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Li X, Li J, Wei S, Gao Y, Pei H, Geng R, Lu Z, Wang P, Zhou W. Maize GOLDEN2-LIKE proteins enhance drought tolerance in rice by promoting stomatal closure. PLANT PHYSIOLOGY 2024; 194:774-786. [PMID: 37850886 PMCID: PMC10828204 DOI: 10.1093/plphys/kiad561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/19/2023]
Abstract
Drought has become one of the most severe abiotic stresses experienced in agricultural production across the world. Plants respond to water deficit via stomatal movements in the leaves, which are mainly regulated by abscisic acid (ABA). A previous study from our lab showed that constitutive expression of maize (Zea mays L.) GOLDEN2-LIKE (GLK) transcription factors in rice (Oryza sativa L.) can improve stomatal conductance and plant photosynthetic capacity under field conditions. In the present study, we uncovered a function of ZmGLK regulation of stomatal movement in rice during drought stress. We found that elevated drought tolerance in rice plants overexpressing ZmGLK1 or GOLDEN2 (ZmG2) was conferred by rapid ABA-mediated stomatal closure. Comparative analysis of RNA-sequencing (RNA-seq) data from the rice leaves and DNA affinity purification sequencing (DAP-seq) results obtained in vitro revealed that ZmGLKs played roles in regulating ABA-related and stress-responsive pathways. Four upregulated genes closely functioning in abiotic stress tolerance with strong binding peaks in the DAP-seq data were identified as putative target genes of ZmGLK1 and ZmG2 in rice. These results demonstrated that maize GLKs play an important role in regulating stomatal movements to coordinate photosynthesis and stress tolerance. This trait is a valuable target for breeding drought-tolerant crop plants without compromising photosynthetic capacity.
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Affiliation(s)
- Xia Li
- Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing 100081, China
| | - Jing Li
- Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing 100081, China
| | - Shaobo Wei
- Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing 100081, China
| | - Yuan Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing 100081, China
| | - Hongcui Pei
- Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing 100081, China
| | - Rudan Geng
- Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing 100081, China
| | - Zefu Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing 100081, China
| | - Peng Wang
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant
Physiology and Ecology, Chinese Academy of Sciences, Shanghai
200032, China
| | - Wenbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing 100081, China
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Qin X, Li Y, Li C, Li X, Wu Y, Wu Q, Wen H, Jiang D, Liu S, Nan W, Liang Y, Zhang H. A Rapid and Simplified Method to Isolate Specific Regulators Based on Biotin-Avidin Binding Affinities in Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:883-893. [PMID: 38118073 DOI: 10.1021/acs.jafc.3c05638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Transcription factors (TFs) are indispensable components of transcriptional regulatory pathways involved in crop growth and development. Herein, we developed a new method for the identification of upstream TFs specific to genes in crops based on the binding affinities of biotin and avidin. First, we constructed and verified the new biotin and avidin system (BAS) by a coprecipitation assay. Subsequently, the feasibility of DNA-based BAS (DBAS) was further proved by in vivo and in vitro assays. Furthermore, we cloned the promoter of rice OsNRT1.1B and the possible regulators were screened and identified. Additionally, partial candidates were validated by the electrophoresis mobility shift assay (EMSA), yeast one-hybrid, and luciferase activity assays. Remarkably, the results showed that the candidates PIP3 and PIP19 both responded to nitrate immediately and overexpression of PIP3 caused retard growth, which indicates that the candidates are functional and the new DBAS method is useful to isolate regulators in crops.
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Affiliation(s)
- Xiaojian Qin
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Yuntong Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Cuiping Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Xiaowei Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Yuanyuan Wu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Qian Wu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Huan Wen
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Dan Jiang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Shifeng Liu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Wenbin Nan
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Yongshu Liang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Hanma Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
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Singh A, Pandey H, Pandey S, Lal D, Chauhan D, Aparna, Antre SH, B S, Kumar A. Drought stress in maize: stress perception to molecular response and strategies for its improvement. Funct Integr Genomics 2023; 23:296. [PMID: 37697159 DOI: 10.1007/s10142-023-01226-6] [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: 07/28/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/13/2023]
Abstract
Given the future demand for food crops, increasing crop productivity in drought-prone rainfed areas has become essential. Drought-tolerant varieties are warranted to solve this problem in major crops, with drought tolerance as a high-priority trait for future research. Maize is one such crop affected by drought stress, which limits production, resulting in substantial economic losses. It became a more serious issue due to global climate change. The most drought sensitive among all stages of maize is the reproductive stages and the most important for overall maize production. The exact molecular basis of reproductive drought sensitivity remains unclear due to genes' complex regulation of drought stress. Understanding the molecular biology and signaling of the unexplored area of reproductive drought tolerance will provide an opportunity to develop climate-smart drought-tolerant next-generation maize cultivars. In recent decades, significant progress has been made in maize to understand the drought tolerance mechanism. However, improving maize drought tolerance through breeding is ineffective due to the complex nature and multigenic control of drought traits. With the help of advanced breeding techniques, molecular genetics, and a precision genome editing approach like CRISPR-Cas, candidate genes for drought-tolerant maize can be identified and targeted. This review summarizes the effects of drought stress on each growth stage of maize, potential genes, and transcription factors that determine drought tolerance. In addition, we discussed drought stress sensing, its molecular mechanisms, different approaches to developing drought-resistant maize varieties, and how molecular breeding and genome editing will help with the current unpredictable climate change.
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Affiliation(s)
- Ashutosh Singh
- Centre for Advanced Studies On Climate Change, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India.
| | | | - Saurabh Pandey
- Department of Agriculture, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
| | - Dalpat Lal
- College of Agriculture, Jodhpur Agriculture University, Jodhpur, Rajasthan, 342304, India
| | - Divya Chauhan
- Banasthali University, Radha Kishanpura, Rajasthan, 304022, India
| | - Aparna
- Departments of Agriculture, Jagan Nath University, Jaipur, Rajasthan, 303901, India
| | - Suresh H Antre
- Advanced Centre of Plant Biotechnology, UAS, GKVK, Bangalore, Karnataka, 560065, India
| | - Santhosh B
- Centre for Advanced Studies On Climate Change, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India
| | - Amarjeet Kumar
- Department of Genetics and Plant Breeding, MTTC & VTC, Selesih, CAU, Imphal, 795001, India
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Rajonandraina T, Ueda Y, Wissuwa M, Kirk GJD, Rakotoson T, Manwaring H, Andriamananjara A, Razafimbelo T. Magnesium supply alleviates iron toxicity-induced leaf bronzing in rice through exclusion and tissue-tolerance mechanisms. FRONTIERS IN PLANT SCIENCE 2023; 14:1213456. [PMID: 37546266 PMCID: PMC10403268 DOI: 10.3389/fpls.2023.1213456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/04/2023] [Indexed: 08/08/2023]
Abstract
Introduction Iron (Fe) toxicity is a widespread nutritional disorder in lowland rice causing growth retardation and leaf symptoms referred to as leaf bronzing. It is partly caused by an imbalance of nutrients other than Fe and supply of these is known to mitigate the toxicity. But the physiological and molecular mechanisms involved are unknown. Methods We investigated the effect of magnesium (Mg) on Fe toxicity tolerance in a field study in the Central Highlands of Madagascar and in hydroponic experiments with excess Fe (300 mg Fe L-1). An RNA-seq analysis was conducted in a hydroponic experiment to elucidate possible mechanisms underlying Mg effects. Results and discussion Addition of Mg consistently decreased leaf bronzing under both field and hydroponic conditions, whereas potassium (K) addition caused minor effects. Plants treated with Mg tended to have smaller shoot Fe concentrations in the field, suggesting enhanced exclusion at the whole-plant level. However, analysis of multiple genotypes showed that Fe toxicity symptoms were also mitigated without a concomitant decrease of Fe concentration, suggesting that increased Mg supply confers tolerance at the tissue level. The hydroponic experiments also suggested that Mg mitigated leaf bronzing without significantly decreasing Fe concentration or oxidative stress as assessed by the content of malondialdehyde, a biomarker for oxidative stress. An RNA-seq analysis revealed that Mg induced more changes in leaves than roots. Subsequent cis-element analysis suggested that NAC transcription factor binding sites were enriched in genes induced by Fe toxicity in leaves. Addition of Mg caused non-significant enrichment of the same binding sites, suggesting that NAC family proteins may mediate the effect of Mg. This study provides clues for mitigating Fe toxicity-induced leaf bronzing in rice.
