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Liang Y, Yang X, Wang C, Wang Y. miRNAs: Primary modulators of plant drought tolerance. JOURNAL OF PLANT PHYSIOLOGY 2024; 301:154313. [PMID: 38991233 DOI: 10.1016/j.jplph.2024.154313] [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: 11/20/2023] [Revised: 06/17/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024]
Abstract
Drought is a principal environmental factor that affects the growth and development of plants. Accordingly, plants have evolved adaptive mechanisms to cope with adverse environmental conditions. One of the mechanisms is gene regulation mediated by microRNAs (miRNAs). miRNAs are regarded as primary modulators of gene expression at the post-transcriptional level and have been shown to participate in drought stress response, including ABA response, auxin signaling, antioxidant defense, and osmotic regulation through downregulating the corresponding targets. miRNA-based genetic reconstructions have the potential to improve the tolerance of plants to drought. However, there are few precise classification and discussion of miRNAs in specific response behaviors to drought stress and their applications. This review summarized and discussed the specific response behaviors of miRNAs under drought stress and the role of miRNAs as regulators in the response of plants to drought and highlighted that the modification of miRNAs might effectively improve the tolerance of plants to drought.
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Affiliation(s)
- Yanting Liang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaoqian Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Chun Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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An Y, Wang Q, Cui Y, Liu X, Wang P, Zhou Y, Kang P, Chen Y, Wang Z, Zhou Q, Wang P. Comparative physiological and transcriptomic analyses reveal genotype specific response to drought stress in Siberian wildrye (Elymus sibiricus). Sci Rep 2024; 14:21060. [PMID: 39256456 PMCID: PMC11387644 DOI: 10.1038/s41598-024-71847-9] [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: 04/11/2024] [Accepted: 08/31/2024] [Indexed: 09/12/2024] Open
Abstract
Siberian wildrye (Elymus sibiricus) is a xero-mesophytic forage grass with high nutritional quality and stress tolerance. Among its numerous germplasm resources, some possess superior drought resistance. In this study, we firstly investigated the physiological differences between the leaves of drought-tolerant (DT) and drought-sensitive (DS) genotypes under different field water contents (FWC) in soil culture. The results showed that, under drought stress, DT maintained a lower leaf water potential for water absorption, sustained higher photosynthetic efficiency, and reduced oxidative damage in leaves by efficiently maintaining the ascorbic acid-glutathione (ASA-GSH) cycle to scavenge reactive oxygen species (ROS) compared to DS. Secondly, using RNA sequencing (RNA-seq), we analyzed the gene expression profiles of DT and DS leaves under osmotic stress of hydroponics induced by PEG-6000. Through differential analysis, we identified 1226 candidate unigenes, from which we subsequently screened out 115/212 differentially expressed genes (DEGs) that were more quickly induced/reduced in DT than in DS under osmotic stress. Among them, Unigene0005863 (EsSnRK2), Unigene0053902 (EsLRK10) and Unigene0031985 (EsCIPK5) may be involved in stomatal closure induced by abscisic acid (ABA) signaling pathway. Unigene0047636 (EsCER1) may positively regulates the synthesis of very-long-chain (VLC) alkanes in cuticular wax biosynthesis, influencing plant responses to abiotic stresses. Finally, the contents of wax and cutin were measured by GC-MS under osmotic stress of hydroponics induced by PEG-6000. Corresponding to RNA-seq, contents of wax monomers, especially alkanes and alcohols, showed significant induction by osmotic stress in DT but not in DS. It is suggested that limiting stomatal and cuticle transpiration under drought stress to maintain higher photosynthetic efficiency and water use efficiency (WUE) is one of the critical mechanisms that confer stronger drought resistance to DT. This study provides some insights into the molecular mechanisms underlying drought tolerance in E. sibiricus. The identified genes may provide a foundation for the selection and breeding of drought-tolerant crops.
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Affiliation(s)
- Yongping An
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Qian Wang
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Yannong Cui
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Xin Liu
- National Key Laboratory of Crop Genetic Improvement, Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ping Wang
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Yue Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Peng Kang
- College of Biological Science and Engineering, North Minzu University, Yinchuan, 750021, China
| | - Youjun Chen
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Zhiwei Wang
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Qingping Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Pei Wang
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China.
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Zhao X, He F, Qi G, Sun S, Shi Z, Niu Y, Wu Z. Transcriptomic and Physiological Studies Unveil that Brassinolide Maintains the Balance of Maize's Multiple Metabolisms under Low-Temperature Stress. Int J Mol Sci 2024; 25:9396. [PMID: 39273343 PMCID: PMC11395154 DOI: 10.3390/ijms25179396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
Low-temperature (LT) is one of the major abiotic stresses that restrict the growth and development of maize seedlings. Brassinolides (BRs) have been shown to enhance LT tolerance in several plant species; the physiological and molecular mechanisms by which BRs enhance maize tolerance are still unclear. Here, we characterized changes in the physiology and transcriptome of N192 and Ji853 seedlings at the three-leaf stage with or without 2 μM 2,4-epibrassinolide (EBR) application at 25 and 15 °C environments via high-performance liquid chromatography and RNA-Sequencing. Physiological analyses revealed that EBR increased the antioxidant enzyme activities, enhanced the cell membrane stability, decreased the malondialdehyde formation, and inhibited the reactive oxygen species (ROS) accumulation in maize seedlings under 15 °C stress; meanwhile, EBR also maintained hormone balance by increasing indole-3-acetic acid and gibberellin 3 contents and decreasing the abscisic acid level under stress. Transcriptome analysis revealed 332 differentially expressed genes (DEGs) enriched in ROS homeostasis, plant hormone signal transduction, and the mitogen-activated protein kinase (MAPK) cascade. These DEGs exhibited synergistic and antagonistic interactions, forming a complex LT tolerance network in maize. Additionally, weighted gene co-expression network analysis (WGCNA) revealed that 109 hub genes involved in LT stress regulation pathways were discovered from the four modules with the highest correlation with target traits. In conclusion, our findings provide new insights into the molecular mechanisms of exogenous BRs in enhancing LT tolerance of maize at the seedling stage, thus opening up possibilities for a breeding program of maize tolerance to LT stress.
