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Zhang X, Yu J, Qu G, Chen S. The cold-responsive C-repeat binding factors in Betula platyphylla Suk. positively regulate cold tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112012. [PMID: 38311248 DOI: 10.1016/j.plantsci.2024.112012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/08/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Cold stress is one of the most destructive abiotic stresses limiting plant growth and development. CBF (C-repeat binding factor) transcription factors and their roles in cold response have been identified in Arabidopsis as well as several other plant species. However, the biological functions and related molecular mechanisms of CBFs in birch (Betula platyphylla Suk.) remain undetermined. In this study, five cold-responsive BpCBF genes, BpCBF1, BpCBF2, BpCBF7, BpCBF10 and BpCBF12 were cloned. Via protoplast transformation, BpCBF7 was found to be localized in nucleus. The result of yeast one hybrid assay validated the binding of BpCBF7 to the CRT/DRE (C-repeat/dehydration responsive element) elements in the promoter of BpERF1.1 gene. By overexpressing and repressing BpCBFs in birch plants, it was proven that BpCBFs play positive roles in the cold tolerance. At the metabolic level, BpCBFs OE lines had lower ROS accumulation, as well as higher activities of antioxidant enzymes (SOD, POD and CAT) and higher accumulation of protective substances (soluble sugar, soluble protein and proline). Via yeast one hybrid and co-transformation of effector and reporter vectors assay, it was proven that BpCBF7 can regulate the expression of BpERF5 and BpZAT10 genes by directly binding to their promoters. An interacting protein of BpCBF7, BpWRKY17, was identified by yeast two hybrid library sequencing and the interaction was validated with in vivo methods. These results indicates that BpCBFs can increase the cold tolerance of birch plants, partly by gene regulation and protein interaction. This study provides a reference for the research on CBF transcription factors and genetic improvement of forest trees upon abiotic stresses.
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Affiliation(s)
- Xiang Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, Heilongjiang, China
| | - Jiajie Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, Heilongjiang, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, Heilongjiang, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, Heilongjiang, China.
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Zhao Z, Liang C, Zhang W, Yang Y, Bi Q, Yu H, Wang L. Genome-wide association analysis identifies a candidate gene controlling seed size and yield in Xanthoceras sorbifolium Bunge. HORTICULTURE RESEARCH 2024; 11:uhad243. [PMID: 38225982 PMCID: PMC10788774 DOI: 10.1093/hr/uhad243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/17/2023] [Indexed: 01/17/2024]
Abstract
Yellow horn (Xanthoceras sorbifolium Bunge) is a woody oilseed tree species whose seed oil is rich in unsaturated fatty acids and rare neuronic acids, and can be used as a high-grade edible oil or as a feedstock for biodiesel production. However, the genetic mechanisms related to seed yield in yellow horn are not well elucidated. This study identified 2 164 863 SNP loci based on 222 genome-wide resequencing data of yellow horn germplasm. We conducted genome-wide association study (GWAS) analysis on three core traits (hundred-grain weight, single-fruit seed mass, and single-fruit seed number) that influence seed yield for the years 2022 and 2020, and identified 399 significant SNP loci. Among these loci, the Chr10_24013014 and Chr10_24012613 loci caught our attention due to their consistent associations across multiple analyses. Through Sanger sequencing, we validated the genotypes of these two loci across 16 germplasms, confirming their consistency with the GWAS analysis results. Downstream of these two significant loci, we identified a candidate gene encoding an AP2 transcription factor protein, which we named XsAP2. RT-qPCR analysis revealed high expression of the XsAP2 gene in seeds, and a significant negative correlation between its expression levels and seed hundred-grain weight, as well as single-fruit seed mass, suggesting its potential role in the normal seed development process. Transgenic Arabidopsis lines with the overexpressed XsAP2 gene exhibited varying degrees of reduction in seed size, number of seeds per silique, and number of siliques per plant compared with wild-type Arabidopsis. Combining these results, we hypothesize that the XsAP2 gene may have a negative regulatory effect on seed yield of yellow horn. These results provide a reference for the molecular breeding of high-yielding yellow horn.
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Affiliation(s)
- Ziquan Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Chongjun Liang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
- College of Forestry, Hainan University, Haikou 570228, China
| | - Wei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Yingying Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Quanxin Bi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Haiyan Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
- College of Forestry, Hainan University, Haikou 570228, China
- College of Forestry, Northwest A&F University, Yangling 712100, China
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3
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Zhou H, Ma J, Liu H, Zhao P. Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions. Int J Mol Sci 2023; 25:25. [PMID: 38203199 PMCID: PMC10778614 DOI: 10.3390/ijms25010025] [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: 11/13/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Cold stress impacts woody tree growth and perennial production, especially when the temperature rapidly changes in late spring. To address this issue, we conducted the genome-wide identification of two important transcription factors (TFs), CBF (C-repeat binding factors) and ICE (inducers of CBF expression), in three walnut (Juglans) genomes. Although the CBF and ICE gene families have been identified in many crops, very little systematic analysis of these genes has been carried out in J. regia and J. sigillata. In this study, we identified a total of 16 CBF and 12 ICE genes in three Juglans genomes using bioinformatics analysis. Both CBF and ICE had conserved domains, motifs, and gene structures, which suggests that these two TFs were evolutionarily conserved. Most ICE genes are located at both ends of the chromosomes. The promoter cis-regulatory elements of CBF and ICE genes are largely involved in light and phytohormone responses. Based on 36 RNA sequencing of leaves from four walnut cultivars ('Zijing', 'Lvling', 'Hongren', and 'Liao1') under three temperature conditions (8 °C, 22 °C, and 5 °C) conditions in late spring, we found that the ICE genes were expressed more highly than CBFs. Both CBF and ICE proteins interacted with cold-related proteins, and many putative miRNAs had interactions with these two TFs. These results determined that CBF1 and ICE1 play important roles in the tolerance of walnut leaves to rapid temperature changes. Our results provide a useful resource on the function of the CBF and ICE genes related to cold tolerance in walnuts.
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Affiliation(s)
- Huijuan Zhou
- Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi’an 710061, China;
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.M.); (H.L.)
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.M.); (H.L.)
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.M.); (H.L.)
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Wu Y, Zhang L, Nie L, Zheng Y, Zhu S, Hou J, Li R, Chen G, Tang X, Wang C, Yuan L. Genome-wide analysis of the DREB family genes and functional identification of the involvement of BrDREB2B in abiotic stress in wucai (Brassica campestris L.). BMC Genomics 2022; 23:598. [PMID: 35978316 PMCID: PMC9382803 DOI: 10.1186/s12864-022-08812-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/30/2022] [Indexed: 11/10/2022] Open
Abstract
Dehydration responsive element binding protein (DREB) is a significant transcription factor class known to be implicated in abiotic stresses. In this study, we systematically conducted a genome-wide identification and expression analysis of the DREB gene family, including gene structures, evolutionary relationships, chromosome distribution, conserved domains, and expression patterns. A total of 65 DREB family gene members were identified in Chinese cabbage (Brassica rapa L.) and were classified into five subgroups based on phylogenetic analysis. Through analysis of the conserved domains of BrDREB family genes, only one exon existed in the gene structure. Through the analysis of cis-acting elements, these genes were mainly involved in hormone regulation and adversity stress. In order to identify the function of BrDREB2B, overexpressed transgenic Arabidopsis was constructed. After different stress treatments, the germination rate, root growth, survival rate, and various plant physiological indicators were measured. The results showed that transgenic Arabidopsis thaliana plants overexpressing BrDREB2B exhibited enhanced tolerance to salt, heat and drought stresses. Taken together, our results are the first to report the BrDREB2B gene response to drought and heat stresses in Chinese cabbage and provide a basis for further studies to determine the function of BrDREBs in response to abiotic stresses.
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Affiliation(s)
- Ying Wu
- College of Horticulture, Anhui Agricultural University, 230036, Hefei, Anhui, China
| | - Liting Zhang
- College of Horticulture, Anhui Agricultural University, 230036, Hefei, Anhui, China
| | - Libing Nie
- College of Horticulture and Forestry, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Yushan Zheng
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China
| | - Shidong Zhu
- College of Horticulture, Anhui Agricultural University, 230036, Hefei, Anhui, China.,Wanjiang Vegetable Industrial Technology Institute, 238200, Maanshan, Anhui, China
| | - Jinfeng Hou
- College of Horticulture, Anhui Agricultural University, 230036, Hefei, Anhui, China.,Wanjiang Vegetable Industrial Technology Institute, 238200, Maanshan, Anhui, China
| | - Renjie Li
- College of Horticulture, Anhui Agricultural University, 230036, Hefei, Anhui, China
| | - Guohu Chen
- College of Horticulture, Anhui Agricultural University, 230036, Hefei, Anhui, China.,Wanjiang Vegetable Industrial Technology Institute, 238200, Maanshan, Anhui, China
| | - Xiaoyan Tang
- College of Horticulture, Anhui Agricultural University, 230036, Hefei, Anhui, China.,Wanjiang Vegetable Industrial Technology Institute, 238200, Maanshan, Anhui, China
| | - Chenggang Wang
- College of Horticulture, Anhui Agricultural University, 230036, Hefei, Anhui, China. .,Wanjiang Vegetable Industrial Technology Institute, 238200, Maanshan, Anhui, China.
| | - Lingyun Yuan
- College of Horticulture, Anhui Agricultural University, 230036, Hefei, Anhui, China. .,Wanjiang Vegetable Industrial Technology Institute, 238200, Maanshan, Anhui, China.
