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Ayyappan V, Sripathi VR, Xie S, Saha MC, Hayford R, Serba DD, Subramani M, Thimmapuram J, Todd A, Kalavacharla VK. Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass. BMC Genomics 2024; 25:223. [PMID: 38424499 PMCID: PMC10903042 DOI: 10.1186/s12864-024-10068-w] [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: 09/05/2022] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress. RESULTS In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls. CONCLUSION Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.
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Affiliation(s)
- Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA.
| | | | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, IN, 47907, USA
| | - Malay C Saha
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | - Rita Hayford
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Desalegn D Serba
- USDA-ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA.
| | - Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA
| | | | - Antonette Todd
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA
| | - Venu Kal Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA
- Center for Integrated Biological and Environmental Research (CIBER), Delaware State University, Dover, DE, 19901, USA
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Sharma A, Choudhary P, Chakdar H, Shukla P. Molecular insights and omics-based understanding of plant-microbe interactions under drought stress. World J Microbiol Biotechnol 2023; 40:42. [PMID: 38105277 DOI: 10.1007/s11274-023-03837-4] [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: 09/29/2023] [Accepted: 11/11/2023] [Indexed: 12/19/2023]
Abstract
The detrimental effects of adverse environmental conditions are always challenging and remain a major concern for plant development and production worldwide. Plants deal with such constraints by physiological, biochemical, and morphological adaptations as well as acquiring mutual support of beneficial microorganisms. As many stress-responsive traits of plants are influenced by microbial activities, plants have developed a sophisticated interaction with microbes to cope with adverse environmental conditions. The production of numerous bioactive metabolites by rhizospheric, endo-, or epiphytic microorganisms can directly or indirectly alter the root system architecture, foliage production, and defense responses. Although plant-microbe interactions have been shown to improve nutrient uptake and stress resilience in plants, the underlying mechanisms are not fully understood. "Multi-omics" application supported by genomics, transcriptomics, and metabolomics has been quite useful to investigate and understand the biochemical, physiological, and molecular aspects of plant-microbe interactions under drought stress conditions. The present review explores various microbe-mediated mechanisms for drought stress resilience in plants. In addition, plant adaptation to drought stress is discussed, and insights into the latest molecular techniques and approaches available to improve drought-stress resilience are provided.
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Affiliation(s)
- Aditya Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Prassan Choudhary
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India
| | - Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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Ndayambaza B, Si J, Deng Y, Jia B, He X, Zhou D, Wang C, Zhu X, Liu Z, Qin J, Wang B, Bai X. The Euphrates Poplar Responses to Abiotic Stress and Its Unique Traits in Dry Regions of China (Xinjiang and Inner Mongolia): What Should We Know? Genes (Basel) 2023; 14:2213. [PMID: 38137039 PMCID: PMC10743205 DOI: 10.3390/genes14122213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
At the moment, drought, salinity, and low-temperature stress are ubiquitous environmental issues. In arid regions including Xinjiang and Inner Mongolia and other areas worldwide, the area of tree plantations appears to be rising, triggering tree growth. Water is a vital resource in the agricultural systems of countries impacted by aridity and salinity. Worldwide efforts to reduce quantitative yield losses on Populus euphratica by adapting tree plant production to unfavorable environmental conditions have been made in response to the responsiveness of the increasing control of water stress. Although there has been much advancement in identifying the genes that resist abiotic stresses, little is known about how plants such as P. euphratica deal with numerous abiotic stresses. P. euphratica is a varied riparian plant that can tolerate drought, salinity, low temperatures, and climate change, and has a variety of water stress adaptability abilities. To conduct this review, we gathered all available information throughout the Web of Science, the Chinese National Knowledge Infrastructure, and the National Center for Biotechnology Information on the impact of abiotic stress on the molecular mechanism and evolution of gene families at the transcription level. The data demonstrated that P. euphratica might gradually adapt its stomatal aperture, photosynthesis, antioxidant activities, xylem architecture, and hydraulic conductivity to endure extreme drought and salt stress. Our analyses will give readers an understanding of how to manage a gene family in desert trees and the influence of abiotic stresses on the productivity of tree plants. They will also give readers the knowledge necessary to improve biotechnology-based tree plant stress tolerance for sustaining yield and quality trees in China's arid regions.
