1
|
Pradhan UK, Mahapatra A, Naha S, Gupta A, Parsad R, Gahlaut V, Rath SN, Meher PK. ASPTF: A computational tool to predict abiotic stress-responsive transcription factors in plants by employing machine learning algorithms. Biochim Biophys Acta Gen Subj 2024; 1868:130597. [PMID: 38490467 DOI: 10.1016/j.bbagen.2024.130597] [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: 10/31/2023] [Revised: 02/26/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND Abiotic stresses pose serious threat to the growth and yield of crop plants. Several studies suggest that in plants, transcription factors (TFs) are important regulators of gene expression, especially when it comes to coping with abiotic stresses. Therefore, it is crucial to identify TFs associated with abiotic stress response for breeding of abiotic stress tolerant crop cultivars. METHODS Based on a machine learning framework, a computational model was envisaged to predict TFs associated with abiotic stress response in plants. To numerically encode TF sequences, four distinct sequence derived features were generated. The prediction was performed using ten shallow learning and four deep learning algorithms. For prediction using more pertinent and informative features, feature selection techniques were also employed. RESULTS Using the features chosen by the light-gradient boosting machine-variable importance measure (LGBM-VIM), the LGBM achieved the highest cross-validation performance metrics (accuracy: 86.81%, auROC: 92.98%, and auPRC: 94.03%). Further evaluation of the proposed model (LGBM prediction method + LGBM-VIM selected features) was also done using an independent test dataset, where the accuracy, auROC and auPRC were observed 81.98%, 90.65% and 91.30%, respectively. CONCLUSIONS To facilitate the adoption of the proposed strategy by users, the approach was implemented as a prediction server called ASPTF, accessible at https://iasri-sg.icar.gov.in/asptf/. The developed approach and the corresponding web application are anticipated to supplement experimental methods in the identification of transcription factors (TFs) responsive to abiotic stress in plants.
Collapse
Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India.
| | - Anuradha Mahapatra
- Department of Bioinformatics, Odisha University of Agriculture & Technology, Bhubaneswar 751003, Odisha, India
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India.
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India.
| | - Rajender Parsad
- ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India.
| | - Vijay Gahlaut
- University Centre for Research & Development, Chandigarh University, Mohali, Punjab, India.
| | - Surya Narayan Rath
- Department of Bioinformatics, Odisha University of Agriculture & Technology, Bhubaneswar 751003, Odisha, India
| | - Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India.
| |
Collapse
|
2
|
Schilling F, Schumacher C, Köhl K, Sprenger H, Kopka J, Peters R, Haas M, Zuther E, Horn R. Whole-genome sequencing of tetraploid potato varieties reveals different strategies for drought tolerance. Sci Rep 2024; 14:5476. [PMID: 38443466 PMCID: PMC10914802 DOI: 10.1038/s41598-024-55669-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
Climate changes leading to increasingly longer seasonal drought periods in large parts of the world increase the necessity for breeding drought-tolerant crops. Cultivated potato (Solanum tuberosum), the third most important vegetable crop worldwide, is regarded as drought-sensitive due to its shallow root architecture. Two German tetraploid potato cultivars differing in drought tolerance and their F1-progeny were evaluated under various drought scenarios. Bulked segregant analyses were combined with whole-genome sequencing (BSA-Seq) using contrasting bulks of drought-tolerant and drought-sensitive F1-clones. Applying QTLseqr, 15 QTLs comprising 588,983 single nucleotide polymorphisms (SNPs) in 2325 genes associated with drought stress tolerance were identified. SeqSNP analyses in an association panel of 34 mostly starch potato varieties using 1-8 SNPs for each of 188 selected genes narrowed the number of candidate genes down to 10. In addition, ent-kaurene synthase B was the only gene present under QTL 10. Eight of the identified genes (StABP1, StBRI1, StKS, StLEA, StPKSP1, StPKSP2, StYAB5, and StZOG1) address plant development, the other three genes (StFATA, StHGD and StSYP) contribute to plant protection under drought stress. Allelic variation in these genes might be explored in future breeding for drought-tolerant potato varieties.
Collapse
Affiliation(s)
- Florian Schilling
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
| | - Christina Schumacher
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
| | - Karin Köhl
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Heike Sprenger
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Department of Food Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Rolf Peters
- Landwirtschaftskammer Niedersachsen, Dethlingen 14, 29633, Munster, Germany
- PotatoConsult UG, Hiddinger Straße 33, 27374, Visselhövede, Germany
| | - Manuela Haas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Ministry of Agriculture, Environment and Climate Protection, Henning-Von-Tresckow-Straße 2-13, 14467, Potsdam, Germany
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Center of Artificial Intelligence in Public Health Research, Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany
| | - Renate Horn
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany.
| |
Collapse
|
3
|
Şimşek Ö, Isak MA, Dönmez D, Dalda Şekerci A, İzgü T, Kaçar YA. Advanced Biotechnological Interventions in Mitigating Drought Stress in Plants. PLANTS (BASEL, SWITZERLAND) 2024; 13:717. [PMID: 38475564 DOI: 10.3390/plants13050717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/20/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024]
Abstract
This comprehensive article critically analyzes the advanced biotechnological strategies to mitigate plant drought stress. It encompasses an in-depth exploration of the latest developments in plant genomics, proteomics, and metabolomics, shedding light on the complex molecular mechanisms that plants employ to combat drought stress. The study also emphasizes the significant advancements in genetic engineering techniques, particularly CRISPR-Cas9 genome editing, which have revolutionized the creation of drought-resistant crop varieties. Furthermore, the article explores microbial biotechnology's pivotal role, such as plant growth-promoting rhizobacteria (PGPR) and mycorrhizae, in enhancing plant resilience against drought conditions. The integration of these cutting-edge biotechnological interventions with traditional breeding methods is presented as a holistic approach for fortifying crops against drought stress. This integration addresses immediate agricultural needs and contributes significantly to sustainable agriculture, ensuring food security in the face of escalating climate change challenges.
Collapse
Affiliation(s)
- Özhan Şimşek
- Horticulture Department, Agriculture Faculty, Erciyes University, Kayseri 38030, Türkiye
| | - Musab A Isak
- Agricultural Sciences and Technology Department, Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri 38030, Türkiye
| | - Dicle Dönmez
- Biotechnology Research and Application Center, Çukurova University, Adana 01330, Türkiye
| | - Akife Dalda Şekerci
- Horticulture Department, Agriculture Faculty, Erciyes University, Kayseri 38030, Türkiye
| | - Tolga İzgü
- National Research Council of Italy (CNR), Institute of BioEconomy, 50019 Florence, Italy
| | - Yıldız Aka Kaçar
- Horticulture Department, Agriculture Faculty, Çukurova University, Adana 01330, Türkiye
| |
Collapse
|
4
|
Ma Z, Zhao B, Zhang H, Duan S, Liu Z, Guo X, Meng X, Li G. Upregulation of Wheat Heat Shock Transcription Factor TaHsfC3-4 by ABA Contributes to Drought Tolerance. Int J Mol Sci 2024; 25:977. [PMID: 38256051 PMCID: PMC10816066 DOI: 10.3390/ijms25020977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Drought stress can seriously affect the yield and quality of wheat (Triticum aestivum). So far, although few wheat heat shock transcription factors (Hsfs) have been found to be involved in the stress response, the biological functions of them, especially the members of the HsfC (heat shock transcription factor C) subclass, remain largely unknown. Here, we identified a class C encoding gene, TaHsfC3-4, based on our previous omics data and analyzed its biological function in transgenic plants. TaHsfC3-4 encodes a protein containing 274 amino acids and shows the basic characteristics of the HsfC class. Gene expression profiles revealed that TaHsfC3-4 was constitutively expressed in many tissues of wheat and was induced during seed maturation. TaHsfC3-4 could be upregulated by PEG and abscisic acid (ABA), suggesting that this Hsf may be involved in the regulation pathway depending on ABA in drought resistance. Further results represented that TaHsfC3-4 was localized in the nucleus but had no transcriptional activation activity. Notably, overexpression of TaHsfC3-4 in Arabidopsis thaliana pyr1pyl1pyl2pyl4 (pyr1pyl124) quadruple mutant plants complemented the ABA-hyposensitive phenotypes of the quadruple mutant including cotyledon greening, root elongation, seedling growth, and increased tolerance to drought, indicating positive roles of TaHsfC3-4 in the ABA signaling pathway and drought tolerance. Furthermore, we identified TaHsfA2-11 as a TaHsfC3-4-interacting protein by yeast two-hybrid (Y2H) screening. The experimental data show that TaHsfC3-4 can indeed interact with TaHsfA2-11 in vitro and in vivo. Moreover, transgenic Arabidopsis TaHsfA2-11 overexpression lines exhibited enhanced drought tolerance, too. In summary, our study confirmed the role of TaHsfC3-4 in response to drought stress and provided a target locus for marker-assisted selection breeding to improve drought tolerance in wheat.