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Zhang H, Gong Y, Sun P, Chen S, Ma C. Genome-wide identification of CBF genes and their responses to cold acclimation in Taraxacum kok-saghyz. PeerJ 2022; 10:e13429. [PMID: 35582615 PMCID: PMC9107785 DOI: 10.7717/peerj.13429] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/21/2022] [Indexed: 01/14/2023] Open
Abstract
C-repeat binding factors (CBFs) are transcription factors that are known to play important roles in plant cold acclimation. They are highly conserved in most higher plants. Taraxacum kok-saghyz (TKS) is an herb native to China and Kazakhstan and is well-known for its production of rubber silk with industrial and economic value. To understand cold acclimation mechanisms, we conducted a genome-wide discovery of the CBF family genes in TKS and revealed ten CBF genes. A bioinformatic analysis of the CBF genes was carried out to analyze the phylogenetic relationship, protein conservative motifs, protein physicochemical properties, gene structure, promoter cis-acting elements, and the gene expression patterns under cold acclimation and control conditions. It was found that most of these genes were highly responsive at the late stage of cold acclimation, indicating that they play important roles in the cold acclimation processes of TKS. This study provides a theoretical basis for the study of the molecular functions of the CBF gene family in TKS, and a useful guidance for the genetic improvement of the cold tolerance traits of TKS and other plants, including crops.
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Affiliation(s)
- Haifeng Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- Key Laboratory of Molecular Biology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Yongyong Gong
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- Key Laboratory of Molecular Biology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Peilin Sun
- Key Laboratory of Nuclear Technology Application, Heilongjiang Institute of Atomic Energy, Harbin, China
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
| | - Chunquan Ma
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- Key Laboratory of Molecular Biology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, China
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Riaz MW, Lu J, Shah L, Yang L, Chen C, Mei XD, Xue L, Manzoor MA, Abdullah M, Rehman S, Si H, Ma C. Expansion and Molecular Characterization of AP2/ERF Gene Family in Wheat ( Triticum aestivum L.). Front Genet 2021; 12:632155. [PMID: 33868370 PMCID: PMC8044323 DOI: 10.3389/fgene.2021.632155] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/04/2021] [Indexed: 01/02/2023] Open
Abstract
The AP2/ERF is a large protein family of transcription factors, playing an important role in signal transduction, plant growth, development, and response to various stresses. AP2/ERF super-family is identified and functionalized in a different plant but no comprehensive and systematic analysis in wheat (Triticum aestivum L.) has been reported. However, a genome-wide and functional analysis was performed and identified 322 TaAP2/ERF putative genes from the wheat genome. According to the phylogenetic and structural analysis, TaAP2/ERF genes were divided into 12 subfamilies (Ia, Ib, Ic, IIa, IIb, IIc, IIIa, IIIb, IIIc, IVa, IVb, and IVc). Furthermore, conserved motifs and introns/exons analysis revealed may lead to functional divergence within clades. Cis-Acting analysis indicated that many elements were involved in stress-related and plant development. Chromosomal location showed that 320 AP2/ERF genes were distributed among 21 chromosomes and 2 genes were present in a scaffold. Interspecies microsynteny analysis revealed that maximum orthologous between Arabidopsis, rice followed by wheat. Segment duplication events have contributed to the expansion of the AP2/ERF family and made this family larger than rice and Arabidopsis. Additionally, AP2/ERF genes were differentially expressed in wheat seedlings under the stress treatments of heat, salt, and drought, and expression profiles were verified by qRT-PCR. Remarkably, the RNA-seq data exposed that AP2/ERF gene family might play a vital role in stress-related. Taken together, our findings provided useful and helpful information to understand the molecular mechanism and evolution of the AP2/ERF gene family in wheat.
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Affiliation(s)
- Muhammad Waheed Riaz
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Liaqat Shah
- Department of Botany, Mir Chakar Khan Rind University, Sibi, Pakistan
| | - Liu Yang
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Can Chen
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Xu Dong Mei
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Liu Xue
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | | | - Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Shamsur Rehman
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Hongqi Si
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China.,National United Engineering Laboratory for Crop Stress Resistance Breeding, Hefei, China.,Anhui Key Laboratory of Crop Biology, Hefei, China
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Ahmed S, Rashid MAR, Zafar SA, Azhar MT, Waqas M, Uzair M, Rana IA, Azeem F, Chung G, Ali Z, Atif RM. Genome-wide investigation and expression analysis of APETALA-2 transcription factor subfamily reveals its evolution, expansion and regulatory role in abiotic stress responses in Indica Rice (Oryza sativa L. ssp. indica). Genomics 2020; 113:1029-1043. [PMID: 33157261 DOI: 10.1016/j.ygeno.2020.10.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/08/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022]
Abstract
Rice is an important cereal crop that serves as staple food for more than half of the world population. Abiotic stresses resulting from changing climatic conditions are continuously threating its yield and production. Genes in APETALA-2 (AP2) family encode transcriptional regulators implicated during regulation of developmental processes and abiotic stress responses but their identification and characterization in indica rice was still missing. In this context, twenty-six genes distributed among eleven chromosomes in Indica rice encoding AP2 transcription-factor subfamily were identified and their diverse haplotypes were studied. Phylogenetic analysis of OsAP2 TF family-members grouped them into three clades indicating conservation of clades among cereals. Segmental duplications were observed to be principal route of evolution, supporting the higher positive selection-pressure, which were estimated to be originated about 10.57 to 56.72 million years ago (MYA). Conserved domain analysis and intron-exon distribution pattern of identified OsAP2s revealed their exclusive distribution among the specific clades of the phylogenetic tree. Moreover, the members of osa-miR172 family were also identified potentially targeting four OsAP2 genes. The real-time quantitative expression profiling of OsAP2s under heat stress conditions in contrasting indica rice genotypes revealed the differential expression pattern of OsAP2s (6 genes up-regulated and 4 genes down-regulated) in stress- and genotype-dependent manner. These findings unveiled the evolutionary pathways of AP2-TF in rice, and can help the functional characterization under developmental and stress responses.
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Affiliation(s)
- Sohaib Ahmed
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Muhammad Abdul Rehman Rashid
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming 650500, China; Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China; Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan.
| | - Syed Adeel Zafar
- National key facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; School of Agriculture Sciences, Zhengzhou University, Zhengzhou 450000, China.
| | - Muhammad Waqas
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Muhammad Uzair
- National key facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Iqrar Ahmad Rana
- Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Republic of Korea.
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan 66000, Pakistan.
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad-38040 Pakistan.
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Li W, Chen Y, Ye M, Lu H, Wang D, Chen Q. Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 (CBF/DREB1) protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum. BMC Evol Biol 2020; 20:142. [PMID: 33143637 PMCID: PMC7607821 DOI: 10.1186/s12862-020-01710-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 10/26/2020] [Indexed: 11/10/2022] Open
Abstract
Background Plants are easily affected by temperature variations, and high temperature (heat stress) and low temperature (cold stress) will lead to poor plant development and reduce crop yields. Therefore, it is very important to identify resistance genes for improving the ability of plants to resist heat stress or cold stress by using modern biotechnology. Members of the C-repeat binding factor/Dehydration responsive element-binding 1 (CBF/DREB1) protein family are related to the stress resistance of many plant species. These proteins affect the growth and development of plants and play vital roles during environmental stress (cold, heat, drought, salt, etc.). In this study, we identified CBF/DREB1 genes from 43 plant species (including algae, moss, ferns, gymnosperms, angiosperms) by using bioinformatic methods to clarify the characteristics of the CBF/DREB1 protein family members and their functions in potato under heat and cold stresses. Results In this study, we identified 292 CBF/DREB1 proteins from 43 plant species. However, no CBF/DREB1 protein was found in algae, moss, ferns, or gymnosperms; members of this protein family exist only in angiosperms. Phylogenetic analysis of all the CBF/DREB1 proteins revealed five independent groups. Among them, the genes of group I do not exist in eudicots and are found only in monocots, indicating that these genes have a special effect on monocots. The analysis of motifs, gene duplication events, and the expression data from the PGSC website revealed the gene structures, evolutionary relationships, and expression patterns of the CBF/DREB1 proteins. In addition, analysis of the transcript levels of the 8 CBF/DREB1 genes in potato (Solanum tuberosum) under low-temperature and high-temperature stresses showed that these genes were related to temperature stresses. In particular, the expression levels of StCBF3 and StCBF4 in the leaves, stems, and roots significantly increased under high-temperature conditions, which suggested that StCBF3 and StCBF4 may be closely related to heat tolerance in potato. Conclusion Overall, members of the CBF/DREB1 protein family exist only in angiosperms and plays an important role in the growth and development of plants. In addition, the CBF/DREB1 protein family is related to the heat and cold resistance of potato. Our research revealed the evolution of the CBF/DREB1 family, and is useful for studying the precise functions of the CBF/DREB1 proteins when the plants are developing and are under temperature stress.
