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Liu J, Wang Z, Chen B, Wang G, Ke H, Zhang J, Jiao M, Wang Y, Xie M, Gu Q, Sun Z, Wu L, Wang X, Ma Z, Zhang Y. Genome-Wide Identification of the Alfin-like Gene Family in Cotton ( Gossypium hirsutum) and the GhAL19 Gene Negatively Regulated Drought and Salt Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:1831. [PMID: 38999670 PMCID: PMC11243875 DOI: 10.3390/plants13131831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/29/2024] [Accepted: 06/30/2024] [Indexed: 07/14/2024]
Abstract
Alfin-like (AL) is a small plant-specific gene family characterized by a PHD-finger-like structural domain at the C-terminus and a DUF3594 structural domain at the N-terminus, and these genes play prominent roles in plant development and abiotic stress response. In this study, we conducted genome-wide identification and analyzed the AL protein family in Gossypium hirsutum cv. NDM8 to assess their response to various abiotic stresses for the first time. A total of 26 AL genes were identified in NDM8 and classified into four groups based on a phylogenetic tree. Moreover, cis-acting element analysis revealed that multiple phytohormone response and abiotic stress response elements were highly prevalent in AL gene promoters. Further, we discovered that the GhAL19 gene could negatively regulate drought and salt stresses via physiological and biochemical changes, gene expression, and the VIGS assay. The study found there was a significant increase in POD and SOD activity, as well as a significant change in MDA in VIGS-NaCl and VIGS-PEG plants. Transcriptome analysis demonstrated that the expression levels of the ABA biosynthesis gene (GhNCED1), signaling genes (GhABI1, GhABI2, and GhABI5), responsive genes (GhCOR47, GhRD22, and GhERFs), and the stress-related marker gene GhLEA14 were regulated in VIGS lines under drought and NaCl treatment. In summary, GhAL19 as an AL TF may negatively regulate tolerance to drought and salt by regulating the antioxidant capacity and ABA-mediated pathway.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Zhicheng Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Bin Chen
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Jin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Mengjia Jiao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Meixia Xie
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Qishen Gu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
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Wei H, Wang X, Wang K, Tang X, Zhang N, Si H. Transcription factors as molecular switches regulating plant responses to drought stress. PHYSIOLOGIA PLANTARUM 2024; 176:e14366. [PMID: 38812034 DOI: 10.1111/ppl.14366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024]
Abstract
Plants often experience abiotic stress, which severely affects their growth. With the advent of global warming, drought stress has become a pivotal factor affecting crop yield and quality. Increasing numbers of studies have focused on elucidating the molecular mechanisms underlying plant responses to drought stress. As molecular switches, transcription factors (TFs) are key participants in drought-resistance regulatory networks in crops. TFs regulate the transcription of downstream genes and are regulated by various upstream regulatory factors. Therefore, understanding the mechanisms of action of TFs in regulating drought stress can help enhance the adaptive capacity of crops under drought conditions. In this review, we summarize the structural characteristics of several common TFs, their multiple drought-response pathways, and recently employed research strategies. We describe the application of new technologies such as analysis of stress granule dynamics and function, multi-omics data, gene editing, and molecular crosstalk between TFs in drought resistance. This review aims to familiarize readers with the regulatory network of TFs in drought resistance and to provide a reference for examining the molecular mechanisms of drought resistance in plants and improving agronomic traits.
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Affiliation(s)
- Han Wei
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Xiao Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Kaitong Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Xun Tang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
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Qi T, Yang W, Hassan MJ, Liu J, Yang Y, Zhou Q, Li H, Peng Y. Genome-wide identification of Aux/IAA gene family in white clover (Trifolium repens L.) and functional verification of TrIAA18 under different abiotic stress. BMC PLANT BIOLOGY 2024; 24:346. [PMID: 38684940 PMCID: PMC11057079 DOI: 10.1186/s12870-024-05034-3] [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: 01/19/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND White clover (Trifolium repens L.) is an excellent leguminous cool-season forage with a high protein content and strong nitrogen-fixing ability. Despite these advantages, its growth and development are markedly sensitive to environmental factors. Indole-3-acetic acid (IAA) is the major growth hormone in plants, regulating plant growth, development, and response to adversity. Nevertheless, the specific regulatory functions of Aux/IAA genes in response to abiotic stresses in white clover remain largely unexplored. RESULTS In this study, we identified 47 Aux/IAA genes in the white clover genome, which were categorized into five groups based on phylogenetic analysis. The TrIAAs promoter region co-existed with different cis-regulatory elements involved in developmental and hormonal regulation, and stress responses, which may be closely related to their diverse regulatory roles. Collinearity analysis showed that the amplification of the TrIAA gene family was mainly carried out by segmental duplication. White clover Aux/IAA genes showed different expression patterns in different tissues and under different stress treatments. In addition, we performed a yeast two-hybrid analysis to investigate the interaction between white clover Aux/IAA and ARF proteins. Heterologous expression indicated that TrIAA18 could enhance stress tolerance in both yeast and transgenic Arabidopsis thaliana. CONCLUSION These findings provide new scientific insights into the molecular mechanisms of growth hormone signaling in white clover and its functional characteristics in response to environmental stress.