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Affiliation(s)
- Xiaoqiang Zhao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Fuqiang He
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Guoxiang Qi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Siqi Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhenzhen Shi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yining Niu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zefeng Wu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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Peer LA, Bhat MY, Lone AA, Dar ZA, Mir BA. Genetic, molecular and physiological crosstalk during drought tolerance in maize (Zea mays): pathways to resilient agriculture. PLANTA 2024; 260:81. [PMID: 39196449 DOI: 10.1007/s00425-024-04517-9] [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: 02/12/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
MAIN CONCLUSION This review comprehensively elucidates maize drought tolerance mechanisms, vital for global food security. It highlights genetic networks, key genes, CRISPR-Cas applications, and physiological responses, guiding resilient variety development. Maize, a globally significant crop, confronts the pervasive challenge of drought stress, impacting its growth and yield significantly. Drought, an important abiotic stress, triggers a spectrum of alterations encompassing maize's morphological, biochemical, and physiological dimensions. Unraveling and understanding these mechanisms assumes paramount importance for ensuring global food security. Approaches like developing drought-tolerant varieties and harnessing genomic and molecular applications emerge as effective measures to mitigate the negative effects of drought. The multifaceted nature of drought tolerance in maize has been unfolded through complex genetic networks. Additionally, quantitative trait loci mapping and genome-wide association studies pinpoint key genes associated with drought tolerance, influencing morphophysiological traits and yield. Furthermore, transcription factors like ZmHsf28, ZmNAC20, and ZmNF-YA1 play pivotal roles in drought response through hormone signaling, stomatal regulation, and gene expression. Genes, such as ZmSAG39, ZmRAFS, and ZmBSK1, have been reported to be pivotal in enhancing drought tolerance through diverse mechanisms. Integration of CRISPR-Cas9 technology, targeting genes like gl2 and ZmHDT103, emerges as crucial for precise genetic enhancement, highlighting its role in safeguarding global food security amid pervasive drought challenges. Thus, decoding the genetic and molecular underpinnings of drought tolerance in maize sheds light on its resilience and paves the way for cultivating robust and climate-smart varieties, thus safeguarding global food security amid climate challenges. This comprehensive review covers quantitative trait loci mapping, genome-wide association studies, key genes and functions, CRISPR-Cas applications, transcription factors, physiological responses, signaling pathways, offering a nuanced understanding of intricate mechanisms involved in maize drought tolerance.
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Affiliation(s)
- Latif A Peer
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India.
| | - Mohd Y Bhat
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Ajaz A Lone
- Dryland Agriculture Research Station, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, 191121, India
| | - Zahoor A Dar
- Dryland Agriculture Research Station, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, 191121, India
| | - Bilal A Mir
- Department of Botany, North Campus, University of Kashmir, Delina, Srinagar, Jammu and Kashmir, 193201, India
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Dou H, Sun J, Wang T, Bi S, Feng X, Sun H, Quan J. Transcriptomic profiling and discovery of key transcription factors involved in adventitious roots formation from root cuttings of mulberry. BMC Genomics 2024; 25:693. [PMID: 39009981 PMCID: PMC11251115 DOI: 10.1186/s12864-024-10593-8] [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: 12/16/2023] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
ARs plays a crucial role in plant morphogenesis and development. The limited and inefficient rooting of scions poses a significant challenge to the efficiency and quality of clonal propagation of forest trees in silvicultural practices. Building on previous research conducted by our team, we found that applying IBA at a concentration of 1000 mg/L significantly enhanced mulberry rooting. This study aims to uncover the molecular mechanisms underlying this effect by analyzing RNA sequencing data from mulberry phloem before and after treatment with IBA over time intervals of 10, 20, 30, and 40 days. We identified 5226 DEGs, which were then classified into GO terms and KEGG pathways, showing significant enrichment in hormone signaling processes. Using WGCNA, we identified eight co-expression modules, two of which were significantly correlated with the IBA treatment. Additionally, 18 transcription factors that potentially facilitate ARs formation in mulberry were identified, and an exploratory analysis on the cis-regulatory elements associated with these transcription factors was conducted. The findings of this study provide a comprehensive understanding of the mechanisms of ARs in mulberry and offer theoretical support for the discovery and utilization of exceptional genetic resources within the species.
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Affiliation(s)
- Hao Dou
- College of Forest, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiajia Sun
- College of Forest, Henan Agricultural University, Zhengzhou, 450002, China
| | - Tiantian Wang
- College of Forest, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shuwen Bi
- College of Forest, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xi Feng
- College of Forest, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huijuan Sun
- College of Forest, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jin'e Quan
- College of Forest, Henan Agricultural University, Zhengzhou, 450002, China.
