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Xia P, Zhang Y, Zhang X. The Potential Relevance of PnDREBs to Panax notoginseng Nitrogen Sensitiveness. Biochem Genet 2024; 62:2631-2651. [PMID: 37999875 DOI: 10.1007/s10528-023-10567-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
The dehydration response element-binding (DREB) transcription factor is a subfamily of AP2/ERF. It actively responds to various abiotic stresses in plants. As one of the representative plants, Panax notoginseng is sensitive to Nitrogen (N). Here, bioinformatics analysis, the identification, chromosomal location, phylogeny, structure, cis-acting elements, and collinearity of PnDREBs were analyzed. In addition, the expression levels of PnDREBs were analyzed by quantitative reverse transcription PCR. In this study, 54 PnDREBs were identified and defined as PnDREB1 to PnDREB54. They were divided into 6 subfamilies (A1-A6). And 44 PnDREBs were irregularly distributed on 10 of 12 chromosomes. Each group showed specific motifs and exon-intron structures. By predicting cis-acting elements, the PnDREBs may participate in biotic stress, abiotic stress, and hormone induction. Collinear analysis showed that fragment duplication events were beneficial to the amplification and evolution of PnDREB members. The expression of PnDREBs showed obvious tissue specificity in its roots, flowers, and leaves. In addition, under the action of ammonium nitrogen and nitrate nitrogen at the 15 mM level, the level of PnDREB genes expression in roots varied to different degrees. In this study, we identified and characterized PnDREBs for the first time, and analyzed that PnDREBs may be related to the response of P. Notoginseng to N sensitiveness. The results of this study lay a foundation for further research on the function of PnDREBs in P. Notoginseng.
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Affiliation(s)
- Pengguo Xia
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
| | - Yan Zhang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Xuemin Zhang
- Tianjin TASLY Modern Chinese Medicine Resources Co., Ltd., Tianjin, 300402, People's Republic of China
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Wang D, Zeng Y, Yang X, Nie S. Characterization of DREB family genes in Lotus japonicus and LjDREB2B overexpression increased drought tolerance in transgenic Arabidopsis. BMC PLANT BIOLOGY 2024; 24:497. [PMID: 39075356 PMCID: PMC11285619 DOI: 10.1186/s12870-024-05225-y] [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: 12/31/2023] [Accepted: 05/30/2024] [Indexed: 07/31/2024]
Abstract
BACKGROUND Drought stress affects plant growth and development. DREB proteins play important roles in modulating plant growth, development, and stress responses, particularly under drought stress. To study the function of DREB transcription factors (TFs), we screened key DREB-regulating TFs for drought in Lotus japonicus. RESULTS Forty-two DREB TFs were identified, and phylogenetic analysis of proteins from L. japonicus classified them into five subfamilies (A1, A2, A4, A5, A6). The gene motif composition of the proteins is conserved within the same subfamily. Based on the cis-acting regulatory element analysis, we identified many growth-, hormone-, and stress-responsive elements within the promoter regions of DREB. We further analyzed the expression pattern of four genes in the A2 subfamily in response to drought stress. We found that the expression of most of the LjDREB A2 subfamily genes, especially LjDREB2B, was induced by drought stress. We further generated LjDREB2B overexpression transgenic Arabidopsis plants. Under drought stress, the growth of wild-type (WT) and overexpressing LjDREB2B (OE) Arabidopsis lines was inhibited; however, OE plants showed better growth. The malondialdehyde content of LjDREB2B overexpressing lines was lower than that of the WT plants, whereas the proline content and antioxidant enzyme activities in the OE lines were significantly higher than those in the WT plants. Furthermore, after drought stress, the expression levels of AtP5CS1, AtP5CS2, AtRD29A, and AtRD29B in the OE lines were significantly higher than those in the WT plants. CONCLUSIONS Our results facilitate further functional analysis of L. japonicus DREB. LjDREB2B overexpression improves drought tolerance in transgenic Arabidopsis. These results indicate that DREB holds great potential for the genetic improvement of drought tolerance in L. japonicus.