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Affiliation(s)
- Tiangang Qi
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Weiqiang Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Muhammad Jawad Hassan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiefang Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yujiao Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qinyu Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Gawande ND, Sankaranarayanan S. Genome wide characterization and expression analysis of CrRLK1L gene family in wheat unravels their roles in development and stress-specific responses. FRONTIERS IN PLANT SCIENCE 2024; 15:1345774. [PMID: 38595759 PMCID: PMC11002176 DOI: 10.3389/fpls.2024.1345774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) genes encode a subfamily of receptor-like kinases (RLK) that regulate diverse processes during plant growth, development, and stress responses. The first CrRLK1L was identified from the Catharanthus roseus, commonly known as Madagascar periwinkle. Subsequently, CrRLK1L gene families have been characterized in many plants. The genome of T. aestivum encodes 15 CrRLK1L genes with 43 paralogous copies, with three homeologs each, except for -2-D and -7-A, which are absent. Chromosomal localization analysis revealed a markedly uneven distribution of CrRLK1L genes across seven different chromosomes, with chromosome 4 housing the highest number of genes, while chromosome 6 lacked any CrRLK1L genes. Tissue-specific gene expression analysis revealed distinct expression patterns among the gene family members, with certain members exhibiting increased expression in reproductive tissues. Gene expression analysis in response to various abiotic and biotic stress conditions unveiled differential regulation of gene family members. Cold stress induces CrRLK1Ls -4-B and -15-A while downregulating -3-A and -7B. Drought stress upregulates -9D, contrasting with the downregulation of -7D. CrRLK1L-15-B and -15-D were highly induced in response to 1 hr of heat, and combined drought and heat stress, whereas -10-B is downregulated. Similarly, in response to NaCl stress, only CrRLK1L1 homeologs were induced. Fusarium graminearum and Claviceps purpurea inoculation induces homeologs of CrRLK1L-6 and -7. The analysis of cis-acting elements in the promoter regions identified elements crucial for plant growth and developmental processes. This comprehensive genome-wide analysis and expression study provides valuable insights into the essential functions of CrRLK1L members in wheat.
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Affiliation(s)
| | - Subramanian Sankaranarayanan
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
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Zhu X, Wang B, Liu W, Wei X, Wang X, Du X, Liu H. Genome-wide analysis of AP2/ERF gene and functional analysis of CqERF24 gene in drought stress in quinoa. Int J Biol Macromol 2023; 253:127582. [PMID: 37866580 DOI: 10.1016/j.ijbiomac.2023.127582] [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: 08/15/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Quinoa is a crop with high nutritional value and strong stress resistance. AP2/ERF transcription factors play a key role in plant growth and development. In this study, 148 AP2/ERF genes were identified in quinoa, which were divided into 5 subfamilies, including ERF, AP2, DREB, RAV and Soloist. The results showed that the number of introns ranged from 0 to 11, and the Motif 1-Motif 4 was highly conserved in most CqAP2/ERF proteins. The 148 CqAP2/ERF genes were distributed on 19 chromosomes. There were 93 pairs of duplicating genes in this family, and gene duplication played a critical role in the expansion of this family. Protein-protein interaction indicated that the proteins in CqAP2/ERF subfamily exhibited complex interactions, and GO enrichment analysis indicated that 148 CqAP2/ERF proteins were involved in transcription factor activity. In addition, CqAP2/ERF gene contains a large number of elements related to hormones in promoter region (IAA, GA, SA, ABA and MeJA) and stresses (salt, drought, low temperature and anaerobic induction). Transcriptome analysis under drought stress indicated that most of the CqAP2/ERF genes were responsive to drought stress, and subcellular localization indicated that CqERF24 was location in the nucleus, qRT-PCR results also showed that most of the genes such as CqERF15, CqERF24, CqDREB03, CqDREB14, CqDREB37 and CqDREB43 also responded to drought stress in roots and leaves. Overexpression of CqERF24 in Arabidopsis thaliana enhanced drought resistance by increasing antioxidant enzyme activity and activation-related stress genes, and the gene is sensitive to ABA, while silencing CqERF24 in quinoa decreased drought tolerance. In addition, overexpression of CqERF24 in quinoa calli enhanced resistance to mannitol. These results lay a solid foundation for further study on the role of AP2/ERF family genes in quinoa under drought stress.
