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Jin J, Yang L, Fan D, Li L, Hao Q. Integration analysis of miRNA-mRNA pairs between two contrasting genotypes reveals the molecular mechanism of jujube (Ziziphus jujuba Mill.) response to high-temperature stress. BMC PLANT BIOLOGY 2024; 24:612. [PMID: 38937704 PMCID: PMC11209981 DOI: 10.1186/s12870-024-05304-0] [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: 08/11/2023] [Accepted: 06/17/2024] [Indexed: 06/29/2024]
Abstract
With global warming, high temperature (HT) has become one of the most common abiotic stresses resulting in significant crop yield losses, especially for jujube (Ziziphus jujuba Mill.), an important temperate economic crop cultivated worldwide. This study aims to explore the coping mechanism of jujube to HT stress at the transcriptional and post-transcriptional levels, including identifying differentially expressed miRNAs and mRNAs as well as elucidating the critical pathways involved. High-throughput sequencing analyses of miRNA and mRNA were performed on jujube leaves, which were collected from "Fucumi" (heat-tolerant) and "Junzao" (heat-sensitive) cultivars subjected to HT stress (42 °C) for 0, 1, 3, 5, and 7 days, respectively. The results showed that 45 known miRNAs, 482 novel miRNAs, and 13,884 differentially expressed mRNAs (DEMs) were identified. Among them, integrated analysis of miRNA target genes prediction and mRNA-seq obtained 1306 differentially expressed miRNAs-mRNAs pairs, including 484, 769, and 865 DEMIs-DEMs pairs discovered in "Fucuimi", "Junzao" and two genotypes comparative groups, respectively. Furthermore, functional enrichment analysis of 1306 DEMs revealed that plant-pathogen interaction, starch and sucrose metabolism, spliceosome, and plant hormone signal transduction were crucial pathways in jujube leaves response to HT stress. The constructed miRNA-mRNA network, composed of 20 DEMIs and 33 DEMs, displayed significant differently expressions between these two genotypes. This study further proved the regulatory role of miRNAs in the response to HT stress in plants and will provide a theoretical foundation for the innovation and cultivation of heat-tolerant varieties.
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Affiliation(s)
- Juan Jin
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi, Xinjiang, 830091, China
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, Xinjiang, 830091, China
| | - Lei Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi, Xinjiang, 830091, China
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, Xinjiang, 830091, China
| | - Dingyu Fan
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi, Xinjiang, 830091, China
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, Xinjiang, 830091, China
| | - Lili Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi, Xinjiang, 830091, China
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, Xinjiang, 830091, China
| | - Qing Hao
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China.
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi, Xinjiang, 830091, China.
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, Xinjiang, 830091, China.
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Lang X, Zhao X, Zhao J, Ren T, Nie L, Zhao W. MicroRNA Profiling Revealed the Mechanism of Enhanced Cold Resistance by Grafting in Melon ( Cucumis melo L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1016. [PMID: 38611545 PMCID: PMC11013280 DOI: 10.3390/plants13071016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Grafting is widely used to improve the resistance to abiotic stresses in cucurbit plants, but the effect and molecular mechanism of grafting on cold stress are still unknown in melon. In this study, phenotypic characteristics, physiological indexes, small-RNA sequencing and expression analyses were performed on grafted plants with pumpkin rootstock (PG) and self-grafted plants (SG) to explore the mechanism of changed cold tolerance by grafting in melon. Compared with SG plants, the cold tolerance was obviously enhanced, the malondialdehyde (MDA) content was significantly decreased and the activities of antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT; peroxidase, POD) were significantly increased in PG plants. Depend on differentially expressed miRNA (DEM) identification and expression pattern analyses, cme-miR156b, cme-miR156f and chr07_30026 were thought to play a key role in enhancing low-temperature resistance resulting from grafting. Subsequently, 24, 37 and 17 target genes of cme-miR156b, cme-miR156f and chr07_30026 were respectively predicted, and 21 target genes were co-regulated by cme-miR156b and cme-miR156f. Among these 57 unique target genes, the putative promoter of 13 target genes contained the low-temperature responsive (LTR) cis-acting element. The results of qRT-PCR indicated that six target genes (MELO3C002370, MELO3C009217, MELO3C018972, MELO3C016713, MELO3C012858 and MELO3C000732) displayed the opposite expression pattern to their corresponding miRNAs. Furthermore, MELO3C002370, MELO3C016713 and MELO3C012858 were significantly downregulated in cold-resistant cultivars and upregulated in cold-sensitive varieties after cold stimulus, and they acted as the key negative regulators of low-temperature response in melon. This study revealed three key miRNAs and three putative target genes involved in the cold tolerance of melon and provided a molecular basis underlying how grafting improved the low-temperature resistance of melon plants.
