1
|
Sultana S, Rahman MM, Das AK, Haque MA, Rahman MA, Islam SMN, Ghosh PK, Keya SS, Tran LSP, Mostofa MG. Role of salicylic acid in improving the yield of two mung bean genotypes under waterlogging stress through the modulation of antioxidant defense and osmoprotectant levels. Plant Physiol Biochem 2024; 206:108230. [PMID: 38100888 DOI: 10.1016/j.plaphy.2023.108230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/06/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Waterlogging (WL) is a major hindrance to the growth and development of leguminous crops, including mung bean. Here, we explored the effect of salicylic acid (SA) pretreatment on growth and yield output of two elite mung bean genotypes (BU Mung bean-4 and BU Mung bean-6) subjected to WL stress. SA pretreatment significantly improved shoot dry weight, individual leaf area, and photosynthetic pigment contents in both genotypes, while those improvements were higher in BU Mung bean-6 when compared with BU Mung bean-4. We also found that SA pretreatment significantly reduced the reactive oxygen species-induced oxidative burden in both BU Mung bean-6 and BU Mung bean-4 by enhancing peroxidase, glutathione S-transferase, catalase, and ascorbate peroxidase activities, as well as total flavonoid contents. SA pretreatment further improved the accumulation of proline and free amino acids in both genotypes, indicating that SA employed these osmoprotectants to enhance osmotic balance. These results were particularly corroborated with the elevated levels of leaf water status and leaf succulence in BU Mung bean-6. SA-mediated improvement in physiological and biochemical mechanisms led to a greater yield-associated feature in BU Mung bean-6 under WL conditions. Collectively, these findings shed light on the positive roles of SA in alleviating WL stress, contributing to yield improvement in mung bean crop.
Collapse
Affiliation(s)
- Sharmin Sultana
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Mezanur Rahman
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Ashim Kumar Das
- Department of Agroforestry and Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Ashraful Haque
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Abiar Rahman
- Department of Agroforestry and Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Shah Mohammad Naimul Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Protik Kumar Ghosh
- Department of Agronomy, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Sanjida Sultana Keya
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Mohammad Golam Mostofa
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
| |
Collapse
|
2
|
Wang X, Xiang Y, Sun M, Xiong Y, Li C, Zhang T, Ma W, Wang Y, Liu X. Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus). BMC Plant Biol 2023; 23:638. [PMID: 38072959 PMCID: PMC10712147 DOI: 10.1186/s12870-023-04651-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Six-spotted spider mite (Eotetranychus sexmaculatus) is one of the most damaging pests of tea (Camellia sinensis). E. sexmaculatus causes great economic loss and affects tea quality adversely. In response to pests, such as spider mites, tea plants have evolved resistance mechanisms, such as expression of defense-related genes and defense-related metabolites. RESULTS To evaluate the biochemical and molecular mechanisms of resistance in C. sinensis against spider mites, "Tianfu-5" (resistant to E. sexmaculatus) and "Fuding Dabai" (susceptible to E. sexmaculatus) were inoculated with spider mites. Transcriptomics and metabolomics based on RNA-Seq and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) technology were used to analyze changes in gene expression and metabolite content, respectively. RNA-Seq data analysis revealed that 246 to 3,986 differentially expressed genes (DEGs) were identified in multiple compared groups, and these DEGs were significantly enriched in various pathways, such as phenylpropanoid and flavonoid biosynthesis, plant-pathogen interactions, MAPK signaling, and plant hormone signaling. Additionally, the metabolome data detected 2,220 metabolites, with 194 to 260 differentially abundant metabolites (DAMs) identified in multiple compared groups, including phenylalanine, lignin, salicylic acid, and jasmonic acid. The combined analysis of RNA-Seq and metabolomic data indicated that phenylpropanoid and flavonoid biosynthesis, MAPK signaling, and Ca2+-mediated PR-1 signaling pathways may contribute to spider mite resistance. CONCLUSIONS Our findings provide insights for identifying insect-induced genes and metabolites and form a basis for studies on mechanisms of host defense against spider mites in C. sinensis. The candidate genes and metabolites identified will be a valuable resource for tea breeding in response to biotic stress.
Collapse
Affiliation(s)
- Xiaoping Wang
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Tea Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.