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Affiliation(s)
| | - Yoshiaki Ueda
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
- PhenoRob Cluster & Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Guy J. D. Kirk
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Tovohery Rakotoson
- Laboratoire des RadioIsotopes (LRI), Université d’Antananarivo, Antananarivo, Madagascar
| | - Hanna Manwaring
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Andry Andriamananjara
- Laboratoire des RadioIsotopes (LRI), Université d’Antananarivo, Antananarivo, Madagascar
| | - Tantely Razafimbelo
- Laboratoire des RadioIsotopes (LRI), Université d’Antananarivo, Antananarivo, Madagascar
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Chen Y, Yang W, Gao R, Chen Y, Zhou Y, Xie J, Zhang F. Genome-Wide Analysis of microRNAs and Their Target Genes in Dongxiang Wild Rice ( Oryza rufipogon Griff.) Responding to Salt Stress. Int J Mol Sci 2023; 24:ijms24044069. [PMID: 36835475 PMCID: PMC9960954 DOI: 10.3390/ijms24044069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Rice (Oryza sativa) is a staple food for more than half of the world's population, and its production is critical for global food security. Moreover, rice yield decreases when exposed to abiotic stresses, such as salinity, which is one of the most detrimental factors for rice production. According to recent trends, as global temperatures continue to rise due to climate change, more rice fields may become saltier. Dongxiang wild rice (Oryza rufipogon Griff., DXWR) is a progenitor of cultivated rice and has a high tolerance to salt stress, making it useful for studying the regulatory mechanisms of salt stress tolerance. However, the regulatory mechanism of miRNA-mediated salt stress response in DXWR remains unclear. In this study, miRNA sequencing was performed to identify miRNAs and their putative target genes in response to salt stress in order to better understand the roles of miRNAs in DXWR salt stress tolerance. A total of 874 known and 476 novel miRNAs were identified, and the expression levels of 164 miRNAs were found to be significantly altered under salt stress. The stem-loop quantitative real-time PCR (qRT-PCR) expression levels of randomly selected miRNAs were largely consistent with the miRNA sequencing results, suggesting that the sequencing results were reliable. The gene ontology (GO) analysis indicated that the predicted target genes of salt-responsive miRNAs were involved in diverse biological pathways of stress tolerance. This study contributes to our understanding of DXWR salt tolerance mechanisms regulated by miRNAs and may ultimately improve salt tolerance in cultivated rice breeding using genetic methods in the future.
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Affiliation(s)
- Yong Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Wanling Yang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Rifang Gao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yaling Chen
- 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
- Correspondence: (J.X.); (F.Z.)
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (J.X.); (F.Z.)
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6
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Comparative Analysis of Physiological, Hormonal and Transcriptomic Responses Reveal Mechanisms of Saline-Alkali Tolerance in Autotetraploid Rice ( Oryza sativa L.). Int J Mol Sci 2022; 23:ijms232416146. [PMID: 36555786 PMCID: PMC9783840 DOI: 10.3390/ijms232416146] [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: 10/14/2022] [Revised: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Saline-alkali soil has posed challenges to the growth of agricultural crops, while polyploidy often show greater adaptability in diverse and extreme environments including saline-alkali stress, but its defense mechanisms in rice remain elusive. Herein, we explored the mechanisms of enhanced saline-alkali tolerance of autotetraploid rice 93-11T relative to diploid rice 93-11D, based on physiological, hormonal and transcriptomic profilings. Physiologically, the enhanced saline-alkali tolerance in 93-11T was manifested in higher soluble sugar accumulation and stronger superoxide dismutase (SOD) and peroxidase (POD) activities in leaves during 24 h after saline-alkali shock. Furthermore, various hormone levels in leaves of 93-11T altered greatly, such as the negative correlation between salicylic acid (SA) and the other four hormones changed to positive correlation due to polyploidy. Global transcriptome profiling revealed that the upregulated differentially expressed genes (DEGs) in leaves and roots of 93-11T were more abundant than that in 93-11D, and there were more DEGs in roots than in leaves under saline-alkali stress. Genes related to phytohormone signal transduction of auxin (AUX) and SA in roots, lignin biosynthesis in leaves or roots, and wax biosynthesis in leaves were obviously upregulated in 93-11T compared with 93-11D under saline-alkali condition. Collectively, 93-11T subjected to saline-alkali stress possibly possesses higher osmotic regulation ability due to cuticular wax synthesis, stronger negative regulation of reactive oxygen species (ROS) production by increasing the SA levels and maintaining relative lower levels of IAA, and higher antioxidant capacity by increasing activities of SOD and POD, as well as lignin biosynthesis. Our research provides new insights for exploring the mechanisms of saline-alkali tolerance in polyploid rice and discovering new gene targets for rice genetic improvement.
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7
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Kumar R, Bahuguna RN, Tiwari M, Pal M, Chinnusamy V, Sreeman S, Muthurajan R, Krishna Jagadish SV. Walking through crossroads-rice responses to heat and biotic stress interactions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4065-4081. [PMID: 35713657 DOI: 10.1007/s00122-022-04131-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Rice, the most important source of calories for humans is prone to severe yield loss due to changing climate including heat stress. Additionally, rice encounters biotic stresses in conjunction with heat stress, which exacerbates the adverse effects, and exponentially increase such losses. Several investigations have identified biotic and heat stress-related quantitative trait loci (QTLs) that may contribute to improved tolerance to these stresses. However, a significant knowledge gap exists in identifying the genomic regions imparting tolerance against combined biotic and heat stress. Hereby, we are presenting a conceptual meta-analysis identifying genomic regions that may be promising candidates for enhancing combined biotic and heat stress tolerance in rice. Fourteen common genomic regions were identified along chromosomes 1, 2, 3, 4, 6, 10 and 12, which harbored 1265 genes related to heat stress and defense responses in rice. Further, the meta expression analysis revealed 24 differentially expressed genes (DEGs) involved in calcium-mediated stress signaling including transcription factors Myb, bHLH, ROS signaling, molecular chaperones HSP110 and pathogenesis related proteins. Additionally, we also proposed a hypothetical model based on GO and MapMan analysis representing the pathways intersecting heat and biotic stresses. These DEGs can be potential candidate genes for improving tolerance to combined biotic and heat stress in rice. We present a framework highlighting plausible connecting links (QTLs/genes) between rice response to heat stress and different biotic factors associated with yield, that can be extended to other crops.
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Affiliation(s)
- Ritesh Kumar
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Rajeev N Bahuguna
- Center for Advanced Studies on Climate Change, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, India
| | - Manish Tiwari
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sheshshayee Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India.
| | - S V Krishna Jagadish
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India.
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India.
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA.
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Liu X, Zong X, Wu X, Liu H, Han J, Yao Z, Ren Y, Ma L, Wang B, Zhang H. Ectopic expression of NAC transcription factor HaNAC3 from Haloxylon ammodendron increased abiotic stress resistance in tobacco. PLANTA 2022; 256:105. [PMID: 36315282 DOI: 10.1007/s00425-022-04021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
HaNAC3 is a transcriptional activator located in the nucleus that may be involved in the response to high temperature, high salt and drought stresses as well as phytohormone IAA and ABA treatments. Our study demonstrated that HaNAC3 increased the tolerance of transgenic tobacco to abiotic stress and was involved in the regulation of a range of downstream genes and metabolic pathways. This also indicates the potential application of HaNAC3 as a plant tolerance gene. NAC transcription factors play a key role in plant growth and development and plant responses to biotic and abiotic stresses. However, the biological functions of NAC transcription factors in the desert plant Haloxylon ammodendron are still poorly understood. In this study, the NAC transcription factor HaNAC3 was isolated and cloned from a typical desert plant H. ammodendron, and its possible biological functions were investigated. Bioinformatics analysis showed that HaNAC3 has the unique N-terminal NAC structural domain of NAC transcription factor. Quantitative real-time fluorescence analysis showed that HaNAC3 was able to participate in the response to simulated drought, high temperature, high salt, and phytohormone IAA and ABA treatments, and was very sensitive to simulated high temperature and phytohormone ABA treatments. Subcellular localization analysis showed that the GFP-HaNAC3 fusion protein was localized in the nucleus of tobacco epidermal cells. The transcriptional self-activation assay showed that HaNAC3 had transcriptional self-activation activity, and the truncation assay confirmed that the transcriptional activation activity was located at the C-terminus. HaNAC3 gene was expressed exogenously in wild-type Nicotiana benthamiana, and the physiological function of HaNAC3 was verified by simulating drought and other abiotic stresses. The results indicated that transgenic tobacco had better resistance to abiotic stresses than wild-type B. fuminata. Further transcriptome analysis showed that HaNAC3 was involved in the regulation of a range of downstream resistance genes, wax biosynthesis and other metabolic pathways. These results suggest that HaNAC3 may have a stress resistance role in H. ammodendron and has potential applications in plant molecular breeding.
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Affiliation(s)
- Xiashun Liu
- College of Life Science, Xinjiang Agricultural University, Ürümqi, China
| | - Xingfeng Zong
- College of Life Science, Xinjiang Agricultural University, Ürümqi, China
| | - Xia Wu
- College of Life Science, Xinjiang Agricultural University, Ürümqi, China
| | - Hao Liu
- College of Life Science, Xinjiang Agricultural University, Ürümqi, China
| | - Jvdong Han
- College of Life Science, Xinjiang Agricultural University, Ürümqi, China
| | - Zhengpei Yao
- College of Life Science, Xinjiang Agricultural University, Ürümqi, China
| | - Yanping Ren
- College of Life Science, Xinjiang Agricultural University, Ürümqi, China
| | - Li Ma
- College of Life Science, Xinjiang Agricultural University, Ürümqi, China
| | - Bo Wang
- College of Life Science, Xinjiang Agricultural University, Ürümqi, China
| | - Hua Zhang
- College of Life Science, Xinjiang Agricultural University, Ürümqi, China.