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Ren Z, Zhang P, Su H, Xie X, Shao J, Ku L, Tian Z, Deng D, Wei L. Regulatory mechanisms used by ZmMYB39 to enhance drought tolerance in maize (Zea mays) seedlings. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108696. [PMID: 38705046 DOI: 10.1016/j.plaphy.2024.108696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/14/2024] [Accepted: 05/01/2024] [Indexed: 05/07/2024]
Abstract
Drought is a significant abiotic stressor that limits maize (Zea mays L.) growth and development. Thus, enhancing drought tolerance is critical for promoting maize production. Our findings demonstrated that ZmMYB39 is an MYB transcription factor with transcriptional activation activity. Drought stress experiments involving ZmMYB39 overexpression and knockout lines indicated that ZmMYB39 positively regulated drought stress tolerance in maize. DAP-Seq, EMSA, dual-LUC, and RT-qPCR provided initial insights into the molecular regulatory mechanisms by which ZmMYB39 enhances drought tolerance in maize. ZmMYB39 directly promoted the expression of ZmP5CS1, ZmPOX1, ZmSOD2, ZmRD22, ZmNAC49, and ZmDREB2A, which are involved in stress resistance. ZmMYB39 enhanced drought tolerance by interacting with and promoting the expression of ZmFNR1, ZmHSP20, and ZmDOF6. Our study offers a theoretical basis for understanding the molecular regulatory networks involved in maize drought stress response. Furthermore, ZmMYB39 serves as a valuable genetic resource for breeding drought-resistant maize.
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Affiliation(s)
- Zhenzhen Ren
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Pengyu Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, China
| | - Huihui Su
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Xiaowen Xie
- Henna Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jing Shao
- Henna Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou, 450046, China
| | - Lixia Ku
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Zhiqiang Tian
- Henna Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou, 450046, China.
| | | | - Li Wei
- Henna Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou, 450046, China.
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Tan H, Guo M, Chen J, Wang J, Yu G. HetFCM: functional co-module discovery by heterogeneous network co-clustering. Nucleic Acids Res 2024; 52:e16. [PMID: 38088228 PMCID: PMC10853805 DOI: 10.1093/nar/gkad1174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/31/2023] [Accepted: 11/23/2023] [Indexed: 02/10/2024] Open
Abstract
Functional molecular module (i.e., gene-miRNA co-modules and gene-miRNA-lncRNA triple-layer modules) analysis can dissect complex regulations underlying etiology or phenotypes. However, current module detection methods lack an appropriate usage and effective model of multi-omics data and cross-layer regulations of heterogeneous molecules, causing the loss of critical genetic information and corrupting the detection performance. In this study, we propose a heterogeneous network co-clustering framework (HetFCM) to detect functional co-modules. HetFCM introduces an attributed heterogeneous network to jointly model interplays and multi-type attributes of different molecules, and applies multiple variational graph autoencoders on the network to generate cross-layer association matrices, then it performs adaptive weighted co-clustering on association matrices and attribute data to identify co-modules of heterogeneous molecules. Empirical study on Human and Maize datasets reveals that HetFCM can find out co-modules characterized with denser topology and more significant functions, which are associated with human breast cancer (subtypes) and maize phenotypes (i.e., lipid storage, drought tolerance and oil content). HetFCM is a useful tool to detect co-modules and can be applied to multi-layer functional modules, yielding novel insights for analyzing molecular mechanisms. We also developed a user-friendly module detection and analysis tool and shared it at http://www.sdu-idea.cn/FMDTool.
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Affiliation(s)
- Haojiang Tan
- School of Software, Shandong University, Jinan 250101, Shandong, China
- Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University, Jinan 250101, Shandong, China
| | - Maozu Guo
- College of Electrical and Information Engineering, Beijing Uni. of Civil Eng. and Arch., Beijing 100044, China
| | - Jian Chen
- College of Agronomy & Biotechnolog, China Agricultural University, Beijing 100193, China
| | - Jun Wang
- Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University, Jinan 250101, Shandong, China
| | - Guoxian Yu
- School of Software, Shandong University, Jinan 250101, Shandong, China
- Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University, Jinan 250101, Shandong, China
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Wu J, Zhang F, Liu G, Abudureheman R, Bai S, Wu X, Zhang C, Ma Y, Wang X, Zha Q, Zhong H. Transcriptome and coexpression network analysis reveals properties and candidate genes associated with grape ( Vitis vinifera L.) heat tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1270933. [PMID: 38023926 PMCID: PMC10643163 DOI: 10.3389/fpls.2023.1270933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023]
Abstract
Temperature is one of the most important environmental factors affecting grape season growth and geographical distribution. With global warming and the increasing occurrence of extreme high-temperature weather, the impact of high temperatures on grape production has intensified. Therefore, identifying the molecular regulatory networks and key genes involved in grape heat tolerance is crucial for improving the resistance of grapes and promoting sustainable development in grape production. In this study, we observed the phenotypes and cellular structures of four grape varieties, namely, Thompson Seedless (TS), Brilliant Seedless (BS), Jumeigui (JMG), and Shine Muscat (SM), in the naturally high-temperature environment of Turpan. Heat tolerance evaluations were conducted. RNA-seq was performed on 36 samples of the four varieties under three temperature conditions (28°C, 35°C, and 42°C). Through differential expression analysis revealed the fewest differentially expressed genes (DEGs) between the heat-tolerant materials BS and JMG, and the DEGs common to 1890 were identified among the four varieties. The number of differentially expressed genes within the materials was similar, with a total of 3767 common DEGs identified among the four varieties. KEGG enrichment analysis revealed that fatty acid metabolism, starch and sucrose metabolism, plant hormone signal transduction, the MAPK signaling pathway, and plant-pathogen interactions were enriched in both between different temperatures of the same material, and between different materials of the same temperature. We also conducted statistical and expression pattern analyses of differentially expressed transcription factors. Based on Weighted correlation network analysis (WGCNA), four specific modules highly correlated with grape heat tolerance were identified by constructing coexpression networks. By calculating the connectivity of genes within the modules and expression analysis, six candidate genes (VIT_04s0044g01430, VIT_17s0000g09190, VIT_01s0011g01350, VIT_01s0011g03330, VIT_04s0008g05610, and VIT_16s0022g00540) related to heat tolerance were discovered. These findings provide a theoretical foundation for further understanding the molecular mechanisms of grape heat tolerance and offer new gene resources for studying heat tolerance in grapes.