| | - Yunjia Xiang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Minshan Sun
- Henan Assist Research Biotechnology Co., Ltd, Zhengzhou, China
| | - Yuanyuan Xiong
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Tea Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Chunhua Li
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Tea Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Ting Zhang
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Tea Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Weiwei Ma
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Tea Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yun Wang
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Tea Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xiao Liu
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Tea Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| |
Collapse
|
3
|
Gedam PA, Khandagale K, Shirsat D, Thangasamy A, Kulkarni O, Kulkarni A, Patil SS, Barvkar VT, Mahajan V, Gupta AJ, Bhagat KP, Khade YP, Singh M, Gawande S. Elucidating the molecular responses to waterlogging stress in onion ( Allium cepa L.) leaf by comparative transcriptome profiling. Front Plant Sci 2023; 14:1150909. [PMID: 37615019 PMCID: PMC10442827 DOI: 10.3389/fpls.2023.1150909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
Introduction Waterlogging is a major stress that severely affects onion cultivation worldwide, and developing stress-tolerant varieties could be a valuable measure for overcoming its adverse effects. Gathering information regarding the molecular mechanisms and gene expression patterns of waterlogging-tolerant and sensitive genotypes is an effective method for improving stress tolerance in onions. To date, the waterlogging tolerance-governing molecular mechanism in onions is unknown. Methods This study identified the differentially expressed genes (DEGs) through transcriptome analysis in leaf tissue of two onion genotypes (Acc. 1666; tolerant and W-344; sensitive) presenting contrasting responses to waterlogging stress. Results Differential gene expression analysis revealed that in Acc. 1666, 1629 and 3271 genes were upregulated and downregulated, respectively. In W-344, 2134 and 1909 genes were upregulated and downregulated, respectively, under waterlogging stress. The proteins coded by these DEGs regulate several key biological processes to overcome waterlogging stress such as phytohormone production, antioxidant enzymes, programmed cell death, and energy production. The clusters of orthologous group pathway analysis revealed that DEGs contributed to the post-translational modification, energy production, and carbohydrate metabolism-related pathways under waterlogging stress. The enzyme assay demonstrated higher activity of antioxidant enzymes in Acc. 1666 than in W-344. The differential expression of waterlogging tolerance related genes, such as those related to antioxidant enzymes, phytohormone biosynthesis, carbohydrate metabolism, and transcriptional factors, suggested that significant fine reprogramming of gene expression occurs in response to waterlogging stress in onion. A few genes such as ADH, PDC, PEP carboxylase, WRKY22, and Respiratory burst oxidase D were exclusively upregulated in Acc. 1666. Discussion The molecular information about DEGs identified in the present study would be valuable for improving stress tolerance and for developing waterlogging tolerant onion varieties.
Collapse
Affiliation(s)
- Pranjali A. Gedam
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Kiran Khandagale
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Dhananjay Shirsat
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - A. Thangasamy
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Onkar Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
| | | | | | - Vijay Mahajan
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Amar Jeet Gupta
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Kiran P. Bhagat
- Indian Council of Agricultural Research (ICAR)-Directorate of Floriculture Research, Pune, India
| | - Yogesh P. Khade
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Major Singh
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Suresh Gawande
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| |
Collapse
|
4
|
Hu J, Duan Y, Yang J, Gan L, Chen W, Yang J, Xiao G, Guan L, Chen J. Transcriptome Analysis Reveals Genes Associated with Flooding Tolerance in Mulberry Plants. Life (Basel) 2023; 13:life13051087. [PMID: 37240733 DOI: 10.3390/life13051087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Mulberry (Morus alba), a widely distributed economic plant, can withstand long-term flooding stress. However, the regulatory gene network underlying this tolerance is unknown. In the present study, mulberry plants were subjected to submergence stress. Subsequently, mulberry leaves were collected to perform quantitative reverse-transcription PCR (qRT-PCR) and transcriptome analysis. Genes encoding ascorbate peroxidase and glutathione S-transferase were significantly upregulated after submergence stress, indicating that they could protect the mulberry plant from flood damage by mediating ROS homeostasis. Genes that regulate starch and sucrose metabolism; genes encoding pyruvate kinase, alcohol dehydrogenase, and pyruvate decarboxylase (enzymes involved in glycolysis and ethanol fermentation); and genes encoding malate dehydrogenase and ATPase (enzymes involved in the TCA cycle) were also obviously upregulated. Hence, these genes likely played a key role in mitigating energy shortage during flooding stress. In addition, genes associated with ethylene, cytokinin, abscisic acid, and MAPK signaling; genes involved in phenylpropanoid biosynthesis; and transcription factor genes also showed upregulation under flooding stress in mulberry plants. These results provide further insights into the adaptation mechanisms and genetics of submergence tolerance in mulberry plants and could aid in the molecular breeding of these plants.
Collapse
Affiliation(s)
- Jingtao Hu
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Yanyan Duan
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Junnian Yang
- College of Teacher Education, Chongqing Three Gorges University, Chongqing 404100, China
| | - Liping Gan
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Wenjing Chen
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Jin Yang
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Guosheng Xiao
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Lingliang Guan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jingsheng Chen
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| |
Collapse
|
5
|
Shang P, Shen B, Zeng B, Bi L, Qu M, Zheng Y, Ye Y, Li W, Zhou X, Yang X, Jiang Y, Zeng B. Integrated Transcriptomic and Metabolomics Analysis of the Root Responses of Orchardgrass to Submergence Stress. Int J Mol Sci 2023; 24. [PMID: 36768412 DOI: 10.3390/ijms24032089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/07/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Submergence stress can severely affect plant growth. Orchardgrass (Dactylis glomerata L.) is an important forage grass, and the molecular mechanisms of orchardgrass to submergence stress are not well understood. The roots of the flood-tolerant cultivar "Dian Bei" were harvested at 0 h, 8 h and 24 h of submergence stress. The combined transcriptomic and metabolomic analyses showed that β-alanine metabolism, flavonoid biosynthesis, and biosynthesis of amino acid pathways were significantly enriched at 8 h and 24 h of submergence stress and were more pronounced at 24 h. Most of the flavonoid biosynthesis-related genes were down-regulated for the synthesis of metabolites such as naringenin, apigenin, naringin, neohesperidin, naringenin chalcone, and liquiritigenin in response to submergence stress. Metabolites such as phenylalanine, tyrosine, and tryptophan were up-regulated under stress. The predominant response of flavonoid and amino acids biosynthesis to submergence stress suggests an important role of these pathways in the submergence tolerance of orchardgrass.