Collapse
Affiliation(s)
- Zhenyu Ma
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Hebei Key Laboratory of Plant Genetic Engineering, Shijiazhuang 050051, China; (Z.M.); (B.Z.); (H.Z.); (S.D.); (Z.L.); (X.G.)
| | - Baihui Zhao
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Hebei Key Laboratory of Plant Genetic Engineering, Shijiazhuang 050051, China; (Z.M.); (B.Z.); (H.Z.); (S.D.); (Z.L.); (X.G.)
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Huaning Zhang
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Hebei Key Laboratory of Plant Genetic Engineering, Shijiazhuang 050051, China; (Z.M.); (B.Z.); (H.Z.); (S.D.); (Z.L.); (X.G.)
| | - Shuonan Duan
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Hebei Key Laboratory of Plant Genetic Engineering, Shijiazhuang 050051, China; (Z.M.); (B.Z.); (H.Z.); (S.D.); (Z.L.); (X.G.)
| | - Zihui Liu
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Hebei Key Laboratory of Plant Genetic Engineering, Shijiazhuang 050051, China; (Z.M.); (B.Z.); (H.Z.); (S.D.); (Z.L.); (X.G.)
| | - Xiulin Guo
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Hebei Key Laboratory of Plant Genetic Engineering, Shijiazhuang 050051, China; (Z.M.); (B.Z.); (H.Z.); (S.D.); (Z.L.); (X.G.)
| | - Xiangzhao Meng
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Hebei Key Laboratory of Plant Genetic Engineering, Shijiazhuang 050051, China; (Z.M.); (B.Z.); (H.Z.); (S.D.); (Z.L.); (X.G.)
| | - Guoliang Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Hebei Key Laboratory of Plant Genetic Engineering, Shijiazhuang 050051, China; (Z.M.); (B.Z.); (H.Z.); (S.D.); (Z.L.); (X.G.)
| |
Collapse
|
5
|
Plessis A. Abiotic stress experiments need a reality check to improve translation to the field. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:1741-1744. [PMID: 36626547 PMCID: PMC10049913 DOI: 10.1093/jxb/erac509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
|
6
|
Wellpott K, Jozefowicz AM, Meise P, Schum A, Seddig S, Mock HP, Winkelmann T, Bündig C. Combined nitrogen and drought stress leads to overlapping and unique proteomic responses in potato. PLANTA 2023; 257:58. [PMID: 36795167 PMCID: PMC9935667 DOI: 10.1007/s00425-023-04085-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Nitrogen deficient and drought-tolerant or sensitive potatoes differ in proteomic responses under combined (NWD) and individual stresses. The sensitive genotype 'Kiebitz' exhibits a higher abundance of proteases under NWD. Abiotic stresses such as N deficiency and drought affect the yield of Solanum tuberosum L. tremendously. Therefore, it is of importance to improve potato genotypes in terms of stress tolerance. In this study, we identified differentially abundant proteins (DAPs) in four starch potato genotypes under N deficiency (ND), drought stress (WD), or combined stress (NWD) in two rain-out shelter experiments. The gel-free LC-MS analysis generated a set of 1177 identified and quantified proteins. The incidence of common DAPs in tolerant and sensitive genotypes under NWD indicates general responses to this stress combination. Most of these proteins were part of the amino acid metabolism (13.9%). Three isoforms of S-adenosyl methionine synthase (SAMS) were found to be lower abundant in all genotypes. As SAMS were found upon application of single stresses as well, these proteins appear to be part of the general stress response in potato. Interestingly, the sensitive genotype 'Kiebitz' showed a higher abundance of three proteases (subtilase, carboxypeptidase, subtilase family protein) and a lower abundance of a protease inhibitor (stigma expressed protein) under NWD stress compared to control plants. The comparably tolerant genotype 'Tomba', however, displayed lower abundances of proteases. This indicates a better coping strategy for the tolerant genotype and a quicker reaction to WD when previously stressed with ND.
Collapse
Affiliation(s)
- Katharina Wellpott
- Department of Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - Anna M Jozefowicz
- Applied Biochemistry, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466, Seeland, Germany
| | - Philipp Meise
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn-Institute (JKI), Bundesforschungsinstitut Für Kulturpflanzen, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Annegret Schum
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn-Institute (JKI), Bundesforschungsinstitut Für Kulturpflanzen, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Sylvia Seddig
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn-Institute (JKI), Bundesforschungsinstitut Für Kulturpflanzen, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Hans-Peter Mock
- Applied Biochemistry, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466, Seeland, Germany
- Universidad de Costa Rica, CIGRAS, 11501-2060, San Pedro, Costa Rica
| | - Traud Winkelmann
- Department of Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - Christin Bündig
- Department of Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany.
| |
Collapse
|
7
|
Alvarez-Morezuelas A, Barandalla L, Ritter E, Ruiz de Galarreta JI. Genome-Wide Association Study of Agronomic and Physiological Traits Related to Drought Tolerance in Potato. PLANTS (BASEL, SWITZERLAND) 2023; 12:734. [PMID: 36840081 PMCID: PMC9963855 DOI: 10.3390/plants12040734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Potato (Solanum tuberosum L.) is often considered a water-sensitive crop and its production can be threatened by drought events, making water stress tolerance a trait of increasing interest. In this study, a panel of 144 tetraploid potato genotypes was evaluated for two consecutive years (2019 and 2020) to observe the variation of several physiological traits such as chlorophyll content and fluorescence, stomatal conductance, NDVI, and leaf area and circumference. In addition, agronomic parameters such as yield, tuber fresh weight, tuber number, starch content, dry matter and reducing sugars were determined. GGP V3 Potato array was used to genotype the population, obtaining a total of 18,259 high-quality SNP markers. Marker-trait association was performed using GWASpoly package in R software and Q + K linear mixed models were considered. This approach allowed us to identify eighteen SNP markers significantly associated with the studied traits in both treatments and years, which were related to genes with known functions. Markers related to chlorophyll content and number of tubers under control and stress conditions, and related to stomatal conductance, NDVI, yield and reducing sugar content under water stress, were identified. Although these markers were distributed throughout the genome, the SNPs associated with the traits under control conditions were found mainly on chromosome 11, while under stress conditions they were detected on chromosome 4. These results contribute to the knowledge of the mechanisms of potato tolerance to water stress and are useful for future marker-assisted selection programs.
Collapse
|
8
|
Yang Z, Qin F. The battle of crops against drought: Genetic dissection and improvement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:496-525. [PMID: 36639908 DOI: 10.1111/jipb.13451] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
With ongoing global climate change, water scarcity-induced drought stress remains a major threat to agricultural productivity. Plants undergo a series of physiological and morphological changes to cope with drought stress, including stomatal closure to reduce transpiration and changes in root architecture to optimize water uptake. Combined phenotypic and multi-omics studies have recently identified a number of drought-related genetic resources in different crop species. The functional dissection of these genes using molecular techniques has enriched our understanding of drought responses in crops and has provided genetic targets for enhancing resistance to drought. Here, we review recent advances in the cloning and functional analysis of drought resistance genes and the development of technologies to mitigate the threat of drought to crop production.
Collapse
Affiliation(s)
- Zhirui Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Feng Qin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
9
|
Transcriptome Analysis of Two Tetraploid Potato Varieties under Water-Stress Conditions. Int J Mol Sci 2022; 23:ijms232213905. [PMID: 36430379 PMCID: PMC9694765 DOI: 10.3390/ijms232213905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Potato (Solanum tuberosum L.) is one of the most important crops worldwide, but due to its sensitivity to drought, its production can be affected by water availability. In this study, the varieties Agria and Zorba were used to determine the expression differences between control and water-stressed plants. For this purpose, they were sequenced by RNAseq, obtaining around 50 million transcripts for each variety and treatment. When comparing the significant transcripts obtained from control and drought-stressed plants of the Agria variety, we detected 931 genes that were upregulated and 2077 genes that were downregulated under stress conditions. When both treatments were compared in Zorba plants, 735 genes were found to be upregulated and 923 genes were found to be downregulated. Significantly more DEGs were found in the Agria variety, indicating a good stress response of this variety. "Abscisic acid and environmental stress-inducible protein TAS14-like" was the most overexpressed gene under drought conditions in both varieties, but expression differences were also found in numerous transcription factors and heat shock proteins. The principal GO term found was "cellular components", more specifically related to the cell membrane and the cell wall, but other metabolic pathways such as carbohydrate metabolism and osmotic adjustment were also identified. These results provide valuable information related to the molecular mechanisms of tolerance to water stress in order to establish the basis for breeding new, more tolerant varieties.