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Affiliation(s)
- Jiuyun Wu
- Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang Grape Engineering Technology Research Center, Turpan, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Fuchun Zhang
- Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang Grape Engineering Technology Research Center, Turpan, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Guohong Liu
- Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang Grape Engineering Technology Research Center, Turpan, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Riziwangguli Abudureheman
- Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang Grape Engineering Technology Research Center, Turpan, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Shijian Bai
- Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang Grape Engineering Technology Research Center, Turpan, China
- Xinjiang Uighur Autonomous Region of Grapes and Melons Research Institution, Turpan, China
| | - Xinyu Wu
- Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang Grape Engineering Technology Research Center, Turpan, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chuan Zhang
- Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang Grape Engineering Technology Research Center, Turpan, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yaning Ma
- Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang Grape Engineering Technology Research Center, Turpan, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xiping Wang
- Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang Grape Engineering Technology Research Center, Turpan, China
- Colleges of Horticulture, Northwest A&F University, Xianyang, China
| | - Qian Zha
- Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang Grape Engineering Technology Research Center, Turpan, China
- Research Institute of Forestry and Pomology, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Haixia Zhong
- Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang Grape Engineering Technology Research Center, Turpan, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
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Li H, Gui Y, Zhu K, Wei J, Zhang R, Yang R, Tang L, Zhou H, Liu X. Comparative transcriptomic analyses of two sugarcane Saccharum L. cultivars differing in drought tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1243664. [PMID: 37885666 PMCID: PMC10598656 DOI: 10.3389/fpls.2023.1243664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
Sugarcane (Saccharum spp.) is an important cash crop, and drought is an important factors limiting its yield. To study the drought resistance mechanism of sugarcane, the transcriptomes of two sugarcane varieties with different levels of drought resistance were compared under different water shortage levels. The results showed that the transcriptomes of the two varieties were significantly different. The differentially expressed genes were enriched in starch and sucrose metabolism, linoleic acid metabolism, glycolysis/gluconeogenesis, and glyoxylate and dicarboxylate metabolic pathways. Unique trend genes of the variety with strong drought resistance (F172) were significantly enriched in photosynthesis, mitogen-activated protein kinases signaling pathway, biosynthesis of various plant secondary metabolites, and cyanoamino acid metabolism pathways. Weighted correlation network analysis indicated that the blue4 and plum1 modules correlated with drought conditions, whereas the tan and salmon4 modules correlated with variety. The unique trend genes expressed in F172 and mapped to the blue4 module were enriched in photosynthesis, purine metabolism, starch and sucrose metabolism, beta-alanine metabolism, photosynthesis-antenna proteins, and plant hormone signal transduction pathways. The expression of genes involved in the photosynthesis-antenna protein and photosynthesis pathways decreased in response to water deficit, indicating that reducing photosynthesis might be a means for sugarcane to respond to drought stress. The results of this study provide insights into drought resistance mechanisms in plants, and the related genes and metabolic pathways identified may be helpful for sugarcane breeding in the future.
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Affiliation(s)
- Haibi Li
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi South Subtropical Agricultural Science Research Institute, Guangxi Academy of Agricultural Sciences, Chongzuo, China
| | - Yiyun Gui
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kai Zhu
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jinju Wei
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ronghua Zhang
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rongzhong Yang
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Liqiu Tang
- Guangxi South Subtropical Agricultural Science Research Institute, Guangxi Academy of Agricultural Sciences, Chongzuo, China
| | - Hui Zhou
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xihui Liu
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
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10
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Wang D, Zhang Y, Chen C, Chen R, Bai X, Qiang Z, Fu J, Qin T. The genetic variation in drought resistance in eighteen perennial ryegrass varieties and the underlying adaptation mechanisms. BMC PLANT BIOLOGY 2023; 23:451. [PMID: 37749497 PMCID: PMC10521523 DOI: 10.1186/s12870-023-04460-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Drought resistance is a complex characteristic closely related to the severity and duration of stress. Perennial ryegrass (Lolium perenne L.) has no distinct drought tolerance but often encounters drought stress seasonally. Although the response of perennial ryegrass to either extreme or moderate drought stress has been investigated, a comprehensive understanding of perennial ryegrass response to both conditions of drought stress is currently lacking. RESULTS In this study, we investigated the genetic variation in drought resistance in 18 perennial ryegrass varieties under both extreme and moderate drought conditions. The performance of these varieties exhibited obvious diversity, and the survival of perennial ryegrass under severe stress was not equal to good growth under moderate drought stress. 'Sopin', with superior performance under both stress conditions, was the best-performing variety. Transcriptome, physiological, and molecular analyses revealed that 'Sopin' adapted to drought stress through multiple sophisticated mechanisms. Under stress conditions, starch and sugar metabolic enzymes were highly expressed, while CslA was expressed at low levels in 'Sopin', promoting starch degradation and soluble sugar accumulation. The expression and activity of superoxide dismutase were significantly higher in 'Sopin', while the activity of peroxidase was lower, allowing for 'Sopin' to maintain a better balance between maintaining ROS signal transduction and alleviating oxidative damage. Furthermore, drought stress-related transcriptional and posttranscriptional regulatory mechanisms, including the upregulation of transcription factors, kinases, and E3 ubiquitin ligases, facilitate abscisic acid and stress signal transduction. CONCLUSION Our study provides insights into the resistance of perennial ryegrass to both extreme and moderate droughts and the underlying mechanisms by which perennial ryegrass adapts to drought conditions.