Collapse
|
6
|
Zhang X, Liu X, Zhou M, Hu Y, Yuan J. PacBio full-length sequencing integrated with RNA-seq reveals the molecular mechanism of waterlogging and its recovery in Paeonia ostii. Front Plant Sci 2022; 13:1030584. [PMID: 36407600 PMCID: PMC9669713 DOI: 10.3389/fpls.2022.1030584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Paeonia ostii, a widely cultivated tree peony species in China, is a resourceful plant with medicinal, ornamental and oil value. However, fleshy roots lead to a low tolerance to waterlogging in P. ostii. In this study, P. ostii roots were sequenced using a hybrid approach combining single-molecule real-time and next-generation sequencing platforms to understand the molecular mechanism underlying the response to this sequentially waterlogging stress, the normal growth, waterlogging treatment (WT), and waterlogging recovery treatment (WRT). Our results indicated that the strategy of P. ostii, in response to WT, was a hypoxic resting syndrome, wherein the glycolysis and fermentation processes were accelerated to maintain energy levels and the tricarboxylic acid cycle was inhibited. P. ostii enhanced waterlogging tolerance by reducing the uptake of nitrate and water from the soil. Moreover, transcription factors, such as AP2/EREBP, WRKY, MYB, and NAC, played essential roles in response to WT and WRT. They were all induced in response to the WT condition, while the decreasing expression levels were observed under the WRT condition. Our results contribute to understanding the defense mechanisms against waterlogging stress in P. ostii.
Collapse
Affiliation(s)
- Xiaoxiao Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Xiang Liu
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Minghui Zhou
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Yonghong Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Junhui Yuan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| |
Collapse
|
7
|
Li Z, Bai D, Zhong Y, Lin M, Sun L, Qi X, Hu C, Fang J. Full-Length Transcriptome and RNA-Seq Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Kiwifruit ( Actinidia valvata). Int J Mol Sci 2022; 23:3237. [PMID: 35328659 DOI: 10.3390/ijms23063237] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 12/13/2022] Open
Abstract
Actinidia valvata possesses waterlogging tolerance; however, the mechanisms underlying this trait are poorly characterized. Here, we performed a transcriptome analysis by combining single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing and investigated the physiological responses of the roots of KR5 (A. valvata, a tolerant genotype) after 0, 12, 24 and 72 h of waterlogging stress. KR5 roots responded to waterlogging stress mainly via carbohydrate and free amino acids metabolism and reactive oxygen species (ROS) scavenging pathways. Trehalose-6-phosphate synthase (TPS) activity, alcohol dehydrogenase (ADH) activity and the total free amino acid content increased significantly under waterlogging stress. The nicotinamide adenine dinucleotide-dependent glutamate synthase/alanine aminotransferase (NADH-GOGAT/AlaAT) cycle was correlated with alanine accumulation. Levels of genes encoding peroxidase (POD) and catalase (CAT) decreased and enzyme activity increased under waterlogging stress. Members of the LATERAL ORGAN BOUNDARIES (LOB), AP2/ERF-ERF, Trihelix and C3H transcription factor families were identified as potential regulators of the transcriptional response. Several hub genes were identified as key factors in the response to waterlogging stress by a weighted gene co-expression network analysis (WGCNA). Our results provide insights into the factors contributing to waterlogging tolerance in kiwifruit, providing a basis for further studies of interspecific differences in an important plant trait and for molecular breeding.
Collapse
|
8
|
Wang J, Wang D, Zhu M, Li F. Exogenous 6-Benzyladenine Improves Waterlogging Tolerance in Maize Seedlings by Mitigating Oxidative Stress and Upregulating the Ascorbate-Glutathione Cycle. Front Plant Sci 2021; 12:680376. [PMID: 34539688 PMCID: PMC8446516 DOI: 10.3389/fpls.2021.680376] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/04/2021] [Indexed: 05/30/2023]
Abstract
The synthetic cytokinin 6-benzyladenine (6-BA) regulates plant growth and prevents the negative consequences of various forms of abiotic stress, including waterlogging in crop plants. The present study aimed to investigate the effects of exogenous 6-BA on the growth, oxidative stress, and ascorbate-glutathione (AsA-GSH) cycle system in the inbred SY-MY13 (waterlogging-resistant) and SY-XT1 (waterlogging-sensitive) seedlings of waxy corn in conditions of waterlogging stress. The results demonstrated that waterlogging stress causes chlorosis and necrosis in waxy corn leaves, inhibiting growth and leading to the accumulation of reactive oxygen species (ROS), which induces oxidative stress and, in turn, reduces membrane lipid peroxidation and the disruption of membrane homeostasis. This is specifically manifested in the increased concentrations of superoxide anion radicals ( O 2 - ), hydrogen peroxide (H2O2), and malondialdehyde (MDA), in addition to increased relative electrical conductivity (REC%) values. The SY-MY13 strain exhibited growth superior to that of SY-XT1 when waterlogged due to its excellent waterlogging resistance. Thus, exogenous 6-BA was found to be effective in enhancing the growth of plants stressed by waterlogging in terms of the weight of the shoots and roots, shoot height, and leaf area. In addition to this, exogenous 6-BA also reduced the accumulation of O 2 - , H2O2, and MDA, increased ascorbate peroxidase (APX), glutathione reductase (GR), dehydroascorbate reductase (DHAR), and monodehydroascorbate reductase (MDHAR) activity, and enhanced ascorbic acid (AsA), and reduced glutathione (GSH) concentration through the regulation of the efficiency of the AsA-GSH cycle system in maize plants. Hence, the application of exogenous 6-BA can alleviate waterlogging-induced damage and improve waterlogging tolerance in waxy corn via the activation of the AsA-GSH cycle system and the elimination of ROS.
