W, Mu P. Genome-wide analysis of FRF gene family and functional identification of HvFRF9 under drought stress in barley. FRONTIERS IN PLANT SCIENCE 2024; 15:1347842. [PMID: 38328701 PMCID: PMC10847358 DOI: 10.3389/fpls.2024.1347842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
Abstract
FHY3 and its homologous protein FAR1 are the founding members of FRS family. They exhibited diverse and powerful physiological functions during evolution, and participated in the response to multiple abiotic stresses. FRF genes are considered to be truncated FRS family proteins. They competed with FRS for DNA binding sites to regulate gene expression. However, only few studies are available on FRF genes in plants participating in the regulation of abiotic stress. With wide adaptability and high stress-resistance, barley is an excellent candidate for the identification of stress-resistance-related genes. In this study, 22 HvFRFs were detected in barley using bioinformatic analysis from whole genome. According to evolution and conserved motif analysis, the 22 HvFRFs could be divided into subfamilies I and II. Most promoters of subfamily I members contained abscisic acid and methyl jasmonate response elements; however, a large number promoters of subfamily II contained gibberellin and salicylic acid response elements. HvFRF9, one of the members of subfamily II, exhibited a expression advantage in different tissues, and it was most significantly upregulated under drought stress. In-situ PCR revealed that HvFRF9 is mainly expressed in the root epidermal cells, as well as xylem and phloem of roots and leaves, indicating that HvFRF9 may be related to absorption and transportation of water and nutrients. The results of subcellular localization indicated that HvFRF9 was mainly expressed in the nuclei of tobacco epidermal cells and protoplast of arabidopsis. Further, transgenic arabidopsis plants with HvFRF9 overexpression were generated to verify the role of HvFRF9 in drought resistance. Under drought stress, leaf chlorosis and wilting, MDA and O2 - contents were significantly lower, meanwhile, fresh weight, root length, PRO content, and SOD, CAT and POD activities were significantly higher in HvFRF9-overexpressing arabidopsis plants than in wild-type plants. Therefore, overexpression of HvFRF9 could significantly enhance the drought resistance in arabidopsis. These results suggested that HvFRF9 may play a key role in drought resistance in barley by increasing the absorption and transportation of water and the activity of antioxidant enzymes. This study provided a theoretical basis for drought resistance in barley and provided new genes for drought resistance breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Ping Mu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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Liu W, Wang Y, Zhang Y, Li W, Wang C, Xu R, Dai H, Zhang L. Characterization of the pyruvate kinase gene family in soybean and identification of a putative salt responsive gene GmPK21. BMC Genomics 2024; 25:88. [PMID: 38254018 PMCID: PMC10802038 DOI: 10.1186/s12864-023-09929-7] [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: 08/18/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND As a key regulatory enzyme in the glycolysis pathway, pyruvate kinase (PK) plays crucial roles in multiple physiological processes during plant growth and is also involved in the abiotic stress response. However, little information is known about PKs in soybean. RESULTS In this study, we identified 27 PK family genes against the genome of soybean cultivar Zhonghuang13. They were classified into 2 subfamilies including PKc and PKp. 22 segmental duplicated gene pairs and 1 tandem duplicated gene pair were identified and all of them experienced a strong purifying selective pressure during evolution. Furthermore, the abiotic stresses (especially salt stress) and hormone responsive cis-elements were present in the promoters of GmPK genes, suggesting their potential roles in abiotic stress tolerance. By performing the qRT-PCR, 6 GmPK genes that continuously respond to both NaCl and ABA were identified. Subsequently, GmPK21, which represented the most significant change under NaCl treatment was chosen for further study. Its encoded protein GmPK21 was localized in the cytoplasm and plasma membrane. The transgenic Arabidopsis overexpressing GmPK21 exhibited weakened salinity tolerance. CONCLUSIONS This study provides genomic information of soybean PK genes and a molecular basis for mining salt tolerance function of PKs in the future.
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Affiliation(s)
- Wei Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
- Shandong Engineering Laboratory of Featured Crops, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Yubin Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
- Shandong Engineering Laboratory of Featured Crops, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Yanwei Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
- Shandong Engineering Laboratory of Featured Crops, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Wei Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
- Shandong Engineering Laboratory of Featured Crops, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Caijie Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
- Shandong Engineering Laboratory of Featured Crops, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Ran Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
- Shandong Engineering Laboratory of Featured Crops, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Haiying Dai
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
- Shandong Engineering Laboratory of Featured Crops, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Lifeng Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China.