- Arid Desert Research Institute, Ürümqi, China.
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9
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Selection of Lentil (Lens Culinaris (Medik.)) Genotypes Suitable for High-Temperature Conditions Based on Stress Tolerance Indices and Principal Component Analysis. Life (Basel) 2022; 12:life12111719. [DOI: 10.3390/life12111719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/16/2022] Open
Abstract
Legumes, including lentil, are a valuable source of carbohydrates, fiber, protein and vitamins and minerals. Their nutritional characteristics have been associated with a reduction in the incidence of various cancers, HDL cholesterol, type 2 diabetes and heart disease. Among these quality parameters, lectins have been associated with reducing certain forms of cancer, activating innate defense mechanisms and managing obesity. Protease inhibitors such as trypsin and chymotrypsin inhibitors have been demonstrated to reduce the incidence of certain cancers and demonstrate potent anti-inflammatory properties. Angiotensin I-converting enzyme (ACE) inhibitor has been associated with a reduction in hypertension. Therefore, legumes, including lentils, should be part of our daily food intake. However, high temperatures at the terminal stage is a major abiotic constraint leading to a reduction in lentil yield and seed quality. Thus, the selection of heat-tolerant genotypes is essential to identifying the potential for high yields with stable performance. To select lentil genotypes, an experiment was conducted with 60 genotypes including local landraces, advanced breeding lines, commercial varieties and exotic germplasm under stress and non-stress conditions from 2019 to 2020. This study was followed by a subset study involving screening based on a few physicochemical parameters and reproductive traits along with field performances. Different tolerance indices (i.e., stress susceptible index (SSI), relative heat index (RHI), tolerance (TOL), mean productivity (MP), stress tolerance index (STI), geometric mean productivity (GMP), yield index (YI), yield stability index (YSI), heat-resistance index (HRI), modified stress-tolerance index (MSTI), abiotic tolerance index (ATI) and stress susceptibility percentage (SSPI)) were used for the selection of the genotypes along with field performance. Biplot analysis was further performed for choosing the most suitable indices. Based on principal components analysis, the GMP, MP, RRI, STI, YI, YSI, ATI and MSTI indices were identified as the most reliable stress indicators, and these indicators might be used for distinguishing heat-tolerant genotypes. Based on the stress indices, the genotypes BLX 05002-3, BLX 10002-20, LRIL-21-1-1-1-1, LRIL-21-1-1-1-1-6 and BLX 09015 were selected as the most stable and heat-tolerant genotypes. In contrast, the genotypes LG 198, Bagura Local, BLX 0200-08-4, RL-12-178, Maitree, 91517 and BLX 11014-8 were selected as the most heat sensitive. Data also exhibited an average yield reduction of 59% due to heat stress on the lentils. Moreover, eight heat-tolerant (HT) genotypes (BLX 09015, PRECOZ, LRL-21-112-1-1-1-1-6, BLX 05002-3, LR-9-25, BLX 05002-6, BARI Masur-8 and RL-12-181), and two heat-susceptible (HS) genotypes (BLX 12009-6, and LG 198) were selected from the screened genotypes and subjected to further analysis by growing them in the following year under similar conditions to investigate the mechanisms associated with heat tolerance. Comparative studies on reproductive function and physiochemical traits revealed significantly higher pollen viability, proline accumulation, relative water content, chlorophyll concentration and a lower membrane stability index in HT genotypes under heat stress. Therefore, these heat-tolerant genotypes could be used as the parents in the hybridization program for achieving heat-tolerant transgressive segregation.
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10
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Jung SE, Kim TH, Shim JS, Bang SW, Bin Yoon H, Oh SH, Kim YS, Oh SJ, Seo JS, Kim JK. Rice NAC17 transcription factor enhances drought tolerance by modulating lignin accumulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111404. [PMID: 35914574 DOI: 10.1016/j.plantsci.2022.111404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/05/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Land plants have developed a comprehensive system to cope with the drought stress, and it is operated by intricate signaling networks, including transcriptional regulation. Herein, we identified the function of OsNAC17, a member of NAC (NAM, ATAF, and CUC2) transcription factor family, in drought tolerance. OsNAC17 is localized to the nucleus, and its expression was significantly induced under drought conditions. A transactivation assay in yeast revealed that the OsNAC17 is a transcriptional activator, harboring an activation domain in the C-terminal region. Overexpressing (OsNAC17OX) transgenic plants showed drought-tolerant, and knock-out (OsNAC17KO) plants exhibited drought susceptible phenotype compared to non-transgenic plants. Further investigation revealed that OsNAC17 positively regulates several lignin biosynthetic genes and promotes lignin accumulation in leaves and roots. Together, our results show that OsNAC17 contributes to drought tolerance through lignin biosynthesis in rice.
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Affiliation(s)
- Se Eun Jung
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, the Republic of Korea
| | - Tae Hwan Kim
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, the Republic of Korea
| | - Jae Sung Shim
- Crop Biotechnology Institute, Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, the Republic of Korea; School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, the Republic of Korea
| | - Seung Woon Bang
- Crop Biotechnology Institute, Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, the Republic of Korea
| | - Ho Bin Yoon
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, the Republic of Korea
| | - Shin Hee Oh
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, the Republic of Korea
| | - Youn Shic Kim
- Crop Biotechnology Institute, Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, the Republic of Korea
| | - Se-Jun Oh
- LaSemilla Co. Ltd, Pyeongchang 25354, the Republic of Korea
| | - Jun Sung Seo
- Crop Biotechnology Institute, Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, the Republic of Korea
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, the Republic of Korea; Crop Biotechnology Institute, Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, the Republic of Korea; LaSemilla Co. Ltd, Pyeongchang 25354, the Republic of Korea.
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Wang Z, Li J, Yang X, Hu Y, Yin Y, Shen X. MdFLP enhances drought tolerance by regulating MdNAC019 in self-rooted apple stocks. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111331. [PMID: 35696930 DOI: 10.1016/j.plantsci.2022.111331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Self-rooted apple stocks are widely used for the production of apples worldwide. However, self-rooted apple stocks are weak due to shallow roots and poor grounding, resulting in poor drought resistance. Therefore, it is essential to understand the molecular mechanisms to develop self-rooted apple stock cultivars with drought resistance. We reported that MdFLP, an R2R3-MYB transcription factor, directly binds to the promoter of MdNAC019, activating its transcription and consequently enhancing drought tolerance in self-rooted apple stocks. In addition, MdFLP indirectly activates the transcriptional expression of abiotic stress-related genes, namely, MdERF6 and MdZAT10. The plants overexpressing MdFLP displayed stronger drought tolerance, whereas MdFLP-RNAi plants showed weak drought tolerance compared with non-transgenic "Gala" plants, indicating that MdFLP regulates drought tolerance in self-rooted apple stocks. Altogether, we believe that our findings provide novel insights into the functions of MdFLP in the regulation of drought tolerance in self-rooted apple stocks.
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Affiliation(s)
- Zenghui Wang
- Shandong Institute of Pomology, Tai'an, Shandong 271000, China
| | - Jialin Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Xuemei Yang
- Shandong Institute of Pomology, Tai'an, Shandong 271000, China
| | - Yanli Hu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, Tai'an, Shandong 271018, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yanlei Yin
- Shandong Institute of Pomology, Tai'an, Shandong 271000, China.
| | - Xiang Shen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, Tai'an, Shandong 271018, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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Rasheed A, Li H, Nawaz M, Mahmood A, Hassan MU, Shah AN, Hussain F, Azmat S, Gillani SFA, Majeed Y, Qari SH, Wu Z. Molecular tools, potential frontiers for enhancing salinity tolerance in rice: A critical review and future prospective. FRONTIERS IN PLANT SCIENCE 2022; 13:966749. [PMID: 35968147 PMCID: PMC9366114 DOI: 10.3389/fpls.2022.966749] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 06/28/2022] [Indexed: 05/08/2023]
Abstract
Improvement of salinity tolerance in rice can minimize the stress-induced yield losses. Rice (Oryza sativa) is one of Asia's most widely consumed crops, native to the subtropical regions, and is generally associated with sensitivity to salinity stress episodes. Salt-tolerant rice genotypes have been developed using conventional breeding methods; however, the success ratio is limited because of the complex nature of the trait and the high cost of development. The narrow genetic base of rice limited the success of conventional breeding methods. Hence, it is critical to launch the molecular tools for screening rice novel germplasm for salt-tolerant genes. In this regard, the latest molecular techniques like quantitative trait loci (QTL) mapping, genetic engineering (GE), transcription factors (TFs) analysis, and clustered regularly interspaced short palindromic repeats (CRISPR) are reliable for incorporating the salt tolerance in rice at the molecular level. Large-scale use of these potent genetic approaches leads to identifying and editing several genes/alleles, and QTL/genes are accountable for holding the genetic mechanism of salinity tolerance in rice. Continuous breeding practices resulted in a huge decline in rice genetic diversity, which is a great worry for global food security. However, molecular breeding tools are the only way to conserve genetic diversity by exploring wild germplasm for desired genes in salt tolerance breeding programs. In this review, we have compiled the logical evidences of successful applications of potent molecular tools for boosting salinity tolerance in rice, their limitations, and future prospects. This well-organized information would assist future researchers in understanding the genetic improvement of salinity tolerance in rice.