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Affiliation(s)
- Wan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yue Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Minghui Ye
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haibin Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Dongdong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Qin Chen
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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9
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Xu L, Feng G, Yang Z, Xu X, Huang L, Yang Q, Zhang X. Genome-wide AP2/ERF gene family analysis reveals the classification, structure, expression profiles and potential function in orchardgrass (Dactylis glomerata). Mol Biol Rep 2020; 47:5225-5241. [PMID: 32577992 DOI: 10.1007/s11033-020-05598-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022]
Abstract
The AP2/ERF transcription factor (TF) family is of great importance in developmental regulation and responses to stress and pathogenic stimuli. Orchardgrass (Dactylis glomerata), a perennial cold-season forage of high quality in the world's temperate zones, contributes to grazing land through mixed sowing with alfalfa (Medicago sativa) and white clover (Trifolium repens). However, little is known about AP2/ERF TFs in orchardgrass. In this study, 193 AP2/ERF genes were classified into five subfamilies and 13 subgroups through phylogenetic analysis. Chromosome structure analysis showed that AP2/ERF family genes in orchardgrass were distributed on seven chromosomes and specific conservative sequences were found in each subgroup. Exon-intron structure and motifs in the same subgroup were almost identical, and the unique motifs contributed to the classification and functional annotation of DgERFs. Expression analysis showed tissue-specific expression of DgERFs in roots and flowers, with most DgERFs widely expressed in roots. The expression levels of each subgroup (subgroups Vc, VIIa, VIIIb, IXa, and XIa) were high at the before-heading and heading stages (BH_DON and H_DON). In addition, 12 DgERFs in various tissues and five DgERFs associated with abiotic stresses were selected for qRT-PCR analysis showed that four dehydration-responsive element binding (DREB) genes and one ERF subfamily gene in orchardgrass were regulated with PEG, heat and salt stresses. DgERF056 belonged to ERF subfamily was involved in the processes of flowering and development stage. This study systematic explored the DgERFs at the genome level for the first time, which lays a foundation for a better understanding of AP2/ERF gene function in Dactylis glomerata and other types of forage.
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Affiliation(s)
- Lei Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,The State Key Laboratory of Grassland Farming Systems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Guangyan Feng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhongfu Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoheng Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qingchuan Yang
- The State Key Laboratory of Grassland Farming Systems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100000, China
| | - Xinquan Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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10
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DREB Genes from Common Bean ( Phaseolus vulgaris L.) Show Broad to Specific Abiotic Stress Responses and Distinct Levels of Nucleotide Diversity. Int J Genomics 2019; 2019:9520642. [PMID: 31249842 PMCID: PMC6525893 DOI: 10.1155/2019/9520642] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/31/2019] [Accepted: 02/19/2019] [Indexed: 12/31/2022] Open
Abstract
We analyzed the nucleotide variability and the expression profile of DREB genes from common bean, a crop of high economic and nutritional value throughout the world but constantly affected by abiotic stresses in cultivation areas. As DREB genes have been constantly associated with abiotic stress tolerance, we systematically categorized 54 putative PvDREB genes distributed in the common bean genome. It involved from AP2 domain location and amino acid conservation analysis (valine at the 14th position) to the identification of conserved motifs within peptide sequences representing six subgroups (A-1 to A-6) of PvDREB proteins. Four genes (PvDREB1F, PvDREB2A, PvDREB5A, and PvDREB6B) were cloned and analyzed for their expression profiles under abiotic stresses and their nucleotide and amino acid diversity in genotypes of Andean and Mesoamerican origin, showing distinct patterns of expression and nucleotide variability. PvDREB1F and PvDREB5A showed high relative inducibilities when genotypes of common bean were submitted to stresses by drought, salt, cold, and ABA. PvDREB2A inducibility was predominantly localized to the stem under drought. PvDREB6B was previously described as an A-2 (DREB2) gene, but a detailed phylogenetic analysis and its expression profile clearly indicated it belongs to group A-6. PvDREB6B was found as a cold- and dehydration-responsive gene, mainly in leaves. Interestingly, PvDREB6B also showed a high nucleotide and amino acid diversity within its coding region, in comparison to the others, implicating in several nonsynonymous amino acid substitutions between Andean and Mesoamerican genotypes. The expression patterns and nucleotide diversity of each DREB found in this study revealed fundamental characteristics for further research aimed at understanding the molecular mechanisms associated with drought, salt, and cold tolerance in common bean, which could be performed based on association mapping and functional analyses.
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11
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Xiang L, Liu C, Luo J, He L, Deng Y, Yuan J, Wu C, Cai Y. A tuber mustard AP2/ERF transcription factor gene, BjABR1, functioning in abscisic acid and abiotic stress responses, and evolutionary trajectory of the ABR1 homologous genes in Brassica species. PeerJ 2018; 6:e6071. [PMID: 30581669 PMCID: PMC6294115 DOI: 10.7717/peerj.6071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/02/2018] [Indexed: 01/05/2023] Open
Abstract
The AP2/ERF superfamily of transcription factors is one of the largest transcription factor families in plants and plays an important role in plant development processes and stress responses. In this study, BjABR1, an AP2/ERF superfamily gene, from tuber mustard (Brassica juncea var. tumida Tsen et Lee), sharing high amino acid sequence similarity with the AtABR1 (Arabidopsis thaliana AP2-like abscisic acid repressor 1) gene, were performed functional research, and the ABR1 homologous genes in Brassica species were identified and performed phylogenetic analysis. The promoter sequence of BjABR1 contained many phytohormone- and stress-related cis-elements; ABA (abscisic acid) and abiotic stresses can induce BjABR1 expression in tuber mustard; overexpression of BjABR1 in Arabidopsis can alleviate plant sensitivity to ABA and salt and osmotic stresses, and the alleviation may be due to changes in stress/ABA-induced gene expression. These results indicated that BjABR1 functions in ABA and abiotic stress responses. By BLAST searches against the genome database of five Brassica species (three diploids, B. rapa, B. nigra, and B. oleracea, and two allotetraploid, B. juncea and B. napus) using the protein sequence of AtABR1, 3, 3, 3, 6, and 5 ABR1 homologous genes in B. nigra, B. rapa, B. oleracea, B. juncea, and B. napus were identified, respectively, and they shared high sequence similarity. By sequence analysis, annotation mistakes of the protein-coding regions of two ABR1 homologous genes, GSBRNA2T00134741001 and BjuB007684, were found and corrected. Then, the evolution analysis of these ABR1 homologous genes showed that the ancestor of the three diploid species had three ABR1 homologous genes and each diploid inherited all the three genes from their ancestor; then, allotetraploid B. juncea inherited all the six genes from B. rapa and B. nigra with no gene lost, while allotetraploid B. napus inherited all the three genes from B. oleracea and two genes from B. rapa with one gene lost, indicating that ABR1 homologous genes possessed greater hereditary conservation in Brassica species. The ABR1 homologous genes between B. rapa and B. oleracea shared much higher sequence similarity compared to that of B. nigra in diploid species, indicating that ABR1 homologous genes in B. nigra had experienced more rapid evolution, and B. rapa and B. oleracea may share closer relationship compared to B. nigra. Moreover, the spatial and temporal expression analysis of six ABR1 homologous genes of tuber mustard showed that they possessed different expression models. These results imply that ABR1 homologous genes are important to Brassica plants, and they may possess similar function in ABA and abiotic stress responses but play a role in different tissues and growing stages of plant. This study will provide the foundation to the functional research of ABR1 homologous genes in the Brassica species and help to reveal and understand the evolution mechanisms of Brassica species.
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Affiliation(s)
- Liuxin Xiang
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Chao Liu
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Jingzhi Luo
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Lin He
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Yushan Deng
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Jie Yuan
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Chaofeng Wu
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Yingfan Cai
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Kaifeng, Henan, China
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12
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Najafi S, Sorkheh K, Nasernakhaei F. Characterization of the APETALA2/Ethylene-responsive factor (AP2/ERF) transcription factor family in sunflower. Sci Rep 2018; 8:11576. [PMID: 30068961 PMCID: PMC6070487 DOI: 10.1038/s41598-018-29526-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/12/2018] [Indexed: 01/09/2023] Open
Abstract
One of the most prominent families of genes in plants is the AP2/ERF which play an important role in regulating plant growth and responses to various stresses. In this research, a genome-wide survey was conducted to recognize the AP2/ERF genes in sunflower (Helianthus annuus L.), and a total of 288 HaAP2/ERF was obtained. Phylogenetic analysis divided them into four sub-families, including 248 ERF, 4 RAV and 35 AP2, and one subgroup of the Soloist family. Localization of chromosome, gene structure, the conserved motif, gene ontology, interaction networks, homology modeling, the modeling of cis-regulatory elements and the analysis of events in the duplication of genes were carried out for HaAP2/ERF genes. Finally, 9AP2/ERF genes were chosen to confirm the gene expression of the selected genes in leaf and root tissues in various abiotic stress conditions by qPCR. The results confirmed that AP2/ERFs genes could effectively resist abiotic stress. Also, proline content was studied under drought, salinity, cold and heat stress. The results indicated that proline was increased under abiotic stress. This research has been done for the first time to determine the HaAP2/ERF family, which prepared valuable data for the evolutionary and practical research regarding AP2/ERF in sunflower.