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Affiliation(s)
- Dan Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Yuting Zhang
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Chunyan Chen
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Ruixin Chen
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Xuechun Bai
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Zhiquan Qiang
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Juanjuan Fu
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Tao Qin
- College of Grassland Agriculture, Northwest A&F University, Yangling, China.
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Li C, Wan Y, Shang X, Fang S. Integration of transcriptomic and metabolomic analysis unveils the response mechanism of sugar metabolism in Cyclocarya paliurus seedlings subjected to PEG-induced drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107856. [PMID: 37354727 DOI: 10.1016/j.plaphy.2023.107856] [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: 04/10/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 06/26/2023]
Abstract
Cyclocarya paliurus (Batal.) Iljinskaja is a multiple function tree species used for functional food and valued timber production. Carbohydrates, especially water-soluble carbohydrates, play an important role in osmotic protection, signal transduction and carbon storage. Under the circumstance of global climate change the abiotic stress would restrict the development of C. paliurus plantation, whereas there is few knowledge on the regulatory mechanisms of sugar metabolism under drought stress in C. paliurus. To investigate the drought response of C. paliurus at molecular level, we conducted an integrated analysis of transcriptomic and metabolomic of C. paliurus at three PEG-induced drought stress levels (0%: control; 15%: moderate drought; 25%: severe drought) in short term. Both moderate and severe drought treatments activated the chemical defense with lowering relative water content, and enhancing the contents of soluble protein, proline and malondialdehyde in the leaves. Meanwhile, alterations in the expression of differentially expressed genes and carbohydrate metabolism profiles were observed among the treatments. Weighted gene co-expression network analysis (WGCNA) showed 3 key modules, 8 structural genes (such as genes encoding beta-fructofuranosidase (INV), sucrose synthase (SUS), raffinose synthase (RS)) and 14 regulatory transcription factors were closely linked to sugar metabolism. Our results provided the foundation to understand the response mechanism of sugar metabolism in C. paliurus under drought stress, and would drive progress in breeding of drought-tolerant varieties and plantation development of the species.
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Affiliation(s)
- Chenhui Li
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yifeng Wan
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xulan Shang
- College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shengzuo Fang
- College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
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12
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Panchal A, Maurya J, Seni S, Singh RK, Prasad M. An insight into the roles of regulatory ncRNAs in plants: An abiotic stress and developmental perspective. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107823. [PMID: 37327647 DOI: 10.1016/j.plaphy.2023.107823] [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: 03/01/2023] [Revised: 04/29/2023] [Accepted: 06/04/2023] [Indexed: 06/18/2023]
Abstract
Different environmental cues lead to changes in physiology, biochemistry and molecular status of plant's growth. Till date, various genes have been accounted for their role in regulating plant development and response to abiotic stress. Excluding genes that code for a functional protein in a cell, a large chunk of the eukaryotic transcriptome consists of non-coding RNAs (ncRNAs) which lack protein coding capacity but are still functional. Recent advancements in Next Generation Sequencing (NGS) technology have led to the unearthing of different types of small and large non-coding RNAs in plants. Non-coding RNAs are broadly categorised into housekeeping ncRNAs and regulatory ncRNAs which work at transcriptional, post-transcriptional and epigenetic levels. Diverse ncRNAs play different regulatory roles in nearly all biological processes including growth, development and response to changing environments. This response can be perceived and counteracted by plants using diverse evolutionarily conserved ncRNAs like miRNAs, siRNAs and lncRNAs to participate in complex molecular regimes by activating gene-ncRNA-mRNA regulatory modules to perform the downstream function. Here, we review the current understanding with a focus on recent advancements in the functional studies of the regulatory ncRNAs at the nexus of abiotic stresses and development. Also, the potential roles of ncRNAs in imparting abiotic stress tolerance and yield improvement in crop plants are also discussed with their future prospects.
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Affiliation(s)
- Anurag Panchal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Jyoti Maurya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Sushmita Seni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India.