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Affiliation(s)
- Xinmei Lang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Xuan Zhao
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Jiateng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Tiantian Ren
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Lanchun Nie
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding 071000, China
- Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, Baoding 071000, China
| | - Wensheng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding 071000, China
- Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, Baoding 071000, China
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Jyoti TP, Chandel S, Singh R. Unveiling the epigenetic landscape of plants using flow cytometry approach. Cytometry A 2024; 105:231-241. [PMID: 38437027 DOI: 10.1002/cyto.a.24834] [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: 09/23/2023] [Revised: 01/12/2024] [Accepted: 02/22/2024] [Indexed: 03/06/2024]
Abstract
Plants are sessile creatures that have to adapt constantly changing environmental circumstances. Plants are subjected to a range of abiotic stressors as a result of unpredictable climate change. Understanding how stress-responsive genes are regulated can help us better understand how plants can adapt to changing environmental conditions. Epigenetic markers that dynamically change in response to stimuli, such as DNA methylation and histone modifications are known to regulate gene expression. Individual cells or particles' physical and/or chemical properties can be measured using the method known as flow cytometry. It may therefore be used to evaluate changes in DNA methylation, histone modifications, and other epigenetic markers, making it a potent tool for researching epigenetics in plants. We explore the use of flow cytometry as a technique for examining epigenetic traits in this thorough discussion. The separation of cell nuclei and their subsequent labeling with fluorescent antibodies, offering information on the epigenetic mechanisms in plants when utilizing flow cytometry. We also go through the use of high-throughput data analysis methods to unravel the complex epigenetic processes occurring inside plant systems.
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Affiliation(s)
- Thakur Prava Jyoti
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Shivani Chandel
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
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He M, Liu J, Tan J, Jian Y, Liu J, Duan Y, Li G, Jin L, Xu J. A Comprehensive Interaction Network Constructed Using miRNAs and mRNAs Provides New Insights into Potato Tuberization under High Temperatures. PLANTS (BASEL, SWITZERLAND) 2024; 13:998. [PMID: 38611527 PMCID: PMC11013713 DOI: 10.3390/plants13070998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024]
Abstract
High temperatures delay tuberization and decrease potato (Solanum tuberosum L.) yields. However, the molecular mechanisms and regulatory networks underlying tuberization under high temperatures remain largely unknown. Here, we performed the mRNA and miRNA sequencing of leaves and stems to identify genes and regulatory networks involved in tuberization under high temperatures. A total of 2804 and 5001 differentially expressed genes (DEGs) under high-temperature stress were identified in leaves and stems, respectively. These genes were significantly enriched in gene ontology terms regarding meristem development, the sucrose biosynthetic process, and response to heat. Meanwhile, 101 and 75 differentially expressed miRNAs (DEmiRNAs) were identified in leaves and stems, respectively. We constructed an interaction network between DEmiRNAs and DEGs, identifying 118 and 150 DEmiRNA-DEG pairs in leaves and stems, respectively. We found three miRNA-mRNA candidate modules involved in tuberization under high temperatures, including stu-miR8030-5p/StCPY714, stu-miR7981f-p5/StAGL8a, and stu-miR10532A/StAGL8b. Our study constructed an interaction network between miRNAs and target genes and proposes candidate miRNA-gene modules that regulate tuber formation under high temperatures. Our study provides new insights for revealing the regulatory mechanism of the high-temperature inhibition of tuberization and also provides gene resources for improving the heat tolerance in potatoes.