Collapse
|
10
|
Alves da Silva A, Oliveira Silva C, do Rosario Rosa V, Silva Santos MF, Naomi Kuki K, Dal-Bianco M, Delmond Bueno R, Alves de Oliveira J, Santos Brito D, Costa AC, Ribeiro C. Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean. PeerJ 2022; 10:e13118. [PMID: 35321407 PMCID: PMC8935993 DOI: 10.7717/peerj.13118] [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: 08/19/2021] [Accepted: 02/23/2022] [Indexed: 01/12/2023] Open
Abstract
Background Soybean is the main oilseed crop grown in the world; however, drought stress affects its growth and physiology, reducing its yield. The objective of this study was to characterize the physiological, metabolic, and genetic aspects that determine differential resistance to water deficit in soybean genotypes. Methods Three soybean genotypes were used in this study, two lineages (L11644 and L13241), and one cultivar (EMBRAPA 48-C48). Plants were grown in pots containing 8 kg of a mixture of soil and sand (2:1) in a greenhouse under sunlight. Soil moisture in the pots was maintained at field capacity until the plants reached the stage of development V4 (third fully expanded leaf). At this time, plants were subjected to three water treatments: Well-Watered (WW) (plants kept under daily irrigation); Water Deficit (WD) (withholding irrigation until plants reached the leaf water potential at predawn of -1.5 ± 0.2 MPa); Rewatered (RW) (plants rehydrated for three days after reached the water deficit). The WW and WD water treatments were evaluated on the eighth day for genotypes L11644 and C48, and on the tenth day for L13241, after interruption of irrigation. For the three genotypes, the treatment RW was evaluated after three days of resumption of irrigation. Physiological, metabolic and gene expression analyses were performed. Results Water deficit inhibited growth and gas exchange in all genotypes. The accumulation of osmolytes and the concentrations of chlorophylls and abscisic acid (ABA) were higher in L13241 under stress. The metabolic adjustment of lineages in response to WD occurred in order to accumulate amino acids, carbohydrates, and polyamines in leaves. The expression of genes involved in drought resistance responses was more strongly induced in L13241. In general, rehydration provided recovery of plants to similar conditions of control treatment. Although the C48 and L11644 genotypes have shown some tolerance and resilience responses to severe water deficit, greater efficiency was observed in the L13241 genotype through adjustments in morphological, physiological, genetic and metabolic characteristics that are combined in the same plant. This study contributes to the advancement in the knowledge about the resistance to drought in cultivated plants and provides bases for the genetic improvement of the soybean culture.
Collapse
Affiliation(s)
- Adinan Alves da Silva
- Ecophysiology and Plant Productivity Laboratory, Instituto Federal Goiano-Campus Rio Verde, Rio Verde, Goiás, Brazil
| | - Cíntia Oliveira Silva
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | | | - Kacilda Naomi Kuki
- Department of Agronomy, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Maximiller Dal-Bianco
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Rafael Delmond Bueno
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Danielle Santos Brito
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Alan Carlos Costa
- Ecophysiology and Plant Productivity Laboratory, Instituto Federal Goiano-Campus Rio Verde, Rio Verde, Goiás, Brazil
| | - Cleberson Ribeiro
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| |
Collapse
|
11
|
Gelaw TA, Sanan-Mishra N. Non-Coding RNAs in Response to Drought Stress. Int J Mol Sci 2021; 22:12519. [PMID: 34830399 PMCID: PMC8621352 DOI: 10.3390/ijms222212519] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.
Collapse
Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Department of Biotechnology, College of Natural and Computational Science, Debre Birhan University, Debre Birhan P.O. Box 445, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
| |
Collapse
|
12
|
Gupta C, Ramegowda V, Basu S, Pereira A. Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance. Front Genet 2021; 12:652189. [PMID: 34249082 PMCID: PMC8264776 DOI: 10.3389/fgene.2021.652189] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Gene regulatory networks underpin stress response pathways in plants. However, parsing these networks to prioritize key genes underlying a particular trait is challenging. Here, we have built the Gene Regulation and Association Network (GRAiN) of rice (Oryza sativa). GRAiN is an interactive query-based web-platform that allows users to study functional relationships between transcription factors (TFs) and genetic modules underlying abiotic-stress responses. We built GRAiN by applying a combination of different network inference algorithms to publicly available gene expression data. We propose a supervised machine learning framework that complements GRAiN in prioritizing genes that regulate stress signal transduction and modulate gene expression under drought conditions. Our framework converts intricate network connectivity patterns of 2160 TFs into a single drought score. We observed that TFs with the highest drought scores define the functional, structural, and evolutionary characteristics of drought resistance in rice. Our approach accurately predicted the function of OsbHLH148 TF, which we validated using in vitro protein-DNA binding assays and mRNA sequencing loss-of-function mutants grown under control and drought stress conditions. Our network and the complementary machine learning strategy lends itself to predicting key regulatory genes underlying other agricultural traits and will assist in the genetic engineering of desirable rice varieties.
Collapse
Affiliation(s)
- Chirag Gupta
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Venkategowda Ramegowda
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Supratim Basu
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| |
Collapse
|
13
|
CANDIDATE GENES IDENTIFICATION OF OIL PALM (Elaeis guineensis Jacq.) INTEREST CHARACTERS USING PUBLISHED DATABASE. BIOVALENTIA: BIOLOGICAL RESEARCH JOURNAL 2021. [DOI: 10.24233/biov.7.1.2021.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Palm oil has supplied more than 30% of vegetable oil consumption worldwide. Rising demand has pushed oil palm plantations to increase the yield. It is well known that genetic has played a significant role in phenotypic performance. Moreover, in recent years, genomic data has emerged tremendously. Unfortunately on the gene related to oil palm yield. Therefore, a preliminary study to classify and select oil palm candidate genes associated with characteristic by scanning existing genes in oil palm or other in-silico species were conducted. Based on Blast2Go results, 22 genes related to oil biosynthesis, two specifically related to fruit number and fruit weight were analysed. Furthermore, 19 candidate genes were able to amplify.
Collapse
|
14
|
Schumacher C, Thümecke S, Schilling F, Köhl K, Kopka J, Sprenger H, Hincha DK, Walther D, Seddig S, Peters R, Zuther E, Haas M, Horn R. Genome-Wide Approach to Identify Quantitative Trait Loci for Drought Tolerance in Tetraploid Potato ( Solanum tuberosum L.). Int J Mol Sci 2021; 22:ijms22116123. [PMID: 34200118 PMCID: PMC8201130 DOI: 10.3390/ijms22116123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 11/20/2022] Open
Abstract
Drought represents a major abiotic stress factor negatively affecting growth, yield and tuber quality of potatoes. Quantitative trait locus (QTL) analyses were performed in cultivated potatoes for drought tolerance index DRYM (deviation of relative starch yield from the experimental median), tuber starch content, tuber starch yield, tuber fresh weight, selected transcripts and metabolites under control and drought stress conditions. Eight genomic regions of major interest for drought tolerance were identified, three representing standalone DRYM QTL. Candidate genes, e.g., from signaling pathways for ethylene, abscisic acid and brassinosteroids, and genes encoding cell wall remodeling enzymes were identified within DRYM QTL. Co-localizations of DRYM QTL and QTL for tuber starch content, tuber starch yield and tuber fresh weight with underlying genes of the carbohydrate metabolism were observed. Overlaps of DRYM QTL with metabolite QTL for ribitol or galactinol may indicate trade-offs between starch and compatible solute biosynthesis. Expression QTL confirmed the drought stress relevance of selected transcripts by overlaps with DRYM QTL. Bulked segregant analyses combined with next-generation sequencing (BSAseq) were used to identify mutations in genes under the DRYM QTL on linkage group 3. Future analyses of identified genes for drought tolerance will give a better insight into drought tolerance in potatoes.
Collapse
Affiliation(s)
- Christina Schumacher
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (C.S.); (S.T.); (F.S.)
| | - Susanne Thümecke
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (C.S.); (S.T.); (F.S.)
| | - Florian Schilling
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (C.S.); (S.T.); (F.S.)
| | - Karin Köhl
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Heike Sprenger
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Dirk Karl Hincha
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Sylvia Seddig
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn Institut, Federal Research Centre for Cultivated Plants, Rudolf-Schick-Platz 3, 18190 Sanitz, Germany;
| | - Rolf Peters
- Landwirtschaftskammer Niedersachsen, Dethlingen 14, 29633 Munster, Germany;
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Manuela Haas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Renate Horn
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (C.S.); (S.T.); (F.S.)
