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Panzade KP, Tribhuvan KU, Pawar DV, Jasrotia RS, Gaikwad K, Dalal M, Kumar RR, Singh MP, Awasthi OP, Padaria JC. Discovering the regulators of heat stress tolerance in Ziziphus nummularia (Burm.f) wight and walk.-arn. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:497-511. [PMID: 38633271 PMCID: PMC11018567 DOI: 10.1007/s12298-024-01431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 12/14/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Ziziphus nummularia an elite heat-stress tolerant shrub, grows in arid regions of desert. However, its molecular mechanism responsible for heat stress tolerance is unexplored. Therefore, we analysed whole transcriptome of Jaisalmer (heat tolerant) and Godhra (heat sensitive) genotypes of Z. nummularia to understand its molecular mechanism responsible for heat stress tolerance. De novo assembly of 16,22,25,052 clean reads yielded 276,029 transcripts. A total of 208,506 unigenes were identified which contains 4290 and 1043 differentially expressed genes (DEG) in TGO (treated Godhra at 42 °C) vs. CGO (control Godhra) and TJR (treated Jaisalmer at 42 °C) vs. CJR (control Jaisalmer), respectively. A total of 987 (67 highly enriched) and 754 (34 highly enriched) pathways were obsorved in CGO vs. TGO and CJR vs. TJR, respectively. Antioxidant pathways and TFs like Homeobox, HBP, ARR, PHD, GRAS, CPP, and E2FA were uniquely observed in Godhra genotype and SET domains were uniquely observed in Jaisalmer genotype. Further transposable elements were highly up-regulated in Godhra genotype but no activation in Jaisalmer genotype. A total of 43,093 and 39,278 simple sequence repeats were identified in the Godhra and Jaisalmer genotypes, respectively. A total of 10 DEGs linked to heat stress were validated in both genotypes for their expression under different heat stresses using quantitative real-time PCR. Comparing expression patterns of the selected DEGs identified ClpB1 as a potential candidate gene for heat tolerance in Z. nummularia. Here we present first characterized transcriptome of Z. nummularia in response to heat stress for the identification and characterization of heat stress-responsive genes. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01431-y.
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Affiliation(s)
- Kishor Prabhakar Panzade
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Kishor U. Tribhuvan
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand 834 003 India
| | - Deepak V. Pawar
- ICAR- Directorate of Weed Research, Maharajpur, Jabalpur, Madhya Pradesh 482004 India
| | - Rahul Singh Jasrotia
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr., San Antonio, TX 78229 USA
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Monika Dalal
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, ICAR–Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Madan Pal Singh
- Division of Plant Physiology, ICAR-Indian Agrcultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Om Prakash Awasthi
- Division of Horticulture, ICAR-Indian Agrcultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Jasdeep Chatrath Padaria
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
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Yu H, Guo Q, Ji W, Wang H, Tao J, Xu P, Chen X, Ali W, Wu X, Shen X, Xie Y, Xu Z. Transcriptome Expression Profiling Reveals the Molecular Response to Salt Stress in Gossypium anomalum Seedlings. PLANTS (BASEL, SWITZERLAND) 2024; 13:312. [PMID: 38276767 PMCID: PMC10819910 DOI: 10.3390/plants13020312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024]
Abstract
Some wild cotton species are remarkably tolerant to salt stress, and hence represent valuable resources for improving salt tolerance of the domesticated allotetraploid species Gossypium hirsutum L. Here, we first detected salt-induced stress changes in physiological and biochemical indexes of G. anomalum, a wild African diploid cotton species. Under 350 mmol/L NaCl treatment, the photosynthetic parameters declined significantly, whereas hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents increased. Catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) activity and proline (PRO) content also significantly increased, reaching peak values at different stages of salt stress. We used RNA-Seq to characterize 15,476 differentially expressed genes in G. anomalum roots after 6, 12, 24, 72, and 144 h of salt stress. Gene Ontology enrichment analysis revealed these genes to be related to sequence-specific DNA and iron ion binding and oxidoreductase, peroxidase, antioxidant, and transferase activity; meanwhile, the top enriched pathways from the Kyoto Encyclopedia of Genes and Genomes database were plant hormone signal transduction, phenylpropanoid biosynthesis, fatty acid degradation, carotenoid biosynthesis, zeatin biosynthesis, starch and sucrose metabolism, and MAPK signaling. A total of 1231 transcription factors were found to be expressed in response to salt stress, representing ERF, MYB, WRKY, NAC, C2H2, bZIP, and HD-ZIP families. Nine candidate genes were validated by quantitative real-time PCR and their expression patterns were found to be consistent with the RNA-Seq data. These data promise to significantly advance our understanding of the molecular response to salt stress in Gossypium spp., with potential value for breeding applications.
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Affiliation(s)
- Huan Yu
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China;
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Qi Guo
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Wei Ji
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Heyang Wang
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Jingqi Tao
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Peng Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xianglong Chen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Wuzhimu Ali
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xuan Wu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xinlian Shen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Yinfeng Xie
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China;
| | - Zhenzhen Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
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Xing M, Huang K, Zhang C, Xi D, Luo H, Pei J, Ruan R, Liu H. Transcriptome Analysis Reveals the Molecular Mechanism and Responsive Genes of Waterlogging Stress in Actinidia deliciosa Planch Kiwifruit Plants. Int J Mol Sci 2023; 24:15887. [PMID: 37958870 PMCID: PMC10649176 DOI: 10.3390/ijms242115887] [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: 09/20/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Waterlogging stress is one of the major natural issues resulting in stunted growth and loss of agricultural productivity. Cultivated kiwifruits are popular for their rich vitamin C content and unique flavor among consumers, while commonly sensitive to waterlogging stress. The wild kiwifruit plants are usually obliged to survive in harsh environments. Here, we carried out a transcriptome analysis by high-throughput RNA sequencing using the root tissues of Actinidia deliciosa (a wild resource with stress-tolerant phenotype) after waterlogging for 0 d, 3 d, and 7 d. Based on the RNA sequencing data, a high number of differentially expressed genes (DEGs) were identified in roots under waterlogging treatment, which were significantly enriched into four biological processes, including stress response, metabolic processes, molecular transport, and mitotic organization, by gene ontology (GO) simplify enrichment analysis. Among these DEGs, the hypoxia-related genes AdADH1 and AdADH2 were correlated well with the contents of acetaldehyde and ethanol, and three transcription factors Acc26216, Acc08443, and Acc16908 were highly correlated with both AdADH1/2 genes and contents of acetaldehyde and ethanol. In addition, we found that there might be an evident difference among the promoter sequences of ADH genes from A. deliciosa and A. chinensis. Taken together, our results provide additional information on the waterlogging response in wild kiwifruit plants.
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Affiliation(s)
| | | | | | | | | | | | | | - Hui Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China; (M.X.); (K.H.); (C.Z.); (D.X.); (H.L.); (J.P.); (R.R.)
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Abdul Aziz M, Masmoudi K. Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms. Int J Mol Sci 2023; 24:9813. [PMID: 37372961 DOI: 10.3390/ijms24129813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023] Open
Abstract
The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na+ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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Cui C, Feng L, Zhou C, Wan H, Zhou B. Transcriptome Revealed GhPP2C43-A Negatively Regulates Salinity Tolerance in an Introgression Line from a Semi-wild Upland Cotton. PLANT & CELL PHYSIOLOGY 2023:pcad036. [PMID: 37115634 DOI: 10.1093/pcp/pcad036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 06/19/2023]
Abstract
Salt damage is one of the major threats to sustainable cotton production owing to the limited arable land in China mainly occupied by the production of staple food crops. Salt-stress tolerant cotton varieties are lacking in production and, the mechanisms underpinning salt-stress tolerance in cotton remain enigmatic. Here, DM37, an intraspecific introgression line from G. hirsutum race yucatanense acc TX-1046 into the G. hirsutum acc TM-1 background, was found to be highly tolerant to salt stress. Its seed germination rate and germination potential were significantly higher than the recipient TM-1 under salt stress. Physiological analysis showed DM37 had higher proline content and Peroxidase activity, as well as lower Na+/K+ ratios at the seedling stage, consistent with higher seedling survival rate after durable salt stress. Furthermore, comparative transcriptome analysis revealed that responsive patterns to salt stress in DM37 were different from TM-1. Weighted Correlation Network Analysis (WGCNA) demonstrated that co-expression modules associated with salt stress in DM37 also differed from TM-1. Out of them, GhPP2C43-A, a phosphatase gene, exhibited negative regulation of salt-stress tolerance verified by VIGS and transgenic Arabidopsis. Gene expression showed GhPP2C43-A in TM-1 was induced by durable salt stress but not in DM37 probably attributing to the variation of cis-element in its promoter, thereby being conferred different salt-stress tolerance. Our result would provide new genes/germplasms from semi-wild cotton in salt-stress tolerant cotton breeding. This study would give us new insights into the mechanisms underpinning the salt-stress tolerance in cotton.
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Affiliation(s)
- Changjiang Cui
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Liuchun Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Chenhui Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
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Bilal Tufail M, Yasir M, Zuo D, Cheng H, Ali M, Hafeez A, Soomro M, Song G. Identification and Characterization of Phytocyanin Family Genes in Cotton Genomes. Genes (Basel) 2023; 14:genes14030611. [PMID: 36980883 PMCID: PMC10048054 DOI: 10.3390/genes14030611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 03/04/2023] Open
Abstract
Phytocyanins (PCs) are a class of plant-specific blue copper proteins that have been demonstrated to play a role in electron transport and plant development. Through analysis of the copper ligand residues, spectroscopic properties, and domain architecture of the protein, PCs have been grouped into four subfamilies: uclacyanins (UCs), stellacyanins (SCs), plantacyanins (PLCs), and early nodulin-like proteins (ENODLs). The present study aimed to identify and characterise the PCs present in three distinct cotton species (Gossypium hirsutum, Gossyium arboreum, and Gossypium raimondii) through the identification of 98, 63, and 69 genes respectively. We grouped PCs into four clades by using bioinformatics analysis and sequence alignment, which exhibit variations in gene structure and motif distribution. PCs are distributed across all chromosomes in each of the three species, with varying numbers of exons per gene and multiple conserved motifs, and with a minimum of 1 and maximum of 11 exons found on one gene. Transcriptomic data and qRT-PCR analysis revealed that two highly differentiated PC genes were expressed at the fibre initiation stage, while three highly differentiated PCs were expressed at the fibre elongation stage. These findings serve as a foundation for further investigations aimed at understanding the contribution of this gene family in cotton fibre production.
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Affiliation(s)
- Muhammad Bilal Tufail
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hailiang Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Mushtaque Ali
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Abdul Hafeez
- Department of Agronomy, Sindh Agriculture University Campus Umerkot, Sindh 69100, Pakistan
| | - Mahtab Soomro
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Correspondence: ; Tel.: +86-037-2256-2377
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Kesawat MS, Satheesh N, Kherawat BS, Kumar A, Kim HU, Chung SM, Kumar M. Regulation of Reactive Oxygen Species during Salt Stress in Plants and Their Crosstalk with Other Signaling Molecules-Current Perspectives and Future Directions. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040864. [PMID: 36840211 PMCID: PMC9964777 DOI: 10.3390/plants12040864] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/19/2023] [Accepted: 02/06/2023] [Indexed: 05/14/2023]
Abstract
Salt stress is a severe type of environmental stress. It adversely affects agricultural production worldwide. The overproduction of reactive oxygen species (ROS) is the most frequent phenomenon during salt stress. ROS are extremely reactive and, in high amounts, noxious, leading to destructive processes and causing cellular damage. However, at lower concentrations, ROS function as secondary messengers, playing a critical role as signaling molecules, ensuring regulation of growth and adjustment to multifactorial stresses. Plants contain several enzymatic and non-enzymatic antioxidants that can detoxify ROS. The production of ROS and their scavenging are important aspects of the plant's normal response to adverse conditions. Recently, this field has attracted immense attention from plant scientists; however, ROS-induced signaling pathways during salt stress remain largely unknown. In this review, we will discuss the critical role of different antioxidants in salt stress tolerance. We also summarize the recent advances on the detrimental effects of ROS, on the antioxidant machinery scavenging ROS under salt stress, and on the crosstalk between ROS and other various signaling molecules, including nitric oxide, hydrogen sulfide, calcium, and phytohormones. Moreover, the utilization of "-omic" approaches to improve the ROS-regulating antioxidant system during the adaptation process to salt stress is also described.