Collapse
Affiliation(s)
- Ji Wang
- College of Agronomy, Specialty Corn Institute, Shenyang Agricultural University, Shenyang, China
| | - Daye Wang
- College of Agronomy, Specialty Corn Institute, Shenyang Agricultural University, Shenyang, China
| | - Min Zhu
- College of Agronomy, Specialty Corn Institute, Shenyang Agricultural University, Shenyang, China
| | - Fenghai Li
- College of Agronomy, Specialty Corn Institute, Shenyang Agricultural University, Shenyang, China
| |
Collapse
|
9
|
Zhang G, Liu Y, Gui R, Wang Z, Li Z, Han Y, Guo X, Sun J. Comparative multi-omics analysis of hypoxic germination tolerance in weedy rice embryos and coleoptiles. Genomics 2021; 113:3337-3348. [PMID: 34298069 DOI: 10.1016/j.ygeno.2021.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/04/2021] [Accepted: 07/17/2021] [Indexed: 10/20/2022]
Abstract
Hypoxic germination tolerance is an important trait for seedling establishment of direct-seeded rice. Our comparative metabolomics analysis revealed that weedy rice accumulated more sugar and amino acids than cultivated rice accumulated in the embryo and coleoptile tissues under hypoxic stress. At the transcriptional level, oxidative phosphorylation activity in weedy rice was higher than in cultivated rice that likely led to more efficient energy metabolism during hypoxic stress. Based on our comparative proteomics analysis, enriched proteins related to cell wall implied that the advantages in energy metabolism of weedy rice were ultimately reflected in the formation of tissue structures. In this study, we found that most of key hypoxic germination tolerance (HGT) genes shared the same genetic backgrounds with Oryza japonica, however, several of them genetically similar to other Oryza plant also play important roles. Our findings suggest weedy rice can serve as genetic resources for the improvement of direct-seeding rice.
Collapse
Affiliation(s)
- Guangchen Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China
| | - Youhong Liu
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Molecular Design and Germplasm Innovation, Haerbin, 150086, China
| | - Rui Gui
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China
| | - Ziming Wang
- College of forestry, Shenyang Agricultural University, Shenyang 110161, China
| | - Zhuan Li
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China
| | - Yuqing Han
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China
| | - Xiaojia Guo
- Jinzhou Institute of Science and Technology, Jinzhou, 121000, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China.
| |
Collapse
|
10
|
Zhang H, Li G, Yan C, Cao N, Yang H, Le M, Zhu F. Depicting the molecular responses of adventitious rooting to waterlogging in melon hypocotyls by transcriptome profiling. 3 Biotech 2021; 11:351. [PMID: 34221821 DOI: 10.1007/s13205-021-02866-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/31/2021] [Indexed: 12/13/2022] Open
Abstract
Waterlogging is a severe abiotic stressor that inhibits crop growth and productivity owing to the decline in the amount of oxygen available to the waterlogged organs. Although melon (Cucumis melo L.) is sensitive to waterlogging, its ability to form adventitious roots facilitates the diffusion of oxygen and allows the plant to survive waterlogging. To provide comprehensive insight into the adventitious rooting in response to waterlogging of melon, global transcriptome changes during this process were investigated. Of the 17,146 genes expressed during waterlogging, 7363 of them were differentially expressed in the pairwise comparisons between different waterlogging treatment time points. A further analysis suggested that the genes involved in sugar cleavage, glycolysis, fermentation, reactive oxygen species scavenging, cell wall modification, cell cycle governing, microtubule remodeling, hormone signals and transcription factors could play crucial roles in the adventitious root production induced by waterlogging. Additionally, ethylene and ERFs were found to be vital factors that function in melon during adventitious rooting. This study broadens our understanding of the mechanisms that underlie adventitious rooting induced by waterlogging and lays the theoretical foundation for further molecular breeding of waterlogging-tolerant melon. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02866-w.