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Affiliation(s)
- Dan Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, China
| | - Yuanyuan Zeng
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, China
| | - Xiuxiu Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, China
| | - Shuming Nie
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, China.
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Zheng K, Lu J, He X, Lan S, Zhai T, Cao S, Lin Y. Genome-Wide Identification and Expression Analysis of GATA Family Genes in Dimocarpus longan Lour. Int J Mol Sci 2024; 25:731. [PMID: 38255805 PMCID: PMC10815313 DOI: 10.3390/ijms25020731] [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: 11/25/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
GATA transcription factors, which are DNA-binding proteins with type IV zinc finger binding domains, have a role in transcriptional regulation in biological organisms. They have an indispensable role in the growth and development of plants, as well as in improvements in their ability to face various environmental stresses. To date, GATAs have been identified in many gene families, but the GATA gene in longan (Dimocarpus longan Lour) has not been studied in previous explorations. Various aspects of genes in the longan GATA family, including their identification and classification, the distribution of their positions on chromosomes, their exon/intron structures, a synteny analysis, their expression at different temperatures, concentration of PEG, early developmental stages of somatic embryos and their expression levels in different tissues, and concentrations of exogenous hormones, were investigated in this study. This study showed that the 22 DlGATAs could be divided into four subfamilies. There were 10 pairs of homologous GATA genes in the synteny analysis of DlGATA and AtGATA. Four segmental replication motifs and one pair of tandem duplication events were present among the DlGATA family members. The cis-acting elements located in promoter regions were also found to be enriched with light-responsive elements, which contained related hormone-responsive elements. In somatic embryos, DlGATA4 is upregulated for expression at the globular embryo (GE) stage. We also found that DlGATA expression was strongly up-regulated in roots and stems. The study demonstrated the expression of DlGATA under hormone (ABA and IAA) treatments in embryogenic callus of longan. Under ABA treatment, DlGATA4 was up-regulated and the other DlGATA genes did not respond significantly. Moreover, as demonstrated with qRT-PCR, the expression of DlGATA genes showed strong up-regulated expression levels under 100 μmol·L-1 concentration IAA treatment. This experiment further studied these and simulated their possible connections with a drought response mechanism, while correlating them with their expression under PEG treatment. Overall, this experiment explored the GATA genes and dug into their evolution, structure, function, and expression profile, thus providing more information for a more in-depth study of the characteristics of the GATA family of genes.
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Affiliation(s)
- Kehui Zheng
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Jiayue Lu
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Xinyu He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Shuoxian Lan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Tingkai Zhai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
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Zhu W, Qi J, Chen J, Ma S, Liu K, Su H, Chai M, Huang Y, Xi X, Cao Z, Qin Y, Cai H. Identification of GA2ox Family Genes and Expression Analysis under Gibberellin Treatment in Pineapple ( Ananas comosus (L.) Merr.). PLANTS (BASEL, SWITZERLAND) 2023; 12:2673. [PMID: 37514287 PMCID: PMC10383957 DOI: 10.3390/plants12142673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
Gibberellin (GAs) plays an important regulatory role in the development and growth of pineapple (Ananas comosus (L.) Merr.). Bioinformatics was used to confirm the differential expression of GA2 gibberellin oxidase gene AcGA2oxs in the pineapple genome, which laid the foundation for exploring its role in pineapple. In this study, 42 GA2ox genes (AcGA2oxs) were identified in the pineapple genome, named from AcGA2ox1 to AcGA2ox42, and divided into four groups according to phylogenetic analysis. We also analyzed the gene structure, conserved motifs and chromosome localization of AcGA2oxs. AcGA2oxs within the same group had similar gene structure and motifs composition. Collinear analysis and cis-element analysis provided the basis for understanding the evolution and function of GA2ox genes in pineapple. In addition, we selected different tissue parts to analyze the expression profile of AcGA2oxs, and the results show that 41 genes were expressed, except for AcGA2ox18. AcGA2ox18 may not be expressed in these sites or may be pseudogenes. qRT-PCR (real-time fluorescence quantitative PCR) was used to detect the relative expression levels of the GA2ox gene family under different concentrations of GA3 treatment, and it was found that AcGA2ox gene expression was upregulated in different degrees under GA3 treatment. These results provide useful information for further study on the evolution and function of the GA2ox family in pineapple.