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Affiliation(s)
- Mahipal Singh Kesawat
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, India
| | - Neela Satheesh
- Department of Food Nutrition and Dietetics, Faculty of Agriculture, Sri Sri University, Cuttack 754006, India
| | - Bhagwat Singh Kherawat
- Krishi Vigyan Kendra, Bikaner II, Swami Keshwanand Rajasthan Agricultural University, Bikaner 334603, India
| | - Ajay Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi-221005, India
| | - Hyun-Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Republic of Korea
| | - Sang-Min Chung
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Goyang 10326, Republic of Korea
| | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Goyang 10326, Republic of Korea
- Correspondence:
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Gao Y, Jiang Z, Shi M, Zhou Y, Huo L, Li X, Xu K. Comparative transcriptome provides insight into responding mechanism of waterlogging stress in Actinidia valvata Dunn. Gene 2022; 845:146843. [PMID: 36041594 DOI: 10.1016/j.gene.2022.146843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/20/2022] [Accepted: 08/23/2022] [Indexed: 11/04/2022]
Abstract
Kiwifruit is one of the most popular fruits, and the area of its cultivation in China has grown rapidly over the last decade. However, kiwifruit vines are vulnerable to waterlogging, especially in the extensive areas of south China where it is grown. This has become an important factor limiting yields. Therefore, it is necessary to clarify the responses of kiwifruit to waterlogging. Here, we have selected Actinidia valvata Dunn which is able to withstand waterlogging conditions and the waterlogging-susceptible Actinidia deliciosa to perform the RNA-seq of roots under waterlogging stress. Seedling roots of Actinidia valvata Dunn and Actinidia deliciosa presented distinct root phenotypes after waterlogging treatments. Genome mapping showed a large genome difference between Actinidia valvata Dunn and Actinidia deliciosa. Transcription factors MYB, MYB-related, AP2-EREBP, bHLH, WRKY, and NAC were identified as the key genes involved in the response to waterlogging stress of kiwifruit. Meanwhile, the MAPK signaling pathway and the glycolysis/gluconeogenesis pathway were identified as the vital pathways involved in the response to waterlogging, and key genes were identified from these two pathways. These results will broaden our understanding of transcriptional response of waterlogging stress and will provide new insights into the molecular mechanisms associated with waterlogging stress. Furthermore, identification of the genes responsible will assist in the breeding of kiwifruit tolerant of waterlogging.
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Affiliation(s)
- Yongbin Gao
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China
| | - Zeyu Jiang
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China
| | - Mengqi Shi
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China
| | - Yifei Zhou
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China
| | - Liuqing Huo
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China
| | - Xiaolong Li
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Kai Xu
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China.
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9
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Liu Y, Han ZJ, Su MX, Zhang M. Transcriptomic Profile Analysis of Populus talassica × Populus euphratica Response and Tolerance under Salt Stress Conditions. Genes (Basel) 2022; 13:genes13061032. [PMID: 35741794 PMCID: PMC9222677 DOI: 10.3390/genes13061032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/31/2022] [Accepted: 06/04/2022] [Indexed: 02/04/2023] Open
Abstract
A new Populus variety with a strong salt tolerance was obtained from cross breeding P. talassica as the female parent and P. euphratica as the male parent. In order to elucidate the molecular mechanism and find out the major differentially expressed genes of salt tolerance of P. talassica × P. euphratica, after being subjected to salt stress, at 0, 200, and 400 mmol/L NaCl, the root, stem, and leaf transcriptomes (denoted as R0, S0, and L0; R200, S200, and L200; and R400, S400, and L400, respectively) of P. talassica × P. euphratica were sequenced. In total, 41,617 differentially expressed genes (DEGs) were identified in all the comparison groups with 21,603 differentially upregulated genes and 20,014 differentially downregulated genes. Gene Ontology analysis showed that DEGs were significantly enriched in biological processes that may be involved in salt stress, such as ‘cell communication’, ‘ion transport’, ‘signaling’, and signal ‘transmission’. Kyoto Encyclopedia of Genes and Genomes analysis showed that DEGs were mainly enriched in pathways of ‘plant–pathogen interaction’, ‘carbon metabolism’, and ‘plant hormone signal transmission’. The pathways and related gene information formed a basis for future research on the mechanisms of salt stress, the development of molecular markers, and the cloning of key genes in P. talassica × P. euphratica.
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Affiliation(s)
- Ying Liu
- College of Life Science and Technology, Tarim University, Alar 843300, China; (Y.L.); (M.X.S.); (M.Z.)
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar 843300, China
| | - Zhan Jiang Han
- College of Life Science and Technology, Tarim University, Alar 843300, China; (Y.L.); (M.X.S.); (M.Z.)
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar 843300, China
- Correspondence:
| | - Meng Xu Su
- College of Life Science and Technology, Tarim University, Alar 843300, China; (Y.L.); (M.X.S.); (M.Z.)
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar 843300, China
| | - Min Zhang
- College of Life Science and Technology, Tarim University, Alar 843300, China; (Y.L.); (M.X.S.); (M.Z.)
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar 843300, China
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Grossi CEM, Santin F, Quintana SA, Fantino E, Ulloa RM. Calcium-dependent protein kinase 2 plays a positive role in the salt stress response in potato. PLANT CELL REPORTS 2022; 41:535-548. [PMID: 33651205 DOI: 10.1007/s00299-021-02676-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
StCDPK2 is an early player in the salt stress response in potato plants; its overexpression promoted ROS scavenging, chlorophyll stability, and the induction of stress-responsive genes conferring tolerance to salinity. The salinity of soils affects plant development and is responsible for great losses in crop yields. Calcium-dependent protein kinases (CDPKs) are sensor-transducers that decode Ca2+ signatures triggered by abiotic stimuli and translate them into physiological responses. Histochemical analyses of potato plants harboring StCDPK2 promoter fused to the reporter gene β-glucuronidase (ProStCDPK2:GUS) revealed that GUS activity was high in the leaf blade and veins, it was restricted to root tips and lateral root primordia, and was observed upon stolon swelling. Comparison with ProStCDPK1:GUS and ProStCDPK3:GUS plants revealed their differential activities in the plant tissues. ProStCDPK2:GUS plants exposed to high salt presented enhanced GUS activity in roots which correlated with the numerous stress-responsive sites predicted in its promoter sequence. Moreover, StCDPK2 expression increased in in vitro potato plants after 2 h of high salt exposure and in greenhouse plants exposed to a dynamic stress condition. As inferred from biometric data and chlorophyll content, plants that overexpress StCDPK2 were more tolerant than wild-type plants when exposed to high salt. Overexpressing plants have a more efficient antioxidant system; they showed reduced accumulation of peroxide and higher catalase activity under salt conditions, and enhanced expression of WRKY6 and ERF5 transcription factors under control conditions. Our results indicate that StCDPK2 is an early player in the salt stress response and support a positive correlation between StCDPK2 overexpression and tolerance towards salt stress.
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Affiliation(s)
- Cecilia Eugenia María Grossi
- Laboratorio de Transducción de Señales en Plantas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires (C.A.B.A., Buenos Aires, Argentina
| | - Franco Santin
- Laboratorio de Transducción de Señales en Plantas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires (C.A.B.A., Buenos Aires, Argentina
- Instituto de Botánica Darwinion (IBODA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Silverio Andrés Quintana
- Laboratorio de Transducción de Señales en Plantas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires (C.A.B.A., Buenos Aires, Argentina
- Departamento de Biotecnología, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Elisa Fantino
- Laboratorio de Transducción de Señales en Plantas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires (C.A.B.A., Buenos Aires, Argentina
- Laboratoire de Recherche Sur le Métabolisme Spécialisé Végétal, Département de Chimie, Biochimie et Physique, Université du Québec à Trois-Rivières, Québec, Canada
| | - Rita María Ulloa
- Laboratorio de Transducción de Señales en Plantas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires (C.A.B.A., Buenos Aires, Argentina.
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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11
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Razzaq A, Saleem F, Wani SH, Abdelmohsen SAM, Alyousef HA, Abdelbacki AMM, Alkallas FH, Tamam N, Elansary HO. De-novo Domestication for Improving Salt Tolerance in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:681367. [PMID: 34603347 PMCID: PMC8481614 DOI: 10.3389/fpls.2021.681367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/12/2021] [Indexed: 05/21/2023]
Abstract
Global agriculture production is under serious threat from rapidly increasing population and adverse climate changes. Food security is currently a huge challenge to feed 10 billion people by 2050. Crop domestication through conventional approaches is not good enough to meet the food demands and unable to fast-track the crop yields. Also, intensive breeding and rigorous selection of superior traits causes genetic erosion and eliminates stress-responsive genes, which makes crops more prone to abiotic stresses. Salt stress is one of the most prevailing abiotic stresses that poses severe damages to crop yield around the globe. Recent innovations in state-of-the-art genomics and transcriptomics technologies have paved the way to develop salinity tolerant crops. De novo domestication is one of the promising strategies to produce superior new crop genotypes through exploiting the genetic diversity of crop wild relatives (CWRs). Next-generation sequencing (NGS) technologies open new avenues to identifying the unique salt-tolerant genes from the CWRs. It has also led to the assembly of highly annotated crop pan-genomes to snapshot the full landscape of genetic diversity and recapture the huge gene repertoire of a species. The identification of novel genes alongside the emergence of cutting-edge genome editing tools for targeted manipulation renders de novo domestication a way forward for developing salt-tolerance crops. However, some risk associated with gene-edited crops causes hurdles for its adoption worldwide. Halophytes-led breeding for salinity tolerance provides an alternative strategy to identify extremely salt tolerant varieties that can be used to develop new crops to mitigate salinity stress.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Shabir Hussain Wani
- Division of Genetics and Plant Breeding, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Shaimaa A. M. Abdelmohsen
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Haifa A. Alyousef
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | - Fatemah H. Alkallas
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nissren Tamam
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Hosam O. Elansary
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
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12
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Singhal RK, Saha D, Skalicky M, Mishra UN, Chauhan J, Behera LP, Lenka D, Chand S, Kumar V, Dey P, Indu, Pandey S, Vachova P, Gupta A, Brestic M, El Sabagh A. Crucial Cell Signaling Compounds Crosstalk and Integrative Multi-Omics Techniques for Salinity Stress Tolerance in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:670369. [PMID: 34484254 PMCID: PMC8414894 DOI: 10.3389/fpls.2021.670369] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/28/2021] [Indexed: 10/29/2023]
Abstract
In the era of rapid climate change, abiotic stresses are the primary cause for yield gap in major agricultural crops. Among them, salinity is considered a calamitous stress due to its global distribution and consequences. Salinity affects plant processes and growth by imposing osmotic stress and destroys ionic and redox signaling. It also affects phytohormone homeostasis, which leads to oxidative stress and eventually imbalances metabolic activity. In this situation, signaling compound crosstalk such as gasotransmitters [nitric oxide (NO), hydrogen sulfide (H2S), hydrogen peroxide (H2O2), calcium (Ca), reactive oxygen species (ROS)] and plant growth regulators (auxin, ethylene, abscisic acid, and salicylic acid) have a decisive role in regulating plant stress signaling and administer unfavorable circumstances including salinity stress. Moreover, recent significant progress in omics techniques (transcriptomics, genomics, proteomics, and metabolomics) have helped to reinforce the deep understanding of molecular insight in multiple stress tolerance. Currently, there is very little information on gasotransmitters and plant growth regulator crosstalk and inadequacy of information regarding the integration of multi-omics technology during salinity stress. Therefore, there is an urgent need to understand the crucial cell signaling crosstalk mechanisms and integrative multi-omics techniques to provide a more direct approach for salinity stress tolerance. To address the above-mentioned words, this review covers the common mechanisms of signaling compounds and role of different signaling crosstalk under salinity stress tolerance. Thereafter, we mention the integration of different omics technology and compile recent information with respect to salinity stress tolerance.