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Affiliation(s)
- Ming He
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (M.H.); (J.L.); (J.T.); (Y.J.); (J.L.); (Y.D.); (G.L.); (L.J.)
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ju Liu
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (M.H.); (J.L.); (J.T.); (Y.J.); (J.L.); (Y.D.); (G.L.); (L.J.)
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Tan
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (M.H.); (J.L.); (J.T.); (Y.J.); (J.L.); (Y.D.); (G.L.); (L.J.)
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinqiao Jian
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (M.H.); (J.L.); (J.T.); (Y.J.); (J.L.); (Y.D.); (G.L.); (L.J.)
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiangang Liu
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (M.H.); (J.L.); (J.T.); (Y.J.); (J.L.); (Y.D.); (G.L.); (L.J.)
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanfeng Duan
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (M.H.); (J.L.); (J.T.); (Y.J.); (J.L.); (Y.D.); (G.L.); (L.J.)
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangcun Li
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (M.H.); (J.L.); (J.T.); (Y.J.); (J.L.); (Y.D.); (G.L.); (L.J.)
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liping Jin
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (M.H.); (J.L.); (J.T.); (Y.J.); (J.L.); (Y.D.); (G.L.); (L.J.)
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianfei Xu
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (M.H.); (J.L.); (J.T.); (Y.J.); (J.L.); (Y.D.); (G.L.); (L.J.)
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Wang Q, Wu Y, Wu W, Lyu L, Li W. A review of changes at the phenotypic, physiological, biochemical, and molecular levels of plants due to high temperatures. PLANTA 2024; 259:57. [PMID: 38307982 DOI: 10.1007/s00425-023-04320-y] [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: 09/17/2023] [Accepted: 12/23/2023] [Indexed: 02/04/2024]
Abstract
MAIN CONCLUSION This review summarizes the physiological, biochemical, and molecular regulatory network changes in plants in response to high temperature. With the continuous rise in temperature, high temperature has become an important issue limiting global plant growth and development, affecting the phenotype and physiological and biochemical processes of plants and seriously restricting crop yield and tree growth speed. As sessile organisms, plants inevitably encounter high temperatures and improve their heat tolerance by activating molecular networks related to heat stress, such as signal transduction, synthesis of metabolites, and gene expression. Heat tolerance is a polygenic trait regulated by a variety of genes, transcription factors, proteins, and metabolites. Therefore, this review summarizes the changes in physiological, biochemical and molecular regulatory networks in plants under high-temperature conditions to lay a foundation for an in-depth understanding of the mechanisms involved in plant heat tolerance responses.
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Affiliation(s)
- Que Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Qian Hu Hou Cun No. 1, Nanjing, 210014, China.
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Qian Hu Hou Cun No. 1, Nanjing, 210014, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Qian Hu Hou Cun No. 1, Nanjing, 210014, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.