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Affiliation(s)
- Xiaolin Zhu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Baoqiang Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Wenyu Liu
- Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Xiaohong Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Xian Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xuefeng Du
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Haixun Liu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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Wu D, Zhang K, Li CY, Xie GW, Lu MT, Qian Y, Shu YP, Shen Q. Genome-wide comprehensive characterization and transcriptomic analysis of AP2/ERF gene family revealed its role in seed oil and ALA formation in perilla (Perilla frutescens). Gene 2023; 889:147808. [PMID: 37722611 DOI: 10.1016/j.gene.2023.147808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/06/2023] [Accepted: 09/15/2023] [Indexed: 09/20/2023]
Abstract
Perilla (Perilla frutescens) is a potential specific oilseed crop with an extremely high α-linolenic acid (ALA) content in its seeds. AP2/ERF transcription factors (TFs) play important roles in multiple biological processes. However, limited information is known about the regulatory mechanism of the AP2/ERF family in perilla's oil accumulation. In this research, we identified 212 AP2/ERF family members in the genome of perilla, and their domain characteristics, collinearity, and sub-genome differentiation were comprehensively analyzed. Transcriptome sequencing revealed that genes encoding key enzymes involved in oil biosynthesis (e.g., ACCs, KASII, GPAT, PDAT and LPAAT) were up-regulated in the high-oil variety. Moreover, the endoplasmic reticulum-localized FAD2 and FAD3 were significantly up-regulated in the high-ALA variety. To investigate the roles of AP2/ERFs in lipid biosynthesis, we conducted a correlation analysis between non-redundant AP2/ERFs and key lipid metabolism genes using WGCNA. A significant correlation was found between 36 AP2/ERFs and 90 lipid metabolism genes. Among them, 12 AP2/ERFs were identified as hub genes and showed significant correlation with lipid synthase genes (e.g., FADs, GPAT and ACSL) and key regulatory TFs (e.g., LEC2, IAA, MYB, UPL3). Furthermore, gene expression analysis identified three AP2/ERFs (WRI, ABI4, and RAVI) potentially playing an important role in the regulation of oil accumulation in perilla. Our study suggests that PfAP2/ERFs are important regulatory TFs in the lipid biosynthesis pathway, providing a foundation for the molecular understanding of oil accumulation in perilla and other oilseed crops.
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Affiliation(s)
- Duan Wu
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Ke Zhang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Chun-Yu Li
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Guan-Wen Xie
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Ming-Ting Lu
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Yong Qian
- Shanghai Standard Technology Co., Ltd, Building 25, 15 Gudan Road, Pudong, Shanghai 201314, China.
| | - Ya-Ping Shu
- Shanghai Standard Technology Co., Ltd, Building 25, 15 Gudan Road, Pudong, Shanghai 201314, China.
| | - Qi Shen
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
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Chen S, Chen Y, Liang M, Qu S, Shen L, Zeng Y, Hou N. Genome-wide identification and molecular expression profile analysis of FHY3/FAR1 gene family in walnut (Juglans sigillata L.) development. BMC Genomics 2023; 24:673. [PMID: 37940838 PMCID: PMC10634098 DOI: 10.1186/s12864-023-09629-2] [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: 05/08/2023] [Accepted: 08/26/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Juglans sigillata L. (walnut) has a high economic value for nuts and wood and has been widely grown and eaten around the world. Light plays an important role in regulating the development of the walnut embryo and promoting nucleolus enlargement, which is one of the factors affecting the yield and quality of walnut. However, little is known about the effect of light on the growth and quality of walnuts. Studies have shown that far red prolonged hypocotyl 3 (FHY3) and far red damaged response (FAR1) play important roles in plant growth, light response, and resistance. Therefore, FHY3/FAR1 genes were identified in walnuts on a genome-wide basis during their growth and development to reveal the potential regulation mechanisms involved in walnut kernel growth and development. RESULTS In the present study, a total of 61 FHY3/FAR1 gene family members in walnuts have been identified, ranging in length from 117 aa to 895 aa. These gene family members have FHY3 or FAR1 conserved domains, which are unevenly distributed on the 15 chromosomes (Chr) of the walnut (except for the Chr16). All 61 FHY3/FAR1 genes were divided into five subclasses (I, II, III, IV, and V) by phylogenetic tree analysis. The results indicated that FHY3/FAR1 genes in the same subclasses with similar structures might be involved in regulating the growth and development of walnut. The gene expression profiles were analyzed in different walnut kernel varieties (Q, T, and F). The result showed that some FHY3/FAR1 genes might be involved in the regulation of walnut kernel ripening and seed coat color formation. Seven genes (OF07056-RA, OF09665-RA, OF24282-RA, OF26012-RA, OF28029-RA, OF28030-RA, and OF08124-RA) were predicted to be associated with flavonoid biosynthetic gene regulation cis-acting elements in promoter sequences. RT-PCR was used to verify the expression levels of candidate genes during the development and color change of walnut kernels. In addition, light responsiveness and MeJA responsiveness are important promoter regulatory elements in the FHY3/FAR1 gene family, which are potentially involved in the light response, growth, and development of walnut plants. CONCLUSION The results of this study provide a valuable reference for supplementing the genomic sequencing results of walnut, and pave the way for further research on the FHY3/FAR1 gene function of walnut.