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Affiliation(s)
| | - Debanjana Saha
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar, India
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Udit N. Mishra
- Faculty of Agriculture, Sri Sri University, Cuttack, India
| | - Jyoti Chauhan
- Narayan Institute of Agricultural Sciences, Gopal Narayan Singh University, Jamuhar, India
| | - Laxmi P. Behera
- Department of Agriculture Biotechnology, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Devidutta Lenka
- Department of Plant Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Subhash Chand
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Vivek Kumar
- Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, India
| | - Prajjal Dey
- Faculty of Agriculture, Sri Sri University, Cuttack, India
| | - Indu
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Saurabh Pandey
- Department of Agriculture, Guru Nanak Dev University, Amritsar, India
| | - Pavla Vachova
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Aayushi Gupta
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Department of Plant Physiology, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Ayman El Sabagh
- Department of Agronomy, Faculty of Agriculture, University of Kafrelsheikh, Kafr El Sheikh, Egypt
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, Turkey
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13
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Zhang Q, Li M, Xia CY, Zhang WJ, Yin ZG, Zhang YL, Fang QX, Liu YC, Zhang MY, Zhang WH, Du JD, Du YL. Transcriptome-based analysis of salt-related genes during the sprout stage of common bean (Phaseolus vulgaris) under salt stress conditions. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1954091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Qi Zhang
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Ming Li
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Chun Yang Xia
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Wen Jing Zhang
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Zhen Gong Yin
- Bean Crops Laboratory, Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, PR China
| | - You Li Zhang
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Qing Xi Fang
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Yang Cheng Liu
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Ming Yu Zhang
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Wen Hui Zhang
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Ji Dao Du
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Daqing, Heilongjiang, PR China
| | - Yan Li Du
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
- Cereals Germplasm Resources Innovation Laboratory, College of Agriculture, National Coarse Cereals Engineering Research Center, Daqing, Heilongjiang, PR China
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Liu H, Wang L, Jing X, Chen Y, Hu F. Functional analysis of CgWRKY57 from Cymbidium goeringii in ABA response. PeerJ 2021; 9:e10982. [PMID: 33665039 PMCID: PMC7908890 DOI: 10.7717/peerj.10982] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/30/2021] [Indexed: 11/20/2022] Open
Abstract
Background The orchid is one of the top ten Chinese flowers and has high ornamental value and elegant color. However, orchids are vulnerable to abiotic stresses during their growth and development, and the molecular mechanism of the abiotic stress response in orchids is unclear. WRKY proteins belong to a transcription factor family that plays important roles in biotic stress, abiotic stress, growth and development in plants, but little is known about the WRKY family in Cymbidium goeringii. Methods The specific fragment of the CgWRKY57 gene of C. goeringii was analyzed by bioinformatics. The expression of the CgWRKY57 gene of C. goeringii under 4 °C, 42 °C water and ABA stress as well as different tissues was detected by real-time fluorescence quantitative PCR. CgWRKY57 gene was overexpressed in wild type Arabidopsis thaliana by inflorescence infection method, and the function of transgenic lines under ABA stress was analyzed. Results CgWRKY57 was cloned from C. goeringii and found to encode 303 amino acids. The CgWRKY57 protein is an acidic, nonsecreted hydrophilic protein without a signal peptide or transmembrane domain. The CgWRKY57 protein is located to the nucleus and may function intracellularly according to its predicted subcellular localization. A domain analysis and homology comparison showed that the CgWRKY57 protein has a "WRKYGQK" domain and belongs to Group III of the WRKY family, and a phylogenetic analysis demonstrated that CgWRKY57 is closely related to OsWRKY47. CgWRKY57 was expressed in the roots, stems, leaves and floral organs of C. goeringii, and its expression level was highest in the roots according to real-time qPCR analysis. There were significant differences in CgWRKY57 expression under 4 °C, 42 °C ABA and water stress treatments, and its expression changed greatly under ABA stress. The expression of CgWRKY57 in transgenic plants was significantly higher than that in wild type plants under ABA stress, and the root length and germination rate were reduced in transgenic plants compared to wild type plants. Conclusions These results indicate that CgWRKY57 overexpression is responsive to ABA stress, and they provide a foundation for future analyses of the biological functions of the WRKY family in C. goeringii.
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Affiliation(s)
- Huanhuan Liu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Lianping Wang
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xijun Jing
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yue Chen
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Fengrong Hu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
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15
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Hafeez A, Gě Q, Zhāng Q, Lǐ J, Gōng J, Liú R, Shí Y, Shāng H, Liú À, Iqbal MS, Dèng X, Razzaq A, Ali M, Yuán Y, Gǒng W. Multi-responses of O-methyltransferase genes to salt stress and fiber development of Gossypium species. BMC PLANT BIOLOGY 2021; 21:37. [PMID: 33430775 PMCID: PMC7798291 DOI: 10.1186/s12870-020-02786-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND O-methyltransferases (OMTs) are an important group of enzymes that catalyze the transfer of a methyl group from S-adenosyl-L-methionine to their acceptor substrates. OMTs are divided into several groups according to their structural features. In Gossypium species, they are involved in phenolics and flavonoid pathways. Phenolics defend the cellulose fiber from dreadful external conditions of biotic and abiotic stresses, promoting strength and growth of plant cell wall. RESULTS An OMT gene family, containing a total of 192 members, has been identified and characterized in three main Gossypium species, G. hirsutum, G. arboreum and G. raimondii. Cis-regulatory elements analysis suggested important roles of OMT genes in growth, development, and defense against stresses. Transcriptome data of different fiber developmental stages in Chromosome Substitution Segment Lines (CSSLs), Recombination Inbred Lines (RILs) with excellent fiber quality, and standard genetic cotton cultivar TM-1 demonstrate that up-regulation of OMT genes at different fiber developmental stages, and abiotic stress treatments have some significant correlations with fiber quality formation, and with salt stress response. Quantitative RT-PCR results revealed that GhOMT10_Dt and GhOMT70_At genes had a specific expression in response to salt stress while GhOMT49_At, GhOMT49_Dt, and GhOMT48_At in fiber elongation and secondary cell wall stages. CONCLUSIONS Our results indicate that O-methyltransferase genes have multi-responses to salt stress and fiber development in Gossypium species and that they may contribute to salt tolerance or fiber quality formation in Gossypium.
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Affiliation(s)
- Abdul Hafeez
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Sindh Agriculture University Tandojam, Hyderabad, Sindh, 70060, Pakistan
| | - Qún Gě
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qí Zhāng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jùnwén Lǐ
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jǔwǔ Gōng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ruìxián Liú
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Yùzhēn Shí
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hǎihóng Shāng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Àiyīng Liú
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Muhammad S Iqbal
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiǎoyīng Dèng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Abdul Razzaq
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Muharam Ali
- Sindh Agriculture University Tandojam, Hyderabad, Sindh, 70060, Pakistan.
| | - Yǒulù Yuán
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Wànkuí Gǒng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Wang D, Lu X, Chen X, Wang S, Wang J, Guo L, Yin Z, Chen Q, Ye W. Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum. BMC Genomics 2020; 21:838. [PMID: 33246403 PMCID: PMC7694341 DOI: 10.1186/s12864-020-07260-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Background Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. We studied a salt-tolerant upland cotton cultivar under temporal salt stress to unfold the salt tolerance molecular mechanisms. Biochemical response to salt stress (400 mM) was measured at 0 h, 3 h, 12 h, 24 h and 48 h post stress intervals and single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) combined with the unique molecular identifiers approach was used to identify differentially expressed genes (DEG). Results Antioxidant enzymes including, catalase (CAT), peroxidase (POD), superoxide dismutase (SOD) were found significantly induced under temporal salt stress, suggesting that reactive oxygen species scavenging antioxidant machinery is an essential component of salt tolerance mechanism in cotton. We identified a wealth of novel transcripts based on the PacBio long reads sequencing approach. Prolonged salt stress duration induces high number of DEGs. Significant numbers of DEGs were found under key terms related to stress pathways such as “response to oxidative stress”, “response to salt stress”, “response to water deprivation”, “cation transport”, “metal ion transport”, “superoxide dismutase”, and “reductase”. Key DEGs related to hormone (abscisic acid, ethylene and jasmonic acid) biosynthesis, ion homeostasis (CBL-interacting serine/threonine-protein kinase genes, calcium-binding proteins, potassium transporter genes, potassium channel genes, sodium/hydrogen exchanger or antiporter genes), antioxidant activity (POD, SOD, CAT, glutathione reductase), transcription factors (myeloblastosis, WRKY, Apetala 2) and cell wall modification were found highly active in response to salt stress in cotton. Expression fold change of these DEGs showed both positive and negative responses, highlighting the complex nature of salt stress tolerance mechanisms in cotton. Conclusion Collectively, this study provides a good insight into the regulatory mechanism under salt stress in cotton and lays the foundation for further improvement of salt stress tolerance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07260-z.
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Affiliation(s)
- Delong Wang
- College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, P. R. China.,State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Xuke Lu
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Xiugui Chen
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Shuai Wang
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Lixue Guo
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Zujun Yin
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, P. R. China
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China.
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17
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Borkiewicz L, Polkowska-Kowalczyk L, Cieśla J, Sowiński P, Jończyk M, Rymaszewski W, Szymańska KP, Jaźwiec R, Muszyńska G, Szczegielniak J. Expression of maize calcium-dependent protein kinase (ZmCPK11) improves salt tolerance in transgenic Arabidopsis plants by regulating sodium and potassium homeostasis and stabilizing photosystem II. PHYSIOLOGIA PLANTARUM 2020; 168:38-57. [PMID: 30714160 DOI: 10.1111/ppl.12938] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
In plants, CALCIUM-DEPENDENT PROTEIN KINASES (CDPKs/CPKs) are involved in calcium signaling in response to endogenous and environmental stimuli. Here, we report that ZmCPK11, one of maize CDPKs, participates in salt stress response and tolerance. Salt stress induced expression and upregulated the activity of ZmCPK11 in maize roots and leaves. Activation of ZmCPK11 upon salt stress was also observed in roots and leaves of transgenic Arabidopsis plants expressing ZmCPK11. The transgenic plants showed a long-root phenotype under control conditions and a short-root phenotype under NaCl, abscisic acid (ABA) or jasmonic acid (JA) treatment. Analysis of ABA and JA content in roots indicated that ZmCPK11 can mediate root growth by regulating the levels of these phytohormones. Moreover, 4-week-old transgenic plants were more tolerant to salinity than the wild-type plants. Their leaves were less chlorotic and showed weaker symptoms of senescence accompanied by higher chlorophyll content and higher quantum efficiency of photosystem II. The expression of Na+ /K+ transporters (HKT1, SOS1 and NHX1) and transcription factors (CBF1, CBF2, CBF3, ZAT6 and ZAT10) with known links to salinity tolerance was upregulated in roots of the transgenic plants upon salt stress. Furthermore, the transgenic plants accumulated less Na+ in roots and leaves under salinity, and showed a higher K+ /Na+ ratio in leaves. These results show that the improved salt tolerance in ZmCPK11-transgenic plants could be due to an upregulation of genes involved in the maintenance of intracellular Na+ and K+ homeostasis and a protection of photosystem II against damage.