- Shandong Engineering Laboratory of Featured Crops, 202 Gongye North Road, Jinan, 250100, Shandong, China.
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Hou Z, Liang J, Cai X, Lin J, Wang X, Liu R, Lu L, Chai G, An C, Chen S, Qin Y, Zheng P. PeHVA22 gene family in passion fruit ( Passiflora edulis): initial characterization and expression profiling diversity. FRONTIERS IN PLANT SCIENCE 2024; 14:1279001. [PMID: 38312363 PMCID: PMC10835403 DOI: 10.3389/fpls.2023.1279001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/28/2023] [Indexed: 02/06/2024]
Abstract
Passion fruit, an economically valuable fruit crop, is highly vulnerable to adverse climate conditions. The HVA22 genes, recognized as abscisic acid (ABA) and stress-inducible, play vital roles in stress response and growth regulation in diverse eukaryotic organisms. Here, six HVA22 genes were firstly identified in passion fruit genome and all predicted to be localized within the endoplasmic reticulum. Phylogenetic analyses showed that all PeHVA22s were divided into four subgroups. The gene structural features of PeHVA22 genes clustered in the same subgroup were relatively conserved, while the gene structure characteristics of PeHVA22s from different subgroups varied significantly. PeHVA22A and PeHVA22C closely clustered with barley HVA22 in Group II, were also induced by ABA and drought stress treatment, suggesting conserved roles similar to barley HVA22. Meanwhile, most PeHVA22s exhibited induced expression post-drought treatment but were suppressed under salt, low and high-temperature conditions, indicating a unique role in drought response. Additionally, PeHVA22s displayed tissue-specific expression patterns across diverse tissues, except for PeHVA22B which maybe a pseudogene. Notably, PeHVA22C, PeHVA22E, and PeHVA22F predominantly expressed in fruit, indicating their involvement in fruit development. Almost all PeHVA22s showed variable expression at different developmental stages of stamens or ovules, implying their roles in passion fruit's sexual reproduction. The intricate roles of PeHVA22s may result from diverse regulatory factors including transcription factors and CREs related to plant growth and development, hormone and stress responsiveness. These observations highlighted that PeHVA22s might play conserved roles in ABA response and drought stress tolerance, and also be participated in the regulation of passion fruit growth and floral development.
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Affiliation(s)
- Zhimin Hou
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianxiang Liang
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinkai Cai
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jingting Lin
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, China
| | - Ruoyu Liu
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Lu
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gaifeng Chai
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chang An
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengzhen Chen
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ping Zheng
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Fu MK, He YN, Yang XY, Tang X, Wang M, Dai WS. Genome-wide identification of the GRF family in sweet orange (Citrus sinensis) and functional analysis of the CsGRF04 in response to multiple abiotic stresses. BMC Genomics 2024; 25:37. [PMID: 38184538 PMCID: PMC10770916 DOI: 10.1186/s12864-023-09952-8] [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: 11/23/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND Citrus is one of the most valuable fruits worldwide and an economic pillar industry in southern China. Nevertheless, it frequently suffers from undesirable environmental stresses during the growth cycle, which severely restricts the growth, development and yield of citrus. In plants, the growth-regulating factor (GRF) family of transcription factors (TF) is extensively distributed and plays an vital part in plant growth and development, hormone response, as well as stress adaptation. However, the systematic identification and functional analysis of GRF TFs in citrus have not been reported. RESULTS Here, a genome-wide identification of GRF TFs was performed in Citrus sinensis, 9 members of CsGRFs were systematically identified and discovered to be scattered throughout 5 chromosomes. Subsequently, physical and chemical properties, phylogenetic relationships, structural characteristics, gene duplication events, collinearity and cis-elements of promoter were elaborately analyzed. In particular, the expression patterns of the CsGRF genes in response to multiple phytohormone and abiotic stress treatments were investigated. Predicated on this result, CsGRF04, which exhibited the most differential expression pattern under multiple phytohormone and abiotic stress treatments was screened out. Virus-induced gene silencing (VIGS) technology was utilized to obtain gene silenced plants for CsGRF04 successfully. After the three stress treatments of high salinity, low temperature and drought, the CsGRF04-VIGS lines showed significantly reduced resistance to high salinity and low temperature stresses, but extremely increased resistance to drought stress. CONCLUSIONS Taken together, our findings systematically analyzed the genomic characterization of GRF family in Citrus sinensis, and excavated a CsGRF04 with potential functions under multiple abiotic stresses. Our study lay a foundation for further study on the function of CsGRFs in abiotic stress and hormone signaling response.