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Affiliation(s)
- Shengqun Chen
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Yingfu Chen
- Guizhou Province Forestry Science and Technology Extension Station, Guiyang, 550000, China
| | - Mei Liang
- Guizhou Province Forestry Science and Technology Extension Station, Guiyang, 550000, China
| | - Shuang Qu
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Lianwen Shen
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Yajun Zeng
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China.
| | - Na Hou
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China.
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Wang Z, Song G, Zhang F, Shu X, Wang N. Functional Characterization of AP2/ERF Transcription Factors during Flower Development and Anthocyanin Biosynthesis Related Candidate Genes in Lycoris. Int J Mol Sci 2023; 24:14464. [PMID: 37833913 PMCID: PMC10572147 DOI: 10.3390/ijms241914464] [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: 08/30/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
The APETALA2/ethylene-responsive transcription factor (AP2/ERF) family has been extensively investigated because of its significant involvement in plant development, growth, fruit ripening, metabolism, and plant stress responses. To date, there has been little investigation into how the AP2/ERF genes influence flower formation and anthocyanin biosynthesis in Lycoris. Herein, 80 putative LrAP2/ERF transcription factors (TFs) with complete open reading frames (ORFs) were retrieved from the Lycoris transcriptome sequence data, which could be divided into five subfamilies dependent on their complete protein sequences. Furthermore, our findings demonstrated that genes belonging to the same subfamily had structural similarities and conserved motifs. LrAP2/ERF genes were analyzed for playing an important role in plant growth, water deprivation, and flower formation by means of gene ontology (GO) enrichment analysis. The expression pattern of the LrAP2/ERF genes differed across tissues and might be important for Lycoris growth and flower development. In response to methyl jasmonate (MeJA) exposure and drought stress, the expression of each LrAP2/ERF gene varied across tissues and time. Moreover, a total of 20 anthocyanin components were characterized using ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis, and pelargonidin-3-O-glucoside-5-O-arabinoside was identified as the major anthocyanin aglycone responsible for the coloration of the red petals in Lycoris. In addition, we mapped the relationships between genes and metabolites and found that LrAP2/ERF16 is strongly linked to pelargonidin accumulation in Lycoris petals. These findings provide the basic conceptual groundwork for future research into the molecular underpinnings and regulation mechanisms of AP2/ERF TFs in anthocyanin accumulation and Lycoris floral development.
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Affiliation(s)
- Zhong Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Guowei Song
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Xiaochun Shu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Ning Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybeans (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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Cao H, Tian Q, Ju M, Duan Y, Li G, Ma Q, Zhang H, Zhang X, Miao H. Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame ( Sesamum indicum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1261238. [PMID: 37810391 PMCID: PMC10558006 DOI: 10.3389/fpls.2023.1261238] [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: 07/19/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023]
Abstract
Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions.
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Affiliation(s)
- Hengchun Cao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Qiuzhen Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Guiting Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Qin Ma
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Xianmei Zhang
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Luohe Academy of Agricultural Sciences, Luohe, Henan, China
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
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Mazhar HSUD, Shafiq M, Ali H, Ashfaq M, Anwar A, Tabassum J, Ali Q, Jilani G, Awais M, Sahu R, Javed MA. Genome-Wide Identification, and In-Silico Expression Analysis of YABBY Gene Family in Response to Biotic and Abiotic Stresses in Potato (Solanum tuberosum). Genes (Basel) 2023; 14:genes14040824. [PMID: 37107580 PMCID: PMC10137784 DOI: 10.3390/genes14040824] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
YABBY is among the specific transcription factor (TF) gene family in plants and plays an important role in the development of the leaves and floral organs. Its specific roles include lateral organ development, the establishment of dorsoventral polarity, and response to abiotic stress. Potato is an important crop worldwide and YABBY genes are not still identified and characterized in potato. So, little has been known about YABBY genes in potato until now. This study was carried out to perform genome-wide analysis, which will provide an in-depth analysis about the role of YABBY genes in potato. There have been seven StYAB genes identified, which are found to be located on seven different chromosomes. Through multiple sequence analyses, it has been predicted that the YABBY domain was present in all seven genes while the C2-C2 domain was found to be absent only in StYAB2. With the help of cis-element analysis, the involvement of StYAB genes in light, stress developmental, and hormonal responsiveness has been found. Furthermore, expression analysis from RNA-seq data of different potato organs indicated that all StYAB genes have a role in the vegetative growth of the potato plant. In addition to this, RNA-seq data also identified StYAB3, StYAB5, and StYAB7 genes showing expression during cadmium, and drought stress, while StYAB6 was highly expressed during a viral attack. Moreover, during the attack of Phytophthora infestans on a potato plant StYAB3, StYAB5, StYAB6, and StYAB7 showed high expression. This study provides significant knowledge about the StYAB gene structures and functions, which can later be used for gene cloning, and functional analysis; this information may be utilized by molecular biologists and plant breeders for the development of new potato lines.