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Wang Y, Wang J, Guo H, Wu X, Hao M, Zhang R. Integrative transcriptome and metabolome analysis reveals the mechanism of exogenous melatonin alleviating drought stress in maize roots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107723. [PMID: 37163805 DOI: 10.1016/j.plaphy.2023.107723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/15/2023] [Accepted: 04/25/2023] [Indexed: 05/12/2023]
Abstract
Melatonin (MT) is essential for plant development and drought adaptation. However, the molecular and metabolic mechanisms underlying MT-induced drought tolerance in maize roots remain largely unclear. Herein, we investigated the effects of MT on drought tolerance in maize roots using integrated transcriptomic and metabolomic analyses, and identified MT-induced genes and metabolites associated with drought resistance. Compared with the untreated control plants, MT application alleviated the deleterious effects of drought on roots, by decreasing the malondialdehyde level and increasing the solute potential, eventually promoting root growth. Transcriptome and metabolome analysis demonstrated that MT significantly upregulates the expression of genes related to flavonoid biosynthesis (PAL, C4H, 4CL, HCT, CHS, CHI, F3'5'H, and DFR), activates drought-responsive transcription factors (ERFs, NACs, MYBs, and bHLHs), and regulates hormone signaling-related genes, especially ethylene response factors (ERF4, ERF81, and ERF110). Moreover, MT increased the accumulation of flavonoid metabolites, particularly apigenin, luteolin, and quercetin, under drought-stress conditions. These findings were further supported by quantitative real-time polymerase chain reaction analysis and total flavonoid measurements. Altogether, our findings suggest that MT promotes maize root growth during drought by regulating flavonoid synthesis pathways, transcription factors, and plant hormone signals. This study provides new insights into the complex mechanisms by which MT enhances crop resistance to drought damage.
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Affiliation(s)
- Yifan Wang
- College of Agronomy, Northwest A&F University, Shaanxi, Yangling, 712100, China
| | - Jiarui Wang
- College of Agronomy, Northwest A&F University, Shaanxi, Yangling, 712100, China
| | - Haoxue Guo
- College of Agronomy, Northwest A&F University, Shaanxi, Yangling, 712100, China
| | - Xi Wu
- College of Agronomy, Northwest A&F University, Shaanxi, Yangling, 712100, China
| | - Miaoyi Hao
- College of Agronomy, Northwest A&F University, Shaanxi, Yangling, 712100, China
| | - Renhe Zhang
- College of Agronomy, Northwest A&F University, Shaanxi, Yangling, 712100, China.
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14
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Liu X, Su L, Li L, Zhang Z, Li X, Liang Q, Li L. Transcriptome profiling reveals characteristics of hairy root and the role of AhGLK1 in response to drought stress and post-drought recovery in peanut. BMC Genomics 2023; 24:119. [PMID: 36927268 PMCID: PMC10018853 DOI: 10.1186/s12864-023-09219-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND HR (hairy root) has emerged as a valuable tissue for the rapid characterization of plant gene function and enzyme activity in vivo. AhGLK1 (Arachis hypogaea L. golden2-like 1) is known to play a role in post-drought recovery. However, it is unclear (a) whether HR has properties that are distinct from those of PR (primary root); and (b) which gene networks are regulated by AhGLK1 in response to drought stress and recovery in peanut. RESULTS We found that cells of the root tip cortex were larger in HR than in PR, while a total of 850 differentially expressed genes (DEGs) were identified in HR compared to PR. Eighty-eight of these DEGs, relating to chlorophyll and photosynthesis, were upregulated in HR. In addition, AhGLK1-OX (AhGLK1-overexpressing) HR showed a green phenotype, and had a higher relative water content than 35 S::eGFP (control) HR during drought stress. RNA-seq analysis showed that 74 DEGs involved both in the drought response and the post-drought recovery process were significantly enriched in the galactose metabolism pathway. GO terms enrichment analysis revealed that 59.19%, 29.79% and 17.02% of the DEGs mapped to the 'biological process' (BP), 'molecular function' (MF) and 'cellular component' (CC) domains, respectively. Furthermore, 20 DEGs involved in post-drought recovery were uniquely expressed in AhGLK1-OX HR and were significantly enriched in the porphyrin metabolism pathway. GO analysis showed that 42.42%, 30.30% and 27.28% of DEGs could be assigned to the BP, MF and CC domains, respectively. Transcription factors including bHLH and MYB family members may play a key role during drought stress and recovery. CONCLUSION Our data reveal that HR has some of the characteristics of leaves, indicating that HR is suitable for studying genes that are mainly expressed in leaves. The RNA-seq results are consistent with previous studies that show chlorophyll synthesis and photosynthesis to be critical for the role of AhGLK1 in improving post-drought recovery growth in peanut. These findings provide in-depth insights that will be of great utility for the exploration of candidate gene functions in relation to drought tolerance and/or post-drought recovery ability in peanut.
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Affiliation(s)
- Xing Liu
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, 519040, Zhuhai, China.,Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Liangchen Su
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, 519040, Zhuhai, China
| | - Limei Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Zhi Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Xiaoyun Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Qingjian Liang
- School of Fishery, Zhejiang Ocean University, 316022, Zhoushan, Zhejiang, China.
| | - Ling Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China.
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15
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Jiang Y, Su S, Chen H, Li S, Shan X, Li H, Liu H, Dong H, Yuan Y. Transcriptome analysis of drought-responsive and drought-tolerant mechanisms in maize leaves under drought stress. PHYSIOLOGIA PLANTARUM 2023; 175:e13875. [PMID: 36775906 DOI: 10.1111/ppl.13875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 01/18/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Maize is a major crop essential for food and feed, but its production is threatened by various biotic and abiotic stresses. Drought is one of the most common abiotic stresses, causing severe crop yield reduction. Although several studies have been devoted to selecting drought-tolerant maize lines and detecting the drought-responsive mechanism of maize, the transcriptomic differences between drought-tolerant and drought-susceptible maize lines are still largely unknown. In our study, RNA-seq was performed on leaves of the drought-tolerant line W9706 and the drought-susceptible line B73 after drought treatment. We identified 3147 differentially expressed genes (DEGs) between these two lines. The upregulated DEGs in W9706 were enriched in specific processes, including ABA signaling, wax biosynthesis, CHO metabolism, signal transduction and brassinosteroid biosynthesis-related processes, while the downregulated DEGs were enriched in specific processes, such as stomatal movement. Altogether, transcriptomic analysis suggests that the different drought resistances were correlated with the differential expression of genes, while the drought tolerance of W9706 is due to the more rapid response to stimulus, higher water retention capacity and stable cellular environment under water deficit conditions.