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Affiliation(s)
- Somayeh Najafi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P. O. Box 61355/144, Ahvaz, Iran
| | - Karim Sorkheh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P. O. Box 61355/144, Ahvaz, Iran.
| | - Fatemeh Nasernakhaei
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P. O. Box 61355/144, Ahvaz, Iran
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13
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Rurek M, Czołpińska M, Pawłowski TA, Staszak AM, Nowak W, Krzesiński W, Spiżewski T. Mitochondrial Biogenesis in Diverse Cauliflower Cultivars under Mild and Severe Drought. Impaired Coordination of Selected Transcript and Proteomic Responses, and Regulation of Various Multifunctional Proteins. Int J Mol Sci 2018; 19:ijms19041130. [PMID: 29642585 PMCID: PMC5979313 DOI: 10.3390/ijms19041130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/09/2018] [Accepted: 04/04/2018] [Indexed: 12/25/2022] Open
Abstract
Mitochondrial responses under drought within Brassica genus are poorly understood. The main goal of this study was to investigate mitochondrial biogenesis of three cauliflower (Brassica oleracea var. botrytis) cultivars with varying drought tolerance. Diverse quantitative changes (decreases in abundance mostly) in the mitochondrial proteome were assessed by two-dimensional gel electrophoresis (2D PAGE) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Respiratory (e.g., complex II, IV (CII, CIV) and ATP synthase subunits), transporter (including diverse porin isoforms) and matrix multifunctional proteins (e.g., components of RNA editing machinery) were diversely affected in their abundance under two drought levels. Western immunoassays showed additional cultivar-specific responses of selected mitochondrial proteins. Dehydrin-related tryptic peptides (found in several 2D spots) immunopositive with dehydrin-specific antisera highlighted the relevance of mitochondrial dehydrin-like proteins for the drought response. The abundance of selected mRNAs participating in drought response was also determined. We conclude that mitochondrial biogenesis was strongly, but diversely affected in various cauliflower cultivars, and associated with drought tolerance at the proteomic and functional levels. However, discussed alternative oxidase (AOX) regulation at the RNA and protein level were largely uncoordinated due to the altered availability of transcripts for translation, mRNA/ribosome interactions, and/or miRNA impact on transcript abundance and translation.
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Affiliation(s)
- Michał Rurek
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | - Magdalena Czołpińska
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | | | - Aleksandra Maria Staszak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland.
- Present address: Department of Plant Physiology, Institute of Biology, Faculty of Biology and Chemistry, University of Białystok, Ciołkowskiego 1J, 15-245 Białystok, Poland.
| | - Witold Nowak
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | - Włodzimierz Krzesiński
- Department of Vegetable Crops, Poznan University of Life Sciences, Dąbrowskiego 159, 60-594 Poznań, Poland.
| | - Tomasz Spiżewski
- Department of Vegetable Crops, Poznan University of Life Sciences, Dąbrowskiego 159, 60-594 Poznań, Poland.
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14
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Abdul Kayum M, Nath UK, Park JI, Biswas MK, Choi EK, Song JY, Kim HT, Nou IS. Genome-Wide Identification, Characterization, and Expression Profiling of Glutathione S-Transferase (GST) Family in Pumpkin Reveals Likely Role in Cold-Stress Tolerance. Genes (Basel) 2018; 9:genes9020084. [PMID: 29439434 PMCID: PMC5852580 DOI: 10.3390/genes9020084] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 11/16/2022] Open
Abstract
Plant growth and development can be adversely affected by cold stress, limiting productivity. The glutathione S-transferase (GST) family comprises important detoxifying enzymes, which play major roles in biotic and abiotic stress responses by reducing the oxidative damage caused by reactive oxygen species. Pumpkins (Cucurbitamaxima) are widely grown, economically important, and nutritious; however, their yield can be severely affected by cold stress. The identification of putative candidate genes responsible for cold-stress tolerance, including the GST family genes, is therefore vital. For the first time, we identified 32 C. maxima GST (CmaGST) genes using a combination of bioinformatics approaches and characterized them by expression profiling. These CmaGST genes represent seven of the 14 known classes of plant GSTs, with 18 CmaGSTs categorized into the tau class. The CmaGSTs were distributed across 13 of pumpkin's 20 chromosomes, with the highest numbers found on chromosomes 4 and 6. The large number of CmaGST genes resulted from gene duplication; 11 and 5 pairs of CmaGST genes were segmental- and tandem-duplicated, respectively. In addition, all CmaGST genes showed organ-specific expression. The expression of the putative GST genes in pumpkin was examined under cold stress in two lines with contrasting cold tolerance: cold-tolerant CP-1 (C. maxima) and cold-susceptible EP-1 (Cucurbita moschata). Seven genes (CmaGSTU3, CmaGSTU7, CmaGSTU8, CmaGSTU9, CmaGSTU11, CmaGSTU12, and CmaGSTU14) were highly expressed in the cold-tolerant line and are putative candidates for use in breeding cold-tolerant crop varieties. These results increase our understanding of the cold-stress-related functions of the GST family, as well as potentially enhancing pumpkin breeding programs.
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Affiliation(s)
- Md Abdul Kayum
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
| | - Manosh Kumar Biswas
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
| | - Eung Kyoo Choi
- Jangchun Seed Company, 72 Sideok-ro, Yakmokmyeon, Chilgok-gun, Kyeongsangbuk-do 39821, Korea.
| | - Jae-Young Song
- National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea.
| | - Hoy-Taek Kim
- University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, Korea.
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15
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Gumi AM, Guha PK, Mazumder A, Jayaswal P, Mondal TK. Characterization of OglDREB2A gene from African rice ( Oryza glaberrima), comparative analysis and its transcriptional regulation under salinity stress. 3 Biotech 2018; 8:91. [PMID: 29430353 PMCID: PMC5796934 DOI: 10.1007/s13205-018-1098-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 01/05/2018] [Indexed: 01/17/2023] Open
Abstract
In this study, AP2 DNA-binding domain-containing transcription factor, OglDREB2A, was cloned from the African rice (Oryza glaberrima) and compared with 3000 rice genotypes. Further, the phylogenetic and various structural analysis was performed using in silico approaches. Further, to understand its allelic variation in rice, SNPs and indels were detected among the 3000 rice genotypes which indicated that while coding region is highly conserved, yet noncoding regions such as UTR and intron contained most of the variation. Phylogenetic analysis of the OglDREB2A sequence in different Oryza as well as in diverse eudicot species revealed that DREB from various Oryza species were diversed much earlier than other genes. Further, structural features and in silico analyses provided insights into different properties of OglDREB2A protein. The neutrality test on the coding region of OglDREB2A from different genotypes of O. glaberrima showed the lack of selection in this gene. Among the different developmental stages, it was upregulated at tillering and flag leaf under salinity treatment indicating its positive role in seedling and reproductive stage tolerance. Real-time PCR analysis also indicated the conserve expression pattern of this gene under salinity stress across the three different Oryza species having different degree of salinity tolerance.
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Affiliation(s)
- Abubakar Mohammad Gumi
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012 India
- Present Address: Department of Biological Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Pritam Kanti Guha
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012 India
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, IARI, New Delhi, 110012 India
| | - Abhishek Mazumder
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, IARI, New Delhi, 110012 India
| | - Pawan Jayaswal
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, IARI, New Delhi, 110012 India
| | - Tapan Kumar Mondal
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012 India
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, IARI, New Delhi, 110012 India
- Present Address: Department of Biological Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
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16
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Wei Y, Chang Y, Zeng H, Liu G, He C, Shi H. RAV transcription factors are essential for disease resistance against cassava bacterial blight via activation of melatonin biosynthesis genes. J Pineal Res 2018; 64. [PMID: 29151275 DOI: 10.1111/jpi.12454] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/30/2017] [Indexed: 12/24/2022]
Abstract
With 1 AP2 domain and 1 B3 domain, 7 MeRAVs in apetala2/ethylene response factor (AP2/ERF) gene family have been identified in cassava. However, the in vivo roles of these remain unknown. Gene expression assays showed that the transcripts of MeRAVs were commonly regulated after Xanthomonas axonopodis pv manihotis (Xam) and MeRAVs were specifically located in plant cell nuclei. Through virus-induced gene silencing (VIGS) in cassava, we found that MeRAV1 and MeRAV2 are essential for plant disease resistance against cassava bacterial blight, as shown by the bacterial propagation of Xam in plant leaves. Through VIGS in cassava leaves and overexpression in cassava leave protoplasts, we found that MeRAV1 and MeRAV2 positively regulated melatonin biosynthesis genes and the endogenous melatonin level. Further investigation showed that MeRAV1 and MeRAV2 are direct transcriptional activators of 3 melatonin biosynthesis genes in cassava, as evidenced by chromatin immunoprecipitation-PCR in cassava leaf protoplasts and electrophoretic mobility shift assay. Moreover, cassava melatonin biosynthesis genes also positively regulated plant disease resistance. Taken together, this study identified MeRAV1 and MeRAV2 as common and upstream transcription factors of melatonin synthesis genes in cassava and revealed a model of MeRAV1 and MeRAV2-melatonin biosynthesis genes-melatonin level in plant disease resistance against cassava bacterial blight.