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Genome-Wide Identification of AP2/ERF Transcription Factor Family and Functional Analysis of DcAP2/ERF#96 Associated with Abiotic Stress in Dendrobium catenatum. Int J Mol Sci 2022; 23:ijms232113603. [PMID: 36362389 PMCID: PMC9659080 DOI: 10.3390/ijms232113603] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
APETALA2/Ethylene Responsive Factor (AP2/ERF) family plays important roles in reproductive development, stress responses and hormone responses in plants. However, AP2/ERF family has not been systematically studied in Dendrobium catenatum. In this study, 120 AP2/ERF family members were identified for the first time in D. catenatum, which were divided into four groups (AP2, RAV, ERF and DREB subfamily) according to phylogenetic analysis. Gene structures and conserved motif analysis showed that each DcAP2/ERF family gene contained at least one AP2 domain, and the distribution of motifs varied among subfamilies. Cis-element analysis indicated that DcAP2/ERF genes contained abundant cis-elements related to hormone signaling and stress response. To further identify potential genes involved in drought stress, 12 genes were selected to detect their expression under drought treatment through qRT-PCR analysis and DcAP2/ERF#96, a nuclear localized ethylene-responsive transcription factor, showed a strong response to PEG treatment. Overexpression of DcAP2/ERF#96 in Arabidopsis showed sensitivity to ABA. Molecular, biochemical and genetic assays indicated that DcAP2ERF#96 interacts with DREB2A and directly inhibits the expression of P5CS1 in response to the ABA signal. Taken together, our study provided a molecular basis for the intensive study of DcAP2/ERF genes and revealed the biological function of DcAP2ERF#96 involved in the ABA signal.
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Goldshmidt A, Ziegler T, Zhou D, Brower‐Toland B, Preuss S, Slewinski T. Tuning of meristem maturation rate increases yield in multiple Triticum aestivum cultivars. PLANT DIRECT 2022; 6:e459. [PMID: 36447652 PMCID: PMC9694431 DOI: 10.1002/pld3.459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 01/02/2020] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Breeding programs aim to improve crop yield and environmental stability for enhanced food security. The principal methodology in breeding for stable yield gain relies on the indirect selection of beneficial genetics by yield evaluation across diverse environmental conditions. This methodology requires substantial resources while delivering a slow pace of yield gain and environmental adaptation. Alternative methods are required to accelerate gain and adaptation, becoming even more imperative in a changing climate. New molecular tools and approaches can enable accelerated creation and deployment of multiple alleles of genes identified to control key traits. With the advent of tools that enable breeding by targeted allelic selection, identifying gene targets associated with an improved crop performance ideotype will become crucial. Previous studies have shown that altered photoperiod regimes increase yield in wheat (Triticum aestivum). In the current study, we have employed such treatments to study the resulting yield ideotype in five spring wheat cultivars. We found that the photoperiod treatment creates a yield ideotype arising from delayed spike establishment rates that are accompanied by increased early shoot expression of TARGET OF EAT1 (TaTOE1) genes. Genes identified in this way could be used for ideotype-based improve crop performance through targeted allele creation and selection in relevant environments.