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Affiliation(s)
- Wenhui Zhu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingang Qi
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingdong Chen
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Suzhuo Ma
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kaichuang Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Han Su
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengnan Chai
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youmei Huang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinpeng Xi
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhuangyuan Cao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Qin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hanyang Cai
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Akbari A, Ismaili A, Amirbakhtiar N, Pouresmael M, Shobbar ZS. Genome-wide transcriptional profiling provides clues to molecular mechanisms underlying cold tolerance in chickpea. Sci Rep 2023; 13:6279. [PMID: 37072529 PMCID: PMC10113226 DOI: 10.1038/s41598-023-33398-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
Chickpea is an important food legume cultivated in several countries. A sudden drop in autumn temperature, freezing winter temperature, and late spring cold events result in significant losses in chickpea production. The current study used RNA sequencing of two cold tolerant (Saral) and sensitive (ILC533) Kabuli chickpea genotypes to identify cold tolerance-associated genes/pathways. A total of 200.85 million raw reads were acquired from the leaf samples by Illumina sequencing, and around 86% of the clean reads (199 million) were mapped to the chickpea reference genome. The results indicated that 3710 (1980 up- and 1730 down-regulated) and 3473 (1972 up- and 1501 down-regulated) genes were expressed differentially under cold stress in the tolerant and sensitive genotypes, respectively. According to the GO enrichment analysis of uniquely down-regulated genes under cold stress in ILC533, photosynthetic membrane, photosystem II, chloroplast part, and photosystem processes were enriched, revealing that the photosynthesis is severely sensitive to cold stress in this sensitive genotype. Many remarkable transcription factors (CaDREB1E, CaMYB4, CaNAC47, CaTCP4, and CaWRKY33), signaling/regulatory genes (CaCDPK4, CaPP2C6, CaMKK2, and CaHSFA3), and protective genes (CaCOR47, CaLEA3, and CaGST) were identified among the cold-responsive genes of the tolerant genotype. These findings would help improve cold tolerance across chickpea genotypes by molecular breeding or genetic engineering.
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Affiliation(s)
- Alireza Akbari
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Ahmad Ismaili
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Nazanin Amirbakhtiar
- Genetic Research Department, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Masoumeh Pouresmael
- Genetic Research Department, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization, Karaj, Iran.
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Comparative Metabolomic Studies of Siberian Wildrye ( Elymus sibiricus L.): A New Look at the Mechanism of Plant Drought Resistance. Int J Mol Sci 2022; 24:ijms24010452. [PMID: 36613896 PMCID: PMC9820681 DOI: 10.3390/ijms24010452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Drought is one of the most important factors affecting plant growth and production due to ongoing global climate change. Elymus sibiricus has been widely applied for ecological restoration and reseeding of degraded grassland in the Qinghai-Tibetan Plateau (QTP) because of its strong adaptability to barren, salted, and drought soils. To explore the mechanism of drought resistance in E. sibiricus, drought-tolerant and drought-sensitive genotypes of E. sibiricus were used in metabolomic studies under simulated long-term and short-term drought stress. A total of 1091 metabolites were detected, among which, 27 DMs were considered to be the key metabolites for drought resistance of E. sibiricus in weighted gene co-expression network analysis (WGCNA). Ten metabolites, including 3-amino-2-methylpropanoic acid, coniferin, R-aminobutyrate, and so on, and 12 metabolites, including L-Proline, L-histidine, N-acetylglycine, and so on, showed differential accumulation patterns under short-term and long-term drought stress, respectively, and thus, could be used as biomarkers for drought-tolerant and drought-sensitive E. sibiricus. In addition, different metabolic accumulation patterns and different drought response mechanisms were also found in drought-tolerant and drought-sensitive genotypes of E. sibiricus. Finally, we constructed metabolic pathways and metabolic patterns for the two genotypes. This metabolomic study on the drought stress response of E. sibiricus can provide resources and a reference for the breeding of new drought-tolerant cultivars of E. sibiricus.