Collapse
Affiliation(s)
- Huanxin Zhang
- Institute of Horticulture, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Guoquan Li
- Institute of Horticulture, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Chengpu Yan
- Institute of Horticulture, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Na Cao
- Institute of Horticulture, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Huidong Yang
- Institute of Horticulture, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Meiwang Le
- Institute of Horticulture, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Fanghong Zhu
- Institute of Horticulture, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| |
Collapse
|
11
|
Kaur G, Vikal Y, Kaur L, Kalia A, Mittal A, Kaur D, Yadav I. Elucidating the morpho-physiological adaptations and molecular responses under long-term waterlogging stress in maize through gene expression analysis. Plant Sci 2021; 304:110823. [PMID: 33568312 DOI: 10.1016/j.plantsci.2021.110823] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 05/25/2023]
Abstract
Waterlogging stress in maize is one of the emerging abiotic stresses in the current climate change scenario. To gain insights in transcriptional reprogramming during late hours of waterlogging stress under field conditions, we aimed to elucidate the transcriptional and anatomical changes in two contrasting maize inbreds viz. I110 (susceptible) and I172 (tolerant). Waterlogging stress reduced dry matter translocations from leaves and stems to ears, resulting in a lack of sink capacity and inadequate grain filling in I110, thus decreased the grain yield drastically. The development of aerenchyma cells within 48 h in I172 enabled hypoxia tolerance. The upregulation of alanine aminotransferase, ubiquitin activating enzyme E1, putative mitogen activated protein kinase and pyruvate kinase in I172 suggested that genes involved in protein degradation, signal transduction and carbon metabolism provided adaptive mechanisms during waterlogging. Overexpression of alcohol dehydrogenase, sucrose synthase, aspartate aminotransferase, NADP dependent malic enzyme and many miRNA targets in I110 indicated that more oxygen and energy consumption might have shortened plant survival during long-term waterlogging exposure. To the best of our knowledge, this is the first report of transcript profiling at late stage (24-96 h) of waterlogging stress under field conditions and provides new visions to understand the molecular basis of waterlogging tolerance in maize.
Collapse
Affiliation(s)
- Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
| | - Loveleen Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Anu Kalia
- Department of Nanoscience, Punjab Agricultural University, Ludhiana, India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Dasmeet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Inderjit Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| |
Collapse
|
12
|
Meena MR, Kumar R, Chinnaswamy A, Karuppaiyan R, Kulshreshtha N, Ram B. Current breeding and genomic approaches to enhance the cane and sugar productivity under abiotic stress conditions. 3 Biotech 2020; 10:440. [PMID: 33014683 DOI: 10.1007/s13205-020-02416-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023] Open
Abstract
Sugarcane (Saccharum spp.) crop is vulnerable to many abiotic stresses such as drought, salinity, waterlogging, cold and high temperature due to climate change. Over the past few decades new breeding and genomic approaches have been used to enhance the genotypic performance under abiotic stress conditions. In sugarcane, introgression of genes from wild species and allied genera for abiotic stress tolerance traits plays a significant role in the development of several stress-tolerant varieties. Moreover, the genomics and transcriptomics approaches have helped to elucidate the key genes/TFs and pathways involved in abiotic stress tolerance in sugarcane. Several novel miRNAs families /proteins or regulatory elements that are responsible for drought, salinity, and cold tolerance have been identified through high-throughput sequencing. The existing sugarcane monoploid genome sequence information opens new gateways and opportunities for researchers to improve the desired traits through efficient genome editing tools, such as the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas) system. TALEN mediated mutations in a highly conserved region of the caffeic acid O-methyltransferase (COMT) of sugarcane significantly reduces the lignin content in the cell wall which is amenable for biofuel production from lignocellulosic biomass. In this review, we focus on current breeding with genomic approaches and their substantial role in enhancing cane production under the abiotic stress conditions, which is expected to provide new insights to plant breeders and biotechnologists to modify their strategy in developing stress-tolerant sugarcane varieties, which can highlight the future demand of cane, bio-energy, and viability of sugar industries.
Collapse
|
13
|
Qiao D, Zhang Y, Xiong X, Li M, Cai K, Luo H, Zeng B. Transcriptome analysis on responses of orchardgrass (Dactylis glomerata L.) leaves to a short term flooding. Hereditas 2020; 157:20. [PMID: 32418541 PMCID: PMC7232843 DOI: 10.1186/s41065-020-00134-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Orchardgrass (Dactylis glomerata L.) is a popular cool-season perennial grass with a high production value, and orchardgrass seed is the fourth top-selling forage grass seed in the world. However, its yield and quality are often affected by flooding. To date, the molecular responses of orchardgrass to flooding were poorly understood. RESULTS Here, we performed mRNA-seq to explore the transcriptomic responses of orchardgrass to a short term flooding (8 h and 24 h). There were 1454 and 565 differentially expressed genes identified in the 8 h and 24 h of flooding, respectively, compared to well control. GO functional enrichment analysis showed that oxidoreductase activity and oxidation-reduction process were highly present, suggesting that flooding induced the response to oxygen stress. Pathways enrichment analysis highlights the importance of glutathione metabolism, peroxidase, glycolysis and plant hormone signal transduction in response to flooding acclimation. Besides, the ROS clearance system is activated by significantly expressed glutathione S-transferase and genes encoding SOD and CAT (CAT1 and CDS2). The significant positive correlation between RNA sequencing data and a qPCR analysis indicated that the identified genes were credible. CONCLUSION In the process of orchardgrass response to flooding stress, multiple differential genes and biological processes have participated in its acclimation to flooding, especially the biological processes involved in the removal of ROS. These results provide a basis for further research on the adaptation mechanism of orchardgrass to flood tolerance.