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Affiliation(s)
- Alexander Goldshmidt
- Bayer Crop ScienceChesterfieldMissouriUSA
- Present address:
The Volcani Agriculture InstituteRishon LeZionIsrael
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Hussain Q, Zheng M, Chang W, Ashraf MF, Khan R, Asim M, Riaz MW, Alwahibi MS, Elshikh MS, Zhang R, Wu J. Genome-Wide Identification and Expression Analysis of SnRK2 Gene Family in Dormant Vegetative Buds of Liriodendron chinense in Response to Abscisic Acid, Chilling, and Photoperiod. Genes (Basel) 2022; 13:genes13081305. [PMID: 35893042 PMCID: PMC9331246 DOI: 10.3390/genes13081305] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Protein kinases play an essential role in plants’ responses to environmental stress signals. SnRK2 (sucrose non-fermenting 1-related protein kinase 2) is a plant-specific protein kinase that plays a crucial role in abscisic acid and abiotic stress responses in some model plant species. In apple, corn, rice, pepper, grapevine, Arabidopsis thaliana, potato, and tomato, a genome-wide study of the SnRK2 protein family was performed earlier. The genome-wide comprehensive investigation was first revealed to categorize the SnRK2 genes in the Liriodendron chinense (L. chinense). The five SnRK2 genes found in the L. chinense genome were highlighted in this study. The structural gene variants, 3D structure, chromosomal distributions, motif analysis, phylogeny, subcellular localization, cis-regulatory elements, expression profiles in dormant buds, and photoperiod and chilling responses were all investigated in this research. The five SnRK2 genes from L. chinense were grouped into groups (I–IV) based on phylogeny analysis, with three being closely related to other species. Five hormones-, six stress-, two growths and biological process-, and two metabolic-related responsive elements were discovered by studying the cis-elements in the promoters. According to the expression analyses, all five genes were up- and down-regulated in response to abscisic acid (ABA), photoperiod, chilling, and chilling, as well as photoperiod treatments. Our findings gave insight into the SnRK2 family genes in L. chinense and opened up new study options.
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Affiliation(s)
- Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China; (Q.H.); (M.Z.); (W.C.); (M.W.R.); (R.Z.)
- Key Laboratory of Modern Silvicultural Technology of Zhejiang Province, Hangzhou 311300, China
| | - Manjia Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China; (Q.H.); (M.Z.); (W.C.); (M.W.R.); (R.Z.)
- Key Laboratory of Modern Silvicultural Technology of Zhejiang Province, Hangzhou 311300, China
| | - Wenwen Chang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China; (Q.H.); (M.Z.); (W.C.); (M.W.R.); (R.Z.)
- Key Laboratory of Modern Silvicultural Technology of Zhejiang Province, Hangzhou 311300, China
| | - Muhammad Furqan Ashraf
- Department of Arctic and Marine Biology, UiT-The Arctic University of Norway, 9009 Tromsø, Norway;
| | - Rayyan Khan
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (R.K.); (M.A.)
| | - Muhammad Asim
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (R.K.); (M.A.)
| | - Muhammad Waheed Riaz
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China; (Q.H.); (M.Z.); (W.C.); (M.W.R.); (R.Z.)
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Mona S. Alwahibi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.S.A.); (M.S.E.)
| | - Mohamed S. Elshikh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.S.A.); (M.S.E.)
| | - Rui Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China; (Q.H.); (M.Z.); (W.C.); (M.W.R.); (R.Z.)
- Key Laboratory of Modern Silvicultural Technology of Zhejiang Province, Hangzhou 311300, China
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China; (Q.H.); (M.Z.); (W.C.); (M.W.R.); (R.Z.)
- Key Laboratory of Modern Silvicultural Technology of Zhejiang Province, Hangzhou 311300, China
- Correspondence:
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Yang T, Gao T, Wang C, Wang X, Chen C, Tian M, Yang W. In silico genome wide identification and expression analysis of the WUSCHEL-related homeobox gene family in Medicago sativa. Genomics Inform 2022; 20:e19. [PMID: 35794699 PMCID: PMC9299560 DOI: 10.5808/gi.22013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/28/2022] [Indexed: 11/20/2022] Open
Abstract
Alfalfa (Medicago sativa) is an important food and feed crop which rich in mineral sources. The WUSCHEL-related homeobox (WOX) gene family plays important roles in plant development and identification of putative gene families, their structure, and potential functions is a primary step for not only understanding the genetic mechanisms behind various biological process but also for genetic improvement. A variety of computational tools, including MAFFT, HMMER, hidden Markov models, Pfam, SMART, MEGA, ProtTest, BLASTn, and BRAD, among others, were used. We identified 34 MsWOX genes based on a systematic analysis of the alfalfa plant genome spread in eight chromosomes. This is an expansion of the gene family which we attribute to observed chromosomal duplications. Sequence alignment analysis revealed 61 conserved proteins containing a homeodomain. Phylogenetic study sung reveal five evolutionary clades with 15 motif distributions. Gene structure analysis reveals various exon, intron, and untranslated structures which are consistent in genes from similar clades. Functional analysis prediction of promoter regions reveals various transcription binding sites containing key growth, development, and stress-responsive transcription factor families such as MYB, ERF, AP2, and NAC which are spread across the genes. Most of the genes are predicted to be in the nucleus. Also, there are duplication events in some genes which explain the expansion of the family. The present research provides a clue on the potential roles of MsWOX family genes that will be useful for further understanding their functional roles in alfalfa plants.
