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Cheng B, Pei W, Wan K, Pan R, Zhang W. LncRNA cis- and trans-regulation provides new insight into drought stress responses in wild barley. PHYSIOLOGIA PLANTARUM 2024; 176:e14424. [PMID: 38973627 DOI: 10.1111/ppl.14424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/11/2024] [Accepted: 06/20/2024] [Indexed: 07/09/2024]
Abstract
Drought is one of the most common abiotic stresses that affect barley productivity. Long noncoding RNA (lncRNA) has been reported to be widely involved in abiotic stress, however, its function in the drought stress response in wild barley remains unclear. In this study, RNA sequencing was performed to identify differentially expressed lncRNAs (DElncRNA) among two wild barley and two cultivated barley genotypes. Then, the cis-regulatory networks were according to the chromosome position and the expression level correction. The GO annotation indicates that these cis-target genes are mainly involved in "ion transport transporter activity" and "metal ion transport transporter activity". Through weighted gene co-expression network analysis (WGCNA), 10 drought-related modules were identified to contract trans-regulatory networks. The KEGG annotation demonstrated that these trans-target genes were enriched for photosynthetic physiology, brassinosteroid biosynthesis, and flavonoid metabolism. In addition, we constructed the lncRNA-mediated ceRNA regulatory network by predicting the microRNA response elements (MREs). Furthermore, the expressions of lncRNAs were verified by RT-qPCR. Functional verification of a candidate lncRNA, MSTRG.32128, demonstrated its positive role in drought response and root growth and development regulation. Hormone content analysis provided insights into the regulatory mechanisms of MSTRG.32128 in root development, revealing its involvement in auxin and ethylene signal transduction pathways. These findings advance our understanding of lncRNA-mediated regulatory mechanisms in barley under drought stress. Our results will provide new insights into the functions of lncRNAs in barley responding to drought stress.
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Affiliation(s)
- Bingyun Cheng
- Research Center of Crop Stresses Resistance Technologies/ MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Yangtze University, Jingzhou, China
| | - Wenyu Pei
- Research Center of Crop Stresses Resistance Technologies/ MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Yangtze University, Jingzhou, China
| | - Kui Wan
- Research Center of Crop Stresses Resistance Technologies/ MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Yangtze University, Jingzhou, China
| | - Rui Pan
- Research Center of Crop Stresses Resistance Technologies/ MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Yangtze University, Jingzhou, China
| | - Wenying Zhang
- Research Center of Crop Stresses Resistance Technologies/ MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Yangtze University, Jingzhou, China
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Caccialupi G, Milc J, Caradonia F, Nasar MF, Francia E. The Triticeae CBF Gene Cluster-To Frost Resistance and Beyond. Cells 2023; 12:2606. [PMID: 37998341 PMCID: PMC10670769 DOI: 10.3390/cells12222606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
The pivotal role of CBF/DREB1 transcriptional factors in Triticeae crops involved in the abiotic stress response has been highlighted. The CBFs represent an important hub in the ICE-CBF-COR pathway, which is one of the most relevant mechanisms capable of activating the adaptive response to cold and drought in wheat, barley, and rye. Understanding the intricate mechanisms and regulation of the cluster of CBF genes harbored by the homoeologous chromosome group 5 entails significant potential for the genetic improvement of small grain cereals. Triticeae crops seem to share common mechanisms characterized, however, by some peculiar aspects of the response to stress, highlighting a combined landscape of single-nucleotide variants and copy number variation involving CBF members of subgroup IV. Moreover, while chromosome 5 ploidy appears to confer species-specific levels of resistance, an important involvement of the ICE factor might explain the greater tolerance of rye. By unraveling the genetic basis of abiotic stress tolerance, researchers can develop resilient varieties better equipped to withstand extreme environmental conditions. Hence, advancing our knowledge of CBFs and their interactions represents a promising avenue for improving crop resilience and food security.
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Affiliation(s)
- Giovanni Caccialupi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy; (J.M.); (F.C.); (M.F.N.); (E.F.)