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Affiliation(s)
- Ming-Kang Fu
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China
| | - Ying-Na He
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China
| | - Xiao-Yue Yang
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China
| | - Xi Tang
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China
| | - Min Wang
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China
| | - Wen-Shan Dai
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China.
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Yousefi Taemeh S, Dehdilani N, Goshayeshi L, Dehghani H. Exploring the Function of Gene Promoter Regulatory Elements Using CRISPR Tools. Methods Mol Biol 2024; 2844:145-156. [PMID: 39068338 DOI: 10.1007/978-1-0716-4063-0_10] [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] [Indexed: 07/30/2024]
Abstract
Gene promoters serve as pivotal regulators of transcription, orchestrating the initiation, rate, and specificity of gene expression, resulting in cellular diversity found among distinct cell types within multicellular organisms. Identification of the sequence and function of promoters' regulatory elements and their complex interaction with transcription factors, enhancers, silencers, and insulators is fundamental to coordinated transcriptional processes within cells. Identifying these regulatory elements and scrutinizing their functions and interactions through the use of synthetic promoters can pave the way for researchers in various fields ranging from uncovering the origins of diseases associated with promoter mutations to harnessing these regulatory components in biotechnological applications.In this chapter, we describe the manipulation of regulatory elements within promoters, with a specific focus on the use of CRISPR technology on enhancers and silencer elements of the Ovalbumin gene promoter. We explain and discuss processes for the deletion of/interference with regulatory elements within the promoter, employing CRISPR-based approaches. Furthermore, we demonstrate that a CRISPR/Cas-manipulated promoter can activate gene transcription in cell types where it is normally inactive. This confirms that CRISPR technology can be effectively used to engineer synthetic promoters with desired characteristics, such as inducibility, tissue-specificity, or enhanced transcriptional strength. Such an approach provides valuable insights into the mechanisms and dynamics of gene expression, thereby offering new opportunities in the fields of biotechnology and medicine.
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Affiliation(s)
- Sara Yousefi Taemeh
- Department of Medical Biochemistry and Microbiology, Biomedical Center (BMC), Uppsala University, Uppsala, Sweden
| | - Nima Dehdilani
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Lena Goshayeshi
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hesam Dehghani
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.
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Duan L, Wang F, Shen H, Xie S, Chen X, Xie Q, Li R, Cao A, Li H. Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis. BMC Genomics 2023; 24:795. [PMID: 38129780 PMCID: PMC10734139 DOI: 10.1186/s12864-023-09717-3] [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: 04/18/2023] [Accepted: 10/04/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND GDSL esterase/lipases (GELPs) play important roles in plant growth, development, and response to biotic and abiotic stresses. Presently, an extensive and in-depth analysis of GELP family genes in cotton is still not clear enough, which greatly limits the further understanding of cotton GELP function and regulatory mechanism. RESULTS A total of 389 GELP family genes were identified in three cotton species of Gossypium hirsutum (193), G. arboreum (97), and G. raimondii (99). These GELPs could be classified into three groups and eight subgroups, with the GELPs in same group to have similar gene structures and conserved motifs. Evolutionary event analysis showed that the GELP family genes tend to be diversified at the spatial dimension and certain conservative at the time dimension, with a trend of potential continuous expansion in the future. The orthologous or paralogous GELPs among different genomes/subgenomes indicated the inheritance from genome-wide duplication during polyploidization, and the paralogous GELPs were derived from chromosomal segment duplication or tandem replication. GELP genes in the A/D subgenome underwent at least three large-scale replication events in the evolutionary process during the period of 0.6-3.2 MYA, with two large-scale evolutionary events between 0.6-1.8 MYA that were associated with tetraploidization, and the large-scale duplication between 2.6-9.1 MYA that occurred during diploidization. The cotton GELPs indicated diverse expression patterns in tissue development, ovule and fiber growth, and in response to biotic and abiotic stresses, combining the existing cis-elements in the promoter regions, suggesting the GELPs involvements of functions to be diversification and of the mechanisms to be a hormone-mediated manner. CONCLUSIONS Our results provide a systematic and comprehensive understanding the function and regulatory mechanism of cotton GELP family, and offer an effective reference for in-depth genetic improvement utilization of cotton GELPs.