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Affiliation(s)
- Adnan Rasheed
- Key Laboratory of Plant Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Huijie Li
- Key Laboratory of Plant Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- College of Humanity and Public Administration, Jiangxi Agricultural University, Nanchang, China
| | - Muhammad Nawaz
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, China
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Fiaz Hussain
- Directorate of Agronomy, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Saira Azmat
- Department of Agriculture, Agriculture Extension and Adaptive Research, Government of the Punjab, Lahore, Pakistan
| | | | - Yasir Majeed
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Sameer H. Qari
- Department of Biology, Al-Jumum University College, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ziming Wu
- Key Laboratory of Plant Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, China
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Zhang J, Sun Y, Zhou Z, Zhang Y, Yang Y, Zan X, Li X, Wan J, Gao X, Chen R, Huang Z, Li L, Xu Z. OsSCL30 overexpression reduces the tolerance of rice seedlings to low temperature, drought and salt. Sci Rep 2022; 12:8385. [PMID: 35589923 PMCID: PMC9120446 DOI: 10.1038/s41598-022-12438-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/11/2022] [Indexed: 01/19/2023] Open
Abstract
Rice is one of the main food crops for the world population. Various abiotic stresses, such as low temperature, drought, and high salinity, affect rice during the entire growth period, determining its yield and quality, and even leading to plant death. In this study, by constructing overexpression vectors D-163 + 1300:OsSCL30 and D-163 + 1300-AcGFP:OsSCL30-GFP, the mechanism of action of OsSCL30 in various abiotic stresses was explored. Bioinformatics analysis showed that OsSCL30 was located on the chromosome 12 of rice Nipponbare, belonging to the plant-specific SCL subfamily of the SR protein family. The 1500 bp section upstream of the open reading frame start site contains stress-related cis-acting elements such as ABRE, MYC, and MYB. Under normal conditions, the expression of OsSCL30 was higher in leaves and leaf sheaths. The results of reverse transcription polymerase chain reaction showed that the expression of OsSCL30 decreased after low temperature, drought and salt treatment. In root cells OsSCL30 was localized in the nuclei. The results of the rice seedling tolerance and recovery tests showed that overexpression of OsSCL30 diminished the resistance to low temperature, drought and salt stresses in transgenic rice and resulted in larger accumulation of reactive oxygen species. This study is of great significance for exploring the response mechanisms of SR proteins under abiotic stresses.
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Affiliation(s)
- Jia Zhang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yihao Sun
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhanmei Zhou
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yifan Zhang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yanmei Yang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaofei Zan
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaohong Li
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jiale Wan
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoling Gao
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Rongjun Chen
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhengjian Huang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lihua Li
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Zhengjun Xu
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Bano N, Fakhrah S, Mohanty CS, Bag SK. Transcriptome Meta-Analysis Associated Targeting Hub Genes and Pathways of Drought and Salt Stress Responses in Cotton ( Gossypium hirsutum): A Network Biology Approach. FRONTIERS IN PLANT SCIENCE 2022; 13:818472. [PMID: 35548277 PMCID: PMC9083274 DOI: 10.3389/fpls.2022.818472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/21/2022] [Indexed: 06/12/2023]
Abstract
Abiotic stress tolerance is an intricate feature controlled through several genes and networks in the plant system. In abiotic stress, salt, and drought are well known to limit cotton productivity. Transcriptomics meta-analysis has arisen as a robust method to unravel the stress-responsive molecular network in crops. In order to understand drought and salt stress tolerance mechanisms, a meta-analysis of transcriptome studies is crucial. To confront these issues, here, we have given details of genes and networks associated with significant differential expression in response to salt and drought stress. The key regulatory hub genes of drought and salt stress conditions have notable associations with functional drought and salt stress-responsive (DSSR) genes. In the network study, nodulation signaling pathways 2 (NSP2), Dehydration-responsive element1 D (DRE1D), ethylene response factor (ERF61), cycling DOF factor 1 (CDF1), and tubby like protein 3 (TLP3) genes in drought and tubby like protein 1 (TLP1), thaumatin-like proteins (TLP), ethylene-responsive transcription factor ERF109 (EF109), ETS-Related transcription Factor (ELF4), and Arabidopsis thaliana homeodomain leucine-zipper gene (ATHB7) genes in salt showed the significant putative functions and pathways related to providing tolerance against drought and salt stress conditions along with the significant expression values. These outcomes provide potential candidate genes for further in-depth functional studies in cotton, which could be useful for the selection of an improved genotype of Gossypium hirsutum against drought and salt stress conditions.
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Affiliation(s)
- Nasreen Bano
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shafquat Fakhrah
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Chandra Sekhar Mohanty
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sumit Kumar Bag
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Jamil F, Mukhtar H, Fouillaud M, Dufossé L. Rhizosphere Signaling: Insights into Plant-Rhizomicrobiome Interactions for Sustainable Agronomy. Microorganisms 2022; 10:microorganisms10050899. [PMID: 35630345 PMCID: PMC9147336 DOI: 10.3390/microorganisms10050899] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 02/01/2023] Open
Abstract
Rhizospheric plant-microbe interactions have dynamic importance in sustainable agriculture systems that have a reduced reliance on agrochemicals. Rhizosphere signaling focuses on the interactions between plants and the surrounding symbiotic microorganisms that facilitate the development of rhizobiome diversity, which is beneficial for plant productivity. Plant-microbe communication comprises intricate systems that modulate local and systemic defense mechanisms to mitigate environmental stresses. This review deciphers insights into how the exudation of plant secondary metabolites can shape the functions and diversity of the root microbiome. It also elaborates on how rhizosphere interactions influence plant growth, regulate plant immunity against phytopathogens, and prime the plant for protection against biotic and abiotic stresses, along with some recent well-reported examples. A holistic understanding of these interactions can help in the development of tailored microbial inoculants for enhanced plant growth and targeted disease suppression.
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Affiliation(s)
- Fatima Jamil
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan;
| | - Hamid Mukhtar
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan;
- Correspondence: (H.M.); (M.F.); Tel.: +92-333-424-5581 (H.M.); +262-262-483-363 (M.F.)
| | - Mireille Fouillaud
- CHEMBIOPRO Chimie et Biotechnologie des Produits Naturels, Faculté des Sciences et Technologies, Université de la Réunion, F-97490 Sainte-Clotilde, Ile de La Réunion, France
- Correspondence: (H.M.); (M.F.); Tel.: +92-333-424-5581 (H.M.); +262-262-483-363 (M.F.)
| | - Laurent Dufossé
- CHEMBIOPRO Chimie et Biotechnologie des Produits Naturels, ESIROI Département Agroalimentaire, Université de la Réunion, F-97490 Sainte-Clotilde, Ile de La Réunion, France;
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Yadav C, Bahuguna RN, Dhankher OP, Singla-Pareek SL, Pareek A. Physiological and molecular signatures reveal differential response of rice genotypes to drought and drought combination with heat and salinity stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:899-910. [PMID: 35592483 PMCID: PMC9110620 DOI: 10.1007/s12298-022-01162-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 05/26/2023]
Abstract
UNLABELLED Rice is the staple food for more than 3.5 billion people worldwide. The sensitivity of rice to heat, drought, and salinity is well documented. However, rice response to combinations of these stresses is not well understood. A contrasting set of rice genotypes for heat (N22, Gharib), drought (Moroberekan, Pusa 1121) and salinity (Pokkali, IR64) were selected to characterize their response under drought, and combination of drought with heat and salinity at the sensitive seedling stage. Sensitive genotypes (IR64, Pusa 1121, Gharib) recorded higher reactive oxygen species accumulation (20-40%), membrane damage (8-65%) and reduction in photosynthetic efficiency (10-23%) across the stress and stress combinations as compared to stress tolerant checks. On the contrary, N22 and Pokkali performed best under drought + heat, and drought + salinity combination, respectively. Moreover, gene expression pattern revealed the highest expression of catalase (CAT), ascorbate peroxidase (APX) and GATA28a in N22 under heat + drought, whereas the highest expression of CAT, APX, superoxide dismutase (SOD), DEHYDRIN, GATA28a and GATA28b in Pokkali under drought + salinity. Interestingly, the phenotypic variation and expression level of genes highlighted the role of different set of physiological traits and genes under drought and drought combination with heat and salinity stress. This study reveals that rice response to stress combinations was unique with rapid readjustment at physiological and molecular levels. Moreover, phenotypic changes under stress combinations showed substantial adaptive plasticity in rice, which warrant further investigations at molecular level. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01162-y.