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Amini Z, Salehi H, Chehrazi M, Etemadi M, Xiang M. miRNAs and Their Target Genes Play a Critical Role in Response to Heat Stress in Cynodon dactylon (L.) Pers. Mol Biotechnol 2023; 65:2004-2017. [PMID: 36913082 DOI: 10.1007/s12033-023-00713-2] [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: 12/27/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023]
Abstract
Annual global temperature is increasing rapidly. Therefore, in the near future, plants will be exposed to severe heat stress. However, the potential of microRNAs-mediated molecular mechanism for modulating the expression of their target genes is unclear. To investigate the changes of miRNAs in thermo-tolerant plants, in this study, we first investigated the impact of four high temperature regimes including 35/30 °C, 40/35 °C, 45/40 °C, and 50/45 °C in a day/night cycle for 21 days on the physiological traits (total chlorophyll, relative water content and electrolyte leakage and total soluble protein), antioxidant enzymes activities (superoxide dismutase, ascorbic peroxidase, catalase and peroxidase), and osmolytes (total soluble carbohydrates and starch) in two bermudagrass accessions named Malayer and Gorgan. The results showed that more chlorophyll and the relative water content, lower ion leakage, more efficient protein and carbon metabolism and activation of defense proteins (such as antioxidant enzymes) in Gorgan accession, led to better maintained plant growth and activity during heat stress. In the next stage, to investigate the role of miRNAs and their target genes in response to heat stress in a thermo-tolerant plant, the impact of severe heat stress (45/40 °C) was evaluated on the expression of three miRNAs (miRNA159a, miRNA160a and miRNA164f) and their target genes (GAMYB, ARF17 and NAC1, respectively). All measurements were performed in leaves and roots simultaneously. Heat stress significantly induced the expression of three miRNAs in leaves of two accession, while having different effects on the expression of these miRNAs in roots. The results showed that a decrease in the expression of the transcription factor ARF17, no change in the expression of the transcription factor NAC1, and an increase in the expression of the transcription factor GAMYB in leaf and root tissues of Gorgan accession led to improved heat tolerance in it. These results also showed that the effect of miRNAs on the modulating expression of target mRNAs in leaves and roots is different under heat stress, and miRNAs and mRNAs show spatiotemporal expression. Therefore, the simultaneous analysis of miRNAs and mRNAs expressions in shoot and roots is needed to comprehensively understand miRNAs regulatory function under heat stress.
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Affiliation(s)
- Zohreh Amini
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Hassan Salehi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran.
| | - Mehrangiz Chehrazi
- Department of Horticultural Science, School of Agriculture, Shahid Chamran University, Ahvaz, Iran
| | - Mohammad Etemadi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Mingying Xiang
- Department of Horticulture and Landscape Architecture, Oklahoma State University, Stillwater, OK, 74078, USA
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Zhou C, Wu S, Li C, Quan W, Wang A. Response Mechanisms of Woody Plants to High-Temperature Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:3643. [PMID: 37896106 PMCID: PMC10610489 DOI: 10.3390/plants12203643] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023]
Abstract
High-temperature stress is the main environmental stress that restricts the growth and development of woody plants, and the growth and development of woody plants are affected by high-temperature stress. The influence of high temperature on woody plants varies with the degree and duration of the high temperature and the species of woody plants. Woody plants have the mechanism of adapting to high temperature, and the mechanism for activating tolerance in woody plants mainly counteracts the biochemical and physiological changes induced by stress by regulating osmotic adjustment substances, antioxidant enzyme activities and transcription control factors. Under high-temperature stress, woody plants ability to perceive high-temperature stimuli and initiate the appropriate physiological, biochemical and genomic changes is the key to determining the survival of woody plants. The gene expression induced by high-temperature stress also greatly improves tolerance. Changes in the morphological structure, physiology, biochemistry and genomics of woody plants are usually used as indicators of high-temperature tolerance. In this paper, the effects of high-temperature stress on seed germination, plant morphology and anatomical structure characteristics, physiological and biochemical indicators, genomics and other aspects of woody plants are reviewed, which provides a reference for the study of the heat-tolerance mechanism of woody plants.
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Affiliation(s)
- Chao Zhou
- Key Laboratory for Information System of Mountainous Area and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang 550001, China; (C.Z.); (C.L.)
| | - Shengjiang Wu
- Guizhou Academy of Tobacco Science, Guiyang 550081, China;
| | - Chaochan Li
- Key Laboratory for Information System of Mountainous Area and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang 550001, China; (C.Z.); (C.L.)
| | - Wenxuan Quan
- Key Laboratory for Information System of Mountainous Area and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang 550001, China; (C.Z.); (C.L.)
| | - Anping Wang
- Key Laboratory for Information System of Mountainous Area and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang 550001, China; (C.Z.); (C.L.)