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Affiliation(s)
- Lidia Borkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Department of Molecular Biology, Maria Curie-Skłodowska University, Lublin, Poland
| | | | - Jarosław Cieśla
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Sowiński
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, Warsaw University, Warsaw, Poland
| | - Maciej Jończyk
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, Warsaw University, Warsaw, Poland
| | - Wojciech Rymaszewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna P Szymańska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Radosław Jaźwiec
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Grażyna Muszyńska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jadwiga Szczegielniak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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18
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Transcription Factor GarWRKY5 Is Involved in Salt Stress Response in Diploid Cotton Species ( Gossypium aridum L.). Int J Mol Sci 2019; 20:ijms20215244. [PMID: 31652670 PMCID: PMC6862181 DOI: 10.3390/ijms20215244] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/15/2019] [Accepted: 10/20/2019] [Indexed: 12/12/2022] Open
Abstract
Cotton is one of the most economically important crops in the world, and it is exposed to various abiotic stresses during its lifecycle, especially salt stress. However, the molecular mechanisms underlying cotton tolerance to salt stress are still not fully understood due to the complex nature of salt response. Therefore, identification of salt stress tolerance-related functional genes will help us understand key components involved in stress response and provide valuable genes for improving salt stress tolerance via genetic engineering in cotton. In the present study, virus-induced gene silencing of GhWRKY5 in cotton showed enhanced salt sensitivity compared to wild-type plants under salt stress. Overexpression of GarWRKY5 in Arabidopsis positively regulated salt tolerance at the stages of seed germination and vegetative growth. Additionally, GarWRKY5-overexpressing plants exhibited higher activities of superoxide dismutase (SOD) and peroxidase (POD) under salt stress. The transcriptome sequencing analysis of transgenic Arabidopsis plants and wild-type plants revealed that there was enriched coexpression of genes involved in reactive oxygen species (ROS) scavenging (including glutamine S-transferases (GSTs) and SODs) and altered response to jasmonic acid and salicylic acid in the GarWRKY5-OE lines. GarWRKY5 is involved in salt stress response by the jasmonic acid- or salicylic acid-mediated signaling pathway based on overexpression of GarWRKY5 in Arabidopsis and virus-induced gene silencing of GarWRKY5 in cotton.
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Yuan Y, Xing H, Zeng W, Xu J, Mao L, Wang L, Feng W, Tao J, Wang H, Zhang H, Wang Q, Zhang G, Song X, Sun XZ. Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage. BMC PLANT BIOLOGY 2019; 19:394. [PMID: 31510912 PMCID: PMC6737726 DOI: 10.1186/s12870-019-1989-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 08/26/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Salinity is a major abiotic stress seriously hindering crop yield. Development and utilization of tolerant varieties is the most economical way to address soil salinity. Upland cotton is a major fiber crop and pioneer plant on saline soil and thus its genetic architecture underlying salt tolerance should be extensively explored. RESULTS In this study, genome-wide association analysis and RNA sequencing were employed to detect salt-tolerant qualitative-trait loci (QTLs) and candidate genes in 196 upland cotton genotypes at the germination stage. Using comprehensive evaluation values of salt tolerance in four environments, we identified 33 significant single-nucleotide polymorphisms (SNPs), including 17 and 7 SNPs under at least two and four environments, respectively. The 17 stable SNPs were located within or near 98 candidate genes in 13 QTLs, including 35 genes that were functionally annotated to be involved in salt stress responses. RNA-seq analysis indicated that among the 98 candidate genes, 13 were stably differentially expressed. Furthermore, 12 of the 13 candidate genes were verified by qRT-PCR. RNA-seq analysis detected 6640, 3878, and 6462 differentially expressed genes at three sampling time points, of which 869 were shared. CONCLUSIONS These results, including the elite cotton accessions with accurate salt tolerance evaluation, the significant SNP markers, the candidate genes, and the salt-tolerant pathways, could improve our understanding of the molecular regulatory mechanisms under salt stress tolerance and genetic manipulation for cotton improvement.
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Affiliation(s)
- Yanchao Yuan
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Key Lab of Plant Biotechnology in Universities of Shandong Province, Changcheng Road 700, Qingdao, China
| | - Huixian Xing
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Wenguan Zeng
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Jialing Xu
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Lili Mao
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Liyuan Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Wei Feng
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Jincai Tao
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Haoran Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Haijun Zhang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Qingkang Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Guihua Zhang
- Heze Academy of Agricultural Sciences, Heze, China
| | - Xianliang Song
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China.
| | - Xue-Zhen Sun
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China.
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20
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Hwang JE, Kim YJ, Shin MH, Hyun HJ, Bohnert HJ, Park HC. A comprehensive analysis of the Korean fir (Abies koreana) genes expressed under heat stress using transcriptome analysis. Sci Rep 2018; 8:10233. [PMID: 29980711 PMCID: PMC6035224 DOI: 10.1038/s41598-018-28552-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 06/22/2018] [Indexed: 11/09/2022] Open
Abstract
Korean fir (Abies koreana), a rare species endemic to South Korea, is sensitive to climate change. Here, we used next-generation massively parallel sequencing technology and de novo transcriptome assembly to gain a comprehensive overview of the Korean fir transcriptome under heat stress. Sequencing control and heat-treated samples of Korean fir, we obtained more than 194,872,650 clean reads from each sample. After de novo assembly and quantitative assessment, 42,056 unigenes were generated with an average length of 908 bp. In total, 6,401 differentially expressed genes were detected, of which 2,958 were up-regulated and 3,443 down-regulated, between the heat-treated and control samples. A gene ontology analysis of these unigenes revealed heat-stress-related terms, such as "response to stimulus". Further, in depth analysis revealed 204 transcription factors and 189 Hsps as differentially expressed. Finally, 12 regulated candidate genes associated with heat stress were examined using quantitative real-time PCR (qRT-PCR). In this study, we present the first comprehensive characterisation of Korean fir subjected to heat stress using transcriptome analysis. It provides an important resource for future studies of Korean fir with the objective of identifying heat stress tolerant lines.
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Affiliation(s)
- Jung Eun Hwang
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea
| | - Yun Jeong Kim
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea
| | - Myung Hwan Shin
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea
| | - Hwa Ja Hyun
- National Institute Forest Science Warm Temperate and Subtropical Forest Research Center, Jeju, Republic of Korea
| | - Hans J Bohnert
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hyeong Cheol Park
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea.
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21
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Gu C, Xu S, Wang Z, Liu L, Zhang Y, Deng Y, Huang S. De novo sequencing, assembly, and analysis of Iris lactea var. chinensis roots' transcriptome in response to salt stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 125:1-12. [PMID: 29413626 DOI: 10.1016/j.plaphy.2018.01.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/22/2018] [Indexed: 06/08/2023]
Abstract
As a halophyte, Iris lactea var. chinensis (I. lactea var. chinensis) is widely distributed and has good drought and heavy metal resistance. Moreover, it is an excellent ornamental plant. I. lactea var. chinensis has extensive application prospects owing to the global impacts of salinization. To better understand its molecular mechanism involved in salt resistance, the de novo sequencing, assembly, and analysis of I. lactea var. chinensis roots' transcriptome in response to salt-stress conditions was performed. On average, 74.17% of the clean reads were mapped to unigenes. A total of 121,093 unigenes were constructed and 56,398 (46.57%) were annotated. Among these, 13,522 differentially expressed genes (DEGs) were identified between salt-treated and control samples Compared to the transcriptional level of control, 7037 DEGs were up-regulated and 6539 down-regulated. In addition, 129 up-regulated and 1609 down-regulated genes were simultaneously detected in all three pairwise comparisons between control and salt-stressed libraries. At least 247 and 250 DEGs encoding transcription factors and transporter proteins were identified. Meanwhile, 130 DEGs regarding reactive oxygen species (ROS) scavenging system were also summarized. Based on real-time quantitative RT-PCR, we verified the changes in the expression patterns of 10 unigenes. Our study identified potential salt-responsive candidate genes and increased the understanding of halophyte responses to salinity stress.
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Affiliation(s)
- Chunsun Gu
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| | - Sheng Xu
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Zhiquan Wang
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Liangqin Liu
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yongxia Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yanming Deng
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Suzhen Huang
- Jiangsu Key Laboratory for Bioresources of Saline Solis, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
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22
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Yao L, Wang J, Li B, Meng Y, Ma X, Si E, Ren P, Yang K, Shang X, Wang H. Transcriptome sequencing and comparative analysis of differentially-expressed isoforms in the roots of Halogeton glomeratus under salt stress. Gene 2017; 646:159-168. [PMID: 29292193 DOI: 10.1016/j.gene.2017.12.058] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/06/2017] [Accepted: 12/28/2017] [Indexed: 11/19/2022]
Abstract
Although Halogeton glomeratus (H. glomeratus) has been confirmed to have a unique mechanism to regulate Na+ efflux from the cytoplasm and compartmentalize Na+ into leaf vacuoles, little is known about the salt tolerance mechanisms of roots under salinity stress. In the present study, transcripts were sequenced using the BGISEQ-500 sequencing platform (BGI, Wuhan, China). After quality control, approximately 24.08 million clean reads were obtained and the average mapping ratio to the reference gene was 70.00%. When comparing salt-treated samples with the control, a total of 550, 590, 1411 and 2063 DEIs were identified at 2, 6, 24 and 72h, respectively. Numerous differentially-expressed isoforms that play important roles in response and adaptation to salt condition are related to metabolic processes, cellular processes, single-organism processes, localization, biological regulation, responses to stimulus, binding, catalytic activity and transporter activity. Fifty-eight salt-induced isoforms were common to different stages of salt stress; most of these DEIs were related to signal transduction and transporters, which maybe the core isoforms regulating Na+ uptake and transport in the roots of H. glomeratus. The expression patterns of 18 DEIs that were detected by quantitative real-time polymerase chain reaction were consistent with their respective changes in transcript abundance as identified by RNA-Seq technology. The present study thoroughly explored potential isoforms involved in salt tolerance on H. glomeratus roots at five time points. Our results may serve as an important resource for the H. glomeratus research community, improving our understanding of salt tolerance in halophyte survival under high salinity stress.
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Affiliation(s)
- Lirong Yao
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China; College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Juncheng Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China; College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Baochun Li
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China; Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yaxiong Meng
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China; College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaole Ma
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China; College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Erjing Si
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China; College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Panrong Ren
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China; College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Ke Yang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China; College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xunwu Shang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Huajun Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China; College of Agronomy, Gansu Agricultural University, Lanzhou, China.
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23
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De Novo Transcriptome Characterization, Gene Expression Profiling and Ionic Responses of Nitraria sibirica Pall. under Salt Stress. FORESTS 2017. [DOI: 10.3390/f8060211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Wei Y, Xu Y, Lu P, Wang X, Li Z, Cai X, Zhou Z, Wang Y, Zhang Z, Lin Z, Liu F, Wang K. Salt stress responsiveness of a wild cotton species (Gossypium klotzschianum) based on transcriptomic analysis. PLoS One 2017; 12:e0178313. [PMID: 28552980 PMCID: PMC5446155 DOI: 10.1371/journal.pone.0178313] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/11/2017] [Indexed: 11/22/2022] Open
Abstract
Cotton is a pioneer of saline land crop, while salt stress still causes its growth inhibition and fiber production decrease. Phenotype identification showed better salt tolerance of a wild diploid cotton species Gossypium klotzschianum. To elucidate the salt-tolerant mechanisms in G. klotzschianum, we firstly detected the changes in hormones, H2O2 and glutathione (GSSH and GSH), then investigated the gene expression pattern of roots and leaves treated with 300 mM NaCl for 0, 3, 12, 48 h, and each time control by RNA-seq on the Illumina-Solexa platform. Physiological determination proved that the significant increase in hormone ABA at 48 h, while that in H2O2 was at 12 h, likewise, the GSH content decrease at 48 h and the GSSH content increase at 48 h, under salt stress. In total, 37,278 unigenes were identified from the transcriptome data, 8,312 and 6,732 differentially expressed genes (DEGs) were discovered to be involved in salt stress tolerance in roots and leaves, respectively. Gene function annotation and expression analysis elucidated hormone biosynthesis and signal transduction, reactive oxygen species (ROS), and salt overly sensitive (SOS) signal transduction related genes revealed the important roles of them in signal transmission, oxidation balance and ion homeostasis in response to salinity stress. This is a report which focuses on primary response to highly salty stress (upto 300 mM NaCl) in cotton using a wild diploid Gossypium species, broadening our understanding of the salt tolerance mechanism in cotton and laying a solid foundation of salt resistant for the genetic improvement of upland cotton with the resistance to salt stress.