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Affiliation(s)
- Lisheng Duan
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Fei Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Haitao Shen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Shuangquan Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Xifeng Chen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Rong Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Aiping Cao
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
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Xie Z, Yang D, Zhou Z, Li K, Yi P, Liu A, Zhou Z, Tu X. A genome-wide analysis of the GRAS gene family in upland cotton and a functional study of the role of the GhGRAS55 gene in regulating early maturity in cotton. Biotechnol J 2023; 18:e2300201. [PMID: 37575005 DOI: 10.1002/biot.202300201] [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: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/15/2023]
Abstract
The members of the GRAS gene family play important roles in regulating plant growth and development, but their functions in regulating early plant maturity traits are still unknown. In this study, we used a series of bioinformatics tools to identify GRAS gene family members and investigate the function of the gene family (GhGRAS55) using a genome-wide database of upland cotton samples. A total of 58 members of the GRAS gene family were identified and screened, which were distributed on 21 chromosomes within the whole cotton genome. The results of the phylogenetic analysis showed that the genes of upland cotton, island cotton, African cotton, Raymond cotton, and Arabidopsis were distributed in subfamilies I-VIII, although subfamily II did not contain any upland cotton or Arabidopsis GRAS family members. The structures and other characteristics of the genes in this family were clarified using bioinformatics technology. The transcriptomic sequencing results for early and late maturing cotton species showed that the expression of most GRAS family genes, such as GhGRAS10, GhGRAS5511, and GhGRAS55, was lower in early maturing species than late maturing species. We also found that cotton plants with GhGRAS55 genes that were silenced by virus-induced gene silencing (VIGS) technology showed early bud emergence phenotypes, so it could be speculated that the GhGRAS55 gene has the function of regulating early maturity in cotton.
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Affiliation(s)
- Zhangshu Xie
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
| | - Dan Yang
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
- Agriculture and Rural Bureau of Jingzhou County, Jingzhou, China
| | - Zhenzhong Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Kan Li
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
| | - Penghui Yi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Aiyu Liu
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
| | - Zhonghua Zhou
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
| | - Xiaoju Tu
- Key Laboratory of Ministry of Education for Crop Physiology and Molecular Biology, Changsha, China
- Cotton Research Institute, Agricultural College, Hunan Agricultural University, Changsha, China
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Yin L, Zhang X, Gao A, Cao M, Yang D, An K, Guo S, Yin H. Genome-Wide Identification and Expression Analysis of 1-Aminocyclopropane-1-Carboxylate Synthase ( ACS) Gene Family in Chenopodium quinoa. PLANTS (BASEL, SWITZERLAND) 2023; 12:4021. [PMID: 38068656 PMCID: PMC10707884 DOI: 10.3390/plants12234021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 04/10/2024]
Abstract
Ethylene plays an important role in plant development and stress resistance. The rate-limiting enzyme in ethylene biosynthesis is 1-aminocyclopropane-1-carboxylic acid synthase (ACS). C. quinoa (Chenopodium quinoa) is an important food crop known for its strong tolerance to abiotic stresses. However, knowledge regarding the ACS gene family in C. quinoa remains restricted. In this study, we successfully identified 12 ACS genes (CqACSs) from the C. quinoa genome. Through thorough analysis of their sequences and phylogenetic relationships, it was verified that 8 out of these 12 CqACS isozymes exhibited substantial resemblance to ACS isozymes possessing ACS activity. Furthermore, these eight isozymes could be categorized into three distinct groups. The four remaining CqACS genes grouped under category IV displayed notable similarities with AtACS10 and AtACS12, known as amido transferases lacking ACS activity. The CqACS proteins bore resemblance to the AtACS proteins and had the characteristic structural features typically observed in plant ACS enzymes. Twelve CqACS genes were distributed across 8 out of the 18 chromosomes of C. quinoa. The CqACS genes were expanded from segment duplication. Many cis-regulatory elements related with various abiotic stresses, phytohormones, and light were found. The expression patterns of ACS genes varied across different tissues of C. quinoa. Furthermore, the analysis of gene expression patterns under abiotic stress showed that CqACS genes can be responsive to various stresses, implying their potential functions in adapting to various abiotic stresses. The findings from this research serve as a foundation for delving deeper into the functional roles of CqACS genes.