Collapse
Affiliation(s)
- Dandan Qiao
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Yajie Zhang
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Xuemei Xiong
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Mingyang Li
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Kai Cai
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Hui Luo
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Bing Zeng
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| |
Collapse
|
14
|
Lin Y, Li W, Zhang Y, Xia C, Liu Y, Wang C, Xu R, Zhang L. Identification of Genes/Proteins Related to Submergence Tolerance by Transcriptome and Proteome Analyses in Soybean. Sci Rep 2019; 9:14688. [PMID: 31604973 PMCID: PMC6789146 DOI: 10.1038/s41598-019-50757-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 09/16/2019] [Indexed: 11/19/2022] Open
Abstract
Flooding can lead to yield reduction of soybean. Therefore, identification of flooding tolerance genes has great significance in production practice. In this study, Qihuang 34, a highly-resistant variety to flooding stress, was selected for submergence treatments. Transcriptome and proteome analyses were conducted, by which twenty-two up-regulated differentially expressed genes (DEGs)/differentially expressed proteins (DEPs) associated with five KEGG pathways were isolated. The number of the DEGs/DEPs enriched in glycolysis/gluconeogenesis was the highest. Four of these genes were confirmed by RT-qPCR, suggesting that glycolysis/gluconeogenesis may be activated to generate energy for plant survival under anaerobic conditions. Thirty-eight down-regulated DEGs/DEPs associated with six KEGG pathways were identified under submergence stress. Eight DEGs/DEPs enriched in phenylpropanoid biosynthesis were assigned to peroxidase, which catalyzes the conversion of coumaryl alcohol to hydroxy-phenyl lignin in the final step of lignin biosynthesis. Three of these genes were confirmed by RT-qPCR. The decreased expression of these genes led to the inhibition of lignin biosynthesis, which may be the cause of plant softening under submergence stress for a long period of time. This study revealed a number of up-/down-regulated pathways and the corresponding DEGs/DEPs, by which, a better understanding of the mechanisms of submergence tolerance in soybean may be achieved.
Collapse
Affiliation(s)
- Yanhui Lin
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Institute of Food Crops, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Wei Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yanwei Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Changjian Xia
- Haikou Cigar Research Institute, Hainan Provincial Branch of China National Tobacco Corporation, Haikou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yun Liu
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Caijie Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ran Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lifeng Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China.
| |
Collapse
|
15
|
Arslan M, Devisetty UK, Porsch M, Große I, Müller JA, Michalski SG. RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. BMC Genomics 2019; 20:489. [PMID: 31195970 PMCID: PMC6567414 DOI: 10.1186/s12864-019-5886-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 06/05/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Juncus effusus L. (family: Juncaceae; order: Poales) is a helophytic rush growing in temperate damp or wet terrestrial habitats and is of almost cosmopolitan distribution. The species has been studied intensively with respect to its interaction with co-occurring plants as well as microbes being involved in major biogeochemical cycles. J. effusus has biotechnological value as component of Constructed Wetlands where the plant has been employed in phytoremediation of contaminated water. Its genome has not been sequenced. RESULTS In this study we carried out functional annotation and polymorphism analysis of de novo assembled RNA-Seq data from 18 genotypes using 249 million paired-end Illumina HiSeq reads and 2.8 million 454 Titanium reads. The assembly comprised 158,591 contigs with a mean contig length of 780 bp. The assembly was annotated using the dammit! annotation pipeline, which queries the databases OrthoDB, Pfam-A, Rfam, and runs BUSCO (Benchmarking Single-Copy Ortholog genes). In total, 111,567 contigs (70.3%) were annotated with functional descriptions, assigned gene ontology terms, and conserved protein domains, which resulted in 30,932 non-redundant gene sequences. Results of BUSCO and KEGG pathway analyses were similar for J. effusus as for the well-studied members of the Poales, Oryza sativa and Sorghum bicolor. A total of 566,433 polymorphisms were identified in transcribed regions with an average frequency of 1 polymorphism in every 171 bases. CONCLUSIONS The transcriptome assembly was of high quality and genome coverage was sufficient for global analyses. This annotated knowledge resource can be utilized for future gene expression analysis, genomic feature comparisons, genotyping, primer design, and functional genomics in J. effusus.
Collapse
Affiliation(s)
- Muhammad Arslan
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr, 15, Leipzig, Germany.,Institute for Biology V (Environmental Research), RWTH Aachen University, Templergraben 55, 52062, Aachen, Germany
| | | | - Martin Porsch
- Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saale), Germany.,Core Facility Deep Sequencing, Martin-Luther-University Halle-Wittenberg, Magdeburger Str. 2, 06112, Halle (Saale), Germany
| | - Ivo Große
- Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Jochen A Müller
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr, 15, Leipzig, Germany.
| | - Stefan G Michalski
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany
| |
Collapse
|
16
|
Fukao T, Barrera-Figueroa BE, Juntawong P, Peña-Castro JM. Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects. Front Plant Sci 2019; 10:340. [PMID: 30967888 PMCID: PMC6439527 DOI: 10.3389/fpls.2019.00340] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/05/2019] [Indexed: 05/20/2023]
Abstract
Soil flooding creates composite and complex stress in plants known as either submergence or waterlogging stress depending on the depth of the water table. In nature, these stresses are important factors dictating the species composition of the ecosystem. On agricultural land, they cause economic damage associated with long-term social consequences. The understanding of the plant molecular responses to these two stresses has benefited from research studying individual components of the stress, in particular low-oxygen stress. To a lesser extent, other associated stresses and plant responses have been incorporated into the molecular framework, such as ion and ROS signaling, pathogen susceptibility, and organ-specific expression and development. In this review, we aim to highlight known or suspected components of submergence/waterlogging stress that have not yet been thoroughly studied at the molecular level in this context, such as miRNA and retrotransposon expression, the influence of light/dark cycles, protein isoforms, root architecture, sugar sensing and signaling, post-stress molecular events, heavy-metal and salinity stress, and mRNA dynamics (splicing, sequestering, and ribosome loading). Finally, we explore biotechnological strategies that have applied this molecular knowledge to develop cultivars resistant to flooding or to offer alternative uses of flooding-prone soils, like bioethanol and biomass production.