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Affiliation(s)
- Yuan Jiang
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Shengzhong Su
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Hao Chen
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Shipeng Li
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Xiaohui Shan
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - He Li
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Hongkui Liu
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Haixiao Dong
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Yaping Yuan
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
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16
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Yang Z, Qin F. The battle of crops against drought: Genetic dissection and improvement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:496-525. [PMID: 36639908 DOI: 10.1111/jipb.13451] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
With ongoing global climate change, water scarcity-induced drought stress remains a major threat to agricultural productivity. Plants undergo a series of physiological and morphological changes to cope with drought stress, including stomatal closure to reduce transpiration and changes in root architecture to optimize water uptake. Combined phenotypic and multi-omics studies have recently identified a number of drought-related genetic resources in different crop species. The functional dissection of these genes using molecular techniques has enriched our understanding of drought responses in crops and has provided genetic targets for enhancing resistance to drought. Here, we review recent advances in the cloning and functional analysis of drought resistance genes and the development of technologies to mitigate the threat of drought to crop production.
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Affiliation(s)
- Zhirui Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Feng Qin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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17
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Hu Z, He Z, Li Y, Wang Q, Yi P, Yang J, Yang C, Borovskii G, Cheng X, Hu R, Zhang W. Transcriptomic and metabolic regulatory network characterization of drought responses in tobacco. FRONTIERS IN PLANT SCIENCE 2023; 13:1067076. [PMID: 36743571 PMCID: PMC9891310 DOI: 10.3389/fpls.2022.1067076] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/30/2022] [Indexed: 06/18/2023]
Abstract
Drought stress usually causes huge economic losses for tobacco industries. Drought stress exhibits multifaceted impacts on tobacco systems through inducing changes at different levels, such as physiological and chemical changes, changes of gene transcription and metabolic changes. Understanding how plants respond and adapt to drought stress helps generate engineered plants with enhanced drought resistance. In this study, we conducted multiple time point-related physiological, biochemical,transcriptomic and metabolic assays using K326 and its derived mutant 28 (M28) with contrasting drought tolerance. Through integrative analyses of transcriptome and metabolome,we observed dramatic changes of gene expression and metabolic profiles between M28 and K326 before and after drought treatment. we found that some of DEGs function as key enzymes responsible for ABA biosynthesis and metabolic pathway, thereby mitigating impairment of drought stress through ABA signaling dependent pathways. Four DEGs were involved in nitrogen metabolism, leading to synthesis of glutamate (Glu) starting from NO-3 /NO-2 that serves as an indicator for stress responses. Importantly, through regulatory network analyses, we detected several drought induced TFs that regulate expression of genes responsible for ABA biosynthesis through network, indicating direct and indirect involvement of TFs in drought responses in tobacco. Thus, our study sheds some mechanistic insights into how plant responding to drought stress through transcriptomic and metabolic changes in tobacco. It also provides some key TF or non-TF gene candidates for engineering manipulation for breeding new tobacco varieties with enhanced drought tolerance.
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Affiliation(s)
- Zhengrong Hu
- Hunan Tobacco Research Institute, Changsha, Hunan, China
| | - Zexue He
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yangyang Li
- Hunan Tobacco Research Institute, Changsha, Hunan, China
| | - Qing Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Pengfei Yi
- Hu'nan Tobacco Company Changde Company, Changde, Hunan, China
| | - Jiashuo Yang
- Hunan Tobacco Research Institute, Changsha, Hunan, China
| | - Chenkai Yang
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China
| | - Gennadii Borovskii
- Siberian Institute of Plant Physiology and Biochemistry Siberian Branch of Russian Academy of Sciences (SB RAS) Irkutsk, Lermontova, Russia
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Risheng Hu
- Hunan Tobacco Research Institute, Changsha, Hunan, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu, China
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18
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Cao Q, Huang L, Li J, Qu P, Tao P, Crabbe MJC, Zhang T, Qiao Q. Integrated transcriptome and methylome analyses reveal the molecular regulation of drought stress in wild strawberry (Fragaria nilgerrensis). BMC PLANT BIOLOGY 2022; 22:613. [PMID: 36575384 PMCID: PMC9795625 DOI: 10.1186/s12870-022-04006-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Fragaria nilgerrensis, which is a diploid wild strawberry with excellent drought-resistance, would provide useful candidate genes for improving drought resistance of cultivated strawberry. So far, its molecular regulatory networks involved in drought stress are unclear. We therefore investigated the drought response regulatory networks of F. nilgerrensis based on the integrated analysis of DNA methylation, transcriptome and physiological traits during four time points under drought stress. RESULTS: The most differentially expressed genes and the physiological changes were found at 8 days (T8) compared with 0 day (T0, control). Methylome analysis revealed slight dynamic changes in genome-wide mC levels under drought conditions, while the most hypomethylated and hypermethylated regions were identified at T4 and T8. Association analysis of the methylome and transcriptome revealed that unexpressed genes exhibited expected hypermethylation levels in mCHG and mCHH contexts, and highly expressed genes exhibited corresponding hypomethylation levels in the gene body, but mCG contexts showed the opposite trend. Then, 835 differentially methylated and expressed genes were identified and grouped into four clustering patterns to characterize their functions. The genes with either negative or positive correlation between methylation and gene expression were mainly associated with kinases, Reactive Oxygen Species (ROS) synthesis, scavenging, and the abscisic acid (ABA) signal pathway. Consistently, weighted gene co-expression network analysis (WGCNA) revealed Hub genes including NCED, CYP707A2, PP2Cs and others that play important roles in the ABA signaling pathway. CONCLUSION F. nilgerrensis drought is dominated by ABA-dependent pathways, possibly accompanied by ABA-independent crosstalk. DNA methylation may affect gene expression, but their correlation was more subtle and multiple types of association exist. Maintaining the balance between ROS regeneration and scavenging is an important factor in drought resistance in F. nilgerrensis. These results deepen our understanding of drought resistance and its application in breeding in strawberry plants.