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Affiliation(s)
- Lu Yin
- College of Life Sciences, Yantai University, Yantai 264005, China; (L.Y.); (X.Z.); (A.G.); (M.C.); (D.Y.); (K.A.)
| | - Xia Zhang
- College of Life Sciences, Yantai University, Yantai 264005, China; (L.Y.); (X.Z.); (A.G.); (M.C.); (D.Y.); (K.A.)
| | - Aihong Gao
- College of Life Sciences, Yantai University, Yantai 264005, China; (L.Y.); (X.Z.); (A.G.); (M.C.); (D.Y.); (K.A.)
| | - Meng Cao
- College of Life Sciences, Yantai University, Yantai 264005, China; (L.Y.); (X.Z.); (A.G.); (M.C.); (D.Y.); (K.A.)
| | - Dongdong Yang
- College of Life Sciences, Yantai University, Yantai 264005, China; (L.Y.); (X.Z.); (A.G.); (M.C.); (D.Y.); (K.A.)
| | - Kexin An
- College of Life Sciences, Yantai University, Yantai 264005, China; (L.Y.); (X.Z.); (A.G.); (M.C.); (D.Y.); (K.A.)
| | - Shanli Guo
- College of Grassland Sciences, Qingdao Agricultural University, Qingdao 266109, China
- High-Efficiency Agricultural Technology Industry Research Institute of Saline and Alkaline Land of Dongying, Qingdao Agricultural University, Dongying 257300, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Agricultural University, Qingdao 266109, China
| | - Haibo Yin
- College of Life Sciences, Yantai University, Yantai 264005, China; (L.Y.); (X.Z.); (A.G.); (M.C.); (D.Y.); (K.A.)
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Li Z, Shi L, Lin X, Tang B, Xing M, Zhu H. Genome-Wide Identification and Expression Analysis of Malate Dehydrogenase Gene Family in Sweet Potato and Its Two Diploid Relatives. Int J Mol Sci 2023; 24:16549. [PMID: 38068872 PMCID: PMC10706315 DOI: 10.3390/ijms242316549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Malate dehydrogenase (MDH; EC 1.1.1.37) plays a vital role in plant growth and development as well as abiotic stress responses, and it is widely present in plants. However, the MDH family genes have not been explored in sweet potato. In this study, nine, ten, and ten MDH genes in sweet potato (Ipomoea batatas) and its two diploid wild relatives, Ipomoea trifida and Ipomoea triloba, respectively, were identified. These MDH genes were unevenly distributed on seven different chromosomes among the three species. The gene duplications and nucleotide substitution analysis (Ka/Ks) revealed that the MDH genes went through segmental duplications during their evolution under purifying selection. A phylogenetic and conserved structure divided these MDH genes into five subgroups. An expression analysis indicated that the MDH genes were omni-presently expressed in distinct tissues and responded to various abiotic stresses. A transcription factor prediction analysis proved that Dof, MADS-box, and MYB were the main transcription factors of sweet potato MDH genes. These findings provide molecular features of the MDH family in sweet potato and its two diploid wild relatives, which further supports functional characterizations.
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Affiliation(s)
| | | | | | | | | | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Z.L.); (L.S.); (X.L.); (B.T.); (M.X.)