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Hamid R, Jacob F, Ghorbanzadeh Z, Jafari L, Alishah O. Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2023; 23:488. [PMID: 37828433 PMCID: PMC10571366 DOI: 10.1186/s12870-023-04495-2] [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: 05/17/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Heterosis is a complex phenomenon wherein the hybrids outperform their parents. Understanding the underlying molecular mechanism by which hybridization leads to higher yields in allopolyploid cotton is critical for effective breeding programs. Here, we integrated DNA methylation, transcriptomes, and small RNA profiles to comprehend the genetic and molecular basis of heterosis in allopolyploid cotton at three developmental stages. RESULTS Transcriptome analysis revealed that numerous DEGs responsive to phytohormones (auxin and salicylic acid) were drastically altered in F1 hybrid compared to the parental lines. DEGs involved in energy metabolism and plant growth were upregulated, whereas DEGs related to basal defense were downregulated. Differences in homoeologous gene expression in F1 hybrid were greatly reduced after hybridization, suggesting that higher levels of parental expression have a vital role in heterosis. Small RNAome and methylome studies showed that the degree of DNA methylation in hybrid is higher when compared to the parents. A substantial number of allele-specific expression genes were found to be strongly regulated by CG allele-specific methylation levels. The hybrid exhibited higher 24-nt-small RNA (siRNA) expression levels than the parents. The regions in the genome with increased levels of 24-nt-siRNA were chiefly related to genes and their flanking regulatory regions, demonstrating a possible effect of these molecules on gene expression. The transposable elements correlated with siRNA clusters in the F1 hybrid had higher methylation levels but lower expression levels, which suggest that these non-additively expressed siRNA clusters, reduced the activity of transposable elements through DNA methylation in the hybrid. CONCLUSIONS These multi-omics data provide insights into how changes in epigenetic mechanisms and gene expression patterns can lead to heterosis in allopolyploid cotton. This makes heterosis a viable tool in cotton breeding.
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Affiliation(s)
- Rasmieh Hamid
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran.
| | - Feba Jacob
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, India
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Leila Jafari
- Horticultural Science Department, Faculty of Agriculture and Natural Resources, University of Hormozgan, Bandar Abbas, Iran
- Research Group of Agroecology in Dryland Areas, University of Hormozgan, Bandar Abbas, Iran
| | - Omran Alishah
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran
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Banerjee S, Mukherjee A, Kundu A. The current scenario and future perspectives of transgenic oilseed mustard by CRISPR-Cas9. Mol Biol Rep 2023; 50:7705-7728. [PMID: 37432544 DOI: 10.1007/s11033-023-08660-6] [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: 09/02/2022] [Accepted: 06/30/2023] [Indexed: 07/12/2023]
Abstract
PURPOSE Production of a designer crop having added attributes is the primary goal of all plant biotechnologists. Specifically, development of a crop with a simple biotechnological approach and at a rapid pace is most desirable. Genetic engineering enables us to displace genes among species. The newly incorporated foreign gene(s) in the host genome can create a new trait(s) by regulating the genotypes and/or phenotypes. The advent of the CRISPR-Cas9 tools has enabled the modification of a plant genome easily by introducing mutation or replacing genomic fragment. Oilseed mustard varieties (e.g., Brassica juncea, Brassica nigra, Brassica napus, and Brassica carinata) are one such plants, which have been transformed with different genes isolated from the wide range of species. Current reports proved that the yield and value of oilseed mustard has been tremendously improved by the introduction of stably inherited new traits such as insect and herbicide resistance. However, the genetic transformation of oilseed mustard remains incompetent due to lack of potential plant transformation systems. To solve numerous complications involved in genetically modified oilseed mustard crop varieties regeneration procedures, scientific research is being conducted to rectify the unwanted complications. Thus, this study provides a broader overview of the present status of new traits introduced in each mentioned varieties of oilseed mustard plant by different genetical engineering tools, especially CRISPR-Cas9, which will be useful to improve the transformation system of oilseed mustard crop plants. METHODS This review presents recent improvements made in oilseed mustard genetic engineering methodologies by using CRISPR-Cas9 tools, present status of new traits introduced in oilseed mustard plant varieties. RESULTS The review highlighted that the transgenic oilseed mustard production is a challenging process and the transgenic varieties of oilseed mustard provide a powerful tool for enhanced mustard yield. Over expression studies and silencing of desired genes provide functional importance of genes involved in mustard growth and development under different biotic and abiotic stress conditions. Thus, it can be expected that in near future CRISPR can contribute enormously in improving the mustard plant's architecture and develop stress resilient oilseed mustard plant species.