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Affiliation(s)
- Tianhui Yang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Ting Gao
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Chuang Wang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Xiaochun Wang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Caijin Chen
- Branch Institute of Guyuan, Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 756000, China
| | - Mei Tian
- Institute of Horticultural Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Weidi Yang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
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Su R, Dossou SSK, Dossa K, Zhou R, Liu A, Zhong Y, Fang S, Zhang X, Wu Z, You J. Genome-wide characterization and identification of candidate ERF genes involved in various abiotic stress responses in sesame (Sesamum indicum L.). BMC PLANT BIOLOGY 2022; 22:256. [PMID: 35606719 PMCID: PMC9128266 DOI: 10.1186/s12870-022-03632-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The adverse effects of climate change on crop production are constraining breeders to develop high-quality environmentally stable varieties. Hence, efforts are being made to identify key genes that could be targeted for enhancing crop tolerance to environmental stresses. ERF transcription factors play an important role in various abiotic stresses in plants. However, the roles of the ERF family in abiotic stresses tolerance are still largely unknown in sesame, the "queen" of oilseed crops. RESULTS In total, 114 sesame ERF genes (SiERFs) were identified and characterized. 96.49% of the SiERFs were distributed unevenly on the 16 linkage groups of the sesame genome. The phylogenetic analysis with the Arabidopsis ERFs (AtERFs) subdivided SiERF subfamily proteins into 11 subgroups (Groups I to X; and VI-L). Genes in the same subgroup exhibited similar structure and conserved motifs. Evolutionary analysis showed that the expansion of ERF genes in sesame was mainly induced by whole-genome duplication events. Moreover, cis-acting elements analysis showed that SiERFs are mostly involved in environmental responses. Gene expression profiles analysis revealed that 59 and 26 SiERFs are highly stimulated under drought and waterlogging stress, respectively. In addition, qRT-PCR analyses indicated that most of SiERFs are also significantly up-regulated under osmotic, submerge, ABA, and ACC stresses. Among them, SiERF23 and SiERF54 were the most induced by both the abiotic stresses, suggesting their potential for targeted improvement of sesame response to multiple abiotic stresses. CONCLUSION This study provides a comprehensive understanding of the structure, classification, evolution, and abiotic stresses response of ERF genes in sesame. Moreover, it offers valuable gene resources for functional characterization towards enhancing sesame tolerance to multiple abiotic stresses.
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Affiliation(s)
- Ruqi Su
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Senouwa Segla Koffi Dossou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Komivi Dossa
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Aili Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Yanping Zhong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Sheng Fang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Ziming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
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Magar MM, Liu H, Yan G. Genome-Wide Analysis of AP2/ERF Superfamily Genes in Contrasting Wheat Genotypes Reveals Heat Stress-Related Candidate Genes. FRONTIERS IN PLANT SCIENCE 2022; 13:853086. [PMID: 35498651 PMCID: PMC9044922 DOI: 10.3389/fpls.2022.853086] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/03/2022] [Indexed: 06/09/2023]
Abstract
The AP2/ERF superfamily is one of the largest groups of transcription factors (TFs) in plants, which plays important roles in regulating plant growth and development under heat stress. A complete genome-wide identification, characterization, and expression analysis of AP2/ERF superfamily genes focusing on heat stress response were conducted in bread wheat. This study identified 630 putative AP2/ERF superfamily TF genes in wheat, with 517 genes containing well-defined AP2-protein domains. They were classified into five sub-families, according to domain content, conserved motif, and gene structure. The unique genes identified in this study were 112 TaERF genes, 77 TaDREB genes, four TaAP2 genes, and one TaRAV gene. The chromosomal distribution analysis showed the unequal distribution of TaAP2/ERF genes in 21 wheat chromosomes, with 127 pairs of segmental duplications and one pair of tandem duplication, highly concentrated in TaERF and TaDREB sub-families. The qRT-PCR validation of differentially expressed genes (DEGs) in contrasting wheat genotypes under heat stress conditions revealed that significant DEGs in tolerant and susceptible genotypes could unequivocally differentiate tolerant and susceptible wheat genotypes. This study provides useful information on TaAP2/ERF superfamily genes and reveals candidate genes in response to heat stress, which forms a foundation for heat tolerance breeding in wheat.