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Affiliation(s)
- Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan province, China
| | - Yanli Chang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan province, China
| | - Hongqiu Zeng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan province, China
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan province, China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan province, China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan province, China
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17
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Hoang XLT, Nhi DNH, Thu NBA, Thao NP, Tran LSP. Transcription Factors and Their Roles in Signal Transduction in Plants under Abiotic Stresses. Curr Genomics 2017. [PMID: 29204078 DOI: 10.2174/1389101918666170227150057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
In agricultural production, abiotic stresses are known as the main disturbance leading to negative impacts on crop performance. Research on elucidating plant defense mechanisms against the stresses at molecular level has been addressed for years in order to identify the major contributors in boosting the plant tolerance ability. From literature, numerous genes from different species, and from both functional and regulatory gene categories, have been suggested to be on the list of potential candidates for genetic engineering. Noticeably, enhancement of plant stress tolerance by manipulating expression of Transcription Factors (TFs) encoding genes has emerged as a popular approach since most of them are early stress-responsive genes and control the expression of a set of downstream target genes. Consequently, there is a higher chance to generate novel cultivars with better tolerance to either single or multiple stresses. Perhaps, the difficult task when deploying this approach is selecting appropriate gene(s) for manipulation. In this review, on the basis of the current findings from molecular and post-genomic studies, our interest is to highlight the current understanding of the roles of TFs in signal transduction and mediating plant responses towards abiotic stressors. Furthermore, interactions among TFs within the stress-responsive network will be discussed. The last section will be reserved for discussing the potential applications of TFs for stress tolerance improvement in plants.
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Affiliation(s)
- Xuan Lan Thi Hoang
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Du Ngoc Hai Nhi
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Nguyen Binh Anh Thu
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Nguyen Phuong Thao
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Lam-Son Phan Tran
- Plant Abiotic Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
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18
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Hoang XLT, Nhi DNH, Thu NBA, Thao NP, Tran LSP. Transcription Factors and Their Roles in Signal Transduction in Plants under Abiotic Stresses. Curr Genomics 2017; 18:483-497. [PMID: 29204078 PMCID: PMC5684650 DOI: 10.2174/1389202918666170227150057] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/07/2016] [Accepted: 10/15/2016] [Indexed: 12/15/2022] Open
Abstract
In agricultural production, abiotic stresses are known as the main disturbance leading to negative impacts on crop performance. Research on elucidating plant defense mechanisms against the stresses at molecular level has been addressed for years in order to identify the major contributors in boosting the plant tolerance ability. From literature, numerous genes from different species, and from both functional and regulatory gene categories, have been suggested to be on the list of potential candidates for genetic engineering. Noticeably, enhancement of plant stress tolerance by manipulating expression of Transcription Factors (TFs) encoding genes has emerged as a popular approach since most of them are early stress-responsive genes and control the expression of a set of downstream target genes. Consequently, there is a higher chance to generate novel cultivars with better tolerance to either single or multiple stresses. Perhaps, the difficult task when deploying this approach is selecting appropriate gene(s) for manipulation. In this review, on the basis of the current findings from molecular and post-genomic studies, our interest is to highlight the current understanding of the roles of TFs in signal transduction and mediating plant responses towards abiotic stressors. Furthermore, interactions among TFs within the stress-responsive network will be discussed. The last section will be reserved for discussing the potential applications of TFs for stress tolerance improvement in plants.
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Affiliation(s)
- Xuan Lan Thi Hoang
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Du Ngoc Hai Nhi
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Nguyen Binh Anh Thu
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Nguyen Phuong Thao
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Lam-Son Phan Tran
- Plant Abiotic Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
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Xing L, Di Z, Yang W, Liu J, Li M, Wang X, Cui C, Wang X, Wang X, Zhang R, Xiao J, Cao A. Overexpression of ERF1-V from Haynaldia villosa Can Enhance the Resistance of Wheat to Powdery Mildew and Increase the Tolerance to Salt and Drought Stresses. FRONTIERS IN PLANT SCIENCE 2017; 8:1948. [PMID: 29238352 PMCID: PMC5712803 DOI: 10.3389/fpls.2017.01948] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/30/2017] [Indexed: 05/04/2023]
Abstract
The APETALA 2/Ethylene-responsive element binding factor (AP2/ERF) transcription factor gene family is widely involved in the biotic and abiotic stress regulation. Haynaldia villosa (VV, 2n = 14), a wild species of wheat, is a potential gene pool for wheat improvement. H. villosa confers high resistance to several wheat diseases and high tolerance to some abiotic stress. In this study, ERF1-V, an ethylene-responsive element-binding factor gene of the AP2/ERF transcription factor gene family from wild H. villosa, was cloned and characterized. Sequence and phylogenetic analysis showed that ERF1-V is a deduced B2 type ERF gene. ERF1-V was first identified as a Blumeria graminis f. sp. tritici (Bgt) up-regulated gene, and later found to be induced by drought, salt and cold stresses. In responses to hormones, ERF1-V was up-regulated by ethylene and abscisic acid, but down-regulated by salicylic acid and jasmonic acid. Over expression of ERF1-V in wheat could improve resistance to powdery mildew, salt and drought stress. Chlorophyll content, malondialdehyde content, superoxide dismutase and peroxidase activity were significantly differences between the recipient Yangmai158 and the transgenic plants following salt treatment. Furthermore, the expression levels of some stress responsive genes were differences after drought or salt treatments. Although ERF1-V was activated by the constitutive promoter, the agronomic traits, including flowering time, plant height, effective tiller number, spikelet number per spike and grain size, did not changed significantly. ERF1-V is a valuable gene for wheat improvement by genetic engineering.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Aizhong Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
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20
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Song GQ, Gao X. Transcriptomic changes reveal gene networks responding to the overexpression of a blueberry DWARF AND DELAYED FLOWERING 1 gene in transgenic blueberry plants. BMC PLANT BIOLOGY 2017; 17:106. [PMID: 28629320 PMCID: PMC5477172 DOI: 10.1186/s12870-017-1053-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 06/06/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Constitutive expression of the CBF/DREB1 for increasing freezing tolerance in woody plants is often associated with other phenotypic changes including dwarf plant and delayed flowering. These phenotypic changes have been observed when Arabidopsis DWARF AND DELAYED FLOWERING 1 (DDF1) was overexpressed in A. thaliana plants. To date, the DDF1 orthologues have not been studied in woody plants. The aim of this study is to investigate transcriptomic responses to the overexpression of blueberry (Vaccinium corymbosum) DDF1 (herein, VcDDF1-OX). RESULTS The VcDDF1-OX resulted in enhanced freezing tolerance in tetraploid blueberry plants and did not result in significant changes in plant size, chilling requirement, and flowering time. Comparative transcriptome analysis of transgenic 'Legacy-VcDDF1-OX' plants containing an overexpressed VcDDF1 with non-transgenic highbush blueberry 'Legacy' plants revealed the VcDDF1-OX derived differentially expressed (DE) genes and transcripts in the pathways of cold-response, plant flowering, DELLA proteins, and plant phytohormones. The increase in freezing tolerance was associated to the expression of cold-regulated genes (CORs) and the ethylene pathway genes. The unchanged plant size, dormancy and flowering were due to the minimal effect of the VcDDF1-OX on the expression of DELLA proteins, flowering pathway genes, and the other phytohormone genes related to plant growth and development. The DE genes in auxin and cytokinin pathways suggest that the VcDDF1-OX has also altered plant tolerance to drought and high salinity. CONCLUSION A DDF1 orthologue in blueberry functioned differently from the DDF1 reported in Arabidopsis. The overexpression of VcDDF1 or its orthologues is a new approach to increase freezing tolerance of deciduous woody plant species with no obvious effect on plant size and plant flowering time.
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Affiliation(s)
- Guo-qing Song
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Xuan Gao
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
- Key Laboratory for the Conservation and Utilization of Important Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
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Nguyen HC, Cao PB, San Clemente H, Ployet R, Mounet F, Ladouce N, Harvengt L, Marque C, Teulieres C. Special trends in CBF and DREB2 groups in Eucalyptus gunnii vs Eucalyptus grandis suggest that CBF are master players in the trade-off between growth and stress resistance. PHYSIOLOGIA PLANTARUM 2017; 159:445-467. [PMID: 27861954 DOI: 10.1111/ppl.12529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
Annotation of the Eucalyptus grandis genome showed a large amplification of the dehydration-responsive element binding 1/C-repeat binding factor (DREB1/CBF) group without recent DREB2 gene duplication compared with other plant species. The present annotation of the CBF and DREB2 genes from a draft of the Eucalyptus gunnii genome sequence reveals at least one additional CBF copy in the E. gunnii genome compared with E. grandis, suggesting that this group is still evolving, unlike the DREB2 group. This study aims to investigate the redundancy/neo- or sub-functionalization of the duplicates and the relative involvement of the two groups in abiotic stress responses in both E. grandis and E. gunnii (lower growth but higher cold resistance). A comprehensive transcriptional analysis using high-throughput quantitative real-time polymerase chain reaction (qRT-PCR) was performed on leaves, stems and roots from the two Eucalyptus species after cold, heat or drought treatment. A large CBF cluster accounted for most of the cold response in all the organs, whereas heat and drought responses mainly involved a small CBF cluster and the DREB2 genes. In addition, CBF putative target genes, known to be involved in plant tolerance and development, were found to be cold-regulated. The higher transcript amounts of both the CBF and target genes in the cold tolerant E. gunnii contrasted with the higher CBF induction rates in the fast growing E. grandis. Altogether, the present results, in agreement with previous data about Eucalyptus transgenic lines over-expressing CBF, suggest that these factors, which promote both stress protection and growth limitation, participate in the trade-off between growth and resistance in this woody species.