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Maqsood H, Munir F, Amir R, Gul A. Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2022; 13:1031679. [PMID: 36507398 PMCID: PMC9731513 DOI: 10.3389/fpls.2022.1031679] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/25/2022] [Indexed: 06/12/2023]
Abstract
Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron-exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.
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Affiliation(s)
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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Hashemi-Petroudi SH, Arab M, Dolatabadi B, Kuo YT, Baez MA, Himmelbach A, Nematzadeh G, Maibody SAMM, Schmutzer T, Mälzer M, Altmann T, Kuhlmann M. Initial Description of the Genome of Aeluropus littoralis, a Halophile Grass. FRONTIERS IN PLANT SCIENCE 2022; 13:906462. [PMID: 35898222 PMCID: PMC9310549 DOI: 10.3389/fpls.2022.906462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/16/2022] [Indexed: 06/01/2023]
Abstract
The use of wild plant species or their halophytic relatives has been considered in plant breeding programs to improve salt and drought tolerance in crop plants. Aeluropus littoralis serves as halophyte model for identification and isolation of novel stress adaptation genes. A. littoralis, a perennial monocot grass, grows in damp or arid areas, often salt-impregnated places and wasteland in cultivated areas, can survive periodically high water salinity, and tolerate high salt concentrations in the soil up to 1,100 mM sodium chloride. Therefore, it serves as valuable genetic resource to understand molecular mechanisms of stress-responses in monocots. The knowledge can potentially be used for improving tolerance to abiotic stresses in economically important crops. Several morphological, anatomical, ecological, and physiological traits of A. littoralis have been investigated so far. After watering with salt water the grass is able to excrete salt via its salt glands. Meanwhile, a number of ESTs (expressed sequence tag), genes and promoters induced by the salt and drought stresses were isolated, sequenced and annotated at a molecular level. Transfer of stress related genes to other species resulted in enhanced stress resistance. Here we describe the genome sequence and structure of A. littoralis analyzed by whole genome sequencing and histological analysis. The chromosome number was determined to be 20 (2n = 2x = 20). The genome size was calculated to be 354 Mb. This genomic information provided here, will support the functional investigation and application of novel genes improving salt stress resistance in crop plants. The utility of the sequence information is exemplified by the analysis of the DREB-transcription factor family.
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Affiliation(s)
- Seyyed Hamidreza Hashemi-Petroudi
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Sari, Iran
- RG Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Mozhdeh Arab
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Behnaz Dolatabadi
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Sari, Iran
- RG Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Yi-Tzu Kuo
- Research Group Chromosome Structure and Function, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Mariana Alejandra Baez
- Research Group Chromosome Structure and Function, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Axel Himmelbach
- Research Group Genomics of Genetic Resources Cereals Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ghorbanali Nematzadeh
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | | | - Thomas Schmutzer
- Institute of Agricultural and Nutritional Sciences, RG Biometrics and Agroinformatics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Mälzer
- RG Structural Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Thomas Altmann
- RG Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Markus Kuhlmann
- RG Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Chakraborty K, Jena P, Mondal S, Dash GK, Ray S, Baig MJ, Swain P. Relative contribution of different members of OsDREB gene family to osmotic stress tolerance in indica and japonica ecotypes of rice. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:356-366. [PMID: 34939275 DOI: 10.1111/plb.13379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Drought/osmotic stress is the single largest production constraint in rain-fed rice cultivation. Different members of the DREB gene family are known to contribute to osmotic stress tolerance. In this study, an attempt was made to understand their relative contribution towards osmotic stress tolerance in indica and japonica ecotypes of rice. Two genotypes (one tolerant and one susceptible) from each ecotype were grown hydroponically, and 21-day-old seedlings were subjected to polyethylene glycol-induced osmotic stress (15% PEG-6000, equivalent to -3.0 bars osmotic potential). The tolerant genotypes CR143 and Moroberekan were found to have superior root traits (total root length, surface area and volume), better plant water status and increased total dry biomass as compared to their susceptible counterparts after 10 days of osmotic stress. Different members of the DREB gene family were differentially induced in response to osmotic shock (1 h after stress) and osmotic stress (24 h after stress), which also differed between the two rice ecotypes. From the gene expression profiles of 10 DREB genes (both DREB1 and DREB2 families), in indica two DREB genes, DREB1B and DREB1G, were significantly correlated with stress tolerance indices, whereas in japonica significant correlations with five DREB genes (DREB1A, DREB1B, DREB1D, DREB1E and DREB2B) were observed. We found that only one member, i.e. DREB1B, showed a significant correlation with drought tolerance indices in both indica and japonica ecotypes. This study provides an overview of the relative contribution of different members of the DREB gene family and their association with drought/osmotic stress tolerance in rice.