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Affiliation(s)
- Chhaya Yadav
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Rajeev Nayan Bahuguna
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003 USA
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
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Abstract
On the world stage, the increase in temperatures due to global warming is already a reality that has become one of the main challenges faced by the scientific community. Since agriculture is highly dependent on climatic conditions, it may suffer a great impact in the short term if no measures are taken to adapt and mitigate the agricultural system. Plant responses to abiotic stresses have been the subject of research by numerous groups worldwide. Initially, these studies were concentrated on model plants, and, later, they expanded their studies in several economically important crops such as rice, corn, soybeans, coffee, and others. However, agronomic evaluations for the launching of cultivars and the classical genetic improvement process focus, above all, on productivity, historically leaving factors such as tolerance to abiotic stresses in the background. Considering the importance of the impact that abiotic stresses can have on agriculture in the short term, new strategies are currently being sought and adopted in breeding programs to understand the physiological, biochemical, and molecular responses to environmental disturbances in plants of agronomic interest, thus ensuring the world food security. Moreover, integration of these approaches is bringing new insights on breeding. We will discuss how water deficit, high temperatures, and salinity exert effects on plants.
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Kumar J, Gupta DS, Kesari R, Verma R, Murugesan S, Basu PS, Soren KR, Gupta S, Singh NP. Comprehensive RNAseq analysis for identification of genes expressed under heat stress in lentil. PHYSIOLOGIA PLANTARUM 2021; 173:1785-1807. [PMID: 33829491 DOI: 10.1111/ppl.13419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Lentils are highly sensitive to abrupt increases in temperature during the mid to late reproductive stages, leading to severe biomass and seed yield reduction. Therefore, we carried out an RNAseq analysis between IG4258 (heat tolerant) and IG3973 (heat sensitive) lentil genotypes at the reproductive stage under both normal and heat stress conditions in the field. It resulted in 209,549 assembled transcripts and among these 161,809 transcripts had coding regions, of which 94,437 transcripts were annotated. The differential gene expression analysis showed upregulation of 678 transcripts and downregulation of 680 transcripts between the tolerant and sensitive genotypes at the early reproductive stage. While 76 transcripts were upregulated and 47 transcripts were downregulated at the late reproductive stage under heat stress conditions. The validation of 12 up-or downregulated transcripts through RT-PCR corresponded well with the expression analysis data of RNAseq, with a correlation of R2 = 0.89. Among these transcripts, the DN364_c1_g1_i9 and DN2218_c0_g1_i5 transcripts encoded enzymes involved in the tryptophan pathway, indicating that tryptophan biosynthesis plays a role under heat stress in lentil. Moreover, KEGG pathways enrichment analysis identified transcripts associated with genes encoding proteins/regulating factors related to different metabolic pathways including signal transduction, fatty acid biosynthesis, rRNA processing, ribosome biogenesis, gibberellin (GA) biosynthesis, and riboflavin biosynthesis. This analysis also identified 6852 genic-SSRs leading to the development of 4968 SSR primers that are potential genomic resources for molecular mapping of heat-tolerant genes in lentil.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Ravi Kesari
- Department of Plant Breeding and Genetics, Bhola Paswan Shastri Agricultural College, Purnea, India
| | - Renu Verma
- Division of Basic Sciences, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | | | - Partha Sarathi Basu
- Division of Basic Sciences, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Khela Ram Soren
- Division of Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sanjeev Gupta
- All India Co-ordinated Research Project on MULLaRP, ICAR-Indian Institute of Pulses Research, Kanpur, India
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Siddiqui ZS, Oh SD, Kim EJ, Jang YJ, Lee SK, Yun DW, Kwon TR, Wajid D, Ansari HH, Park SC, Cho JI. Physiological and photochemical evaluation of pepper methionine sulfoxide reductase B2 (CaMsrB2) expressing transgenic rice in saline habitat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:198-209. [PMID: 34365290 DOI: 10.1016/j.plaphy.2021.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Two pepper methionine sulfoxide reductase B2 (CaMsrB2) gene expressing transgenic rice lines (L-8 and L-23) were interrogated with respect to their physiological and photochemical attributes along with control (WT, Ilmi) as a standard against varying levels of salt concentration which are 75 mM, 150 mM and 225 mM. Against various levels of salt (NaCl) concentration, recurring detrimental effects of extreme salt stress was observed and more pronounced in the wild type plants as compared to our transgenic lines. As the exacerbated effects of salinity is responsible for pushing the plants to their ecological tolerance, our transgenic lines performed well uplifted in different realms of physiology and photochemistry such as relative water content (RWC = 60-75%), stomatal conductance (gs = 70-190 mmolm-2s-1), performance index (PIABS = 1.0-4.5), maximal photochemical yield of PSII (FV/FM = 0.48-0.72) and chlorophyll content index (CCI = 5-7.2 au) in comparison to the control. Relative gene expression, ion analysis and antioxidants activity were analyzed in all treatments to ensure the hypothesis obtained from data of physiology and photochemistry. Photosynthetic apparatus is known to lose energy in various forms such as NPQ, DIO/CS, damages of reaction center (FV/FO) which are the markers of poor health were clearly decreased in the L-23 line as compared to L-8 and WT. Present study revealed the protruding tolerance of L-23 and L-8 transgenic lines with L-23 line in the lead in comparison to control and L-8 transgenic lines.
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Affiliation(s)
- Zamin Shaheed Siddiqui
- Stress Physiology and Phenomic Lab., Department of Botany, University of Karachi, Karachi, 75270, Pakistan.
| | - Sung-Dug Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, South Korea
| | - Eun-Ji Kim
- Crop Production and Physiology Division, National Institute of Crop Science, Rural Development Administration, Wanju, 55365, South Korea
| | - Ye-Jin Jang
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, South Korea
| | - Seong-Kon Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, South Korea
| | - Doh-Won Yun
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, South Korea
| | - Taek-Ryoun Kwon
- Technology Cooperation Bureau, Rural Development Administration, Jeonju, 54875, South Korea
| | - Danish Wajid
- Stress Physiology and Phenomic Lab., Department of Botany, University of Karachi, Karachi, 75270, Pakistan
| | - Hafiza Hamna Ansari
- Stress Physiology and Phenomic Lab., Department of Botany, University of Karachi, Karachi, 75270, Pakistan
| | - Soo-Chul Park
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, South Korea.
| | - Jung-Il Cho
- Crop Production and Physiology Division, National Institute of Crop Science, Rural Development Administration, Wanju, 55365, South Korea.
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20
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Epigenetic control of abiotic stress signaling in plants. Genes Genomics 2021; 44:267-278. [PMID: 34515950 DOI: 10.1007/s13258-021-01163-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Although plants may be regularly exposed to various abiotic stresses, including drought, salt, cold, heat, heavy metals, and UV-B throughout their lives, it is not possible to actively escape from such stresses due to the immobile nature of plants. To overcome adverse environmental stresses, plants have developed adaptive systems that allow appropriate responses to diverse environmental cues; such responses can be achieved by fine-tuning or controlling genetic and epigenetic regulatory systems. Epigenetic mechanisms such as DNA or histone modifications and modulation of chromatin accessibility have been shown to regulate the expression of stress-responsive genes in struggles against abiotic stresses. OBJECTIVE Herein, the current progress in elucidating the epigenetic regulation of abiotic stress signaling in plants has been summarized in order to further understand the systems plants utilize to effectively respond to abiotic stresses. METHODS This review focuses on the action mechanisms of various components that epigenetically regulate plant abiotic stress responses, mainly in terms of DNA methylation, histone methylation/acetylation, and chromatin remodeling. CONCLUSIONS This review can be considered a basis for further research into understanding the epigenetic control system for abiotic stress responses in plants. Moreover, the knowledge of such systems can be effectively applied in developing novel methods to generate abiotic stress resistant crops.
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Rahimi Y, Ingvarsson PK, Bihamta MR, Alipour H, Taleei A, Khoshnoodi Jabar Abadi S. Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey. FRONTIERS IN PLANT SCIENCE 2021; 12:710867. [PMID: 34484273 PMCID: PMC8415571 DOI: 10.3389/fpls.2021.710867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
A well-developed root system benefits host plants by optimizing water absorption and nutrient uptake and thereby increases plant productivity. In this study we have characterized the root transcriptome using RNA-seq and subsequential functional analysis in a set of drought tolerant and susceptible genotypes. The goal of the study was to elucidate and characterize water deficit-responsive genes in wheat landraces that had been through long-term field and biochemical screening for drought tolerance. The results confirm genotype differences in water-deficit tolerance in line with earlier results from field trials. The transcriptomics survey highlighted a total of 14,187 differentially expressed genes (DEGs) that responded to water deficit. The characterization of these genes shows that all chromosomes contribute to water-deficit tolerance, but to different degrees, and the B genome showed higher involvement than the A and D genomes. The DEGs were mainly mapped to flavonoid, phenylpropanoid, and diterpenoid biosynthesis pathways, as well as glutathione metabolism and hormone signaling. Furthermore, extracellular region, apoplast, cell periphery, and external encapsulating structure were the main water deficit-responsive cellular components in roots. A total of 1,377 DEGs were also predicted to function as transcription factors (TFs) from different families regulating downstream cascades. TFs from the AP2/ERF-ERF, MYB-related, B3, WRKY, Tify, and NAC families were the main genotype-specific regulatory factors. To further characterize the dynamic biosynthetic pathways, protein-protein interaction (PPI) networks were constructed using significant KEGG proteins and putative TFs. In PPIs, enzymes from the CYP450, TaABA8OH2, PAL, and GST families play important roles in water-deficit tolerance in connection with MYB13-1, MADS-box, and NAC transcription factors.