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Affiliation(s)
- Hong C Nguyen
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Phi B Cao
- Hung Vuong University, Nong Trang Ward, Viettri City, Vietnam
| | - Hélène San Clemente
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Raphaël Ployet
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Fabien Mounet
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Nathalie Ladouce
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Luc Harvengt
- FCBA Biotechnology and Advanced Silviculture Dept, Genetics & Biotechnology Team, Cestas, France
| | - Christiane Marque
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Chantal Teulieres
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
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Kavas M, Kızıldoğan AK, Abanoz B. Comparative genome-wide phylogenetic and expression analysis of SBP genes from potato (Solanum tuberosum). Comput Biol Chem 2017; 67:131-140. [PMID: 28081487 DOI: 10.1016/j.compbiolchem.2017.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/27/2016] [Accepted: 01/03/2017] [Indexed: 11/28/2022]
Abstract
Flowering time is a very important phase in transition to reproductive stage of life in higher plants. SQUAMOSA promoter-binding protein (SBP) gene family encodes plant-specific transcription factors that are involved in regulation of several developmental processes, especially flowering. Although SBP-box genes have been identified in different plants, there have been no study indicating the regulatory effect of SBP box in potato flowering. Here, we report for the first time the identification and characterization of SBP-box transcription factors as well as determination of expression level of SBP-box genes in Solanum tuberosum L. an important crop worldwide. Fifteen different SBP-box transcription factor genes were identified in potato genome. They were found to be distributed in nine chromosomes and eight of them included miR156 and miRNA157 target sites. Characterization of amino acid sequences were performed and protein interactions were predicted. In addition, expression levels of five S. tuberosum SBP-box genes were analysed by both in silico and qRT-PCR. All these results provide a better understanding of functional role of SBP-box gene family members in flowering time in potato.
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Affiliation(s)
- Musa Kavas
- Ondokuz Mayıs University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey.
| | - Aslıhan Kurt Kızıldoğan
- Ondokuz Mayıs University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey
| | - Büşra Abanoz
- Ondokuz Mayıs University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey
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Li H, Wang Y, Wu M, Li L, Li C, Han Z, Yuan J, Chen C, Song W, Wang C. Genome-Wide Identification of AP2/ERF Transcription Factors in Cauliflower and Expression Profiling of the ERF Family under Salt and Drought Stresses. FRONTIERS IN PLANT SCIENCE 2017; 8:946. [PMID: 28642765 PMCID: PMC5462956 DOI: 10.3389/fpls.2017.00946] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/22/2017] [Indexed: 05/18/2023]
Abstract
The AP2/ERF transcription factors (TFs) comprise one of the largest gene superfamilies in plants. These TFs perform vital roles in plant growth, development, and responses to biotic and abiotic stresses. In this study, 171 AP2/ERF TFs were identified in cauliflower (Brassica oleracea L. var. botrytis), one of the most important horticultural crops in Brassica. Among these TFs, 15, 9, and 1 TFs were classified into the AP2, RAV, and Soloist family, respectively. The other 146 TFs belong to ERF family, which were further divided into the ERF and DREB subfamilies. The ERF subfamily contained 91 TFs, while the DREB subfamily contained 55 TFs. Phylogenetic analysis results indicated that the AP2/ERF TFs can be classified into 13 groups, in which 25 conserved motifs were confirmed. Some motifs were group- or subgroup- specific, implying that they are significant to the functions of the AP2/ERF TFs of these clades. In addition, 35 AP2/ERF TFs from the 13 groups were selected randomly and then used for expression pattern analysis under salt and drought stresses. The majority of these AP2/ERF TFs exhibited positive responses to these stress conditions. In specific, Bra-botrytis-ERF054a, Bra-botrytis-ERF056, and Bra-botrytis-CRF2a demonstrated rapid responses. By contrast, six AP2/ERF TFs were showed to delay responses to both stresses. The AP2/ERF TFs exhibiting specific expression patterns under salt or drought stresses were also confirmed. Further functional analysis indicated that ectopic overexpression of Bra-botrytis-ERF056 could increase tolerance to both salt and drought treatments. These findings provide new insights into the AP2/ERF TFs present in cauliflower, and offer candidate AP2/ERF TFs for further studies on their roles in salt and drought stress tolerance.
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Affiliation(s)
- Hui Li
- College of Life Sciences, Nankai UniversityTianjin, China
- College of Horticulture and Landscape, Tianjin Agricultural UniversityTianjin, China
| | - Yu Wang
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Mei Wu
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Lihong Li
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Cong Li
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Zhanpin Han
- College of Horticulture and Landscape, Tianjin Agricultural UniversityTianjin, China
| | - Jiye Yuan
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Chengbin Chen
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Wenqin Song
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Chunguo Wang
- College of Life Sciences, Nankai UniversityTianjin, China
- *Correspondence: Chunguo Wang
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RETRACTED ARTICLE: Cadmium permeates through calcium channels and activates transcriptomic complexity in wheat roots in response to cadmium stress. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0488-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Bahieldin A, Atef A, Edris S, Gadalla NO, Ali HM, Hassan SM, Al-Kordy MA, Ramadan AM, Makki RM, Al-Hajar ASM, El-Domyati FM. Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant. BMC PLANT BIOLOGY 2016; 16:216. [PMID: 27716054 PMCID: PMC5053207 DOI: 10.1186/s12870-016-0908-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 09/27/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND The ultimate goal of this work was to detect the role of transcription factors (TFs) concordantly expressed with genes related to programmed cell death (PCD) during PCD and salt stress. This work was based on the hypothesis that TFs and their driven genes likely co-express under different stimuli. The conserved superfamily ethylene responsive factor (AP2/ERF) draw attention of the present study as it participates in the response to biotic and abiotic stimuli as well as to program cell death (PCD). RESULTS RNA-Seq analysis was done for tobacco (N. benthamiana) leaves exposed to oxalic acid (OA) at 20 mM for 0, 2, 6, 12 and 24 h to induce PCD. Genes up-regulated after 2 h of OA treatment with known function during PCD were utilized as landmarks to select TFs with concordant expression. Knockdown mutants of these TFs were generated in tobacco via virus induced gene silencing (VIGS) in order to detect their roles during PCD. Based on the results of PCD assay, knockout (KO) T-DNA insertion mutants of Arabidopsis as well as over-expression lines of two selected TFs, namely ERF109 and TFIID5, analogs to those in tobacco, were tested under salt stress (0, 100, 150 and 200 mM NaCl). CONCLUSIONS Results of knockdown mutant tobacco cells confirmed the influence of these two TFs during PCD. Knockout insertion mutants and over-expression lines indicated the role of ERF109 in conferring salt tolerance in Arabidopsis.
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Affiliation(s)
- Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Ahmed Atef
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Nour O. Gadalla
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Hani M. Ali
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Sabah M. Hassan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Magdy A. Al-Kordy
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Ahmed M. Ramadan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Rania M. Makki
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Abdulrahman S. M. Al-Hajar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Fotouh M. El-Domyati
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
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Han J, Thamilarasan SK, Natarajan S, Park JI, Chung MY, Nou IS. De Novo Assembly and Transcriptome Analysis of Bulb Onion (Allium cepa L.) during Cold Acclimation Using Contrasting Genotypes. PLoS One 2016; 11:e0161987. [PMID: 27627679 PMCID: PMC5023330 DOI: 10.1371/journal.pone.0161987] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/16/2016] [Indexed: 12/03/2022] Open
Abstract
Bulb onion (Allium cepa) is the second most widely cultivated and consumed vegetable crop in the world. During winter, cold injury can limit the production of bulb onion. Genomic resources available for bulb onion are still very limited. To date, no studies on heritably durable cold and freezing tolerance have been carried out in bulb onion genotypes. We applied high-throughput sequencing technology to cold (2°C), freezing (-5 and -15°C), and control (25°C)-treated samples of cold tolerant (CT) and cold susceptible (CS) genotypes of A. cepa lines. A total of 452 million paired-end reads were de novo assembled into 54,047 genes with an average length of 1,331 bp. Based on similarity searches, these genes were aligned with entries in the public non-redundant (nr) database, as well as KEGG and COG database. Differentially expressed genes (DEGs) were identified using log10 values with the FPKM method. Among 5,167DEGs, 491 genes were differentially expressed at freezing temperature compared to the control temperature in both CT and CS libraries. The DEG results were validated with qRT-PCR. We performed GO and KEGG pathway enrichment analyses of all DEGs and iPath interactive analysis found 31 pathways including those related to metabolism of carbohydrate, nucleotide, energy, cofactors and vitamins, other amino acids and xenobiotics biodegradation. Furthermore, a large number of molecular markers were identified from the assembled genes, including simple sequence repeats (SSRs) 4,437 and SNP substitutions of transition and transversion types of CT and CS. Our study is the first to provide a transcriptome sequence resource for Allium spp. with regard to cold and freezing stress. We identified a large set of genes and determined their DEG profiles under cold and freezing conditions using two different genotypes. These data represent a valuable resource for genetic and genomic studies of Allium spp.