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Affiliation(s)
- K Chakraborty
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - P Jena
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - S Mondal
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - G K Dash
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - S Ray
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - M J Baig
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - P Swain
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
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Anwar M, Saleem MA, Dan M, Malik W, Ul-Allah S, Ahmad MQ, Qayyum A, Amjid MW, Zia ZU, Afzal H, Asif M, Ur Rahman MA, Hu Z. Morphological, physiological and molecular assessment of cotton for drought tolerance under field conditions. Saudi J Biol Sci 2022; 29:444-452. [PMID: 35002440 PMCID: PMC8717151 DOI: 10.1016/j.sjbs.2021.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 08/31/2021] [Accepted: 09/05/2021] [Indexed: 11/29/2022] Open
Abstract
Climate change could be an existential threat to many crops. Drought and heat stress are becoming harder for cultivated crops. Cotton in Pakistan is grown under natural high temperature and low moisture, could be used as a source of heat and drought tolerance. Therefore, the study was conducted to morphological, physiological and molecular characterization of cotton genotypes under field conditions. A total of 25 cotton genotypes were selected from the gene pool of Pakistan based on tolerance to heat and drought stress. In field trail, the stress related traits like boll retention percentage, plant height, number of nodes and inter-nodal distance were recorded. In physiological assessment, traits such as photosynthesis rate, stomatal conductance, transpiration rate, leaf temperature, relative water content and excised leaf water loss were observed. At molecular level, a set of 19 important transcription factors, controlling drought/heat stress tolerance (HSPCB, GHSP26, HSFA2, HSP101, HSP3, DREB1A, DREB2A, TPS, GhNAC2, GbMYB5, GhWRKY41, GhMKK3, GhMPK17, GhMKK1, GhMPK2, APX1, HSC70, ANNAT8, and GhPP2A1) were analyzed from all genotypes. Data analyses depicted that boll retention percentage, photosynthesis, stomatal conductance, relative water content under the stress conditions were associated with the presence of important drought & heat TF/genes which depicts high genetic potential of Pakistani cotton varieties against abiotic stress. The variety MNH-886 appeared in medium plant height, high boll retention percentage, high relative water content, photosynthesis rate, stomatal conductance, transpiration rate and with maximum number transcription factors under study. The variety may be used as source material for heat and drought tolerant cotton breeding. The results of this study may be useful for the cotton breeders to develop genotype adoptable to environmental stresses under climate change scenario.