Collapse
Affiliation(s)
- Takeshi Fukao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | | | - Piyada Juntawong
- Center for Advanced Studies in Tropical Natural Resources, National Research University – Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Julián Mario Peña-Castro
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec, Mexico
| |
Collapse
|
17
|
Ren CG, Kong CC, Yan K, Xie ZH. Transcriptome analysis reveals the impact of arbuscular mycorrhizal symbiosis on Sesbania cannabina expose to high salinity. Sci Rep 2019; 9:2780. [PMID: 30808908 PMCID: PMC6391373 DOI: 10.1038/s41598-019-39463-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 01/07/2019] [Indexed: 12/21/2022] Open
Abstract
Arbuscular mycorrhiza can improve the salt-tolerance of host plant. A systematic study of mycorrhizal plant responses to salt stress may provide insights into the acquired salt tolerance. Here, the transcriptional profiles of mycorrhizal Sesbania cannabina shoot and root under saline stress were obtained by RNA-Seq. Using weighted gene coexpression network analysis and pairwise comparisons, we identified coexpressed modules, networks and hub genes in mycorrhizal S. cannabina in response to salt stress. In total, 10,371 DEGs were parsed into five coexpression gene modules. One module was positively correlated with both salt treatment and arbuscular mycorrhizal (AM) inoculation, and associated with photosynthesis and ROS scavenging in both enzymatic and nonenzymatic pathways. The hub genes in the module were mostly transcription factors including WRKY, MYB, ETHYLENE RESPONSE FACTOR, and TCP members involved in the circadian clock and might represent central regulatory components of acquired salinity tolerance in AM S. cannabina. The expression patterns of 12 genes involved in photosynthesis, oxidation-reduction processes, and several transcription factors revealed by qRT-PCR confirmed the RNA-Seq data. This large-scale assessment of Sesbania genomic resources will help in exploring the molecular mechanisms underlying plant–AM fungi interaction in salt stress responses.
Collapse
Affiliation(s)
- Cheng-Gang Ren
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, China
| | - Cun-Cui Kong
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, China
| | - Kun Yan
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, China
| | - Zhi-Hong Xie
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, China.
| |
Collapse
|
18
|
Pan R, He D, Xu L, Zhou M, Li C, Wu C, Xu Y, Zhang W. Proteomic analysis reveals response of differential wheat (Triticum aestivum L.) genotypes to oxygen deficiency stress. BMC Genomics 2019; 20:60. [PMID: 30658567 PMCID: PMC6339445 DOI: 10.1186/s12864-018-5405-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/21/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Waterlogging is one of the main abiotic stresses that limit wheat production. Quantitative proteomics analysis has been applied in the study of crop abiotic stress as an effective way in recent years (e.g. salt stress, drought stress, heat stress and waterlogging stress). However, only a few proteins related to primary metabolism and signal transduction, such as UDP - glucose dehydrogenase, UGP, beta glucosidases, were reported to response to waterlogging stress in wheat. The differentially expressed proteins between genotypes of wheat in response to waterlogging are less-defined. In this study, two wheat genotypes, one is sensitive to waterlogging stress (Seri M82, named as S) and the other is tolerant to waterlogging (CIGM90.863, named as T), were compared in seedling roots under hypoxia conditions to evaluate the different responses at proteomic level. RESULTS A total of 4560 proteins were identified and the number of differentially expressed proteins (DEPs) were 361, 640, 788 in S and 33, 207, 279 in T in 1, 2, 3 days, respectively. These DEPs included 270 common proteins, 681 S-specific and 50 T-specific proteins, most of which were misc., protein processing, DNA and RNA processing, amino acid metabolism and stress related proteins induced by hypoxia. Some specific proteins related to waterlogging stress, including acid phosphatase, oxidant protective enzyme, S-adenosylmethionine synthetase 1, were significantly different between S and T. A total of 20 representative genes encoding DEPs, including 7 shared DEPs and 13 cultivar-specific DEPs, were selected for further RT-qPCR analysis. Fourteen genes showed consistent dynamic expression patterns at mRNA and protein levels. CONCLUSIONS Proteins involved in primary metabolisms and protein processing were inclined to be affected under hypoxia stress. The negative effects were more severe in the sensitive genotype. The expression patterns of some specific proteins, such as alcohol dehydrogenases and S-adenosylmethionine synthetase 1, could be applied as indexes for improving the waterlogging tolerance in wheat. Some specific proteins identified in this study will facilitate the subsequent protein function validation and biomarker development.