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Affiliation(s)
- Yousef Rahimi
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pär K. Ingvarsson
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mohammad Reza Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia University, Urmia, Iran
| | - Alireza Taleei
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
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Jeyasri R, Muthuramalingam P, Satish L, Pandian SK, Chen JT, Ahmar S, Wang X, Mora-Poblete F, Ramesh M. An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10071472. [PMID: 34371676 PMCID: PMC8309266 DOI: 10.3390/plants10071472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 05/06/2023]
Abstract
Abiotic stresses (AbS), such as drought, salinity, and thermal stresses, could highly affect the growth and development of plants. For decades, researchers have attempted to unravel the mechanisms of AbS for enhancing the corresponding tolerance of plants, especially for crop production in agriculture. In the present communication, we summarized the significant factors (atmosphere, soil and water) of AbS, their regulations, and integrated omics in the most important cereal crops in the world, especially rice, wheat, sorghum, and maize. It has been suggested that using systems biology and advanced sequencing approaches in genomics could help solve the AbS response in cereals. An emphasis was given to holistic approaches such as, bioinformatics and functional omics, gene mining and agronomic traits, genome-wide association studies (GWAS), and transcription factors (TFs) family with respect to AbS. In addition, the development of omics studies has improved to address the identification of AbS responsive genes and it enables the interaction between signaling pathways, molecular insights, novel traits and their significance in cereal crops. This review compares AbS mechanisms to omics and bioinformatics resources to provide a comprehensive view of the mechanisms. Moreover, further studies are needed to obtain the information from the integrated omics databases to understand the AbS mechanisms for the development of large spectrum AbS-tolerant crop production.
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Affiliation(s)
- Rajendran Jeyasri
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, India; (R.J.); (P.M.); (L.S.); (S.K.P.)
| | - Pandiyan Muthuramalingam
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, India; (R.J.); (P.M.); (L.S.); (S.K.P.)
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641062, India
| | - Lakkakula Satish
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, India; (R.J.); (P.M.); (L.S.); (S.K.P.)
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Shunmugiah Karutha Pandian
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, India; (R.J.); (P.M.); (L.S.); (S.K.P.)
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 81148, Taiwan;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile;
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an 716000, China;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile;
- Correspondence: (F.M.-P.); (M.R.)
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, India; (R.J.); (P.M.); (L.S.); (S.K.P.)
- Correspondence: (F.M.-P.); (M.R.)
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Park SI, Kwon HJ, Cho MH, Song JS, Kim BG, Baek J, Kim SL, Ji H, Kwon TR, Kim KH, Yoon IS. The OsERF115/AP2EREBP110 Transcription Factor Is Involved in the Multiple Stress Tolerance to Heat and Drought in Rice Plants. Int J Mol Sci 2021; 22:ijms22137181. [PMID: 34281241 PMCID: PMC8269390 DOI: 10.3390/ijms22137181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 01/26/2023] Open
Abstract
The AP2/EREBP family transcription factors play important roles in a wide range of stress tolerance and hormone signaling. In this study, a heat-inducible rice ERF gene was isolated and functionally characterized. The OsERF115/AP2EREBP110 was categorized to Group-IIIc of the rice AP2/EREBP family and strongly induced by heat and drought treatment. The OsERF115/AP2EREBP110 protein targeted to nuclei and suppressed the ABA-induced transcriptional activation of Rab16A promoter in rice protoplasts. Overexpression of OsERF115/AP2EREBP110 enhanced thermotolerance of seeds and vegetative growth stage plants. The OsERF115/AP2EREBP110 overexpressing (OE) plants exhibited higher proline level and increased expression of a proline biosynthesis P5CS1 gene. Phenotyping of water use dynamics of the individual plant indicates that the OsERF115/AP2EREBP110-OE plant exhibited better water saving traits under heat and drought combined stress. Our combined results suggest the potential use of OsERF115/AP2EREBP110 as a candidate gene for genetic engineering approaches to develop heat and drought stress-tolerant crops.
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Affiliation(s)
- Seong-Im Park
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Hyeok Jin Kwon
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Mi Hyeon Cho
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Ji Sun Song
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Beom-Gi Kim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea;
| | - JeongHo Baek
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Song Lim Kim
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - HyeonSo Ji
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Taek-Ryoun Kwon
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Kyung-Hwan Kim
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - In Sun Yoon
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
- Correspondence:
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24
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Butt H, Bazin J, Alshareef S, Eid A, Benhamed M, Reddy ASN, Crespi M, Mahfouz MM. Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation. Commun Biol 2021; 4:529. [PMID: 33953336 PMCID: PMC8100303 DOI: 10.1038/s42003-021-02051-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/26/2021] [Indexed: 01/02/2023] Open
Abstract
The SF3B complex, a multiprotein component of the U2 snRNP of the spliceosome, plays a crucial role in recognizing branch point sequence and facilitates spliceosome assembly and activation. Several chemicals that bind SF3B1 and PHF5A subunits of the SF3B complex inhibit splicing. We recently generated a splicing inhibitor-resistant SF3B1 mutant named SF3B1GEX1ARESISTANT 4 (SGR4) using CRISPR-mediated directed evolution, whereas splicing inhibitor-resistant mutant of PHF5A (Overexpression-PHF5A GEX1A Resistance, OGR) was generated by expressing an engineered version PHF5A-Y36C. Global analysis of splicing in wild type and these two mutants revealed the role of SF3B1 and PHF5A in splicing regulation. This analysis uncovered a set of genes whose intron retention is regulated by both proteins. Further analysis of these retained introns revealed that they are shorter, have a higher GC content, and contain shorter and weaker polypyrimidine tracts. Furthermore, splicing inhibition increased seedlings sensitivity to salt stress, consistent with emerging roles of splicing regulation in stress responses. In summary, we uncovered the functions of two members of the plant branch point recognition complex. The novel strategies described here should be broadly applicable in elucidating functions of splicing regulators, especially in studying the functions of redundant paralogs in plants. Butt et al. used CRISPR-mediated directed evolution to generate rice mutants for the spliceosome components SF3B1 and PHF5A. They demonstrate that these mutants have different levels of sensitivity to salt treatments and suggest that the strategies they employed can be used in the future to study functions of redundant paralogs in plants.
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Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jeremie Bazin
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Sahar Alshareef
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Moussa Benhamed
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Martin Crespi
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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25
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Yadav AK, Kumar A, Grover N, Ellur RK, Bollinedi H, Krishnan SG, Bhowmick PK, Vinod KK, Nagarajan M, Singh AK. Genome-Wide Association Study Reveals Marker-Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice. PLANTS (BASEL, SWITZERLAND) 2021; 10:559. [PMID: 33809618 PMCID: PMC8000697 DOI: 10.3390/plants10030559] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 11/16/2022]
Abstract
Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker-trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.
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Affiliation(s)
- Ashutosh Kumar Yadav
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Aruna Kumar
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Nitasha Grover
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Haritha Bollinedi
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Subbaiyan Gopala Krishnan
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Prolay Kumar Bhowmick
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Kunnummal Kurungara Vinod
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Mariappan Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR—Indian Agricultural Research Institute, Aduthurai 612101, Tamil Nadu, India;
| | - Ashok Kumar Singh
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
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26
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Nair MM, Shylaraj KS. Introgression of dual abiotic stress tolerance QTLs ( Saltol QTL and Sub1 gene) into Rice ( Oryza sativa L.) variety Aiswarya through marker assisted backcross breeding. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:497-514. [PMID: 33854279 PMCID: PMC7981364 DOI: 10.1007/s12298-020-00893-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/08/2020] [Accepted: 10/06/2020] [Indexed: 06/12/2023]
Abstract
Salinity and submergence are two very prominent abiotic stress conditions affecting rice yield adversely in the coastal agro ecosystem. Marker Assisted Backcross Breeding (MABB) is an efficient and fast track molecular tool to incorporate a desired stress tolerant QTL/gene into an improved cultivar. The present study was carried out for the introgression of Saltol QTL responsible for salinity tolerance and Sub1 gene responsible for submergence tolerance into the high yielding rice variety Aiswarya independently through MABB. Final objective of the study is to develop dual stress tolerant (tolerance to salinity and submergence) Aiswarya rice variety by pyramiding the both target QTLs introgressed BC2F2 progenies having maximum background homozygosity. The donors of Saltol QTL and Sub1 gene used in the present study were FL478 and Swarna Sub1, respectively. Based on the background genome analysis of the introgressed plants, the plants with > 85-90% background similarity were selected for pyramiding of Saltol QTL and Sub1 gene into the elite background of rice variety Aiswarya. Those selected introgressed lines with Saltol QTL and Sub1 gene will be again crossed to pyramid both Saltol QTL and Sub1 gene into the rice variety Aiswarya. Such a mega rice variety pyramided with dual stress tolerant QTLs is the expected outcome of this study and can be recommended for cultivation in the flood prone saline coastal agroecosystem.