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Affiliation(s)
- Yangyang Wei
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
- National Key Laboratory of Crop Genetic Improvement (Wuhan), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Pu Lu
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhenqing Li
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhenmei Zhang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement (Wuhan), Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail: (ZL); (FL); (KW)
| | - Fang Liu
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
- * E-mail: (ZL); (FL); (KW)
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
- * E-mail: (ZL); (FL); (KW)
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Long XH, Liu LP, Shao TY, Shao HB, Liu ZP. Developing and sustainably utilize the coastal mudflat areas in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 569-570:1077-1086. [PMID: 27396318 DOI: 10.1016/j.scitotenv.2016.06.170] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 06/20/2016] [Indexed: 05/08/2023]
Abstract
Coastal mudflat areas are regarded as the important reserve land resource in China. Rational exploitation and development of the mudflat areas can relieve the stress of inadequate land resources. Probing into the developing models of resource exploitation of coastal tidal mudflats is one of the important components of achieving the sustainable development in the coastal areas. Therefore, the development history of coastal mudflats after 1950s in China is briefly introduced in this paper. Then, the status in quo of the modes of development and utilization of coastal mudflat in China the paper is reviewed with a special attention payed to the agricultural use of coastal resource, especially halophytes and improved salt-tolerant varieties planting, agricultural dyke pond and coastal saline-alkali soil remediation. Based on related research frontier, sustainable developmental prospects of these coastal areas are presented as well.
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Affiliation(s)
- Xiao-Hua Long
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Li-Ping Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Tian-Yun Shao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong-Bo Shao
- Institute of Agro-biotechnology, Jiangsu, Academy of Agricultural Sciences, Nanjing 210014,China; Yantai Institute of Coastal Zone Research,Chinese Academy of Sciences,Yantai264003,China.
| | - Zhao-Pu Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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Kottapalli P, Ulloa M, Kottapalli KR, Payton P, Burke J. SNP Marker Discovery in Pima Cotton ( Gossypium barbadense L.) Leaf Transcriptomes. GENOMICS INSIGHTS 2016; 9:51-60. [PMID: 27721653 PMCID: PMC5049682 DOI: 10.4137/gei.s40377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 11/17/2022]
Abstract
The objective of this study was to explore the known narrow genetic diversity and discover single-nucleotide polymorphic (SNP) markers for marker-assisted breeding within Pima cotton (Gossypium barbadense L.) leaf transcriptomes. cDNA from 25-day plants of three diverse cotton genotypes [Pima S6 (PS6), Pima S7 (PS7), and Pima 3-79 (P3-79)] was sequenced on Illumina sequencing platform. A total of 28.9 million reads (average read length of 138 bp) were generated by sequencing cDNA libraries of these three genotypes. The de novo assembly of reads generated transcriptome sets of 26,369 contigs for PS6, 25,870 contigs for PS7, and 24,796 contigs for P3-79. A Pima leaf reference transcriptome was generated consisting of 42,695 contigs. More than 10,000 single-nucleotide polymorphisms (SNPs) were identified between the genotypes, with 100% SNP frequency and a minimum of eight sequencing reads. The most prevalent SNP substitutions were C-T and A-G in these cotton genotypes. The putative SNPs identified can be utilized for characterizing genetic diversity, genotyping, and eventually in Pima cotton breeding through marker-assisted selection.
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Affiliation(s)
- Pratibha Kottapalli
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
| | - Mauricio Ulloa
- USDA-ARS, PA, CSRL, Plant Stress and Germplasm Development Research, Lubbock, TX, USA
| | | | - Paxton Payton
- USDA-ARS, PA, CSRL, Plant Stress and Germplasm Development Research, Lubbock, TX, USA
| | - John Burke
- USDA-ARS, PA, CSRL, Plant Stress and Germplasm Development Research, Lubbock, TX, USA
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Gharat SA, Parmar S, Tambat S, Vasudevan M, Shaw BP. Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes. PLoS One 2016; 11:e0163485. [PMID: 27682829 PMCID: PMC5040429 DOI: 10.1371/journal.pone.0163485] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/10/2016] [Indexed: 01/02/2023] Open
Abstract
Although salt tolerance is a feature representative of halophytes, most studies on this topic in plants have been conducted on glycophytes. Transcriptome profiles are also available for only a limited number of halophytes. Hence, the present study was conducted to understand the molecular basis of salt tolerance through the transcriptome profiling of the halophyte Suaeda maritima, which is an emerging plant model for research on salt tolerance. Illumina sequencing revealed 72,588 clustered transcripts, including 27,434 that were annotated using BLASTX. Salt application resulted in the 2-fold or greater upregulation of 647 genes and downregulation of 735 genes. Of these, 391 proteins were homologous to proteins in the COGs (cluster of orthologous groups) database, and the majorities were grouped into the poorly characterized category. Approximately 50% of the genes assigned to MapMan pathways showed homology to S. maritima. The majority of such genes represented transcription factors. Several genes also contributed to cell wall and carbohydrate metabolism, ion relation, redox responses and G protein, phosphoinositide and hormone signaling. Real-time PCR was used to validate the results of the deep sequencing for the most of the genes. This study demonstrates the expression of protein kinase C, the target of diacylglycerol in phosphoinositide signaling, for the first time in plants. This study further reveals that the biochemical and molecular responses occurring at several levels are associated with salt tolerance in S. maritima. At the structural level, adaptations to high salinity levels include the remodeling of cell walls and the modification of membrane lipids. At the cellular level, the accumulation of glycinebetaine and the sequestration and exclusion of Na+ appear to be important. Moreover, this study also shows that the processes related to salt tolerance might be highly complex, as reflected by the salt-induced enhancement of transcription factor expression, including hormone-responsive factors, and that this process might be initially triggered by G protein and phosphoinositide signaling.
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Affiliation(s)
- Sachin Ashruba Gharat
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Shaifaly Parmar
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Subodh Tambat
- Bionivid Technology Private Limited, 3rd Floor, 4C-209, 4th Cross, Near New Horizon College, Kasturi Nagar, Bangalore, 560043, Karnataka, India
| | - Madavan Vasudevan
- Bionivid Technology Private Limited, 3rd Floor, 4C-209, 4th Cross, Near New Horizon College, Kasturi Nagar, Bangalore, 560043, Karnataka, India
| | - Birendra Prasad Shaw
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
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RNA sequencing reveals differential thermal regulation mechanisms between sexes of Glanville fritillary butterfly in the Tianshan Mountains, China. Mol Biol Rep 2016; 43:1423-1433. [PMID: 27649991 DOI: 10.1007/s11033-016-4076-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 09/09/2016] [Indexed: 10/21/2022]
Abstract
The Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae) has been extensively studied as a model species in metapopulation ecology. We investigated in the earlier studies that female butterflies exhibit higher thermal tolerance than males in the Tianshan Mountains of China. We aim to understand the molecular mechanism of differences of thermal responses between sexes. We used RNA-seq approach and performed de novo assembly of transcriptome to compare the gene expression patterns between two sexes after heat stress. All the reads were assembled into 84,376 transcripts and 72,701 unigenes. The number of differential expressed genes (DEGs) between control and heat shock samples was 175 and 268 for males and females, respectively. Heat shock proteins genes (hsps) were up-regulated in response to heat stress in both males and females. Most of the up-regulated hsps showed higher fold changes in males than in females. Females expressed more ribosomal subunit protein genes, transcriptional elongation factor genes, and methionine-rich storage protein genes, participating in protein synthesis. It indicated that protein synthesis is needed for females to replace the damaged proteins due to heat shock. In addition, aspartate decarboxylase might contribute to thermal tolerance in females. These differences in gene expression may at least partly explain the response to high temperature stress, and the fact that females exhibit higher thermal tolerance.
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Li S, Zhong X, Kan X, Gu L, Sun H, Zhang G, Liu X. De novo transcriptome analysis of Thitarodes jiachaensis before and after infection by the caterpillar fungus, Ophiocordyceps sinensis. Gene 2016; 580:96-103. [DOI: 10.1016/j.gene.2016.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 01/05/2016] [Accepted: 01/05/2016] [Indexed: 11/16/2022]
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Nan G, Zhang Y, Li S, Lee I, Takano T, Liu S. NaCl stress-induced transcriptomics analysis of Salix linearistipularis (syn. Salix mongolica). ACTA ACUST UNITED AC 2016; 23:1. [PMID: 26933650 PMCID: PMC4772304 DOI: 10.1186/s40709-016-0038-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 01/29/2016] [Indexed: 11/30/2022]
Abstract
Background Salix linearistipularis (syn. S. mongolica) is a woody halophyte, which is distributed naturally in saline-alkali soil of Songnen plain, Heilongjiang, China. It plays an important role in maintaining ecological balance and in improving saline soil. Furthermore, S. linearistipularis is also a genetic resource; however, there is no available information of genomic background for salt tolerance mechanism. We conducted the transcriptome analysis of S. linearistipularis to understand the mechanisms of salt tolerance by using RNA-seq technology. Results The transcription profiles of both the salt stress (SLH-treated) and the control (SLH-control) sample for S. linearistipularis were obtained by using RNA-seq in this study. By comparative analysis, only 3034 of 53,362 all-unigenes between two samples were expressed differently at more than 1.5-fold (\documentclass[12pt]{minimal}
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\begin{document}$$\left| {fold - change} \right| \ge 1.5$$\end{document}fold-change≥1.5, FDR ≤ 0.05), including 1397 up-regulated genes and 1637 down-regulated genes. In total, 2199 genes were classified into 50 Gene Ontology (GO) terms and 1103 genes were involved in 116 biological pathways. To find salt stress related genes, all-unigenes of S. linearistipularis were classified into three categories according to their degree of the differentially expressed genes (DEGs) at 0–1.5-fold (non differently expressed genes, N-DEGs), at 1.5–4.0-fold and more than 4.0-fold. The pathways of three categorized genes were compared with the DEGs of Arabidopsis thaliana, showing that 22, 10 and 1 pathway of S. linearistipularis were overlapped with A. thaliana. Degree of the overlapping was categorized as 0–1.5-fold, 1.5–4.0-fold and more than 4.0-folds. Conclusion Our study revealed that the N-DEGs of 22 pathways in S. linearistipularis were overlapped with the DEGs of A. thaliana. This result suggests that those overlapped genes that contrasted with the up- or down-regulated genes in A. thaliana were possibility evolved into housekeeping genes in S. linearistipularis under salt stress. Electronic supplementary material The online version of this article (doi:10.1186/s40709-016-0038-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guixian Nan
- Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Hexing Road No. 26, Xiangfang, Harbin, 150040 Heilongjiang China ; College of Agriculture, Yanbian University, Yanji, 133002 China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081 China
| | - Song Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081 China
| | - Imshik Lee
- Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Hexing Road No. 26, Xiangfang, Harbin, 150040 Heilongjiang China ; Institute of Physics, Nankai University, Nankai District, Tianjin, 300071 China
| | - Tetsuo Takano
- Asian Natural Environment Science Center (ANESC), The University of Tokyo, Midori Cho 1-1-1, Nishitokyo, Tokyo 188-0002 Japan
| | - Shenkui Liu
- Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Hexing Road No. 26, Xiangfang, Harbin, 150040 Heilongjiang China
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Chandra S, Singh D, Pathak J, Kumari S, Kumar M, Poddar R, Balyan HS, Gupta PK, Prabhu KV, Mukhopadhyay K. De Novo Assembled Wheat Transcriptomes Delineate Differentially Expressed Host Genes in Response to Leaf Rust Infection. PLoS One 2016; 11:e0148453. [PMID: 26840746 PMCID: PMC4739524 DOI: 10.1371/journal.pone.0148453] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/17/2016] [Indexed: 11/20/2022] Open
Abstract
Pathogens like Puccinia triticina, the causal organism for leaf rust, extensively damages wheat production. The interaction at molecular level between wheat and the pathogen is complex and less explored. The pathogen induced response was characterized using mock- or pathogen inoculated near-isogenic wheat lines (with or without seedling leaf rust resistance gene Lr28). Four Serial Analysis of Gene Expression libraries were prepared from mock- and pathogen inoculated plants and were subjected to Sequencing by Oligonucleotide Ligation and Detection, which generated a total of 165,767,777 reads, each 35 bases long. The reads were processed and multiple k-mers were attempted for de novo transcript assembly; 22 k-mers showed the best results. Altogether 21,345 contigs were generated and functionally characterized by gene ontology annotation, mining for transcription factors and resistance genes. Expression analysis among the four libraries showed extensive alterations in the transcriptome in response to pathogen infection, reflecting reorganizations in major biological processes and metabolic pathways. Role of auxin in determining pathogenesis in susceptible and resistant lines were imperative. The qPCR expression study of four LRR-RLK (Leucine-rich repeat receptor-like protein kinases) genes showed higher expression at 24 hrs after inoculation with pathogen. In summary, the conceptual model of induced resistance in wheat contributes insights on defense responses and imparts knowledge of Puccinia triticina-induced defense transcripts in wheat plants.