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Affiliation(s)
- Sangeeta Banerjee
- Department of Microbiology, Techno India University, EM-4, Sector-V, Saltlake City, Kolkata, West Bengal, 700091, India
| | - Ananya Mukherjee
- Division of Plant Biology, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, WB, 700091, India
| | - Atreyee Kundu
- Department of Microbiology, Techno India University, EM-4, Sector-V, Saltlake City, Kolkata, West Bengal, 700091, India.
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Ma Z, Hu L. MicroRNA: A Dynamic Player from Signalling to Abiotic Tolerance in Plants. Int J Mol Sci 2023; 24:11364. [PMID: 37511124 PMCID: PMC10379455 DOI: 10.3390/ijms241411364] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding single-stranded RNA molecules composed of approximately 20-24 nucleotides in plants. They play an important regulatory role in plant growth and development and as a signal in abiotic tolerance. Some abiotic stresses include drought, salt, cold, high temperature, heavy metals and nutritional elements. miRNAs affect gene expression by manipulating the cleavage, translational expression or DNA methylation of target messenger RNAs (mRNAs). This review describes the current progress in the field considering two aspects: (i) the way miRNAs are produced and regulated and (ii) the way miRNA/target genes are used in plant responses to various abiotic stresses. Studying the molecular mechanism of action of miRNAs' downstream target genes could optimize the genetic manipulation of crop growth and development conditions to provide a more theoretically optimized basis for improving crop production. MicroRNA is a novel signalling mechanism in interplant communication relating to abiotic tolerance.
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Affiliation(s)
- Ziming Ma
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Lanjuan Hu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
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11
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Genome-Wide Identification and Characterization of the Oat ( Avena sativa L.) WRKY Transcription Factor Family. Genes (Basel) 2022; 13:genes13101918. [PMID: 36292803 PMCID: PMC9601435 DOI: 10.3390/genes13101918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 11/04/2022] Open
Abstract
The WRKY family is widely involved in the regulation of plant growth and stress response and is one of the largest gene families related to plant environmental adaptation. However, no systematic studies on the WRKY family in oat (Avena sativa L.) have been conducted to date. The recently published complete genome sequence of oat enables the systematic analysis of the AsWRKYs. Based on a genome-wide study of oat, we identified 162 AsWRKYs that were unevenly distributed across 21 chromosomes; a phylogenetic tree of WRKY domains divided these genes into three groups (I, II, and III). We also analyzed the gene duplication events and identified a total of 111 gene pairs that showed strong purifying selection during the evolutionary process. Surprisingly, almost all genes evolved after the completion of subgenomic differentiation of hexaploid oat. Further studies on the functional analysis indicated that AsWRKYs were widely involved in various biological processes. Notably, expression patterns of 16 AsWRKY genes revealed that the response of AsWRKYs were affected by stress level and time. In conclusion, this study provides a reference for further analysis of the role of WRKY transcription factors in species evolution and functional differentiation.
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12
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Ahmad M. Genomics and transcriptomics to protect rice ( Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger. FRONTIERS IN PLANT SCIENCE 2022; 13:1002596. [PMID: 36340401 PMCID: PMC9630331 DOI: 10.3389/fpls.2022.1002596] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.