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Affiliation(s)
- Meenu M. Nair
- Rice Research Station, Kerala Agricultural University, Vytilla P.O, Kochi, 682019 Kerala India
| | - K. S. Shylaraj
- Rice Research Station, Kerala Agricultural University, Vytilla P.O, Kochi, 682019 Kerala India
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27
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Lu X, Liu S, Zhi S, Chen J, Ye G. Comparative transcriptome profile analysis of rice varieties with different tolerance to zinc deficiency. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:375-390. [PMID: 33296551 DOI: 10.1111/plb.13227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Zinc (Zn) is an indispensable element for rice growth. Zn deficiency results in brown blotches and streaks 2-3 weeks after transplanting, as well as stunting, reduced tillering, and low productivity of rice plants. These processes are controlled by different families of expressed genes. A comparative transcriptome profile analysis was conducted using the roots of two Zn deficiency tolerant varieties (UCP122 and KALIBORO26) and two sensitive varieties (IR26 and IR64) by merging data from untreated control (CK) and Zn deficiency treated samples. Results revealed a total of 4,688 differentially expressed genes (DEGs) between the normal Zn and deficient conditions, with 2,702 and 1,489 unique DEGs upregulated and downregulated, respectively. Functional enrichment analysis identified transcription factors (TFs), such as WRKY, MYB, ERF, and bHLH which are important in the regulation of the Zn deficiency response. Furthermore, chitinases, jasmonic acid, and phenylpropanoid pathways were found to be important in the Zn deficiency response. The metal tolerance protein (MTP) genes also appeared to play an important role in conferring tolerance to Zn deficiency. A heavy metal-associated domain-containing protein 7 was associated with tolerance to Zn deficiency and negatively regulated downstream genes. Collectively, our findings provide valuable expression patterns and candidate genes for the study of molecular mechanisms underlying the response to Zn deficiency and for improvements in breeding for tolerance to Zn deficiency in rice.
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Affiliation(s)
- X Lu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - S Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University, Nanchang, China
| | - S Zhi
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, China
| | - J Chen
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - G Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University, Nanchang, China
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
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28
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Razi K, Muneer S. Drought stress-induced physiological mechanisms, signaling pathways and molecular response of chloroplasts in common vegetable crops. Crit Rev Biotechnol 2021; 41:669-691. [PMID: 33525946 DOI: 10.1080/07388551.2021.1874280] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Drought stress is one of the most adverse abiotic stresses that hinder plants' growth and productivity, threatening sustainable crop production. It impairs normal growth, disturbs water relations and reduces water-use efficiency in plants. However, plants have evolved many physiological and biochemical responses at the cellular and organism levels, in order to cope with drought stress. Photosynthesis, which is considered one of the most crucial biological processes for survival of plants, is greatly affected by drought stress. A gradual decrease in CO2 assimilation rates, reduced leaf size, stem extension and root proliferation under drought stress, disturbs plant water relations, reducing water-use efficiency, disrupts photosynthetic pigments and reduces the gas exchange affecting the plants adversely. In such conditions, the chloroplast, organelle responsible for photosynthesis, is found to counteract the ill effects of drought stress by its critical involvement as a sensor of changes occurring in the environment, as the first process that drought stress affects is photosynthesis. Beside photosynthesis, chloroplasts carry out primary metabolic functions such as the biosynthesis of starch, amino acids, lipids, and tetrapyroles, and play a central role in the assimilation of nitrogen and sulfur. Because the chloroplasts are central organelles where the photosynthetic reactions take place, modifications in their physiology and protein pools are expected in response to the drought stress-induced variations in leaf gas exchanges and the accumulation of ROS. Higher expression levels of various transcription factors and other proteins including heat shock-related protein, LEA proteins seem to be regulating the heat tolerance mechanisms. However, several aspects of plastid alterations, following a water deficit environment are still poorly characterized. Since plants adapt to various stress tolerance mechanisms to respond to drought stress, understanding mechanisms of drought stress tolerance in plants will lead toward the development of drought tolerance in crop plants. This review throws light on major droughts stress-induced molecular/physiological mechanisms in response to severe and prolonged drought stress and addresses the molecular response of chloroplasts in common vegetable crops. It further highlights research gaps, identifying unexplored domains and suggesting recommendations for future investigations.
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Affiliation(s)
- Kaukab Razi
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu, India.,School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Neang S, de Ocampo M, Egdane JA, Platten JD, Ismail AM, Seki M, Suzuki Y, Skoulding NS, Kano-Nakata M, Yamauchi A, Mitsuya S. A GWAS approach to find SNPs associated with salt removal in rice leaf sheath. ANNALS OF BOTANY 2020; 126:1193-1202. [PMID: 33009812 PMCID: PMC7684702 DOI: 10.1093/aob/mcaa139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/02/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND AND AIMS The ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice. METHODS In this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl- concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress. KEY RESULTS For the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress. CONCLUSIONS These GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress.
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Affiliation(s)
- Sarin Neang
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | | | - James A Egdane
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | | | | | - Masahide Seki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Japan
| | | | - Mana Kano-Nakata
- International Center for Research and Education in Agriculture, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Shiro Mitsuya
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
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Renau-Morata B, Carrillo L, Dominguez-Figueroa J, Vicente-Carbajosa J, Molina RV, Nebauer SG, Medina J. CDF transcription factors: plant regulators to deal with extreme environmental conditions. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3803-3815. [PMID: 32072179 DOI: 10.1093/jxb/eraa088] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/03/2020] [Indexed: 05/23/2023]
Abstract
In terrestrial environments, water and nutrient availabilities and temperature conditions are highly variable, and especially in extreme environments limit survival, growth, and reproduction of plants. To sustain growth and maintain cell integrity under unfavourable environmental conditions, plants have developed a variety of biochemical and physiological mechanisms, orchestrated by a large set of stress-responsive genes and a complex network of transcription factors. Recently, cycling DOF factors (CDFs), a group of plant-specific transcription factors (TFs), were identified as components of the transcriptional regulatory networks involved in the control of abiotic stress responses. The majority of the members of this TF family are activated in response to a wide range of adverse environmental conditions in different plant species. CDFs regulate different aspects of plant growth and development such as photoperiodic flowering-time control and root and shoot growth. While most of the functional characterization of CDFs has been reported in Arabidopsis, recent data suggest that their diverse roles extend to other plant species. In this review, we integrate information related to structure and functions of CDFs in plants, with special emphasis on their role in plant responses to adverse environmental conditions.
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Affiliation(s)
- Begoña Renau-Morata
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Camino de Vera s/n, Valencia, Spain
| | - Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Autopista M40 (km 38), Madrid, Spain
| | - Jose Dominguez-Figueroa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Autopista M40 (km 38), Madrid, Spain
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Autopista M40 (km 38), Madrid, Spain
| | - Rosa V Molina
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Camino de Vera s/n, Valencia, Spain
| | - Sergio G Nebauer
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Camino de Vera s/n, Valencia, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Autopista M40 (km 38), Madrid, Spain
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Muthu V, Abbai R, Nallathambi J, Rahman H, Ramasamy S, Kambale R, Thulasinathan T, Ayyenar B, Muthurajan R. Pyramiding QTLs controlling tolerance against drought, salinity, and submergence in rice through marker assisted breeding. PLoS One 2020; 15:e0227421. [PMID: 31910435 PMCID: PMC6946594 DOI: 10.1371/journal.pone.0227421] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/18/2019] [Indexed: 01/13/2023] Open
Abstract
Increases in rice productivity are significantly hampered because of the increase in the occurrence of abiotic stresses, including drought, salinity, and submergence. Developing a rice variety with inherent tolerance against these major abiotic stresses will help achieve a sustained increase in rice production under unfavorable conditions. The present study was conducted to develop abiotic stress-tolerant rice genotypes in the genetic background of the popular rice variety Improved White Ponni (IWP) by introgressing major effect quantitative trait loci (QTLs) conferring tolerance against drought (qDTY1.1, qDTY2.1), salinity (Saltol), and submergence (Sub1) through a marker assisted backcross breeding approach. Genotyping of early generation backcrossed inbred lines (BILs) resulted in the identification of three progenies, 3-11-9-2, 3-11-11-1, and 3-11-11-2, possessing all four target QTLs and maximum recovery of the recurrent parent genome (88.46%). BILs exhibited consistent agronomic and grain quality characters compared to those of IWP and enhanced performance against dehydration, salinity, and submergence stress compared with the recurrent parent IWP. BILs exhibited enhanced tolerance against salinity during germination and increased shoot length, root length, and vigor index compared to those of IWP. All three BILs exhibited reduced symptoms of injury because of salinity (NaCl) and dehydration (PEG) than did IWP. At 12 days of submergence stress, BILs exhibited enhanced survival and greater recovery, whereas IWP failed completely. BILs were found to exhibit on par grain and cooking quality characteristics with their parents. Results of this study clearly demonstrated the effects of the target QTLs in reducing damage caused by drought, salinity, and submergence and lead to the development of a triple stress tolerant version of IWP.