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Affiliation(s)
- Boniface Ndayambaza
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (B.N.); (B.J.); (X.H.); (D.Z.); (C.W.); (X.Z.); (Z.L.); (J.Q.); (B.W.); (X.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhua Si
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (B.N.); (B.J.); (X.H.); (D.Z.); (C.W.); (X.Z.); (Z.L.); (J.Q.); (B.W.); (X.B.)
| | - Yanfang Deng
- Qilian Mountain National Park Qinghai Provincial Administration, Xining 810000, China;
| | - Bing Jia
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (B.N.); (B.J.); (X.H.); (D.Z.); (C.W.); (X.Z.); (Z.L.); (J.Q.); (B.W.); (X.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohui He
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (B.N.); (B.J.); (X.H.); (D.Z.); (C.W.); (X.Z.); (Z.L.); (J.Q.); (B.W.); (X.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Faculty of Resources and Environment, Baotou Teachers’ College, Inner Mongolia University of Science and Technology, Baotou 014030, China
| | - Dongmeng Zhou
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (B.N.); (B.J.); (X.H.); (D.Z.); (C.W.); (X.Z.); (Z.L.); (J.Q.); (B.W.); (X.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunlin Wang
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (B.N.); (B.J.); (X.H.); (D.Z.); (C.W.); (X.Z.); (Z.L.); (J.Q.); (B.W.); (X.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinglin Zhu
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (B.N.); (B.J.); (X.H.); (D.Z.); (C.W.); (X.Z.); (Z.L.); (J.Q.); (B.W.); (X.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zijin Liu
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (B.N.); (B.J.); (X.H.); (D.Z.); (C.W.); (X.Z.); (Z.L.); (J.Q.); (B.W.); (X.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Qin
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (B.N.); (B.J.); (X.H.); (D.Z.); (C.W.); (X.Z.); (Z.L.); (J.Q.); (B.W.); (X.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Boyang Wang
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (B.N.); (B.J.); (X.H.); (D.Z.); (C.W.); (X.Z.); (Z.L.); (J.Q.); (B.W.); (X.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Bai
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (B.N.); (B.J.); (X.H.); (D.Z.); (C.W.); (X.Z.); (Z.L.); (J.Q.); (B.W.); (X.B.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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Manchanda P, Chaudhary P, Deswal R. Photosynthesis regulation, cell membrane stabilization and methylglyoxal detoxification seems major altered pathways under cold stress as revealed by integrated multi-omics meta-analysis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1395-1407. [PMID: 38076772 PMCID: PMC10709295 DOI: 10.1007/s12298-023-01367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/01/2023] [Accepted: 10/01/2023] [Indexed: 12/17/2023]
Abstract
Climate change has altered cold weather patterns, resulting in irregular cold weather conditions, and changing the global plant distribution pattern affecting plant development processes resulting in severe yield losses. Although molecular mechanisms and interconnections are quite well studied, a cumulative understanding of plant responses to cold stress (CS) is still lacking. Through meta-analysis, integration of data at the multi-omics level and its correlation with known physiological changes to map and understand the global changes in response to CS was made. Meta-analysis was conducted using the metafor R package program based on physiological parameters like relative electrolytic leakage, malondialdehyde, soluble sugar, proline and antioxidant enzymes activity. Proline and soluble sugars showed the highest (> 1.5 mean fold) change over control thus qualifying as global markers for studying CS. Surprisingly most up-regulated (> 15-fold) DEGs corresponded with the dehydrin family and glyoxalase superfamily proteins. Functional annotations of DEGs corresponded with photosynthesis and glycolysis pathway. Proteins responsible for cell signalling and increased soluble sugars were common in all the datasets studied thus correlating with the transcriptome and proteomic data. Proline and soluble sugars were positively regulated in all the metabolomics datasets. This study supported the earlier known players like proline and soluble sugars. Surprisingly, a new player glyoxalase seems to be contributing in CS. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01367-9.
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Affiliation(s)
- Preet Manchanda
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007 India
| | - Parneeta Chaudhary
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007 India
| | - Renu Deswal
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007 India
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