- Correspondence:
| |
Collapse
|
15
|
Jogawat A, Yadav B, Lakra N, Singh AK, Narayan OP. Crosstalk between phytohormones and secondary metabolites in the drought stress tolerance of crop plants: A review. PHYSIOLOGIA PLANTARUM 2021; 172:1106-1132. [PMID: 33421146 DOI: 10.1111/ppl.13328] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/08/2020] [Accepted: 01/01/2021] [Indexed: 05/21/2023]
Abstract
Drought stress negatively affects crop performance and weakens global food security. It triggers the activation of downstream pathways, mainly through phytohormones homeostasis and their signaling networks, which further initiate the biosynthesis of secondary metabolites (SMs). Roots sense drought stress, the signal travels to the above-ground tissues to induce systemic phytohormones signaling. The systemic signals further trigger the biosynthesis of SMs and stomatal closure to prevent water loss. SMs primarily scavenge reactive oxygen species (ROS) to protect plants from lipid peroxidation and also perform additional defense-related functions. Moreover, drought-induced volatile SMs can alert the plant tissues to perform drought stress mitigating functions in plants. Other phytohormone-induced stress responses include cell wall and cuticle thickening, root and leaf morphology alteration, and anatomical changes of roots, stems, and leaves, which in turn minimize the oxidative stress, water loss, and other adverse effects of drought. Exogenous applications of phytohormones and genetic engineering of phytohormones signaling and biosynthesis pathways mitigate the drought stress effects. Direct modulation of the SMs biosynthetic pathway genes or indirect via phytohormones' regulation provides drought tolerance. Thus, phytohormones and SMs play key roles in plant development under the drought stress environment in crop plants.
Collapse
Affiliation(s)
| | - Bindu Yadav
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Nita Lakra
- Department of Biotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Amit Kumar Singh
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Om Prakash Narayan
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts, USA
| |
Collapse
|
16
|
Unravelling Differences in Candidate Genes for Drought Tolerance in Potato ( Solanum tuberosum L.) by Use of New Functional Microsatellite Markers. Genes (Basel) 2021; 12:genes12040494. [PMID: 33800602 PMCID: PMC8067248 DOI: 10.3390/genes12040494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/26/2022] Open
Abstract
Potato is regarded as drought sensitive and most vulnerable to climate changes. Its cultivation in drought prone regions or under conditions of more frequent drought periods, especially in subtropical areas, requires intensive research to improve drought tolerance in order to guarantee high yields under limited water supplies. A candidate gene approach was used to develop functional simple sequence repeat (SSR) markers for association studies in potato with the aim to enhance breeding for drought tolerance. SSR primer combinations, mostly surrounding interrupted complex and compound repeats, were derived from 103 candidate genes for drought tolerance. Validation of the SSRs was performed in an association panel representing 34 mainly starch potato cultivars. Seventy-five out of 154 SSR primer combinations (49%) resulted in polymorphic, highly reproducible banding patterns with polymorphic information content (PIC) values between 0.11 and 0.90. Five SSR markers identified allelic differences between the potato cultivars that showed significant associations with drought sensitivity. In all cases, the group of drought-sensitive cultivars showed predominantly an additional allele, indicating that selection against these alleles by marker-assisted breeding might confer drought tolerance. Further studies of these differences in the candidate genes will elucidate their role for an improved performance of potatoes under water-limited conditions.
Collapse
|
17
|
Gupta C, Ramegowda V, Basu S, Pereira A. Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance. Front Genet 2021. [PMID: 34249082 DOI: 10.1101/2020.04.29.068379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Gene regulatory networks underpin stress response pathways in plants. However, parsing these networks to prioritize key genes underlying a particular trait is challenging. Here, we have built the Gene Regulation and Association Network (GRAiN) of rice (Oryza sativa). GRAiN is an interactive query-based web-platform that allows users to study functional relationships between transcription factors (TFs) and genetic modules underlying abiotic-stress responses. We built GRAiN by applying a combination of different network inference algorithms to publicly available gene expression data. We propose a supervised machine learning framework that complements GRAiN in prioritizing genes that regulate stress signal transduction and modulate gene expression under drought conditions. Our framework converts intricate network connectivity patterns of 2160 TFs into a single drought score. We observed that TFs with the highest drought scores define the functional, structural, and evolutionary characteristics of drought resistance in rice. Our approach accurately predicted the function of OsbHLH148 TF, which we validated using in vitro protein-DNA binding assays and mRNA sequencing loss-of-function mutants grown under control and drought stress conditions. Our network and the complementary machine learning strategy lends itself to predicting key regulatory genes underlying other agricultural traits and will assist in the genetic engineering of desirable rice varieties.
Collapse
Affiliation(s)
- Chirag Gupta
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Venkategowda Ramegowda
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Supratim Basu
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| |
Collapse
|
18
|
Locateli G, Peralta RM, Koehnlein EA. Recommended Consumption of Fruits and Vegetables Increases the Intake of Polyphenols and Flavonoids in Brazilian Adults. CURRENT NUTRITION & FOOD SCIENCE 2020. [DOI: 10.2174/1573401315666190704155121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Adequate consumption of fruits and vegetables (FV) is associated with reduced
risks of various diseases, especially due to their nutrient, fiber, and bioactive compound content.
Polyphenols are included in this last class. In Brazil, as in several other regions of the world,
consumption of FV is low. Data on the importance of the recommended intake of FV for the ingestion
of these compounds and subclasses are scarce.
Objective:
To estimate the intake of polyphenols by Brazilian adults and to verify the impact of the
recommended consumption of FV for this intake.
Methods:
Data from 21,959 adults were obtained from the Brazilian Dairy Survey of the Household
Budget Survey (POF 2008-2009). Food intake was estimated from a single food register. Polyphenol
intake was calculated using the Phenol-Explorer database. To evaluate the impact of FV on the consumption
of polyphenols, the population was divided into two groups according to the FV intake as
recommended by the World Health Organization.
Results:
The average consumption of phenolic compounds was 441.04 mg among individuals consuming
less than 400 g of FV daily, and 651.86 mg those consuming equal or more than 400 g daily.
In addition, individuals consuming 400 g or more FV per day consumed approximately 12 times
more phenolic from FV, especially flavonoids and the anthocyanin and flavanone subclasses.
Conclusions:
The high consumption of FV is essential for a higher dietary intake and diversity of
polyphenols and flavonoids compounds by the Brazilian population.
Collapse
Affiliation(s)
- Gelvani Locateli
- Post Graduate Program Health Sciences, Community University of the Region of Chapeco, Chapeco, Santa Catarina, Brazil
| | | | | |
Collapse
|
19
|
Jiang Z, Jin F, Shan X, Li Y. iTRAQ-Based Proteomic Analysis Reveals Several Strategies to Cope with Drought Stress in Maize Seedlings. Int J Mol Sci 2019; 20:ijms20235956. [PMID: 31779286 PMCID: PMC6928945 DOI: 10.3390/ijms20235956] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 12/11/2022] Open
Abstract
Drought stress, especially during the seedling stage, seriously limits the growth of maize and reduces production in the northeast of China. To investigate the molecular mechanisms of drought response in maize seedlings, proteome changes were analyzed. Using an isotopic tagging relative quantitation (iTRAQ) based method, a total of 207 differentially accumulated protein species (DAPS) were identified under drought stress in maize seedlings. The DAPS were classified into ten essential groups and analyzed thoroughly, which involved in signaling, osmotic regulation, protein synthesis and turnover, reactive oxygen species (ROS) scavenging, membrane trafficking, transcription related, cell structure and cell cycle, fatty acid metabolism, carbohydrate and energy metabolism, as well as photosynthesis and photorespiration. The enhancements of ROS scavenging, osmotic regulation, protein turnover, membrane trafficking, and photosynthesis may play important roles in improving drought tolerance of maize seedlings. Besides, the inhibitions of some protein synthesis and slowdown of cell division could reduce the growth rate and avoid excessive water loss, which is possible to be the main reasons for enhancing drought avoidance of maize seedlings. The incongruence between protein and transcript levels was expectedly observed in the process of confirming iTRAQ data by quantitative real-time polymerase chain reaction (qRT-PCR) analysis, which further indicated that the multiplex post-transcriptional regulation and post-translational modification occurred in drought-stressed maize seedlings. Finally, a hypothetical strategy was proposed that maize seedlings coped with drought stress by improving drought tolerance (via. promoting osmotic adjustment and antioxidant capacity) and enhancing drought avoidance (via. reducing water loss). Our study provides valuable insight to mechanisms underlying drought response in maize seedlings.