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Affiliation(s)
- Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Muhammad Asif Saleem
- Department of Plant Breeding & Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Ma Dan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agriculture Sciences, Anyang 455000, China
| | - Waqas Malik
- Department of Plant Breeding & Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Sami Ul-Allah
- College of Agriculture, Bahauddin Zakariya University, Bahadur Sub-campus, Layyah, Pakistan
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding & Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Abdul Qayyum
- Department of Plant Breeding & Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Waqas Amjid
- State Key Lab. of Crop Genetics & Germplasm, Nanjing Agriculture University, China
| | | | - Hammad Afzal
- Department of Plant Breeding & Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Asif
- Department of Plant Breeding & Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Aneeq Ur Rahman
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.,Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
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11
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ain-Ali QU, Mushtaq N, Amir R, Gul A, Tahir M, Munir F. Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum. PLoS One 2021; 16:e0261215. [PMID: 34914734 PMCID: PMC8675703 DOI: 10.1371/journal.pone.0261215] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/27/2021] [Indexed: 12/24/2022] Open
Abstract
Dehydration Responsive Element Binding (DREB) regulates the expression of numerous stress-responsive genes, and hence plays a pivotal role in abiotic stress responses and tolerance in plants. The study aimed to develop a complete overview of the cis-acting regulatory elements (CAREs) present in S. tuberosum DREB gene promoters. A total of one hundred and four (104) cis-regulatory elements (CREs) were identified from 2.5kbp upstream of the start codon (ATG). The in-silico promoter analysis revealed variable sets of cis-elements and functional diversity with the predominance of light-responsive (30%), development-related (20%), abiotic stress-responsive (14%), and hormone-responsive (12%) elements in StDREBs. Among them, two light-responsive elements (Box-4 and G-box) were predicted in 64 and 61 StDREB genes, respectively. Two development-related motifs (AAGAA-motif and as-1) were abundant in StDREB gene promoters. Most of the DREB genes contained one or more Myeloblastosis (MYB) and Myelocytometosis (MYC) elements associated with abiotic stress responses. Hormone-responsive element i.e. ABRE was found in 59 out of 66 StDREB genes, which implied their role in dehydration and salinity stress. Moreover, six proteins were chosen corresponding to A1-A6 StDREB subgroups for secondary structure analysis and three-dimensional protein modeling followed by model validation through PROCHECK server by Ramachandran Plot. The predicted models demonstrated >90% of the residues in the favorable region, which further ensured their reliability. The present study also anticipated pocket binding sites and disordered regions (DRs) to gain insights into the structural flexibility and functional annotation of StDREB proteins. The protein association network determined the interaction of six selected StDREB proteins with potato proteins encoded by other gene families such as MYB and NAC, suggesting their similar functional roles in biological and molecular pathways. Overall, our results provide fundamental information for future functional analysis to understand the precise molecular mechanisms of the DREB gene family in S. tuberosum.
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Affiliation(s)
- Qurat-ul ain-Ali
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Nida Mushtaq
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Tahir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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12
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Haddoudi L, Hdira S, Hanana M, Romero I, Haddoudi I, Mahjoub A, Ben Jouira H, Djébali N, Ludidi N, Sanchez-Ballesta MT, Abdelly C, Badri M. Evaluation of the Morpho-Physiological, Biochemical and Molecular Responses of Contrasting Medicago truncatula Lines under Water Deficit Stress. PLANTS (BASEL, SWITZERLAND) 2021; 10:2114. [PMID: 34685923 PMCID: PMC8537959 DOI: 10.3390/plants10102114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/29/2021] [Accepted: 09/10/2021] [Indexed: 12/02/2022]
Abstract
Medicago truncatula is a forage crop of choice for farmers, and it is a model species for molecular research. The growth and development and subsequent yields are limited by water availability mainly in arid and semi-arid regions. Our study aims to evaluate the morpho-physiological, biochemical and molecular responses to water deficit stress in four lines (TN6.18, JA17, TN1.11 and A10) of M. truncatula. The results showed that the treatment factor explained the majority of the variation for the measured traits. It appeared that the line A10 was the most sensitive and therefore adversely affected by water deficit stress, which reduced its growth and yield parameters, whereas the tolerant line TN6.18 exhibited the highest root biomass production, a significantly higher increase in its total protein and soluble sugar contents, and lower levels of lipid peroxidation with greater cell membrane integrity. The expression analysis of the DREB1B gene using RT-qPCR revealed a tissue-differential expression in the four lines under osmotic stress, with a higher induction rate in roots of TN6.18 and JA17 than in A10 roots, suggesting a key role for DREB1B in water deficit tolerance in M. truncatula.
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Affiliation(s)
- Loua Haddoudi
- Centre of Biotechnology of Borj Cedria, Laboratory of Extremophile Plants, B.P. 901, Hammam-Lif 2050, Tunisia; (L.H.); (S.H.); (M.H.); (A.M.); (H.B.J.); (C.A.)