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47
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Chen H, Zhang S, Du K, Kang X. Genome-wide identification, characterization, and expression analysis of CCT transcription factors in poplar. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108101. [PMID: 37922648 DOI: 10.1016/j.plaphy.2023.108101] [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: 07/29/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023]
Abstract
The CCT [CONSTANS (CO), CO-like, and TIMING OF CAB EXPRESSION1 (TOC1)] gene family is involved in photoperiodic flowering and adaptation to different environments. In this study, 39 CCT family genes from the poplar genome were identified and characterized, including 18 COL, 7 PRR, and 14 CMF TFs. Phylogenetics analysis showed that the PtrCCT gene family could be classified into five classes (Classes I-V) that have close relationships with Arabidopsis thaliana. Eight pairs of PtrCCTs had collinear relationships through interchromosomal synteny analysis in poplar, suggesting segmental duplication played a vital role in the expansion of the poplar CCT gene family. Besides, synteny analyses of the CCT members among poplar and different species provided more clues for PtrCCT gene family evolution. Cis-acting elements in the promoters of PtrCCTs predicted their involvement in light responses, hormone responses, biotic/abiotic stress responses, and plant growth and development. Eight members of the PpnCCT gene family were differentially expressed in the apical buds and leaves of triploid poplar compared to diploids. We then focused on PpnCCT39 upregulated in triploid poplars and showed that PpnCCT39 was localized in the nucleus, chloroplast, and cytoplasm and could interact with CLPP1 in the chloroplast. Overexpression of PpnCCT39 in poplar increased chlorophyll contents and enhanced photosynthetic rate. This study provided comprehensive information for the CCT gene family and set up a basis for its function identification in poplar.
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Affiliation(s)
- Hao Chen
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Shuwen Zhang
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Kang Du
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Xiangyang Kang
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China.
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48
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Li X, Zhu T, Wang X, Zhu M. Genome-wide identification of glutamate receptor-like gene family in soybean. Heliyon 2023; 9:e21655. [PMID: 38027661 PMCID: PMC10651524 DOI: 10.1016/j.heliyon.2023.e21655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 10/02/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Glutamate receptor-like genes (GLRs) are essential in the growth and development of plants and many physiological and biochemical processes; however, related information in soybean is lacking. In this study, 105 GLRs, including 67 Glycine soja and 38 Glycine max GLRs, were identified and divided into two clades (Clades II and III) according to their phylogenetic relationships. GLR members in the same branch had a relatively conservative motif composition and genetic structure. Furthermore, the soybean GLR family mainly experienced purification selection during evolution. Cis-acting element analysis, gene ontology, and Kyoto Encyclopedia of Genes and Genomic annotations indicated the complexity of the gene regulation and functional diversity of the soybean GLR. Moreover, transcriptome data analysis showed that these GLRs had different expression profiles in different tissues, and Clade III members had higher and more common expression patterns. Additionally, the expression profiles under jasmonic acid treatment and salt stress indicate that the GLR participated in the jasmonic acid signaling pathway and plays a role in salt treatment. This study provides information for a comprehensive understanding of the soybean GLR family and a reference for further functional research and genetic improvement.
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Affiliation(s)
- Xinran Li
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, China
| | - Tianhao Zhu
- College of Mathematical Sciences, Harbin Engineering University, Harbin, China
| | - Xuying Wang
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, China
| | - Miao Zhu
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, China
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49
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Jadhao KR, Kale SS, Chavan NS, Janjal PH. Genome-wide analysis of the SPL transcription factor family and its response to water stress in sunflower (Helianthus annuus). Cell Stress Chaperones 2023; 28:943-958. [PMID: 37938528 PMCID: PMC10746691 DOI: 10.1007/s12192-023-01388-z] [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: 08/14/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/09/2023] Open
Abstract
SPL (SQUAMOSA promoter binding proteins-like) are plant-specific transcription factors that play essential roles in a variety of developmental processes as well as the ability to withstand biotic and abiotic stresses. To date, numerous species have been investigated for the SPL gene family, but so far, no SPL family genes have been thoroughly identified and characterized in the sunflower (Helianthus annuus). In this study, 25 SPL genes were identified in the sunflower genome and were unevenly distributed on 11 chromosomes. According to phylogeny analysis, 59 SPL genes from H. annuus, O. sativa, and A. thaliana were clustered into seven groups. Furthermore, the SPL genes in groups-I and II were demonstrated to be potential targets of miR156. Synteny analysis showed that 7 paralogous gene pairs exist in HaSPL genes and 26 orthologous gene pairs exist between sunflower and rice, whereas 21 orthologous gene pairs were found between sunflower and Arabidopsis. Segmental duplication appears to have played a vital role in the expansion processes of sunflower SPL genes, and because of selection pressure, all duplicated genes have undergone purifying selection. Tissue-specific gene expression analysis of the HaSBP genes proved their diverse spatiotemporal expression patterns, which were predominantly expressed in floral organs and differentially expressed in stem, axil, and root tissues. The expression pattern of HaSPL genes under water stress showed broad involvement of HaSPLs in the response to flood and drought stresses. This genome-wide identification investigation provides detailed information on the sunflower SPL transcription factor gene family and establishes a strong platform for future research on sunflower responses to abiotic stress tolerance.