Collapse
Affiliation(s)
- Zhilei Jiang
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Changchun 130033, China; (Z.J.); (F.J.)
| | - Fengxue Jin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Changchun 130033, China; (Z.J.); (F.J.)
| | - Xiaohui Shan
- College of Plant Science, Jilin University, Changchun 130062, China
- Correspondence: (X.S.); (Y.L.)
| | - Yidan Li
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Changchun 130033, China; (Z.J.); (F.J.)
- Correspondence: (X.S.); (Y.L.)
| |
Collapse
|
20
|
Iquebal MA, Sharma P, Jasrotia RS, Jaiswal S, Kaur A, Saroha M, Angadi UB, Sheoran S, Singh R, Singh GP, Rai A, Tiwari R, Kumar D. RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat. Sci Rep 2019; 9:13917. [PMID: 31558740 PMCID: PMC6763491 DOI: 10.1038/s41598-019-49915-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 08/12/2019] [Indexed: 01/08/2023] Open
Abstract
Drought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is first sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refinement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For effective future use of findings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under field drought conditions along with genomic resources, warranted in endeavour of wheat productivity.
Collapse
Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Amandeep Kaur
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Monika Saroha
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India.
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India.
| |
Collapse
|
21
|
Rodrigues J, Inzé D, Nelissen H, Saibo NJM. Source-Sink Regulation in Crops under Water Deficit. TRENDS IN PLANT SCIENCE 2019; 24:652-663. [PMID: 31109763 DOI: 10.1016/j.tplants.2019.04.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 05/21/2023]
Abstract
To meet the food demands of an increasing world population, it is necessary to improve crop production; a task that is made more challenging by the changing climate. Several recent reports show that increasing the capacity of plants to assimilate carbon (source strength), or to tap into the internal carbon reservoir (sink strength), has the potential to improve plant productivity in the field under water-deficit conditions. Here, we review the effects of water deficit on the source-sink communication, as well as the respective regulatory mechanisms underpinning plant productivity. We also highlight stress-tolerant traits that can contribute to harness source and sink strengths towards producing high-yielding and drought-tolerant crops, depending on the drought scenario.
Collapse
Affiliation(s)
- Joana Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, UNL, 2780-157 Oeiras, Portugal; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, UNL, 2780-157 Oeiras, Portugal.
| |
Collapse
|
22
|
Overexpression of ScMYBAS1 alternative splicing transcripts differentially impacts biomass accumulation and drought tolerance in rice transgenic plants. PLoS One 2018; 13:e0207534. [PMID: 30517137 PMCID: PMC6281192 DOI: 10.1371/journal.pone.0207534] [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: 06/26/2018] [Accepted: 11/01/2018] [Indexed: 02/05/2023] Open
Abstract
Drought is the most significant environmental stress for agricultural production worldwide, and tremendous efforts have been made to improve crop yield under the increasing water scarcity. Transcription factors are major players in the regulation of water stress-related genes in plants. Recently, different MYB transcription factors were characterized for their involvement in drought response. A sugarcane R2R3-MYB gene (ScMYBAS1) and its four alternative forms of transcript (ScMYAS1-2, ScMYBAS1-3, ScMYBAS1-4 and ScMYBAS1-5) were identified in this study. The subcellular localization, in Nicotiniana benthamiana, of the TFs fused in frame with GFP revealed that ScMYBAS1-2-GFP and ScMYBAS1-3-GFP were observed in the nucleus. The overexpression of ScMYBAS1-2 and ScMYBAS1-3 spliced transcripts in rice promoted change in plant growth under both well-watered and drought conditions. The ScMYBAS1-2 and ScMYBAS1-3 transgenic lines revealed a higher relative water content (RWC) compared to the wild type before maximum stress under drought conditions. The ScMYBAS1-2 transgenic lines showed a reduction in biomass (total dry weight). Conversely, ScMYBAS1-3 showed an increased biomass (total dry weight) relative to the wild-type. The overexpression of ScMYBAS1-3 in rice transgenic lines showed involvement with drought tolerance and biomass and, for this reason, was considered a good target for plant transformation, particularly for use in developing genotypes with drought tolerance and biomass accumulation.
Collapse
|
23
|
Martins SJ, Rocha GA, de Melo HC, de Castro Georg R, Ulhôa CJ, de Campos Dianese É, Oshiquiri LH, da Cunha MG, da Rocha MR, de Araújo LG, Vaz KS, Dunlap CA. Plant-associated bacteria mitigate drought stress in soybean. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:13676-13686. [PMID: 29502259 DOI: 10.1007/s11356-018-1610-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 02/25/2018] [Indexed: 06/08/2023]
Abstract
Agriculture accounts for ~ 70% of all water use and the world population is increasing annually; soon more people will need to be fed, while also using less water. The use of plant-associated bacteria (PAB) is an eco-friendly alternative that can increase crop water use efficiency. This work aimed to study the effect of some PAB on increasing soybean tolerance to drought stress, the mechanisms of the drought tolerance process, and the effect of the PAB on promoting plant growth and on the biocontrol of Sclerotinia sclerotiorum. PAB were isolated from soybean rhizosphere and S. sclerotiorum sclerotia. The strains identified as UFGS1 (Bacillus subtilis), UFGS2 (Bacillus thuringiensis), UFGRB2 and UFGRB3 (Bacillus cereus) were selected on their ability to grow in media with reduced water activity. Soybean plants were inoculated with the PAB and evaluated for growth promotion, physiological and molecular parameters, after drought stress. Under drought stress, UFGS2 and UFGRB2 sustained potential quantum efficiency of PSII (Fv/Fm), while a decrease was found in the control plants. Moreover, UFGS2 and UFGRB3 maintained the photosynthetic rates in non-stressed conditions compared to the control. UFGS2-treated plants showed a higher stomatal conductance and higher transpiration than the control, after drought stress. Some PAB-treated plants also had other beneficial phenotypes, such as increases in fresh and dried biomass relative to the control. Differential gene expression analysis of genes involved in plant stress pathways shows changes in expression in PAB-treated plants. Results from this study suggest that PAB can mitigate drought stress in soybean and may improve water efficiency under certain conditions.
Collapse
Affiliation(s)
- Samuel Julio Martins
- College of Agronomy, Federal University of Goiás, Campus Samambaia, Rodovia GO-462 km 0, CP 3037, Goiânia, GO, 74690-900, Brazil.
| | - Geisiane Alves Rocha
- College of Agronomy, Federal University of Goiás, Campus Samambaia, Rodovia GO-462 km 0, CP 3037, Goiânia, GO, 74690-900, Brazil
| | - Hyrandir Cabral de Melo
- Laboratory of Plant Physiology, Institute of Biology, Federal University of Goiás, Goiânia, Brazil
| | - Raphaela de Castro Georg
- Laboratory of Enzymology, Institute of Biology, Federal University of Goiás, Goiânia, 74001-970, Brazil
| | - Cirano José Ulhôa
- Laboratory of Enzymology, Institute of Biology, Federal University of Goiás, Goiânia, 74001-970, Brazil
| | - Érico de Campos Dianese
- College of Agronomy, Federal University of Goiás, Campus Samambaia, Rodovia GO-462 km 0, CP 3037, Goiânia, GO, 74690-900, Brazil
| | - Leticia Harumi Oshiquiri
- Laboratory of Enzymology, Institute of Biology, Federal University of Goiás, Goiânia, 74001-970, Brazil
| | - Marcos Gomes da Cunha
- College of Agronomy, Federal University of Goiás, Campus Samambaia, Rodovia GO-462 km 0, CP 3037, Goiânia, GO, 74690-900, Brazil
| | - Mara Rúbia da Rocha
- College of Agronomy, Federal University of Goiás, Campus Samambaia, Rodovia GO-462 km 0, CP 3037, Goiânia, GO, 74690-900, Brazil
| | | | - Karina Santana Vaz
- College of Agronomy, Federal University of Goiás, Campus Samambaia, Rodovia GO-462 km 0, CP 3037, Goiânia, GO, 74690-900, Brazil
| | - Christopher A Dunlap
- US Department of Agriculture, Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, Peoria, IL, USA
| |
Collapse
|
24
|
Woldesemayat AA, Modise DM, Gemeildien J, Ndimba BK, Christoffels A. Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PLoS One 2018; 13:e0192678. [PMID: 29590108 PMCID: PMC5873934 DOI: 10.1371/journal.pone.0192678] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/29/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Crop response to the changing climate and unpredictable effects of global warming with adverse conditions such as drought stress has brought concerns about food security to the fore; crop yield loss is a major cause of concern in this regard. Identification of genes with multiple responses across environmental stresses is the genetic foundation that leads to crop adaptation to environmental perturbations. METHODS In this paper, we introduce an integrated approach to assess candidate genes for multiple stress responses across-species. The approach combines ontology based semantic data integration with expression profiling, comparative genomics, phylogenomics, functional gene enrichment and gene enrichment network analysis to identify genes associated with plant stress phenotypes. Five different ontologies, viz., Gene Ontology (GO), Trait Ontology (TO), Plant Ontology (PO), Growth Ontology (GRO) and Environment Ontology (EO) were used to semantically integrate drought related information. RESULTS Target genes linked to Quantitative Trait Loci (QTLs) controlling yield and stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and closely related species were identified. Based on the enriched GO terms of the biological processes, 1116 sorghum genes with potential responses to 5 different stresses, such as drought (18%), salt (32%), cold (20%), heat (8%) and oxidative stress (25%) were identified to be over-expressed. Out of 169 sorghum drought responsive QTLs associated genes that were identified based on expression datasets, 56% were shown to have multiple stress responses. On the other hand, out of 168 additional genes that have been evaluated for orthologous pairs, 90% were conserved across species for drought tolerance. Over 50% of identified maize and rice genes were responsive to drought and salt stresses and were co-located within multifunctional QTLs. Among the total identified multi-stress responsive genes, 272 targets were shown to be co-localized within QTLs associated with different traits that are responsive to multiple stresses. Ontology mapping was used to validate the identified genes, while reconstruction of the phylogenetic tree was instrumental to infer the evolutionary relationship of the sorghum orthologs. The results also show specific genes responsible for various interrelated components of drought response mechanism such as drought tolerance, drought avoidance and drought escape. CONCLUSIONS We submit that this approach is novel and to our knowledge, has not been used previously in any other research; it enables us to perform cross-species queries for genes that are likely to be associated with multiple stress tolerance, as a means to identify novel targets for engineering stress resistance in sorghum and possibly, in other crop species.