Collapse
Affiliation(s)
- Rui Pan
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
| | - Dongli He
- College of Life Sciences, Hubei University, Wuhan, 430074 China
| | - Le Xu
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
| | - Meixue Zhou
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, Hobart, Tasmania 7250 Australia
| | - Chengdao Li
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA Australia
| | - Chu Wu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 China
| | - Yanhao Xu
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
| |
Collapse
|
19
|
Peng Y, Zhou Z, Zhang Z, Yu X, Zhang X, Du K. Molecular and physiological responses in roots of two full-sib poplars uncover mechanisms that contribute to differences in partial submergence tolerance. Sci Rep 2018; 8:12829. [PMID: 30150759 PMCID: PMC6110812 DOI: 10.1038/s41598-018-30821-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/31/2018] [Indexed: 11/22/2022] Open
Abstract
Poplar is a major afforestation tree species in flood-prone areas. Here, we compared molecular and physiological responses in the roots of two full-sib poplar clones, LS1 (flood-tolerant) and LS2 (flood-susceptive), subjected to stagnant flooding using transcript and metabolite profiling. LS1 displayed less phenotypic damage and superior leaf gas exchange and plant growth compared with those of LS2. We concluded that three characteristics might contribute to the differences in flood tolerance between LS1 and LS2. First, fermentation was initiated through lactic dehydrogenation in LS1 roots under flooding and subsequently dominated by alcohol fermentation. However, lactic dehydrogenase was persistently active in flooded LS2. Second, 13 differentially expressed genes associated with energy and O2 consumption processes under soil flooding had lower transcript levels in LS1 than those in LS2, which might contribute to better energy-/O2-saving abilities and behaviours in flood-tolerant LS1 than those in flood-susceptible LS2 under hypoxic stress. Third, LS1 possessed increased reactive oxygen species scavenging abilities compared with those of LS2 under edaphic flooding. Our data are a valuable contribution to understanding the mechanisms involved in the flood tolerance of poplar.
Collapse
Affiliation(s)
- YanJie Peng
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - ZhiXiang Zhou
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Zhe Zhang
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - XiaoLi Yu
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - XinYe Zhang
- Hubei Academy of Forestry, Wuhan, 430075, P. R. China
| | - KeBing Du
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| |
Collapse
|
20
|
Zhu X, Li X, Jiu S, Zhang K, Wang C, Fang J. Analysis of the regulation networks in grapevine reveals response to waterlogging stress and candidate gene-marker selection for damage severity. R Soc Open Sci 2018; 5:172253. [PMID: 30110413 PMCID: PMC6030322 DOI: 10.1098/rsos.172253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/22/2018] [Indexed: 05/31/2023]
Abstract
Owing to the climate change impacts, waterlogging is one of the most hazardous abiotic stresses to crops, which also can result in a serious reduction in the quantity and quality of grape berry and wine production during the rainy season. Therefore, the exploration of the response mechanism of grape to waterlogging is necessary, for which the analysis of the transcriptomic regulation networks of grapevine leaves in response to waterlogging stress was carried out. In this study, 12 634 genes were detected in both waterlogging stress and control grapevine plants, out of which 6837 genes were differentially expressed. A comparative analysis revealed that genes functioning in the antioxidant system, glycolysis and fermentation pathway, chlorophyll metabolism, amino acid metabolism and hormones were activated to reduce injury to grapes under the waterlogging stress. Meanwhile, genes encoding class-2 non-symbiotic haemoglobin were determined as important in waterlogging acclimation. Additionally, the expression variations of three marker genes were found to be informative and can be used to predict the viability of the grapevines subjected to waterlogging. This research not only probes the molecular mechanism underlying grapevine waterlogging tolerance but also puts forward an idea about the application of gene expression information to practical management.
Collapse
|
21
|
Ren CG, Kong CC, Xie ZH. Role of abscisic acid in strigolactone-induced salt stress tolerance in arbuscular mycorrhizal Sesbania cannabina seedlings. BMC Plant Biol 2018; 18:74. [PMID: 29724168 PMCID: PMC5934815 DOI: 10.1186/s12870-018-1292-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 04/24/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Strigolactones (SLs) are considered to be a novel class of phytohormone involved in plant defense responses. Currently, their relationships with other plant hormones, such as abscisic acid (ABA), during responses to salinity stress are largely unknown. RESULTS In this study, the relationship between SL and ABA during the induction of H2O2 - mediated tolerance to salt stress were studied in arbuscular mycorrhizal (AM) Sesbania cannabina seedlings. The SL levels increased after ABA treatments and decreased when ABA biosynthesis was inhibited in AM plants. Additionally, the expression levels of SL-biosynthesis genes in AM plants increased following treatments with exogenous ABA and H2O2. Furthermore, ABA-induced SL production was blocked by a pre-treatment with dimethylthiourea, which scavenges H2O2. In contrast, ABA production was unaffected by dimethylthiourea. Abscisic acid induced only partial and transient increases in the salt tolerance of TIS108 (a SL synthesis inhibitor) treated AM plants, whereas SL induced considerable and prolonged increases in salt tolerance after a pre-treatment with tungstate. CONCLUSIONS These results strongly suggest that ABA is regulating the induction of salt tolerance by SL in AM S. cannabina seedlings.
Collapse
Affiliation(s)
- Cheng-Gang Ren
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003 China
| | - Cun-Cui Kong
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003 China
| | - Zhi-Hong Xie
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003 China
| |
Collapse
|