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Affiliation(s)
- Mushtaq Ahmad
- Visiting Scientist Plant Sciences, University of Nebraska, Lincoln, NE, United States
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13
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Huang LZ, Zhou M, Ding YF, Zhu C. Gene Networks Involved in Plant Heat Stress Response and Tolerance. Int J Mol Sci 2022; 23:ijms231911970. [PMID: 36233272 PMCID: PMC9569452 DOI: 10.3390/ijms231911970] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 12/03/2022] Open
Abstract
Global warming is an environmental problem that cannot be ignored. High temperatures seriously affect the normal growth and development of plants, and threaten the development of agriculture and the distribution and survival of species at risk. Plants have evolved complex but efficient mechanisms for sensing and responding to high temperatures, which involve the activation of numerous functional proteins, regulatory proteins, and non-coding RNAs. These mechanisms consist of large regulatory networks that regulate protein and RNA structure and stability, induce Ca2+ and hormone signal transduction, mediate sucrose and water transport, activate antioxidant defense, and maintain other normal metabolic pathways. This article reviews recent research results on the molecular mechanisms of plant response to high temperatures, highlighting future directions or strategies for promoting plant heat tolerance, thereby helping to identify the regulatory mechanisms of heat stress responses in plants.
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Affiliation(s)
| | | | - Yan-Fei Ding
- Correspondence: (Y.-F.D.); (C.Z.); Tel.: +86-571-8683-6090 (C.Z.)
| | - Cheng Zhu
- Correspondence: (Y.-F.D.); (C.Z.); Tel.: +86-571-8683-6090 (C.Z.)
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14
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Arora H, Singh RK, Sharma S, Sharma N, Panchal A, Das T, Prasad A, Prasad M. DNA methylation dynamics in response to abiotic and pathogen stress in plants. PLANT CELL REPORTS 2022; 41:1931-1944. [PMID: 35833989 DOI: 10.1007/s00299-022-02901-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
DNA methylation is a dynamic epigenetic mechanism that plays a significant role in gene expression and also maintains chromatin stability. The process is conserved in both plants and animals, and crucial for development and stress responses. Differential DNA methylation during adverse environmental conditions or pathogen attack facilitates the selective expression of defense-related genes. Both stress-induced DNA hypomethylation and hypermethylation play beneficial roles in activating the defense response. These DNA marks may be carried to the next generation making the progenies 'primed' for abiotic and biotic stress responses. Over the recent years, rapid advancements in the area of high throughput sequencing have enabled the detection of methylation status at genome levels in several plant species. Epigenotyping offers an alternative tool to plant breeders in addition to conventional markers for the selection of the desired offspring. In this review, we briefly discuss the mechanism of DNA methylation, recent understanding of DNA methylation-mediated gene regulation during abiotic and biotic stress responses, and stress memory in plants.
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Affiliation(s)
- Heena Arora
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shambhavi Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Institute of Life Sciences, NALCO Nagar, Bhubaneswar, 751023, India
| | - Anurag Panchal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Tuhin Das
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India.
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15
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Siddiqui MH, Khan MN, Singh VP. Hot and dry: how plants can thrive in future climates. PLANT CELL REPORTS 2022; 41:497-499. [PMID: 35175359 DOI: 10.1007/s00299-022-02843-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
| | - M Nasir Khan
- Department of Biology, College of Haql, University of Tabuk, Tabuk, Saudi Arabia
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
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Tang Y, Yan X, Gu C, Yuan X. Biogenesis, Trafficking, and Function of Small RNAs in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:825477. [PMID: 35251095 PMCID: PMC8891129 DOI: 10.3389/fpls.2022.825477] [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: 11/30/2021] [Accepted: 01/19/2022] [Indexed: 05/03/2023]
Abstract
Small RNAs (sRNAs) encoded by plant genomes have received widespread attention because they can affect multiple biological processes. Different sRNAs that are synthesized in plant cells can move throughout the plants, transport to plant pathogens via extracellular vesicles (EVs), and transfer to mammals via food. Small RNAs function at the target sites through DNA methylation, RNA interference, and translational repression. In this article, we reviewed the systematic processes of sRNA biogenesis, trafficking, and the underlying mechanisms of its functions.
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Affiliation(s)
- Yunjia Tang
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaoning Yan
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Chenxian Gu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaofeng Yuan
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- *Correspondence: Xiaofeng Yuan,
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