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Genome-Wide Investigation and Functional Verification of the ZIP Family Transporters in Wild Emmer Wheat. Int J Mol Sci 2022; 23:ijms23052866. [PMID: 35270007 PMCID: PMC8911026 DOI: 10.3390/ijms23052866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/18/2022] [Accepted: 02/19/2022] [Indexed: 12/02/2022] Open
Abstract
The zinc/iron-regulated transporter-like protein (ZIP) family has a crucial role in Zn homeostasis of plants. Although the ZIP genes have been systematically studied in many plant species, the significance of this family in wild emmer wheat (Triticum turgidum ssp. dicoccoides) is not yet well understood. In this study, a genome-wide investigation of ZIPs genes based on the wild emmer reference genome was conducted, and 33 TdZIP genes were identified. Protein structure analysis revealed that TdZIP proteins had 1 to 13 transmembrane (TM) domains and most of them were predicted to be located on the plasma membrane. These TdZIPs can be classified into three clades in a phylogenetic tree. They were annotated as being involved in inorganic ion transport and metabolism. Cis-acting analysis showed that several elements were involved in hormone, stresses, grain-filling, and plant development. Expression pattern analysis indicated that TdZIP genes were highly expressed in different tissues. TdZIP genes showed different expression patterns in response to Zn deficiency and that 11 genes were significantly induced in either roots or both roots and shoots of Zn-deficient plants. Yeast complementation analysis showed that TdZIP1A-3, TdZIP6B-1, TdZIP6B-2, TdZIP7A-3, and TdZIP7B-2 have the capacity to transport Zn. Overexpression of TdZIP6B-1 in rice showed increased Zn concentration in roots compared with wild-type plants. The expression levels of TdZIP6B-1 in transgenic rice were upregulated in normal Zn concentration compared to that of no Zn. This work provides a comprehensive understanding of the ZIP gene family in wild emmer wheat and paves the way for future functional analysis and genetic improvement of Zn deficiency tolerance in wheat.
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Bashir SS, Hussain A, Hussain SJ, Wani OA, Zahid Nabi S, Dar NA, Baloch FS, Mansoor S. Plant drought stress tolerance: understanding its physiological, biochemical and molecular mechanisms. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2021.2020161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Sheikh Shanawaz Bashir
- Department of Botany, School of Chemical and Life Science, Jamia Hamdard University, New Delhi, India
| | - Anjuman Hussain
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Sofi Javed Hussain
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Owais Ali Wani
- Department of Soil Science, FoA, Wadura, Sopore, Sher-e-Kashmir University of Agricultural Sciences & Technology Shalimar Kashmir, Srinagar, Jammu and Kashmir, India
| | - Sheikh Zahid Nabi
- Division of Biochemistry, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Niyaz A. Dar
- ARSSSS Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology, Shalimar Kashmir, Srinagar, Jammu and Kashmir, India
| | - Faheem Shehzad Baloch
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Sheikh Mansoor
- Division of Biochemistry, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
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Sabir IA, Manzoor MA, Shah IH, Liu X, Jiu S, Wang J, Alam P, Abdullah M, Zhang C. Identification and Comprehensive Genome-Wide Analysis of Glutathione S-Transferase Gene Family in Sweet Cherry ( Prunus avium) and Their Expression Profiling Reveals a Likely Role in Anthocyanin Accumulation. FRONTIERS IN PLANT SCIENCE 2022; 13:938800. [PMID: 35903236 PMCID: PMC9315441 DOI: 10.3389/fpls.2022.938800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/16/2022] [Indexed: 05/08/2023]
Abstract
Glutathione S-transferases (GSTs) in plants are multipurpose enzymes that are involved in growth and development and anthocyanins transportation. However, members of the GST gene family were not identified in sweet cherry (Prunus avium). To identify the GST genes in sweet cherry, a genome-wide analysis was conducted. In this study, we identified 67 GST genes in P. avium genome and nomenclature according to chromosomal distribution. Phylogenetic tree analysis revealed that PavGST genes were classified into seven chief subfamily: TCHQD, Theta, Phi, Zeta, Lambda, DHAR, and Tau. The majority of the PavGST genes had a relatively well-maintained exon-intron and motif arrangement within the same group, according to gene structure and motif analyses. Gene structure (introns-exons) and conserved motif analysis revealed that the majority of the PavGST genes showed a relatively well-maintained motif and exons-introns configuration within the same group. The chromosomal localization, GO enrichment annotation, subcellular localization, syntenic relationship, Ka/Ks analysis, and molecular characteristics were accomplished using various bioinformatics tools. Mode of gene duplication showed that dispersed duplication might play a key role in the expansion of PavGST gene family. Promoter regions of PavGST genes contain numerous cis-regulatory components, which are involved in multiple stress responses, such as abiotic stress and phytohormones responsive factors. Furthermore, the expression profile of sweet cherry PavGSTs showed significant results under LED treatment. Our findings provide the groundwork for future research into induced LED anthocyanin and antioxidants deposition in sweet cherries.
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Affiliation(s)
- Irfan Ali Sabir
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Iftikhar Hussain Shah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Muhammad Abdullah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Caixi Zhang,
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