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Affiliation(s)
- Saket Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Dharmendra Singh
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Jyoti Pathak
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Supriya Kumari
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Raju Poddar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Puspendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Kumble Vinod Prabhu
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
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Muriira NG, Xu W, Muchugi A, Xu J, Liu A. De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea). BMC Genomics 2015; 16:723. [PMID: 26395839 PMCID: PMC4580217 DOI: 10.1186/s12864-015-1908-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/09/2015] [Indexed: 11/18/2022] Open
Abstract
Background The Sodom apple (Calotropis gigantea), a member of the Asclepiadaceae family, is a large evergreen shrub native to continental Asia and northern Africa. As an important medicinal shrub and a fiber resource plant, there is an urgent need for developing molecular markers to facilitate breeding and genetic improvement of varieties. Results In this study, using the Illumina high throughput sequencing technique we obtained about 45 million paired end sequencing reads, De novo assembled and generated a total of 133,634 transcripts with a mean of 1837.47 bp in length. Based on protein homology searches against available databases, a total of 21,851 unigenes were functionally annotated. In particular, many transcripts that encode for putative proteins involved in fiber and secondary metabolite biosynthesis were identified and analyzed. Key fiber genes identified were validated experimentally through Real-Time PCR technique. Various transcription factors involved in regulating plant response to abiotic stress were also identified. In addition, based on the unigene sequences assembled, 11,623 microsatellites loci were detected, which provide very useful resources for developing microsatellite molecular markers. Conclusion This study is the first report on transcriptome information in the Calotropis species and provides rich gene transcript resources for conducting further studies on understanding the molecular basis of fiber and secondary metabolite biosynthesis, serving the genetic improvement and resource utilization in Calotropis plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1908-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nkatha G Muriira
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,World Agroforestry Centre, East and Central Asia Office, 132 Lanhei Road, Kunming, 650201, China. .,World Agroforestry Centre (ICRAF), P.O. Box 30677-00100, Nairobi, Kenya.
| | - Wei Xu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Alice Muchugi
- World Agroforestry Centre (ICRAF), P.O. Box 30677-00100, Nairobi, Kenya.
| | - Jianchu Xu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,World Agroforestry Centre, East and Central Asia Office, 132 Lanhei Road, Kunming, 650201, China.
| | - Aizhong Liu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China.
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Wang Z, Wang B, Chen G, Jian J, Lu Y, Xu Y, Wu Z. Transcriptome analysis of the pearl oyster (Pinctada fucata) hemocytes in response to Vibrio alginolyticus infection. Gene 2015; 575:421-428. [PMID: 26363408 DOI: 10.1016/j.gene.2015.09.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 07/16/2015] [Accepted: 09/07/2015] [Indexed: 10/23/2022]
Abstract
The pearl oyster Pinctada fucata is cultured widely for production of marine pearls in China, while mass mortalities, likely related to pathogenic infections, have occurred frequently in juvenile, mother and operated oysters. To address this issue, understanding host defense mechanisms of P. fucata against pathogenic challenge is extremely important. In the present study, a comparative analysis of hemocyte transcriptomes of P. fucata before and after Vibrio alginolyticus infection was conducted using the Illumina/Hiseq-2000 RNA-Seq technology. A total of 56,345,139 clean reads were generated and then assembled into 74,007 unigenes with an average length of 680 bp and an N50 of 1197 bp. Unigenes were annotated by comparing against non-redundant protein sequence (nr), non-redundant nucleotide (nt), Swiss-Prot, Pfam, Gene Ontology database (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and 29,615 unigenes (40.01%) were annotated in at least one database. There were 636 genes (518 up-regulated and 118 down-regulated) that were significantly differentially expressed after bacterial challenge, and among which 369 were associated with 122 pathways, including classical immune-related pathways, such as 'MAPK signaling pathway', 'Chemokine signaling pathway', 'Apoptosis' and 'Wnt signaling pathway'. These findings provide information on the pearl oyster innate immunity and may contribute to developing strategies for management of diseases and long-term sustainability of P. fucata culture.
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Affiliation(s)
- Zhongliang Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animals, Zhanjiang 524025, China
| | - Bei Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524025, China
| | - Gang Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animals, Zhanjiang 524025, China
| | - Jichang Jian
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524025, China
| | - Yishan Lu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524025, China
| | - Youhou Xu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou 535099, China
| | - Zaohe Wu
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524025, China; Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
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Gardin JAC, Gouzy J, Carrère S, Délye C. ALOMYbase, a resource to investigate non-target-site-based resistance to herbicides inhibiting acetolactate-synthase (ALS) in the major grass weed Alopecurus myosuroides (black-grass). BMC Genomics 2015; 16:590. [PMID: 26265378 PMCID: PMC4534104 DOI: 10.1186/s12864-015-1804-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 07/31/2015] [Indexed: 12/29/2022] Open
Abstract
Background Herbicide resistance in agrestal weeds is a global problem threatening food security. Non-target-site resistance (NTSR) endowed by mechanisms neutralising the herbicide or compensating for its action is considered the most agronomically noxious type of resistance. Contrary to target-site resistance, NTSR mechanisms are far from being fully elucidated. A part of weed response to herbicide stress, NTSR is considered to be largely driven by gene regulation. Our purpose was to establish a transcriptome resource allowing investigation of the transcriptomic bases of NTSR in the major grass weed Alopecurus myosuroides L. (Poaceae) for which almost no genomic or transcriptomic data was available. Results RNA-Seq was performed from plants in one F2 population that were sensitive or expressing NTSR to herbicides inhibiting acetolactate-synthase. Cloned plants were sampled over seven time-points ranging from before until 73 h after herbicide application. Assembly of over 159M high-quality Illumina reads generated a transcriptomic resource (ALOMYbase) containing 65,558 potentially active contigs (N50 = 1240 nucleotides) predicted to encode 32,138 peptides with 74 % GO annotation, of which 2017 were assigned to protein families presumably involved in NTSR. Comparison with the fully sequenced grass genomes indicated good coverage and correct representation of A. myosuroides transcriptome in ALOMYbase. The part of the herbicide transcriptomic response common to the resistant and the sensitive plants was consistent with the expected effects of acetolactate-synthase inhibition, with striking similarities observed with published Arabidopsis thaliana data. A. myosuroides plants with NTSR were first affected by herbicide action like sensitive plants, but ultimately overcame it. Analysis of differences in transcriptomic herbicide response between resistant and sensitive plants did not allow identification of processes directly explaining NTSR. Five contigs associated to NTSR in the F2 population studied were tentatively identified. They were predicted to encode three cytochromes P450 (CYP71A, CYP71B and CYP81D), one peroxidase and one disease resistance protein. Conclusions Our data confirmed that gene regulation is at the root of herbicide response and of NTSR. ALOMYbase proved to be a relevant resource to support NTSR transcriptomic studies, and constitutes a valuable tool for future research aiming at elucidating gene regulations involved in NTSR in A. myosuroides. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1804-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jérôme Gouzy
- INRA, UMR441 LIPM, F-31326, Castanet-Tolosan, France.
| | | | - Christophe Délye
- INRA, UMR1347 Agroécologie, 17 rue de Sully, F-21000, Dijon, France.
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Shi G, Guo X, Guo J, Liu L, Hua J. Analyzing serial cDNA libraries revealed reactive oxygen species and gibberellins signaling pathways in the salt response of Upland cotton (Gossypium hirsutum L.). PLANT CELL REPORTS 2015; 34:1005-23. [PMID: 25700980 DOI: 10.1007/s00299-015-1761-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/27/2015] [Accepted: 02/08/2015] [Indexed: 05/22/2023]
Abstract
By comparing series full-length cDNA libraries stressed and control, the dynamic process of salt stress response in Upland cotton was studied, and reactive oxygen species and gibberellins signaling pathways were proposed. The Upland cotton is the most important fiber plant with highly salt tolerance. However, the molecular mechanism underlying salt tolerance in domesticated cotton was unclear. Here, seven full-length cDNA libraries were constructed for seedling roots of Upland cotton 'Zhong G 5' at 0, 3, 12 and 48 h after the treatment of control or 150 mM NaCl stress. About 3300 colonies in each library were selected robotically for 5'-end pyrosequencing, resulting in 20,358 expressed sequence tags (ESTs) totally. And 8516 uniESTs were then assembled, including 2914 contigs and 5602 singletons, and explored for Gene Ontology (GO) function. GO comparison between serial stress libraries and control reflected the growth regulation, stimulus response, signal transduction and biology regulation processes were conducted dynamically in response to salt stress. MYB, MYB-related, WRKY, bHLH, GRAS and ERF families of transcription factors were significantly enriched in the early response. 65 differentially expressed genes (DEGs), mainly associated with reactive oxygen species (ROS) scavenging, gibberellins (GAs) metabolism, signal transduction, transcription regulation, stress response and transmembrane transport, were identified and confirmed by quantitative real-time PCR. Overexpression of selected DEGs increased tolerance against salt stress in transgenic yeast. Results in this study supported that a ROS-GAs interacting signaling pathway of salt stress response was activated in Upland cotton. Our results provided valuable gene resources for further investigation of the molecular mechanism of salinity tolerance.
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Affiliation(s)
- Gongyao Shi
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China,
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Pan L, Liu Y, Wei Q, Xiao C, Ji Q, Bao G, Wu X. Solexa-Sequencing Based Transcriptome Study of Plaice Skin Phenotype in Rex Rabbits (Oryctolagus cuniculus). PLoS One 2015; 10:e0124583. [PMID: 25955442 PMCID: PMC4425669 DOI: 10.1371/journal.pone.0124583] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 02/19/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Fur is an important genetically-determined characteristic of domestic rabbits; rabbit furs are of great economic value. We used the Solexa sequencing technology to assess gene expression in skin tissues from full-sib Rex rabbits of different phenotypes in order to explore the molecular mechanisms associated with fur determination. METHODOLOGY/PRINCIPAL FINDINGS Transcriptome analysis included de novo assembly, gene function identification, and gene function classification and enrichment. We obtained 74,032,912 and 71,126,891 short reads of 100 nt, which were assembled into 377,618 unique sequences by Trinity strategy (N50=680 nt). Based on BLAST results with known proteins, 50,228 sequences were identified at a cut-off E-value ≥ 10-5. Using Blast to Gene Ontology (GO), Clusters of Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we obtained several genes with important protein functions. A total of 308 differentially expressed genes were obtained by transcriptome analysis of plaice and un-plaice phenotype animals; 209 additional differentially expressed genes were not found in any database. These genes included 49 that were only expressed in plaice skin rabbits. The novel genes may play important roles during skin growth and development. In addition, 99 known differentially expressed genes were assigned to PI3K-Akt signaling, focal adhesion, and ECM-receptor interactin, among others. Growth factors play a role in skin growth and development by regulating these signaling pathways. We confirmed the altered expression levels of seven target genes by qRT-PCR. And chosen a key gene for SNP to found the differentially between plaice and un-plaice phenotypes rabbit. CONCLUSIONS/SIGNIFICANCE The rabbit transcriptome profiling data provide new insights in understanding the molecular mechanisms underlying rabbit skin growth and development.