Collapse
Affiliation(s)
- Adugna Abdi Woldesemayat
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Belleville, South Africa
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Science Campus, Florida, Johannesburg, South Africa
- * E-mail: ,
| | - David M. Modise
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, University of South Africa, Science Campus, Florida, Johannesburg, South Africa
| | - Junaid Gemeildien
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Belleville, South Africa
| | - Bongani K. Ndimba
- Department of Biotechnology, University of the Western Cape, Cape Town, Western Cape, South Africa
- Agricultural Research Council, Infruitech-Nietvoorbij, Stellenbosch, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Belleville, South Africa
| |
Collapse
|
25
|
Leaf wax trait in crops for drought and biotic stress tolerance: regulators of epicuticular wax synthesis and role of small RNAs. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40502-017-0333-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
26
|
Shavrukov Y, Kurishbayev A, Jatayev S, Shvidchenko V, Zotova L, Koekemoer F, de Groot S, Soole K, Langridge P. Early Flowering as a Drought Escape Mechanism in Plants: How Can It Aid Wheat Production? FRONTIERS IN PLANT SCIENCE 2017; 8:1950. [PMID: 29204147 PMCID: PMC5698779 DOI: 10.3389/fpls.2017.01950] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/30/2017] [Indexed: 05/18/2023]
Abstract
Drought escape (DE) is a classical adaptive mechanism which involves rapid plant development to enable the completion of the full life-cycle prior to a coming drought event. This strategy is widely used in populations of native plants, and is also applicable to cereal crops such as wheat. Early flowering time and a shorter vegetative phase can be very important for wheat production in conditions of terminal drought since this can minimize exposure to dehydration during the sensitive flowering and post-anthesis grain filling periods. A gradual shift toward early flowering has been observed over the last century of wheat breeding in countries with a Mediterranean-type climate and frequent terminal drought. This trend is predicted to continue for wheat production in the coming years in response to global climate warming. The advantage of early flowering wheat is apparent under conditions of impending terminal drought, and modern varieties are significantly more productive due to minimization of the risk associated with drought stress. Under favorable conditions, a short vegetative phase can result in reduced plant biomass due to the reduction in time available for photosynthetic production and seed nutrient accumulation. However, high yield potential has been reported for the development of both shallow and deep roots, representing plasticity in response to drought in combination with the early flowering trait. Wheat productivity can be high both in well-watered and drought-affected field trials, where an efficient strategy of DE was associated with quick growth, yield potential and water use efficiency. Therefore, early flowering provides a promising strategy for the production of advanced drought-adapted wheat cultivars.
Collapse
Affiliation(s)
- Yuri Shavrukov
- School of Biological Sciences, Flinders University, Bedford Park, SA, Australia
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Akhylbek Kurishbayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Vladimir Shvidchenko
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Lyudmila Zotova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | | | | | - Kathleen Soole
- School of Biological Sciences, Flinders University, Bedford Park, SA, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| |
Collapse
|
27
|
Landi S, De Lillo A, Nurcato R, Grillo S, Esposito S. In-field study on traditional Italian tomato landraces: The constitutive activation of the ROS scavenging machinery reduces effects of drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 118:150-160. [PMID: 28633087 DOI: 10.1016/j.plaphy.2017.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/31/2017] [Accepted: 06/12/2017] [Indexed: 05/18/2023]
Abstract
The involvement and the efficiency of the antioxidants scavenging system upon drought were examined by comparing traditional tomato landraces with respect to an industrial commercial genotype (Red Setter); for the first time, comprehensive analyses of physiological, biochemical and molecular parameters were investigated directly under real field conditions, in a typical agricultural environment of Southern Italy. The characterization of the responses upon drought evidenced peculiar changes in stomatal conductance, ascorbate peroxidase and catalase activities and expression in drought tolerant tomato landraces, with respect to the industrial genotype. An in silico analysis (promoter and co-expression study) coupled to a phylogenetic investigation of selected enzymes was performed, reinforcing the hypothesis of a basal activation of ROS scavenging machinery in the Mediterranean landraces. Thus our data suggest a constitutive increase in the expression and activities of specific enzymes involved in ROS detoxification that can play a pivotal role in the drought response shown by tomato landraces. Therefore, traditional landraces could represent an important source of useful genetic variability for the improvement of commercial varieties; their ROS detoxifying capabilities denote peculiar aspects worth being explored to better describe their specific stress tolerance.
Collapse
Affiliation(s)
- Simone Landi
- Institute of Biosciences and Bioresources, Research Division, National Research Council of Italy (IBBR-CNR), Portici, 80055, Naples, Italy; Dipartimento di Biologia, Università di Napoli ''Federico II'', Via Cinthia, I-80126 Napoli, Italy
| | - Alessia De Lillo
- Dipartimento di Biologia, Università di Napoli ''Federico II'', Via Cinthia, I-80126 Napoli, Italy
| | - Roberta Nurcato
- Institute of Biosciences and Bioresources, Research Division, National Research Council of Italy (IBBR-CNR), Portici, 80055, Naples, Italy
| | - Stefania Grillo
- Institute of Biosciences and Bioresources, Research Division, National Research Council of Italy (IBBR-CNR), Portici, 80055, Naples, Italy
| | - Sergio Esposito
- Dipartimento di Biologia, Università di Napoli ''Federico II'', Via Cinthia, I-80126 Napoli, Italy.
| |
Collapse
|
28
|
Ghosh Dasgupta M, Dharanishanthi V. Identification of PEG-induced water stress responsive transcripts using co-expression network in Eucalyptus grandis. Gene 2017; 627:393-407. [DOI: 10.1016/j.gene.2017.06.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/12/2017] [Accepted: 06/28/2017] [Indexed: 12/23/2022]
|
29
|
Gramazio P, Prohens J, Plazas M, Mangino G, Herraiz FJ, Vilanova S. Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background. FRONTIERS IN PLANT SCIENCE 2017; 8:1477. [PMID: 28912788 PMCID: PMC5582342 DOI: 10.3389/fpls.2017.01477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/09/2017] [Indexed: 05/29/2023]
Abstract
Advanced backcrosses (ABs) and introgression lines (ILs) of eggplant (Solanum melongena) can speed up genetics and genomics studies and breeding in this crop. We have developed the first full set of ABs and ILs in eggplant using Solanum incanum, a wild eggplant that has a relatively high tolerance to drought, as a donor parent. The development of these ABs and IL eggplant populations had a low efficiency in the early stages, because of the lack of molecular markers and genomic tools. However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. A set of 73 selected ABs covered 99% of the S. incanum genome, while 25 fixed immortal ILs, each carrying a single introgressed fragment in homozygosis, altogether spanned 61.7% of the S. incanum genome. The introgressed size fragment in the ILs contained between 0.1 and 10.9% of the S. incanum genome, with a mean value of 4.3%. Sixty-eight candidate genes involved in drought tolerance were identified in the set of ILs. This first set of ABs and ILs of eggplant will be extremely useful for the genetic dissection of traits of interest for eggplant, and represents an elite material for introduction into the breeding pipelines for developing new eggplant cultivars adapted to the challenges posed by the climate-change scenario.