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Affiliation(s)
- Kundansing R Jadhao
- Department of Bioinformatics, MGM College of Agricultural Biotechnology, Aurangabad, 431007, India.
| | - Sonam S Kale
- Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431003, India
| | - Nilesh S Chavan
- Department of Microbiology and Environmental Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431003, India
| | - Pandharinath H Janjal
- Department of Bioinformatics, MGM College of Agricultural Biotechnology, Aurangabad, 431007, India
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50
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Tao X, Zhao Y, Ma L, Wu J, Zeng R, Jiao J, Li R, Ma W, Lian Y, Wang W, Pu Y, Yang G, Liu L, Li X, Sun W. Cloning and functional analysis of the BrCUC2 gene in Brassica rapa L. FRONTIERS IN PLANT SCIENCE 2023; 14:1274567. [PMID: 37965013 PMCID: PMC10642757 DOI: 10.3389/fpls.2023.1274567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023]
Abstract
The CUP-SHAPED COTYLEDON2 (CUC2) gene plays an important role in the formation of apical meristem and organ edges in plants. The apical meristematic tissue of Brassica rapa (B. rapa) is associated with cold resistance, however, the role of the CUC2 gene in cold resistance of B.rapa is unclear. In this study, we used bioinformatics software to analyze the structure of BrCUC2 gene, real-time fluorescence quantitative PCR to detect the expression level of BrCUC2, constructed transgenic Arabidopsis thaliana by the flower dipping method and subcellular localization for functional validation. The results showed that, we isolated a 1104 bp open reading frame of BrCUC2 from the winter B. rapa cultivar 'Longyou 7'. The BrCUC2 contains a highly conserved domain belonging to the NAM superfamily. Its homologus CUC genes contain similar conserved motifs and are closely related to Brassica oleracea (B.oleracea), and the N-terminal of amino acid sequence contains NAC domain. BrCUC2 protein was localized in the nucleus and self-activation tests showed that pGBKT7-BrCUC2 had self-activation. Tissue-specific expression analysis and promoter β-Glucuronidase (GUS) activity showed that BrCUC2 had high expression levels in B. rapa growth points and A. thaliana leaf edges, stems and growth points. After low-temperature stress, BrCUC2 showed greater expression in 'Longyou 7,' which presents strong cold resistance and concave growth points, than in 'Longyou 99,' which presents weak cold resistance and protruding growth points. BrCUC2 promoter contains multiple elements related to stress responses. BrCUC2 overexpression revealed that the phenotype did not differ from that of the wild type during the seedling stage but showed weak growth and a dwarf phenotype during the flowering and mature stages. After low-temperature treatment, the physiological indexes and survival rate of BrCUC2-overexpression lines of Arabidopsis thaliana (A. thaliana) were better than those of the wild type within 12 h, although differences were not observed after 24 h. These results showed that BrCUC2 improved the low-temperature tolerance of transgenic A. thaliana within a short time. It can provide a foundation for the study of cold resistance in winter B. rapa.
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Affiliation(s)
- Xiaolei Tao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Yuhong Zhao
- Gansu Yasheng Agricultural Research Institute Co. Ltd, Crop Office, Lanzhou, China
| | - Li Ma
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Junyan Wu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Rui Zeng
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - JinTang Jiao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Rong Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Weiming Ma
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Yintao Lian
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Wangtian Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Yuanyuan Pu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Gang Yang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Lijun Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Xuecai Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
| | - Wancang Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Gansu Agricultural University, Lanzhou, China
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