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Affiliation(s)
- Lei Pan
- Animal Husbandry and Veterinary Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yan Liu
- Animal Husbandry and Veterinary Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Qiang Wei
- Animal Husbandry and Veterinary Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Chenwen Xiao
- Animal Husbandry and Veterinary Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Quanan Ji
- Animal Husbandry and Veterinary Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Guolian Bao
- Animal Husbandry and Veterinary Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou Uuniversity, Yangzhou, Jiangsu, China
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Fan X, Guo Q, Xu P, Gong Y, Shu H, Yang Y, Ni W, Zhang X, Shen X. Transcriptome-wide identification of salt-responsive members of the WRKY gene family in Gossypium aridum. PLoS One 2015; 10:e0126148. [PMID: 25951083 PMCID: PMC4423833 DOI: 10.1371/journal.pone.0126148] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/30/2015] [Indexed: 12/28/2022] Open
Abstract
WRKY transcription factors are plant-specific, zinc finger-type transcription factors. The WRKY superfamily is involved in abiotic stress responses in many crops including cotton, a major fiber crop that is widely cultivated and consumed throughout the world. Salinity is an important abiotic stress that results in considerable yield losses. In this study, we identified 109 WRKY genes (GarWRKYs) in a salt-tolerant wild cotton species Gossypium aridum from transcriptome sequencing data to elucidate the roles of these factors in cotton salt tolerance. According to their structural features, the predicted members were divided into three groups (Groups I-III), as previously described for Arabidopsis. Furthermore, 28 salt-responsive GarWRKY genes were identified from digital gene expression data and subjected to real-time quantitative RT-PCR analysis. The expression patterns of most GarWRKY genes revealed by this analysis are in good agreement with those revealed by RNA-Seq analysis. RT-PCR analysis revealed that 27 GarWRKY genes were expressed in roots and one was exclusively expressed in roots. Analysis of gene orthology and motif compositions indicated that WRKY members from Arabidopsis, rice and soybean generally shared the similar motifs within the same subgroup, suggesting they have the similar function. Overexpression-GarWRKY17 and -GarWRKY104 in Arabidopsis revealed that they could positively regulate salt tolerance of transgenic Arabidopsis during different development stages. The comprehensive data generated in this study provide a platform for elucidating the functions of WRKY transcription factors in salt tolerance of G. aridum. In addition, GarWRKYs related to salt tolerance identified in this study will be potential candidates for genetic improvement of cultivated cotton salt stress tolerance.
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Affiliation(s)
- Xinqi Fan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, P. R. China, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qi Guo
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, P. R. China, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Peng Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, P. R. China, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - YuanYong Gong
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, P. R. China, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongmei Shu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, P. R. China, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yang Yang
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, P. R. China, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wanchao Ni
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, P. R. China, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xianggui Zhang
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, P. R. China, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xinlian Shen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, P. R. China, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- * E-mail:
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Duhoux A, Carrère S, Gouzy J, Bonin L, Délye C. RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance. PLANT MOLECULAR BIOLOGY 2015; 87:473-87. [PMID: 25636204 DOI: 10.1007/s11103-015-0292-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/26/2015] [Indexed: 05/03/2023]
Abstract
Non-target-site resistance (NTSR) to herbicides that disrupts agricultural weed control is a worldwide concern for food security. NTSR is considered a polygenic adaptive trait driven by differential gene regulation in resistant plants. Little is known about its genetic determinism, which precludes NTSR diagnosis and evolutionary studies. We used Illumina RNA-sequencing to investigate transcriptomic differences between plants from the global major weed rye-grass sensitive or resistant to the acetolactate-synthase (ALS) inhibiting herbicide pyroxsulam. Plants were collected before and along a time-course after herbicide application. De novo transcriptome assembly yielded a resource (LOLbase) including 92,381 contigs representing potentially active transcripts that were assigned putative annotations. Early effects of ALS inhibition consistent with the literature were observed in resistant and sensitive plants, proving LOLbase data were relevant to study herbicide response. Comparison of resistant and sensitive plants identified 30 candidate NTSR contigs. Further validation using 212 plants resistant or sensitive to pyroxsulam and/or to the ALS inhibitors iodosulfuron + mesosulfuron confirmed four contigs (two cytochromes P450, one glycosyl-transferase and one glutathione-S-transferase) were NTSR markers which combined expression levels could reliably identify resistant plants. This work confirmed that NTSR is driven by differential gene expression and involves different mechanisms. It provided tools and foundation for subsequent NTSR investigations.
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Affiliation(s)
- Arnaud Duhoux
- UMR1347 Agroécologie, INRA, 17 rue Sully, 21000, Dijon, France
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Long Y, Wang Y, Wu S, Wang J, Tian X, Pei X. De novo assembly of transcriptome sequencing in Caragana korshinskii Kom. and characterization of EST-SSR markers. PLoS One 2015; 10:e0115805. [PMID: 25629164 PMCID: PMC4309406 DOI: 10.1371/journal.pone.0115805] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/27/2014] [Indexed: 01/05/2023] Open
Abstract
Caragana korshinskii Kom. is widely distributed in various habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in the Asian and African deserts. To date, no previous genomic information or EST-SSR marker has been reported in Caragana Fabr. genus. In this study, more than two billion bases of high-quality sequence of C. korshinskii were generated by using illumina sequencing technology and demonstrated the de novo assembly and annotation of genes without prior genome information. These reads were assembled into 86,265 unigenes (mean length = 709 bp). The similarity search indicated that 33,955 and 21,978 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 26,232 a unigenes were separately assigned to Gene Ontology (GO) database. When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database, 5,598 unigenes were assigned to 5 main categories including 32 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (2,862, 43.7%), suggesting the active metabolic processes in the desert tree. In addition, a total of 19,150 EST-SSRs were identified from 15,484 unigenes, and the characterizations of EST-SSRs were further compared with other four species in Fabraceae. 126 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among the 9 germplasms in Caranaga Fabr. genus, PCR success rate were 93.7% and the phylogenic tree was constructed based on the genotypic data. This research generated a substantial fraction of transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding.
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Affiliation(s)
- Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanyan Wang
- College of Plant science and technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shanshan Wu
- College of Plant science and technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiao Wang
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinjie Tian
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinwu Pei
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- * E-mail:
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Sundaresan S, Philosoph-Hadas S, Riov J, Mugasimangalam R, Kuravadi NA, Kochanek B, Salim S, Tucker ML, Meir S. De novo Transcriptome Sequencing and Development of Abscission Zone-Specific Microarray as a New Molecular Tool for Analysis of Tomato Organ Abscission. FRONTIERS IN PLANT SCIENCE 2015; 6:1258. [PMID: 26834766 PMCID: PMC4712312 DOI: 10.3389/fpls.2015.01258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/24/2015] [Indexed: 05/19/2023]
Abstract
Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum) can be induced by flower removal or leaf deblading, respectively, which leads to auxin depletion, resulting in increased sensitivity of the abscission zone (AZ) to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq) to obtain a comprehensive transcriptome of tomato flower AZ (FAZ) and leaf AZ (LAZ) during abscission. RNA-Seq was performed on a pool of total RNA extracted from tomato FAZ and LAZ, at different abscission stages, followed by de novo assembly. The assembled clusters contained transcripts that are already known in the Solanaceae (SOL) genomics and NCBI databases, and over 8823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing the novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehensive set of transcripts, and for mining for naturally occurring antisense transcripts. We focused on comparing the global transcriptomes generated from the FAZ and the LAZ to establish the divergences and similarities in their transcriptional networks, and particularly to characterize the processes and transcriptional regulators enriched in gene clusters that are differentially regulated in these two AZs. This study is the first attempt to analyze the global gene expression in different AZs in tomato by combining the RNA-Seq technique with oligonucleotide microarrays. Our AZ-specific microarray chip provides a cost-effective approach for expression profiling and robust analysis of multiple samples in a rapid succession.
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Affiliation(s)
- Srivignesh Sundaresan
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Sonia Philosoph-Hadas
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
| | - Joseph Riov
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Raja Mugasimangalam
- Department of Bioinformatics, QTLomics Technologies Pvt. LtdBangalore, India
| | - Nagesh A. Kuravadi
- Department of Bioinformatics, QTLomics Technologies Pvt. LtdBangalore, India
| | - Bettina Kochanek
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
| | - Shoshana Salim
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
| | - Mark L. Tucker
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
| | - Shimon Meir
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
- *Correspondence: Shimon Meir
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Yamamoto N, Takano T, Tanaka K, Ishige T, Terashima S, Endo C, Kurusu T, Yajima S, Yano K, Tada Y. Comprehensive analysis of transcriptome response to salinity stress in the halophytic turf grass Sporobolus virginicus. FRONTIERS IN PLANT SCIENCE 2015; 6:241. [PMID: 25954282 PMCID: PMC4404951 DOI: 10.3389/fpls.2015.00241] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/26/2015] [Indexed: 05/06/2023]
Abstract
The turf grass Sporobolus virginicus is halophyte and has high salinity tolerance. To investigate the molecular basis of its remarkable tolerance, we performed Illumina high-throughput RNA sequencing on roots and shoots of a S. virginicus genotype under normal and saline conditions. The 130 million short reads were assembled into 444,242 unigenes. A comparative analysis of the transcriptome with rice and Arabidopsis transcriptome revealed six turf grass-specific unigenes encoding transcription factors. Interestingly, all of them showed root specific expression and five of them encode bZIP type transcription factors. Another remarkable transcriptional feature of S. virginicus was activation of specific pathways under salinity stress. Pathway enrichment analysis suggested transcriptional activation of amino acid, pyruvate, and phospholipid metabolism. Up-regulation of several unigenes, previously shown to respond to salt stress in other halophytes was also observed. Gene Ontology enrichment analysis revealed that unigenes assigned as proteins in response to water stress, such as dehydrin and aquaporin, and transporters such as cation, amino acid, and citrate transporters, and H(+)-ATPase, were up-regulated in both shoots and roots under salinity. A correspondence analysis of the enriched pathways in turf grass cells, but not in rice cells, revealed two groups of unigenes similarly up-regulated in the turf grass in response to salt stress; one of the groups, showing excessive up-regulation under salinity, included unigenes homologos to salinity responsive genes in other halophytes. Thus, the present study identified candidate genes involved in salt tolerance of S. virginicus. This genetic resource should be valuable for understanding the mechanisms underlying high salt tolerance in S. virginicus. This information can also provide insight into salt tolerance in other halophytes.