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Arjmand MP, Lahiji HS, Golfazani MM, Biglouei MH. New insights on the regulatory network of drought-responsive key genes in Arabidopsis thaliana. Genetica 2023; 151:29-45. [PMID: 36474134 DOI: 10.1007/s10709-022-00177-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Drought stress is complex abiotic stress that seriously affects crop productivity and yield. Many genes with various functions are induced in response to drought stress. The present study aimed to identify drought-responsive hub genes and their related regulation network in Arabidopsis thaliana under drought stress. In this study, RNA-sequencing data of well-watered and drought treatment samples of Arabidopsis were analyzed, and differential expression genes were identified. The gene ontology enrichment and protein-protein interaction network analyses were performed for differential expression genes. Then, the most important hub genes, gene ontology enrichment, co-expression network, and prediction of related miRNAs of hub genes were investigated by in silico approaches. A total of 2462 genes were expressed differentially, of which 1926 transcripts were up-regulated under drought stress, and the rest were down-regulated. WRKY33, WRKY40, AT1G19020, STZ, SYP122, CNI1, CML37, BCS1, AT3G02840, and AT5G54490 were identified as hub genes in drought stress. The gene ontology analysis showed that hub genes significantly enriched in response to hypoxia, chitin, wounding, and salicylic acid-mediated signaling pathway. The hub genes were co-expressed with important drought-responsive genes such as WRKY46, WRKY60, CML38, ERF6, ERF104, and ERF1A. They were regulated by many stress-responsive miRNAs, such as ath-miR5021, miR413, miR5998, and miR162, that could be used as candidate miRNAs for regulating key genes under drought stress. It seems that the regulation network was involved in signaling pathways and protein degradation under drought stress, and it consists of several important genes and miRNAs that are potential candidates for plant improvement and breeding programs.
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Affiliation(s)
- Maryam Pasandideh Arjmand
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | | | | | - Mohammad Hassan Biglouei
- Department of Water Engineering, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
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Wu W, Zhu S, Xu L, Zhu L, Wang D, Liu Y, Liu S, Hao Z, Lu Y, Yang L, Shi J, Chen J. Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress. BMC PLANT BIOLOGY 2022; 22:25. [PMID: 35012508 PMCID: PMC8744262 DOI: 10.1186/s12870-021-03371-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/29/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Liriodendron chinense (Lchi) is a tree species within the Magnoliaceae family and is considered a basal angiosperm. The too low or high temperature or soil drought will restrict its growth as the adverse environmental conditions, thus improving L. chinense abiotic tolerance was the key issues to study. WRKYs are a major family of plant transcription factors known to often be involved in biotic and abiotic stress responses. So far, it is still largely unknown if and how the LchiWRKY gene family is tied to regulating L. chinense stress responses. Therefore, studying the involvement of the WRKY gene family in abiotic stress regulation in L. chinense could be very informative in showing how this tree deals with such stressful conditions. RESULTS In this research, we performed a genome-wide analysis of the Liriodendron chinense (Lchi) WRKY gene family, studying their classification relationships, gene structure, chromosomal locations, gene duplication, cis-element, and response to abiotic stress. The 44 members of the LchiWRKY gene family contain a significant amount of sequence diversity, with their lengths ranging from 525 bp to 40,981 bp. Using classification analysis, we divided the 44 LchiWRKY genes into three phylogenetic groups (I, II, II), with group II then being further divided into five subgroups (IIa, IIb, IIc, IId, IIe). Comparative phylogenetic analysis including the WRKY families from 17 plant species suggested that LchiWRKYs are closely related to the Magnolia Cinnamomum kanehirae WRKY family, and has fewer family members than higher plants. We found the LchiWRKYs to be evenly distributed across 15 chromosomes, with their duplication events suggesting that tandem duplication may have played a major role in LchiWRKY gene expansion model. A Ka/Ks analysis indicated that they mainly underwent purifying selection and distributed in the group IId. Motif analysis showed that LchiWRKYs contained 20 motifs, and different phylogenetic groups contained conserved motif. Gene ontology (GO) analysis showed that LchiWRKYs were mainly enriched in two categories, i.e., biological process and molecular function. Two group IIc members (LchiWRKY10 and LchiWRKY37) contain unique WRKY element sequence variants (WRKYGKK and WRKYGKS). Gene structure analysis showed that most LchiWRKYs possess 3 exons and two different types of introns: the R- and V-type which are both contained within the WRKY domain (WD). Additional promoter cis-element analysis