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Affiliation(s)
- Jeongsukhyeon Han
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | | | - Sathishkumar Natarajan
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
- * E-mail:
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27
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Guo B, Wei Y, Xu R, Lin S, Luan H, Lv C, Zhang X, Song X, Xu R. Genome-Wide Analysis of APETALA2/Ethylene-Responsive Factor (AP2/ERF) Gene Family in Barley (Hordeum vulgare L.). PLoS One 2016; 11:e0161322. [PMID: 27598245 PMCID: PMC5012588 DOI: 10.1371/journal.pone.0161322] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 08/03/2016] [Indexed: 12/29/2022] Open
Abstract
APETALA2/Ethylene-Responsive Factor (AP2/ERF) gene family is plant specific transcription factor. It plays critical roles in development process, tolerance to biotic and abiotic stresses, and responses to plant hormones. However, limited data are available on the contributions of AP2/ERF gene family in barley (Hordeum vulgare L.). In the present study, 121 HvAP2/ERF genes in barley were identified by using bioinformatics methods. A total of 118 HvAP2/ERF (97.5%) genes were located on seven chromosomes. According to phylogenetic classification of AP2/ERF family in Arabidopsis, HvAP2/ERF proteins were divided into AP2 (APETALA2), RAV (Related to ABI3/VP), DREB (dehydration responsive element binding), ERF (ethylene responsive factors) and soloist sub families. The analysis of duplication events indicated that tandem repeat and segmental duplication contributed to the expansion of the AP2/ERF family in barley. HvDREB1s/2s genes displayed various expression patterns under abiotic stress and phytohormone. Taken together, the data generated in this study will be useful for genome-wide analysis to determine the precise role of the HvAP2/ERF gene during barley development, abiotic stress and phytohormone responses with the ultimate goal of improving crop production.
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Affiliation(s)
- Baojian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yafeng Wei
- JiangSu Yanjiang Institute of Agricultural Sciences, Nantong, China
| | - Ruibin Xu
- College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, China
| | - Shen Lin
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Haiye Luan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Chao Lv
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Xinzhong Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Xiyun Song
- College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, China
| | - Rugen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
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Glutathione Transferases Superfamily: Cold-Inducible Expression of Distinct GST Genes in Brassica oleracea. Int J Mol Sci 2016; 17:ijms17081211. [PMID: 27472324 PMCID: PMC5000609 DOI: 10.3390/ijms17081211] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 02/08/2023] Open
Abstract
Plants, as sessile organisms, can suffer serious growth and developmental consequences under cold stress conditions. Glutathione transferases (GSTs, EC 2.5.1.18) are ubiquitous and multifunctional conjugating proteins, which play a major role in stress responses by preventing oxidative damage by reactive oxygen species (ROS). Currently, understanding of their function(s) during different biochemical and signaling pathways under cold stress condition remain unclear. In this study, using combined computational strategy, we identified 65 Brassica oleracea glutathione transferases (BoGST) and characterized them based on evolutionary analysis into 11 classes. Inter-species and intra-species duplication was evident between BoGSTs and Arabidopsis GSTs. Based on localization analyses, we propose possible pathways in which GST genes are involved during cold stress. Further, expression analysis of the predicted putative functions for GST genes were investigated in two cold contrasting genotypes (cold tolerance and susceptible) under cold condition, most of these genes were highly expressed at 6 h and 1 h in the cold tolerant (CT) and cold susceptible (CS) lines, respectively. Overall, BoGSTU19, BoGSTU24, BoGSTF10 are candidate genes highly expressed in B. oleracea. Further investigation of GST superfamily in B. oleracea will aid in understanding complex mechanism underlying cold tolerance in plants.
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Shanmugam A, Thamilarasan SK, Park JI, Jung MY, Nou IS. Characterization and abiotic stress-responsive expression analysis of SGT1 genes in Brassica oleracea. Genome 2016; 59:243-51. [PMID: 26966988 DOI: 10.1139/gen-2015-0128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
SGT1 genes are involved in enhancing plant responses to various biotic and abiotic stresses. Brassica oleracea is known to contain two types of SGT1 genes, namely suppressor of G2 allele of SKP1 and suppressor of GCR2. In this study, through systematic analysis, four putative SGT1 genes were identified and characterized in B. oleracea. In phylogenetic analysis, the genes clearly formed separate groups, namely BolSGT1a, BolSGT1b (both suppressor of G2 allele of SKP1 types), and BolSGT1 (suppressor of GCR2). Functional domain analysis and organ-specific expression patterns suggested possible roles for BolSGT1 genes during stress conditions. BolSGT1 genes showed significant changes in expression in response to heat, cold, drought, salt, or ABA treatment. Interaction network analysis supported the expression analysis, and showed that the BolSGT1a and BolSGT1b genes are strongly associated with co-regulators during stress conditions. However, the BolSGT1 gene did not show any strong association. Hence, BolSGT1 might be a stress resistance-related gene that functions without a co-regulator. Our results show that BolSGT1 genes are potential target genes to improve B. oleracea resistance to abiotic stresses such as heat, cold, and salt.
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Affiliation(s)
- Ashokraj Shanmugam
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 57922, Republic of Korea
| | - Senthil Kumar Thamilarasan
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 57922, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 57922, Republic of Korea
| | - Mi Young Jung
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 57922, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 57922, Republic of Korea
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Du C, Hu K, Xian S, Liu C, Fan J, Tu J, Fu T. Dynamic transcriptome analysis reveals AP2/ERF transcription factors responsible for cold stress in rapeseed (Brassica napus L.). Mol Genet Genomics 2016; 291:1053-67. [PMID: 26728151 DOI: 10.1007/s00438-015-1161-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/14/2015] [Indexed: 02/02/2023]
Abstract
The APETALA2/ethylene response factor (AP2/ERF) transcription factor (TF) superfamily plays an important regulatory role in signal transduction of the plant responses to various stresses including low temperature. Significant progress has been made in understanding the mechanism of cold resistance in Brassica napus, an important oilseed crop. However, comprehensive studies on the induction and activity of these TFs under low temperature have been lacking. In this study, 132 AP2/ERF genes were identified by transcriptome sequencing of rapeseed leaves exposed to 0, 2, 6, 12, and 24 h of low (4 °C) temperature stress. The genes were classified into 4 subfamilies (AP2, DREB, ERF, and RAV) and 13 subgroups, among which the DREB subfamily and ERF subfamily contained 114 genes, no genes were assigned to soloist or DREB A3 subgroups. One hundred and eighteen genes were located on chromosomes A1 to C9. GO functional analysis and promoter sequence analysis revealed that these genes are involved in many molecular pathways that may enhance cold resistance in plants, such as the low-temperature responsiveness, methyl jasmonate, abscisic acid, and ethylene-responsiveness pathways. Their expression patterns revealed dynamic control at different times following initiation of cold stress; the RAV and DREB subfamilies were expressed at the early stage of cold stress, whereas the AP2 subfamily was expressed later. Quantitative PCR analyses of 13 cold-induced AP2/ERF TFs confirmed the accuracy of above results. This study is the first dynamic analysis of the AP2/ERF TFs responsible for cold stress in rapeseed. These findings will serve as a reference for future functional research on transcription in rapeseed.
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Affiliation(s)
- Chunfang Du
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, People's Republic of China.,Cotton Research Institute, Shanxi Academy of Agricultural Sciences, Yuncheng, 044000, People's Republic of China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shuanshi Xian
- Cotton Research Institute, Shanxi Academy of Agricultural Sciences, Yuncheng, 044000, People's Republic of China
| | - Chunqing Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianchun Fan
- Cotton Research Institute, Shanxi Academy of Agricultural Sciences, Yuncheng, 044000, People's Republic of China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, People's Republic of China
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Qu C, Zhao H, Fu F, Wang Z, Zhang K, Zhou Y, Wang X, Wang R, Xu X, Tang Z, Lu K, Li JN. Genome-Wide Survey of Flavonoid Biosynthesis Genes and Gene Expression Analysis between Black- and Yellow-Seeded Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1755. [PMID: 27999578 PMCID: PMC5139615 DOI: 10.3389/fpls.2016.01755] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/07/2016] [Indexed: 05/20/2023]
Abstract
Flavonoids, the compounds that impart color to fruits, flowers, and seeds, are the most widespread secondary metabolites in plants. However, a systematic analysis of these loci has not been performed in Brassicaceae. In this study, we isolated 649 nucleotide sequences related to flavonoid biosynthesis, i.e., the Transparent Testa (TT) genes, and their associated amino acid sequences in 17 Brassicaceae species, grouped into Arabidopsis or Brassicaceae subgroups. Moreover, 36 copies of 21 genes of the flavonoid biosynthesis pathway were identified in Arabidopsis thaliana, 53 were identified in Brassica rapa, 50 in Brassica oleracea, and 95 in B. napus, followed the genomic distribution, collinearity analysis and genes triplication of them among Brassicaceae species. The results showed that the extensive gene loss, whole genome triplication, and diploidization that occurred after divergence from the common ancestor. Using qRT-PCR methods, we analyzed the expression of 18 flavonoid biosynthesis genes in 6 yellow- and black-seeded B. napus inbred lines with different genetic background, found that 12 of which were preferentially expressed during seed development, whereas the remaining genes were expressed in all B. napus tissues examined. Moreover, 14 of these genes showed significant differences in expression level during seed development, and all but four of these (i.e., BnTT5, BnTT7, BnTT10, and BnTTG1) had similar expression patterns among the yellow- and black-seeded B. napus. Results showed that the structural genes (BnTT3, BnTT18, and BnBAN), regulatory genes (BnTTG2 and BnTT16) and three encoding transfer proteins (BnTT12, BnTT19, and BnAHA10) might play an crucial roles in the formation of different seed coat colors in B. napus. These data will be helpful for illustrating the molecular mechanisms of flavonoid biosynthesis in Brassicaceae species.