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Affiliation(s)
- Naoki Yamamoto
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji UniversityTama-ku, Kawasaki, Japan
| | - Tomoyuki Takano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji UniversityTama-ku, Kawasaki, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of AgricultureSetagaya-ku, Japan
| | - Taichiro Ishige
- NODAI Genome Research Center, Tokyo University of AgricultureSetagaya-ku, Japan
| | - Shin Terashima
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji UniversityTama-ku, Kawasaki, Japan
| | - Chisato Endo
- School of Bioscience and Biotechnology, Tokyo University of TechnologyHachioji, Japan
| | - Takamitsu Kurusu
- School of Bioscience and Biotechnology, Tokyo University of TechnologyHachioji, Japan
| | - Shunsuke Yajima
- NODAI Genome Research Center, Tokyo University of AgricultureSetagaya-ku, Japan
- Department of Bioscience, Tokyo University of AgricultureSetagaya-ku, Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji UniversityTama-ku, Kawasaki, Japan
- *Correspondence: Kentaro Yano, Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Yuichi Tada
- School of Bioscience and Biotechnology, Tokyo University of TechnologyHachioji, Japan
- Yuichi Tada, School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan
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Li W, Zhao F, Fang W, Xie D, Hou J, Yang X, Zhao Y, Tang Z, Nie L, Lv S. Identification of early salt stress responsive proteins in seedling roots of upland cotton (Gossypium hirsutum L.) employing iTRAQ-based proteomic technique. FRONTIERS IN PLANT SCIENCE 2015; 6:732. [PMID: 26442045 PMCID: PMC4566050 DOI: 10.3389/fpls.2015.00732] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/28/2015] [Indexed: 05/17/2023]
Abstract
Soil salinity is a major abiotic stress that limits plant growth and agricultural productivity. Upland cotton (Gossypium hirsutum L.) is highly tolerant to salinity; however, large-scale proteomic data of cotton in response to salt stress are still scant. Here, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic technique was employed to identify the early differentially expressed proteins (DEPs) from salt-treated cotton roots. One hundred and twenty-eight DEPs were identified, 76 of which displayed increased abundance and 52 decreased under salt stress conditions. The majority of the proteins have functions related to carbohydrate and energy metabolism, transcription, protein metabolism, cell wall and cytoskeleton metabolism, membrane and transport, signal transduction, in addition to stress and defense. It is worth emphasizing that some novel salt-responsive proteins were identified, which are involved in cell cytoskeleton metabolism (actin-related protein2, ARP2, and fasciclin-like arabinogalactan proteins, FLAs), membrane transport (tonoplast intrinsic proteins, TIPs, and plasma membrane intrinsic proteins, PIPs), signal transduction (leucine-rich repeat receptor-like kinase encoding genes, LRR-RLKs) and stress responses (thaumatin-like protein, TLP, universal stress protein, USP, dirigent-like protein, DIR, desiccation-related protein PCC13-62). High positive correlation between the abundance of some altered proteins (superoxide dismutase, SOD, peroxidase, POD, glutathione S-transferase, GST, monodehydroascorbate reductase, MDAR, and malate dehydrogenase, MDH) and their enzyme activity was evaluated. The results demonstrate that the iTRAQ-based proteomic technique is reliable for identifying and quantifying a large number of cotton root proteins. qRT-PCR was used to study the gene expression levels of the five above-mentioned proteins; four patterns are consistent with those of induced protein. These results showed that the proteome of cotton roots under NaCl stress is complex. The comparative protein profiles of roots under salinity vs control improves the understanding of the molecular mechanisms involved in the tolerance of plants to salt stress. This work provides a good basis for further functional elucidation of these DEPs using genetic and/or other approaches, and, consequently, candidate genes for genetic engineering to improve crop salt tolerance.
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Affiliation(s)
- Wu Li
- College of Life Sciences, Henan UniversityKaifeng, China
- Economic Crop Research Institute, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Fu'an Zhao
- Economic Crop Research Institute, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Weiping Fang
- Economic Crop Research Institute, Henan Academy of Agricultural SciencesZhengzhou, China
- *Correspondence: Weiping Fang, Economic Crop Research Institute, Henan Academy of Agricultural Sciences, NO. 115, Huayuan Road, Zhengzhou 450002, China
| | - Deyi Xie
- Economic Crop Research Institute, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Jianan Hou
- Economic Crop Research Institute, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Xiaojie Yang
- Economic Crop Research Institute, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Yuanming Zhao
- Economic Crop Research Institute, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Zhongjie Tang
- Economic Crop Research Institute, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Lihong Nie
- Economic Crop Research Institute, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Shuping Lv
- Economic Crop Research Institute, Henan Academy of Agricultural SciencesZhengzhou, China
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Kurusu T, Kuchitsu K, Tada Y. Plant signaling networks involving Ca(2+) and Rboh/Nox-mediated ROS production under salinity stress. FRONTIERS IN PLANT SCIENCE 2015; 6:427. [PMID: 26113854 PMCID: PMC4461821 DOI: 10.3389/fpls.2015.00427] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/26/2015] [Indexed: 05/02/2023]
Abstract
Salinity stress, which induces both ionic and osmotic damage, impairs plant growth and causes severe reductions in crop yield. Plants are equipped with defense responses against salinity stress such as regulation of ion transport including Na(+) and K(+), accumulation of compatible solutes and stress-related gene expression. The initial Ca(2+) influx mediated by plasma membrane ion channels has been suggested to be crucial for the adaptive signaling. NADPH oxidase (Nox)-mediated production of reactive oxygen species (ROS) has also been suggested to play crucial roles in regulating adaptation to salinity stress in several plant species including halophytes. Respiratory burst oxidase homolog (Rboh) proteins show the ROS-producing Nox activity, which are synergistically activated by the binding of Ca(2+) to EF-hand motifs as well as Ca(2+)-dependent phosphorylation. We herein review molecular identity, structural features and roles of the Ca(2+)-permeable channels involved in early salinity and osmotic signaling, and comparatively discuss the interrelationships among spatiotemporal dynamic changes in cytosolic concentrations of free Ca(2+), Rboh-mediated ROS production, and downstream signaling events during salinity adaptation in planta.
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Affiliation(s)
- Takamitsu Kurusu
- School of Bioscience and Biotechnology, Tokyo University of TechnologyHachioji, Japan
- Department of Applied Biological Science, Tokyo University of ScienceNoda, Japan
- Research Institute for Science and Technology, Tokyo University of ScienceNoda, Japan
- *Correspondence: Takamitsu Kurusu, School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan
| | - Kazuyuki Kuchitsu
- Department of Applied Biological Science, Tokyo University of ScienceNoda, Japan
- Research Institute for Science and Technology, Tokyo University of ScienceNoda, Japan
| | - Yuichi Tada
- School of Bioscience and Biotechnology, Tokyo University of TechnologyHachioji, Japan
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Yang SY, Hao DL, Song ZZ, Yang GZ, Wang L, Su YH. RNA-Seq analysis of differentially expressed genes in rice under varied nitrogen supplies. Gene 2014; 555:305-17. [PMID: 25447912 DOI: 10.1016/j.gene.2014.11.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/29/2014] [Accepted: 11/07/2014] [Indexed: 01/03/2023]
Abstract
Ammonium is the main inorganic nitrogen source in paddy soil. Rice (Oryza sativa), an ammonium-preferring and -tolerant grain crop, is a valuable resource for researching ammonium-uptake mechanism and understanding the molecular networks that the plant copes with ammonium variation. To generate a broad survey of early responses affected by varied ammonium supplies in rice, RNA samples were prepared from the roots and shoots of rice plants subjected to nitrogen-free (0mM ammonium), 1mM ammonium and high ammonium (10mM ammonium) for a short period of 4h (1mM ammonium treatment as the control), respectively, and the transcripts were sequenced using the Illumina/HiSeq™ 2000 RNA sequencing (RNA-Seq) platform. By comparative analysis, 394 differentially expressed genes (DEGs) were identified in roots, among which, 143 and 251 DEGs were up- and down-regulated under nitrogen-free condition, respectively. In shoots, 468 (119 up-regulated/349 down-regulated) DEGs were found under such condition. However, with high ammonium treatment, only 63 genes (6 up-regulated/57 down-regulated) in roots and 115 genes in shoots (93 up-regulated/22 down-regulated) were differentially expressed. According to KEGG analysis, when exposed to nitrogen-free condition, DEGs participating in the carbohydrate and amino acid metabolisms were down-regulated (with 1 exception) in roots as well as in shoots, implying reduced carbohydrate and nitrogen metabolisms. Under high ammonium supply, all DEGs associated with carbohydrate and amino acid metabolisms were down-regulated in roots and to the contrary, up-regulated in shoots. Aldehyde dehydrogenase (ALDH, NAD(+)) [EC: 1.2.1.3] seemed to have played an important role in rice shoots under high ammonium condition, analysis results implicated a coordinative regulation of carbohydrate with amino acid metabolisms under nitrogen deficiency as well as the high ammonium conditions during a short period of several hours in rice. Moreover, transcripts with abundance variation might be precious gene resources in responding to different ammonium supplies in rice.
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Affiliation(s)
- Shun-ying Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong-li Hao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-zhong Song
- Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, Nanjing 210008, China
| | - Guang-zhe Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Li Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-hua Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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Peng Z, He S, Gong W, Sun J, Pan Z, Xu F, Lu Y, Du X. Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes. BMC Genomics 2014; 15:760. [PMID: 25189468 PMCID: PMC4169805 DOI: 10.1186/1471-2164-15-760] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/04/2014] [Indexed: 12/26/2022] Open
Abstract
Background Cotton (Gossypium spp.) is one of the major fibre crops of the world. Although it is classified as salt tolerant crop, cotton growth and productivity are adversely affected by high salinity, especially at germination and seedling stages. Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology. Results We investigated two distinct salt stress phases—dehydration (4 h) and ionic stress (osmotic restoration; 24 h)—that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. A comparative transcriptomics was used to monitor gene and miRNA differential expression at two time points (4 and 24 h) in leaves of the two cotton genotypes under salinity conditions. The expression patterns of differentially co-expressed unigenes were divided into six groups using short time-servies expression miner software. During a 24-h salt exposure, 819 transcription factor unigenes were differentially expressed in both genotypes, with 129 unigenes specifically expressed in the salt-tolerant genotype. Under salt stress, 108 conserved miRNAs from known families were differentially expressed at two time points in the salt-tolerant genotype. We further analyzed the predicted target genes of these miRNAs along with the transcriptome for each time point. Important expressed genes encoding membrane receptors, transporters, and pathways involved in biosynthesis and signal transduction of calcium-dependent protein kinase, mitogen-activated protein kinase, and hormones (abscisic acid and ethylene) were up-regulated. We also analyzed the salt stress response of some key miRNAs and their target genes and found that the expressions of five of nine target genes exhibited significant inverse correlations with their corresponding miRNAs. On the basis of these results, we constructed molecular regulatory pathways and a potential regulatory network for these salt-responsive miRNAs. Conclusions Our comprehensive transcriptome analysis has provided new insights into salt-stress response of upland cotton. The results should contribute to the development of genetically modified cotton with salt tolerance. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-760) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Yanli Lu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000 Anyang, Henan, China.
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Hiz MC, Canher B, Niron H, Turet M. Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions. PLoS One 2014; 9:e92598. [PMID: 24651267 PMCID: PMC3961409 DOI: 10.1371/journal.pone.0092598] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 02/24/2014] [Indexed: 12/02/2022] Open
Abstract
Salinity is one of the important abiotic stress factors that limit crop production. Common bean, Phaseolus vulgaris L., a major protein source in developing countries, is highly affected by soil salinity and the information on genes that play a role in salt tolerance is scarce. We aimed to identify differentially expressed genes (DEGs) and related pathways by comprehensive analysis of transcriptomes of both root and leaf tissues of the tolerant genotype grown under saline and control conditions in hydroponic system. We have generated a total of 158 million high-quality reads which were assembled into 83,774 all-unigenes with a mean length of 813 bp and N50 of 1,449 bp. Among the all-unigenes, 58,171 were assigned with Nr annotations after homology analyses. It was revealed that 6,422 and 4,555 all-unigenes were differentially expressed upon salt stress in leaf and root tissues respectively. Validation of the RNA-seq quantifications (RPKM values) was performed by qRT-PCR (Quantitative Reverse Transcription PCR) analyses. Enrichment analyses of DEGs based on GO and KEGG databases have shown that both leaf and root tissues regulate energy metabolism, transmembrane transport activity, and secondary metabolites to cope with salinity. A total of 2,678 putative common bean transcription factors were identified and classified under 59 transcription factor families; among them 441 were salt responsive. The data generated in this study will help in understanding the fundamentals of salt tolerance in common bean and will provide resources for functional genomic studies.
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Affiliation(s)
- Mahmut Can Hiz
- Bogazici University Department of Molecular Biology and Genetics, Istanbul, Turkey
- * E-mail:
| | - Balkan Canher
- Bogazici University Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Harun Niron
- Bogazici University Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Muge Turet
- Bogazici University Department of Molecular Biology and Genetics, Istanbul, Turkey
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