- Faculty of Mathematical, Physical and Natural Sciences of Tunis, Campus Universitaire El-Manar, University of Tunis El Manar, Tunis 2092, Tunisia
| | - Sabrine Hdira
- Centre of Biotechnology of Borj Cedria, Laboratory of Extremophile Plants, B.P. 901, Hammam-Lif 2050, Tunisia; (L.H.); (S.H.); (M.H.); (A.M.); (H.B.J.); (C.A.)
- Faculty of Mathematical, Physical and Natural Sciences of Tunis, Campus Universitaire El-Manar, University of Tunis El Manar, Tunis 2092, Tunisia
| | - Mohsen Hanana
- Centre of Biotechnology of Borj Cedria, Laboratory of Extremophile Plants, B.P. 901, Hammam-Lif 2050, Tunisia; (L.H.); (S.H.); (M.H.); (A.M.); (H.B.J.); (C.A.)
| | - Irene Romero
- Laboratory of Biotechnology and Postharvest Quality, Institute of Food Science, Technology and Nutrition (ICTAN-CSIC), Jose Antonio Novais, 10, 28040 Madrid, Spain; (I.R.); (M.T.S.-B.)
| | - Imen Haddoudi
- Department of Ecosystem Biology, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic;
| | - Asma Mahjoub
- Centre of Biotechnology of Borj Cedria, Laboratory of Extremophile Plants, B.P. 901, Hammam-Lif 2050, Tunisia; (L.H.); (S.H.); (M.H.); (A.M.); (H.B.J.); (C.A.)
| | - Hatem Ben Jouira
- Centre of Biotechnology of Borj Cedria, Laboratory of Extremophile Plants, B.P. 901, Hammam-Lif 2050, Tunisia; (L.H.); (S.H.); (M.H.); (A.M.); (H.B.J.); (C.A.)
| | - Naceur Djébali
- Centre of Biotechnology of Borj Cedria, Laboratory of Bioactive Substances, B.P. 901, Hammam-Lif 2050, Tunisia;
| | - Ndiko Ludidi
- Plant Biotechnology Research Group, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa;
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa
| | - Maria Teresa Sanchez-Ballesta
- Laboratory of Biotechnology and Postharvest Quality, Institute of Food Science, Technology and Nutrition (ICTAN-CSIC), Jose Antonio Novais, 10, 28040 Madrid, Spain; (I.R.); (M.T.S.-B.)
| | - Chedly Abdelly
- Centre of Biotechnology of Borj Cedria, Laboratory of Extremophile Plants, B.P. 901, Hammam-Lif 2050, Tunisia; (L.H.); (S.H.); (M.H.); (A.M.); (H.B.J.); (C.A.)
| | - Mounawer Badri
- Centre of Biotechnology of Borj Cedria, Laboratory of Extremophile Plants, B.P. 901, Hammam-Lif 2050, Tunisia; (L.H.); (S.H.); (M.H.); (A.M.); (H.B.J.); (C.A.)
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13
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Mushtaq N, Munir F, Gul A, Amir R, Zafar Paracha R. Genome-wide analysis, identification, evolution and genomic organization of dehydration responsive element-binding (DREB) gene family in Solanum tuberosum. PeerJ 2021; 9:e11647. [PMID: 34221730 PMCID: PMC8236231 DOI: 10.7717/peerj.11647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/29/2021] [Indexed: 01/19/2023] Open
Abstract
Background The dehydration responsive element-binding (DREB) gene family plays a crucial role as transcription regulators and enhances plant tolerance to abiotic stresses. Although the DREB gene family has been identified and characterized in many plants, knowledge about it in Solanum tuberosum (Potato) is limited. Results In the present study, StDREB gene family was comprehensively analyzed using bioinformatics approaches. We identified 66 StDREB genes through genome wide screening of the Potato genome based on the AP2 domain architecture and amino acid conservation analysis (Valine at position 14th). Phylogenetic analysis divided them into six distinct subgroups (A1–A6). The categorization of StDREB genes into six subgroups was further supported by gene structure and conserved motif analysis. Potato DREB genes were found to be distributed unevenly across 12 chromosomes. Gene duplication proved that StDREB genes experienced tandem and segmental duplication events which led to the expansion of the gene family. The Ka/Ks ratios of the orthologous pairs also demonstrated the StDREB genes were under strong purification selection in the course of evolution. Interspecies synteny analysis revealed 45 and 36 StDREB genes were orthologous to Arabidopsis and Solanum lycopersicum, respectively. Moreover, subcellular localization indicated that StDREB genes were predominantly located within the nucleus and the StDREB family’s major function was DNA binding according to gene ontology (GO) annotation. Conclusions This study provides a comprehensive and systematic understanding of precise molecular mechanism and functional characterization of StDREB genes in abiotic stress responses and will lead to improvement in Solanum tuberosum.