Collapse
Affiliation(s)
- Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Mariola Plazas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de ValènciaValencia, Spain
| | - Giulio Mangino
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Francisco J. Herraiz
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| |
Collapse
|
30
|
Effects of drought stress on global gene expression profile in leaf and root samples of Dongxiang wild rice ( Oryza rufipogon). Biosci Rep 2017; 37:BSR20160509. [PMID: 28424372 PMCID: PMC6434088 DOI: 10.1042/bsr20160509] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 04/05/2017] [Accepted: 04/19/2017] [Indexed: 11/17/2022] Open
Abstract
Drought is a serious constraint to rice production throughout the world, and although Dongxiang wild rice (Oryza rufipogon, DXWR) possesses a high degree of drought resistance, the underlying mechanisms of this trait remains unclear. In the present study, cDNA libraries were constructed from the leaf and root tissues of drought-stressed and untreated DXWR seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in drought-stress response. The results indicated that 11231 transcripts were differentially expressed in the leaves (4040 up-regulated and 7191 down-regulated) and 7025 transcripts were differentially expressed in the roots (3097 up-regulated and 3928 down-regulated). Among these differentially expressed genes (DEGs), the detection of many transcriptional factors and functional genes demonstrated that multiple regulatory pathways were involved in drought resistance. Meanwhile, the DEGs were also annotated with gene ontology (GO) terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway mapping, respectively. A set of the most interesting candidate genes was then identified by combining the DEGs with previously identified drought-resistant quantitative trait loci (QTL). The present work provides abundant genomic information for functional dissection of the drought resistance of DXWR, and findings will further help the current understanding of the biological regulatory mechanisms of drought resistance in plants and facilitate the breeding of new drought-resistant rice cultivars.
Collapse
|
31
|
|
32
|
Menguer PK, Sperotto RA, Ricachenevsky FK. A walk on the wild side: Oryza species as source for rice abiotic stress tolerance. Genet Mol Biol 2017; 40:238-252. [PMID: 28323300 PMCID: PMC5452139 DOI: 10.1590/1678-4685-gmb-2016-0093] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023] Open
Abstract
Oryza sativa, the common cultivated rice, is one of the most important crops for human consumption, but production is increasingly threatened by abiotic stresses. Although many efforts have resulted in breeding rice cultivars that are relatively tolerant to their local environments, climate changes and population increase are expected to soon call for new, fast generation of stress tolerant rice germplasm, and current within-species rice diversity might not be enough to overcome such needs. The Oryza genus contains other 23 wild species, with only Oryza glaberrima being also domesticated. Rice domestication was performed with a narrow genetic diversity, and the other Oryza species are a virtually untapped genetic resource for rice stress tolerance improvement. Here we review the origin of domesticated Oryza sativa from wild progenitors, the ecological and genomic diversity of the Oryza genus, and the stress tolerance variation observed for wild Oryza species, including the genetic basis underlying the tolerance mechanisms found. The summary provided here is important to indicate how we should move forward to unlock the full potential of these germplasms for rice improvement.
Collapse
Affiliation(s)
- Paloma Koprovski Menguer
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Raul Antonio Sperotto
- Setor de Genética e Biologia Molecular do Museu de Ciências Naturais (MCN), Centro de Ciências Biológicas e da Saúde (CCBS), Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Centro Universitário UNIVATES, Lajeado, RS, Brazil
| | - Felipe Klein Ricachenevsky
- Programa de Pós-Graduação em Agrobiologia, Departamento de Biologia, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| |
Collapse
|
33
|
Wang Z, Wang F, Hong Y, Huang J, Shi H, Zhu JK. Two Chloroplast Proteins Suppress Drought Resistance by Affecting ROS Production in Guard Cells. PLANT PHYSIOLOGY 2016; 172:2491-2503. [PMID: 27744298 PMCID: PMC5129706 DOI: 10.1104/pp.16.00889] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 10/13/2016] [Indexed: 05/06/2023]
Abstract
Chloroplast as the site for photosynthesis is an essential organelle in plants, but little is known about its role in stomatal regulation and drought resistance. In this study, we show that two chloroplastic proteins essential for thylakoid formation negatively regulate drought resistance in Arabidopsis (Arabidopsis thaliana). By screening a mutant pool with T-DNA insertions in nuclear genes encoding chloroplastic proteins, we identified an HCF106 knockdown mutant exhibiting increased resistance to drought stress. The hcf106 mutant displayed elevated levels of reactive oxygen species (ROS) in guard cells, improved stomatal closure, and reduced water loss under drought conditions. The HCF106 protein was found to physically interact with THF1, a previously identified chloroplastic protein crucial for thylakoid formation. The thf1 mutant phenotypically resembled the hcf106 mutant and displayed more ROS accumulation in guard cells, increased stomatal closure, reduced water loss, and drought resistant phenotypes compared to the wild type. The hcf106thf1 double mutant behaved similarly as the thf1 single mutant. These results suggest that HCF106 and THF1 form a complex to modulate chloroplast function and that the complex is important for ROS production in guard cells and stomatal control in response to environmental stresses. Our results also suggest that modulating chloroplastic proteins could be a way for improving drought resistance in crops.
Collapse
Affiliation(s)
- Zhen Wang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences (Z.W., F.W., Y.H., J.-K.Z.), University of Chinese Academy of Sciences (Z.W., F.W., Y.H.), Chinese Academy of Sciences, Shanghai 200032, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.H.)
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 (H.S.); and
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (J.-K.Z.)
| | - Fuxing Wang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences (Z.W., F.W., Y.H., J.-K.Z.), University of Chinese Academy of Sciences (Z.W., F.W., Y.H.), Chinese Academy of Sciences, Shanghai 200032, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.H.)
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 (H.S.); and
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (J.-K.Z.)
| | - Yechun Hong
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences (Z.W., F.W., Y.H., J.-K.Z.), University of Chinese Academy of Sciences (Z.W., F.W., Y.H.), Chinese Academy of Sciences, Shanghai 200032, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.H.)
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 (H.S.); and
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (J.-K.Z.)
| | - Jirong Huang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences (Z.W., F.W., Y.H., J.-K.Z.), University of Chinese Academy of Sciences (Z.W., F.W., Y.H.), Chinese Academy of Sciences, Shanghai 200032, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.H.)
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 (H.S.); and
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (J.-K.Z.)
| | - Huazhong Shi
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences (Z.W., F.W., Y.H., J.-K.Z.), University of Chinese Academy of Sciences (Z.W., F.W., Y.H.), Chinese Academy of Sciences, Shanghai 200032, China;
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.H.);
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 (H.S.); and
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (J.-K.Z.)
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences (Z.W., F.W., Y.H., J.-K.Z.), University of Chinese Academy of Sciences (Z.W., F.W., Y.H.), Chinese Academy of Sciences, Shanghai 200032, China;
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.H.);
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 (H.S.); and
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (J.-K.Z.)
| |
Collapse
|
34
|
Sprenger H, Kurowsky C, Horn R, Erban A, Seddig S, Rudack K, Fischer A, Walther D, Zuther E, Köhl K, Hincha DK, Kopka J. The drought response of potato reference cultivars with contrasting tolerance. PLANT, CELL & ENVIRONMENT 2016; 39:2370-2389. [PMID: 27341794 DOI: 10.1111/pce.12780] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/14/2016] [Accepted: 06/14/2016] [Indexed: 05/21/2023]
Abstract
Systems responses to drought stress of four potato reference cultivars with differential drought tolerance (Solanum tuberosum L.) were investigated by metabolome profiling and RNA sequencing. Systems analysis was based on independent field and greenhouse trials. Robust differential drought responses across all cultivars under both conditions comprised changes of proline, raffinose, galactinol, arabitol, arabinonic acid, chlorogenic acid and 102 transcript levels. The encoded genes contained a high proportion of heat shock proteins and proteins with signalling or regulatory functions, for example, a homolog of abscisic acid receptor PYL4. Constitutive differences of the tolerant compared with the sensitive cultivars included arbutin, octopamine, ribitol and 248 transcripts. The gene products of many of these transcripts were pathogen response related, such as receptor kinases, or regulatory proteins, for example, a homolog of the Arabidopsis FOUR LIPS MYB-regulator of stomatal cell proliferation. Functional enrichment analyses imply heat stress as a major acclimation component of potato leaves to long-term drought stress. Enhanced heat stress during drought can be caused by loss of transpiration cooling. This effect and CO2 limitation are the main consequences of drought-induced or abscisic acid-induced stomatal closure. Constitutive differences in metabolite and transcript levels between tolerant and sensitive cultivars indicate interactions of drought tolerance and pathogen resistance in potato.