indicated that 12 cis-elements that play different functions in environmental adaptability occur across all LchiWRKY groups. Heat, cold, and drought stress mainly induced the expression of group II and I LchiWRKYs, some of which had undergone gene duplication during evolution, and more than half of which had three exons. LchiWRKY33 mainly responded to cold stress and LchiWRKY25 mainly responded to heat stress, and LchiWRKY18 mainly responded to drought stress, which was almost 4-fold highly expressed, while 5 LchiWRKYs (LchiWRKY5, LchiWRKY23, LchiWRKY14, LchiWRKY27, and LchiWRKY36) responded equally three stresses with more than 6-fold expression. Subcellular localization analysis showed that all LchiWRKYs were localized in the nucleus, and subcellular localization experiments of LchiWRKY18 and 36 also showed that these two transcription factors were expressed in the nucleus. CONCLUSIONS This study shows that in Liriodendron chinense, several WRKY genes like LchiWRKY33, LchiWRKY25, and LchiWRKY18, respond to cold or heat or drought stress, suggesting that they may indeed play a role in regulating the tree's response to such conditions. This information will prove a pivotal role in directing further studies on the function of the LchiWRKY gene family in abiotic stress response and provides a theoretical basis for popularizing afforestation in different regions of China.
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Affiliation(s)
- Weihuang Wu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Sheng Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Lin Xu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Zhu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dandan Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yang Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Siqin Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Ye Lu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
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Islam MQ, Hasan MN, Hoque H, Jewel NA, Bhuiyan MFH, Prodhan SH. Characterization of transcription factor MYB59 and expression profiling in response to low K + and NO 3- in indica rice (Oryza sativa L.). J Genet Eng Biotechnol 2021; 19:167. [PMID: 34704216 PMCID: PMC8548439 DOI: 10.1186/s43141-021-00248-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/18/2021] [Indexed: 11/11/2022]
Abstract
Background Nitrogen and potassium are crucial supplements for plant development and growth. Plants can detect potassium and nitrate ions in soils and in like way, they modify root-to-shoot transport of these ions to adjust the conveyance among roots and shoots. Transcription factor MYB59 plays essential roles in numerous physiological processes inclusive of hormone response, abiotic stress tolerance, plant development, and metabolic regulation. In this study, we retrieved 56 MYB59 proteins from different plant species. Multiple sequence alignment, phylogenetic tree, conserved motif, chromosomal localization, and cis-regulatory elements of the retrieved sequences were analyzed. Gene structure, protein 3D structure, and DNA binding of OsMYB59 indica were also predicted. Finally, we characterized OsMYB59 and its function under low K+/NO3− conditions in Oryza sativa subsp. indica. Results Data analysis showed that MYB59s from various groups separated in terms of conserved functional domains and gene structure, where members of genus Oryza clustered together. Plants showed reduced height and yellowish appearance when grown on K+ and NO3− deficient medium. Quantitative real-time PCR uncovered that the OsMYB59 reacted to abiotic stresses where its expression was increased in BRRI dhan56 but decreased in other varieties on K+ deficient medium. In addition, OsMYB59 transcript level increased on NO3− deficient medium. Conclusions Our results can help to explain the biological functions of indica rice MYB59 protein and gave a theoretical premise to additionally describe its biological roles in response to abiotic stresses particularly drought. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00248-6.
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Affiliation(s)
- Md Qamrul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Hammadul Hoque
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Nurnabi Azad Jewel
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Fahmid Hossain Bhuiyan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Shamsul H Prodhan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
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Javadi SM, Shobbar ZS, Ebrahimi A, Shahbazi M. Correction to: New insights on key genes involved in drought stress response of barley: gene networks reconstruction, hub, and promoter analysis. J Genet Eng Biotechnol 2021; 19:78. [PMID: 34047869 PMCID: PMC8163899 DOI: 10.1186/s43141-021-00158-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Seyedeh Mehri Javadi
- Department of Biotechnology and Plant Breeding, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Asa Ebrahimi
- Department of Biotechnology and Plant Breeding, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Shahbazi
- Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
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