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Affiliation(s)
- Nida Mushtaq
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- Research Centre for Modelling & Simulation, National University of Sciences and Technology, Islamabad, Pakistan
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14
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Wang L, Liu Y, Chai M, Chen H, Aslam M, Niu X, Qin Y, Cai H. Genome-wide identification, classification, and expression analysis of the HSF gene family in pineapple ( Ananas comosus). PeerJ 2021; 9:e11329. [PMID: 33987013 PMCID: PMC8086565 DOI: 10.7717/peerj.11329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/31/2021] [Indexed: 11/28/2022] Open
Abstract
Transcription factors (TFs), such as heat shock transcription factors (HSFs), usually play critical regulatory functions in plant development, growth, and response to environmental cues. However, no HSFs have been characterized in pineapple thus far. Here, we identified 22 AcHSF genes from the pineapple genome. Gene structure, motifs, and phylogenetic analysis showed that AcHSF families were distinctly grouped into three subfamilies (12 in Group A, seven in Group B, and four in Group C). The AcHSF promoters contained various cis-elements associated with stress, hormones, and plant development processes, for instance, STRE, WRKY, and ABRE binding sites. The majority of HSFs were expressed in diverse pineapple tissues and developmental stages. The expression of AcHSF-B4b/AcHSF-B4c and AcHSF-A7b/AcHSF-A1c were enriched in the ovules and fruits, respectively. Six genes (AcHSF-A1a , AcHSF-A2, AcHSF-A9a, AcHSF-B1a, AcHSF-B2a, and AcHSF-C1a) were transcriptionally modified by cold, heat, and ABA. Our results provide an overview and lay the foundation for future functional characterization of the pineapple HSF gene family.
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Affiliation(s)
- Lulu Wang
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Yanhui Liu
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Mengnan Chai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Huihuang Chen
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Mohammad Aslam
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Xiaoping Niu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Yuan Qin
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Hanyang Cai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
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15
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Huang Y, Liu Y, Zhang M, Chai M, He Q, Jakada BH, Chen F, Chen H, Jin X, Cai H, Qin Y. Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple ( Ananas comosus (L.) Merr.). PeerJ 2020; 8:e10014. [PMID: 33024641 PMCID: PMC7518161 DOI: 10.7717/peerj.10014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/01/2020] [Indexed: 01/27/2023] Open
Abstract
Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 ERF genes (AcoERFs) were identified in pineapple genome, named from AcoERF1 to AcoERF74, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of AcoERFs, and the AcoERFs within the same group possess similar gene structures and motif compositions. Three genes (AcoERF71, AcoERF73 and AcoERF74) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and cis-elements analysis of ERF genes provided deep insight into the evolution and function of pineapple ERF genes. Furthermore, we analyzed the expression profiling of AcoERF in different tissues and developmental stages, and 22 AcoERF genes were expressed in all examined tissues, in which five genes (AcoERF13, AcoERF16, AcoERF31, AcoERF42, and AcoERF65) had high expression levels. Additionally, nine AcoERF genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple.
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Affiliation(s)
- Youmei Huang
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Yanhui Liu
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Man Zhang
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Mengnan Chai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Qing He
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Bello Hassan Jakada
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Fangqian Chen
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Huihuang Chen
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Xingyue Jin
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Hanyang Cai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Yuan Qin
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi Province, China
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