Collapse
Affiliation(s)
- Heike Sprenger
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Christina Kurowsky
- Institut für Biowissenschaften und Pflanzengenetik, University of Rostock, Albert-Einstein-Straße 3, D-18059, Rostock, Germany
| | - Renate Horn
- Institut für Biowissenschaften und Pflanzengenetik, University of Rostock, Albert-Einstein-Straße 3, D-18059, Rostock, Germany
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Sylvia Seddig
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn Institut, Federal Research Centre for Cultivated Plants, Rudolf-Schick-Platz 3, D-18190, Sanitz, Germany
| | - Katharina Rudack
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn Institut, Federal Research Centre for Cultivated Plants, Rudolf-Schick-Platz 3, D-18190, Sanitz, Germany
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Karin Köhl
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Dirk K Hincha
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany.
| |
Collapse
|
35
|
Wang X, Cai X, Xu C, Wang Q, Dai S. Drought-Responsive Mechanisms in Plant Leaves Revealed by Proteomics. Int J Mol Sci 2016; 17:E1706. [PMID: 27763546 PMCID: PMC5085738 DOI: 10.3390/ijms17101706] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/06/2016] [Accepted: 09/22/2016] [Indexed: 02/04/2023] Open
Abstract
Plant drought tolerance is a complex trait that requires a global view to understand its underlying mechanism. The proteomic aspects of plant drought response have been extensively investigated in model plants, crops and wood plants. In this review, we summarize recent proteomic studies on drought response in leaves to reveal the common and specialized drought-responsive mechanisms in different plants. Although drought-responsive proteins exhibit various patterns depending on plant species, genotypes and stress intensity, proteomic analyses show that dominant changes occurred in sensing and signal transduction, reactive oxygen species scavenging, osmotic regulation, gene expression, protein synthesis/turnover, cell structure modulation, as well as carbohydrate and energy metabolism. In combination with physiological and molecular results, proteomic studies in leaves have helped to discover some potential proteins and/or metabolic pathways for drought tolerance. These findings provide new clues for understanding the molecular basis of plant drought tolerance.
Collapse
Affiliation(s)
- Xiaoli Wang
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Xiaofeng Cai
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Chenxi Xu
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Quanhua Wang
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Shaojun Dai
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| |
Collapse
|
36
|
Landi S, Nurcato R, De Lillo A, Lentini M, Grillo S, Esposito S. Glucose-6-phosphate dehydrogenase plays a central role in the response of tomato (Solanum lycopersicum) plants to short and long-term drought. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 105:79-89. [PMID: 27085599 DOI: 10.1016/j.plaphy.2016.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 05/03/2023]
Abstract
The present study was undertaken to investigate the expression, occurrence and activity of glucose 6 phosphate dehydrogenase (G6PDH - EC 1.1.1.49), the key-enzyme of the Oxidative Pentose Phosphate Pathway (OPPP), in tomato plants (Solanum lycopersicum cv. Red Setter) exposed to short- and long-term drought stress. For the first time, drought effects have been evaluated in plants under different growth conditions: in hydroponic laboratory system, and in greenhouse pots under controlled conditions; and in open field, in order to evaluate drought response in a representative agricultural environment. Interestingly, changes observed appear strictly associated to the induction of well known stress response mechanisms, such as the increase of proline synthesis, accumulation of chaperone Hsp70, and ascorbate peroxidase. Results show significant increase in total activity of G6PDH, and specifically in expression and occurrence of cytosolic isoform (cy-G6PDH) in plants grown in any cultivation system upon drought. Intriguingly, the results clearly suggest that abscissic acid (ABA) pathway and signaling cascade (protein phosphatase 2C PP2C) could be strictly related to increased G6PDH expression, occurrence and activities. We hypothesized for G6PDH a specific role as one of the main reductants' suppliers to counteract the effects of drought stress, in the light of converging evidences given by young and adult tomato plants under stress of different duration and intensity.
Collapse
Affiliation(s)
- Simone Landi
- Università di Napoli ''Federico II", Dipartimento di Biologia, Via Cinthia, I-80126, Napoli, Italy; National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Portici, 80055, Naples, Italy
| | - Roberta Nurcato
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Portici, 80055, Naples, Italy
| | - Alessia De Lillo
- Università di Napoli ''Federico II", Dipartimento di Biologia, Via Cinthia, I-80126, Napoli, Italy
| | - Marco Lentini
- Università di Napoli ''Federico II", Dipartimento di Biologia, Via Cinthia, I-80126, Napoli, Italy
| | - Stefania Grillo
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Portici, 80055, Naples, Italy
| | - Sergio Esposito
- Università di Napoli ''Federico II", Dipartimento di Biologia, Via Cinthia, I-80126, Napoli, Italy.
| |
Collapse
|
37
|
Koroban NV, Kudryavtseva AV, Krasnov GS, Sadritdinova AF, Fedorova MS, Snezhkina AV, Bolsheva NL, Muravenko OV, Dmitriev AA, Melnikova NV. The role of microRNA in abiotic stress response in plants. Mol Biol 2016. [DOI: 10.1134/s0026893316020102] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
38
|
Zhang F, Luo X, Zhou Y, Xie J. Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.). Biotechnol Lett 2015; 38:711-21. [PMID: 26667133 DOI: 10.1007/s10529-015-2012-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/02/2015] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To identify drought stress-responsive conserved microRNA (miRNA) from Dongxiang wild rice (Oryza rufipogon Griff., DXWR) on a genome-wide scale, high-throughput sequencing technology was used to sequence libraries of DXWR samples, treated with and without drought stress. RESULTS 505 conserved miRNAs corresponding to 215 families were identified. 17 were significantly down-regulated and 16 were up-regulated under drought stress. Stem-loop qRT-PCR revealed the same expression patterns as high-throughput sequencing, suggesting the accuracy of the sequencing result was high. Potential target genes of the drought-responsive miRNA were predicted to be involved in diverse biological processes. Furthermore, 16 miRNA families were first identified to be involved in drought stress response from plants. CONCLUSION These results present a comprehensive view of the conserved miRNA and their expression patterns under drought stress for DXWR, which will provide valuable information and sequence resources for future basis studies.
Collapse
Affiliation(s)
- Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Xiangdong Luo
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Yi Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jiankun Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
| |
Collapse
|
39
|
Singh D, Laxmi A. Transcriptional regulation of drought response: a tortuous network of transcriptional factors. FRONTIERS IN PLANT SCIENCE 2015; 6:895. [PMID: 26579147 PMCID: PMC4625044 DOI: 10.3389/fpls.2015.00895] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/08/2015] [Indexed: 05/18/2023]
Abstract
Drought is one of the leading factors responsible for the reduction in crop yield worldwide. Due to climate change, in future, more areas are going to be affected by drought and for prolonged periods. Therefore, understanding the mechanisms underlying the drought response is one of the major scientific concerns for improving crop yield. Plants deploy diverse strategies and mechanisms to respond and tolerate drought stress. Expression of numerous genes is modulated in different plants under drought stress that help them to optimize their growth and development. Plant hormone abscisic acid (ABA) plays a major role in plant response and tolerance by regulating the expression of many genes under drought stress. Transcription factors being the major regulator of gene expression play a crucial role in stress response. ABA regulates the expression of most of the target genes through ABA-responsive element (ABRE) binding protein/ABRE binding factor (AREB/ABF) transcription factors. Genes regulated by AREB/ABFs constitute a regulon termed as AREB/ABF regulon. In addition to this, drought responsive genes are also regulated by ABA-independent mechanisms. In ABA-independent regulation, dehydration-responsive element binding protein (DREB), NAM, ATAF, and CUC regulons play an important role by regulating many drought-responsive genes. Apart from these major regulons, MYB/MYC, WRKY, and nuclear factor-Y (NF-Y) transcription factors are also involved in drought response and tolerance. Our understanding about transcriptional regulation of drought is still evolving. Recent reports have suggested the existence of crosstalk between different transcription factors operating under drought stress. In this article, we have reviewed various regulons working under drought stress and their crosstalk with each other.
Collapse
|