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Affiliation(s)
- Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
- Food and Bioproduct Science, University of SaskatchewanSaskatoon, SK, Canada
| | - Huiyan Zhao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue UniversityWest Lafayette, IN, USA
| | - Zhen Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Kai Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Yan Zhou
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Xin Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Rui Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Zhanglin Tang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
- *Correspondence: Kun Lu
| | - Jia-Na Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
- Jia-Na Li
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Song X, Wang J, Ma X, Li Y, Lei T, Wang L, Ge W, Guo D, Wang Z, Li C, Zhao J, Wang X. Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1186. [PMID: 27570529 PMCID: PMC4982375 DOI: 10.3389/fpls.2016.01186] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/22/2016] [Indexed: 05/03/2023]
Abstract
The AP2/ERF superfamily, one of the most important transcription factor families, plays crucial roles in response to biotic and abiotic stresses. So far, a comprehensive evolutionary inference of its origination and expansion has not been available. Here, we identified 515 AP2/ERF genes in B. napus, a neo-tetraploid forming ~7500 years ago, and found that 82.14% of them were duplicated in the tetraploidization. A prominent subgenome bias was revealed in gene expression, tissue-specific, and gene conversion. Moreover, a large-scale analysis across plants and alga suggested that this superfamily could have been originated from AP2 family, expanding to form other families (ERF, and RAV). This process was accompanied by duplicating and/or alternative deleting AP2 domain, intragenic domain sequence conversion, and/or by acquiring other domains, resulting in copy number variations, alternatively contributing to functional innovation. We found that significant positive selection occurred at certain critical nodes during the evolution of land plants, possibly responding to changing environment. In conclusion, the present research revealed origination, functional innovation, and evolutionary trajectory of the AP2/ERF superfamily, contributing to understanding their roles in plant stress tolerance.
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Affiliation(s)
- Xiaoming Song
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Jinpeng Wang
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Xiao Ma
- Library, North China University of Science and TechnologyTangshan, China
| | - Yuxian Li
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Tianyu Lei
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Li Wang
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Weina Ge
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Di Guo
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Zhenyi Wang
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Chunjin Li
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Jianjun Zhao
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
- Jianjun Zhao
| | - Xiyin Wang
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
- *Correspondence: Xiyin Wang
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Kavas M, Kizildogan A, Gökdemir G, Baloglu MC. Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean. EXCLI JOURNAL 2015; 14:1187-206. [PMID: 27152109 PMCID: PMC4849109 DOI: 10.17179/excli2015-600] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 11/01/2015] [Indexed: 12/17/2022]
Abstract
Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the AP2-ERF genes in the common bean genome. In this study, a comprehensive genome-wide in silico analysis identified 180 AP2-ERF superfamily genes in common bean (Phaseolus vulgaris). Based on the amino acid alignment and phylogenetic analyses, superfamily members were classified into four subfamilies: DREB (54), ERF (95), AP2 (27) and RAV (3), as well as one soloist. The physical and chemical characteristics of amino acids, interaction between AP2-ERF proteins, cis elements of promoter region of AP2-ERF genes and phylogenetic trees were predicted and analyzed. Additionally, expression levels of AP2-ERF genes were evaluated by in silico and qRT-PCR analyses. In silico micro-RNA target transcript analyses identified nearly all PvAP2-ERF genes as targets of by 44 different plant species' miRNAs were identified in this study. The most abundant target genes were PvAP2/ERF-20-25-62-78-113-173. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST analyses. Interactome analysis revealed that the transcription factor PvAP2-ERF78, an ortholog of Arabidopsis At2G28550, was potentially interacted with at least 15 proteins, indicating that it was very important in transcriptional regulation. Here we present the first study to identify and characterize the AP2-ERF transcription factors in common bean using whole-genome analysis, and the findings may serve as a references for future functional research on the transcription factors in common bean.
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Affiliation(s)
- Musa Kavas
- Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey
| | - Aslihan Kizildogan
- Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey
| | - Gökhan Gökdemir
- Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey
| | - Mehmet Cengiz Baloglu
- Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey
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Dong X, Yi H, Han CT, Nou IS, Hur Y. GDSL esterase/lipase genes in Brassica rapa L.: genome-wide identification and expression analysis. Mol Genet Genomics 2015; 291:531-42. [DOI: 10.1007/s00438-015-1123-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/18/2015] [Indexed: 11/29/2022]
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Kavas M, Baloğlu MC, Atabay ES, Ziplar UT, Daşgan HY, Ünver T. Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration. Mol Genet Genomics 2015; 291:129-43. [PMID: 26193947 DOI: 10.1007/s00438-015-1095-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/11/2015] [Indexed: 11/28/2022]
Abstract
Members of basic helix-loop-helix (bHLH) gene family found in all eukaryotes play crucial roles in response to stress. Though, most eukaryotes carry the proteins of this family, biological functions of the most bHLH family members are not deeply evaluated in plants. In this study, we conducted a comprehensive genome-wide analysis of bHLH transcription factors in salt tolerant common bean. We identified 155 bHLH protein-encoding genes (PvbHLH) by using in silico comparative genomics tools. Based on the phylogenetic tree, PvbHLH genes were classified into 8 main groups with 21 subfamilies. Exon-intron analysis indicated that proteins belonging to same main groups exhibited a closely related gene structure. While, the PvbHLH gene family has been mainly expanded through segmental duplications, a total of 11 tandem duplication were detected. Genome-wide expression analysis of bHLH genes showed that 63 PvbHLH genes were differentially expressed in at least one tissue. Three of them displayed higher expression values in both leaf and root tissues. The in silico micro-RNA target transcript analyses revealed that totally 100 PvHLH genes targeted by 86 plant miRNAs. The most abundant transcripts, which were targeted by all 18 plant miRNA, were belonging to PvHLH-22 and PvHLH-44 genes. The expression of 16 PvbHLH genes in the root and leaf tissues of salt-stressed common bean was evaluated using qRT-PCR. Among them, two of PvbHLHs, PvbHLH-54, PvbHLH-148, were found to be up-regulated in both tissues in correlation with RNA-seq measurements. The results of this study could help improve understanding of biological functions of common bean bHLH family under salt stress. Additionally, it may provide basic resources for analyzing bHLH protein function for improving economic, agronomic and ecological benefit in common bean and other species.
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Affiliation(s)
- Musa Kavas
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey.
| | - Mehmet Cengiz Baloğlu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Elif Seda Atabay
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey
| | | | - Hayriye Yıldız Daşgan
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Turgay Ünver
- Department of Biology, Faculty of Science, Çankırı Karatekin University, Cankiri, Turkey
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Chen R, Li Q, Tan H, Chen J, Xiao Y, Ma R, Gao S, Zerbe P, Chen W, Zhang L. Gene-to-metabolite network for biosynthesis of lignans in MeJA-elicited Isatis indigotica hairy root cultures. FRONTIERS IN PLANT SCIENCE 2015; 6:952. [PMID: 26579184 PMCID: PMC4630570 DOI: 10.3389/fpls.2015.00952] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 10/19/2015] [Indexed: 05/06/2023]
Abstract
Root and leaf tissue of Isatis indigotica shows notable anti-viral efficacy, and are widely used as "Banlangen" and "Daqingye" in traditional Chinese medicine. The plants' pharmacological activity is attributed to phenylpropanoids, especially a group of lignan metabolites. However, the biosynthesis of lignans in I. indigotica remains opaque. This study describes the discovery and analysis of biosynthetic genes and AP2/ERF-type transcription factors involved in lignan biosynthesis in I. indigotica. MeJA treatment revealed differential expression of three genes involved in phenylpropanoid backbone biosynthesis (IiPAL, IiC4H, Ii4CL), five genes involved in lignan biosynthesis (IiCAD, IiC3H, IiCCR, IiDIR, and IiPLR), and 112 putative AP2/ERF transcription factors. In addition, four intermediates of lariciresinol biosynthesis were found to be induced. Based on these results, a canonical correlation analysis using Pearson's correlation coefficient was performed to construct gene-to-metabolite networks and identify putative key genes and rate-limiting reactions in lignan biosynthesis. Over-expression of IiC3H, identified as a key pathway gene, was used for metabolic engineering of I. indigotica hairy roots, and resulted in an increase in lariciresinol production. These findings illustrate the utility of canonical correlation analysis for the discovery and metabolic engineering of key metabolic genes in plants.
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Affiliation(s)
- Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical UniversityShanghai, China
| | - Qing Li
- Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Hexin Tan
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical UniversityShanghai, China
| | - Junfeng Chen
- Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Ying Xiao
- Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Ruifang Ma
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical UniversityShenyang, China
| | - Shouhong Gao
- Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Philipp Zerbe
- Department of Plant Biology, University of California, DavisDavis, CA, USA
| | - Wansheng Chen
- Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical UniversityShanghai, China
- *Correspondence: Lei Zhang
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