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Affiliation(s)
- Qiang Cao
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Lin Huang
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Jiamin Li
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Peng Qu
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Pang Tao
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, 650205, Kunming, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, OX26UD, UK
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Park Square, LU1 3JU, Luton, UK
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, 650500, Kunming, China.
| | - Qin Qiao
- College of Horticulture and Landscape, Yunnan Agricultural University, 650201, Kunming, China.
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Lv L, Chen X, Li H, Huang J, Liu Y, Zhao A. Different adaptive patterns of wheat with different drought tolerance under drought stresses and rehydration revealed by integrated metabolomic and transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:1008624. [PMID: 36311061 PMCID: PMC9608176 DOI: 10.3389/fpls.2022.1008624] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/26/2022] [Indexed: 05/27/2023]
Abstract
Wheat as a staple food crop is enduring ever-frequent intermittent and changing drought with the climate change. It is of great significance to highlight the adaptive approaches under such variable conditions at multiple levels to provide a comprehensive understanding of drought tolerance and facilitate the genetic breeding of wheat. Therefore, three wheat lines with different drought tolerance (drought-tolerant mutant Mu > common wheat CK > drought susceptible mutant mu) were analyzed under moderate and severe drought stresses as well as rehydration. Samples were subjected to transcriptomic and metabolomic profiling in combination with physiological and biochemical determination. The moderate drought stress rendered 198 and 115 differentially expressed metabolites (DEMs) in CK and Mu, respectively. The severe drought stress rendered 166, 151 and 137 DEMs in CK, Mu and mu, respectively. The rehydration rendered 150 and 127 DEMs in CK and Mu. 12,557 and 10,402 differentially expressed genes (DEGs) were identified for CK and Mu under moderate drought stress, respectively. 9,893, 7,924, and 9,387 DEGs were identified for CK, Mu, and mu under severe drought stress, respectively. 13,874 and 14,839 were identified in CK and Mu under rehydration, respectively. Metabolomics results showed that amino acid was the most differentially expressed metabolites, followed by phenolic acids. Flavonoids played an important role in drought tolerance. Most enriched pathways under drought included biosynthesis of secondary metabolites, metabolic pathways and photosynthesis. Metabolites and genes involved in osmotic regulation, antioxidase activities, and ABA signaling were more enriched in Mu than in CK and mu. Various drought-responsive genes and metabolites in Mu showed different trends with those in CK and mu. Increased amino acids biosynthetic capability and ROS scavenging ability resulted from higher antioxidase activities and increased flavonoids may be the mechanisms underlying the drought tolerance characteristic of Mu. Recovery from reversible ROS damage and rapid amino acid biosynthesis may contribute to the rapid recovery of Mu. The present study provides new insights for mechanisms of wheat under complex drought conditions.
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Insights into the Response of Perennial Ryegrass to Abiotic Stress: Underlying Survival Strategies and Adaptation Mechanisms. LIFE (BASEL, SWITZERLAND) 2022; 12:life12060860. [PMID: 35743891 PMCID: PMC9224976 DOI: 10.3390/life12060860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022]
Abstract
Perennial ryegrass (Lolium perenne L.) is an important turfgrass and gramineous forage widely grown in temperate regions around the world. However, its perennial nature leads to the inevitable exposure of perennial ryegrass to various environmental stresses on a seasonal basis and from year to year. Like other plants, perennial ryegrass has evolved sophisticated mechanisms to make appropriate adjustments in growth and development in order to adapt to the stress environment at both the physiological and molecular levels. A thorough understanding of the mechanisms of perennial ryegrass response to abiotic stresses is crucial for obtaining superior stress-tolerant varieties through molecular breeding. Over the past decades, studies of perennial ryegrass at the molecular and genetic levels have revealed a lot of useful information to understand the mechanisms of perennial ryegrass adaptation to an adverse environment. Unfortunately, molecular mechanisms by which perennial ryegrass adapts to abiotic stresses have not been reviewed thus far. In this review, we summarize the recent works on the genetic and molecular mechanisms of perennial ryegrass response to the major abiotic stresses (i.e., drought, salinity, and extreme temperatures) and discuss new directions for future studies. Such knowledge will provide valuable information for molecular breeding in perennial ryegrass to improve stress resistance and promote the sustainability of agriculture and the environment.
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