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Affiliation(s)
- Valarmathi Muthu
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Ragavendran Abbai
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Hifzur Rahman
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Sasikala Ramasamy
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Rohit Kambale
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Thiyagarajan Thulasinathan
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Bharathi Ayyenar
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
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Meena M, Divyanshu K, Kumar S, Swapnil P, Zehra A, Shukla V, Yadav M, Upadhyay RS. Regulation of L-proline biosynthesis, signal transduction, transport, accumulation and its vital role in plants during variable environmental conditions. Heliyon 2019; 5:e02952. [PMID: 31872123 PMCID: PMC6909094 DOI: 10.1016/j.heliyon.2019.e02952] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/28/2019] [Accepted: 11/25/2019] [Indexed: 12/19/2022] Open
Abstract
Background In response to various environmental stresses, many plant species synthesize L-proline in the cytosol and accumulates in the chloroplasts. L-Proline accumulation in plants is a well-recognized physiological reaction to osmotic stress prompted by salinity, drought and other abiotic stresses. L-Proline plays several protective functions such as osmoprotectant, stabilizing cellular structures, enzymes, and scavenging reactive oxygen species (ROS), and keeps up redox balance in adverse situations. In addition, ample-studied osmoprotective capacity, L-proline has been also ensnared in the regulation of plant improvement, including flowering, pollen, embryo, and leaf enlargement. Scope and conclusions Albeit, ample is now well-known about L-proline metabolism, but certain characteristics of its biological roles are still indistinct. In the present review, we discuss the L-proline accumulation, metabolism, signaling, transport and regulation in the plants. We also discuss the effects of exogenous L-proline during different environmental conditions. L-Proline biosynthesis and catabolism are controlled by several cellular mechanisms, of which we identify only very fewer mechanisms. So, in the future, there is a requirement to identify such types of cellular mechanisms.
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Affiliation(s)
- Mukesh Meena
- Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, India.,Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Kumari Divyanshu
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Sunil Kumar
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Prashant Swapnil
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.,International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Andleeb Zehra
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Vaishali Shukla
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Mukesh Yadav
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - R S Upadhyay
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
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Tang M, Xu L, Wang Y, Cheng W, Luo X, Xie Y, Fan L, Liu L. Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.). BMC Genomics 2019; 20:772. [PMID: 31651257 PMCID: PMC6814140 DOI: 10.1186/s12864-019-6121-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022] Open
Abstract
Background Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stresses. Therefore, the identification and characterization of HSFs is imperative to dissect the mechanism responsible for plant stress responses. Although the HSF gene family has been extensively studied in several plant species, its characterization, evolutionary history and expression patterns in the radish (Raphanus sativus L.) remain limited. Results In this study, 33 RsHSF genes were obtained from the radish genome, which were classified into three main groups based on HSF protein domain structure. Chromosomal localization analysis revealed that 28 of 33 RsHSF genes were located on nine chromosomes, and 10 duplicated RsHSF genes were grouped into eight gene pairs by whole genome duplication (WGD). Moreover, there were 23 or 9 pairs of orthologous HSFs were identified between radish and Arabidopsis or rice, respectively. Comparative analysis revealed a close relationship among radish, Chinese cabbage and Arabidopsis. RNA-seq data showed that eight RsHSF genes including RsHSF-03, were highly expressed in the leaf, root, cortex, cambium and xylem, indicating that these genes might be involved in plant growth and development. Further, quantitative real-time polymerase chain reaction (RT-qPCR) indicated that the expression patterns of 12 RsHSF genes varied upon exposure to different abiotic stresses including heat, salt, and heavy metals. These results indicated that the RsHSFs may be involved in abiotic stress response. Conclusions These results could provide fundamental insights into the characteristics and evolution of the HSF family and facilitate further dissection of the molecular mechanism responsible for radish abiotic stress responses.
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Affiliation(s)
- Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Wanwan Cheng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yang Xie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Lianxue Fan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Liu LYD, Hsiao YC, Chen HC, Yang YW, Chang MC. Construction of gene causal regulatory networks using microarray data with the coefficient of intrinsic dependence. BOTANICAL STUDIES 2019; 60:22. [PMID: 31512008 PMCID: PMC6738364 DOI: 10.1186/s40529-019-0268-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/17/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND In the past two decades, biologists have been able to identify the gene signatures associated with various phenotypes through the monitoring of gene expressions with high-throughput biotechnologies. These gene signatures have in turn been successfully applied to drug development, disease prevention, crop improvement, etc. However, ignoring the interactions among genes has weakened the predictive power of gene signatures in practical applications. Gene regulatory networks, in which genes are represented by nodes and the associations between genes are represented by edges, are typically constructed to analyze and visualize such gene interactions. More specifically, the present study sought to measure gene-gene associations by using the coefficient of intrinsic dependence (CID) to capture more nonlinear as well as cause-effect gene relationships. RESULTS A stepwise procedure using the CID along with the partial coefficient of intrinsic dependence (pCID) was demonstrated for the rebuilding of simulated networks and the well-known CBF-COR pathway under cold stress using Arabidopsis microarray data. The procedure was also applied to the construction of bHLH gene regulatory pathways under abiotic stresses using rice microarray data, in which OsbHLH104, a putative phytochrome-interacting factor (OsPIF14), and OsbHLH060, a positive regulator of iron homeostasis (OsPRI1) were inferred as the most affiliated genes. The inferred regulatory pathways were verified through literature reviews. CONCLUSIONS The proposed method can efficiently decipher gene regulatory pathways and may assist in achieving higher predictive power in practical applications. The lack of any mention in the literature of some of the regulatory event may have been due to the high complexity of the regulatory systems in the plant transcription, a possibility which could potentially be confirmed in the near future given ongoing rapid developments in bio-technology.
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Affiliation(s)
- Li-yu Daisy Liu
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
| | - Ya-Chun Hsiao
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
| | - Hung-Chi Chen
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106 Taiwan
| | - Yun-Wei Yang
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
| | - Men-Chi Chang
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
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Zheng D, Wang L, Chen L, Pan X, Lin K, Fang Y, Wang XE, Zhang W. Salt-Responsive Genes are Differentially Regulated at the Chromatin Levels Between Seedlings and Roots in Rice. PLANT & CELL PHYSIOLOGY 2019; 60:1790-1803. [PMID: 31111914 DOI: 10.1093/pcp/pcz095] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 05/06/2019] [Indexed: 06/09/2023]
Abstract
The elucidation of epigenetic responses of salt-responsive genes facilitates understanding of the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms are associated with the expression of salt-responsive genes in rice and other crops. In this study, we reported tissue-specific gene expression and tissue-specific changes in chromatin modifications or signatures between seedlings and roots in response to salt treatment. Our study indicated that among six of individual mark examined (H3K4me3, H3K27me3, H4K12ac, H3K9ac, H3K27ac and H3K36me3), a positive association between salt-related changes in histone marks and the expression of differentially expressed genes (DEGs) was observed only for H3K9ac and H4K12ac in seedlings and H3K36me3 in roots. In contrast, chromatin states (CSs) with combinations of six histone modification marks played crucial roles in the differential expression of salt-responsive genes between seedlings and roots. Most importantly, CS7 containing the bivalent marks H3K4me3 and H3K27me3, with a mutual exclusion of functions with each other, displayed distinct functions in the expression of DEGs in both tissues. Specifically, H3K27me3 in CS7 mainly suppressed the expression of DEGs in roots, while H3K4me3 affected the expression of down- and up-regulated genes, possibly by antagonizing the repressive role of H3K27me3 in seedlings. Our findings indicate distinct impacts of the CSs on the differential expression of salt-responsive genes between seedlings and roots in rice, which provides an important background for understanding chromatin-based epigenetic mechanisms that might confer salt tolerance in plants.
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Affiliation(s)
- Dongyang Zheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Lei Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Lifen Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Xiucai Pan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
| | - Kande Lin
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Yuan Fang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Xiu-E Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, P.R. China
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Smita S, Katiyar A, Lenka SK, Dalal M, Kumar A, Mahtha SK, Yadav G, Chinnusamy V, Pandey DM, Bansal KC. Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis. Funct Integr Genomics 2019; 20:29-49. [PMID: 31286320 DOI: 10.1007/s10142-019-00697-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/31/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
Abstract
Abiotic stress tolerance is a complex trait regulated by multiple genes and gene networks in plants. A range of abiotic stresses are known to limit rice productivity. Meta-transcriptomics has emerged as a powerful approach to decipher stress-associated molecular network in model crops. However, retaining specificity of gene expression in tolerant and susceptible genotypes during meta-transcriptome analysis is important for understanding genotype-dependent stress tolerance mechanisms. Addressing this aspect, we describe here "abiotic stress tolerant" (ASTR) genes and networks specifically and differentially expressing in tolerant rice genotypes in response to different abiotic stress conditions. We identified 6,956 ASTR genes, key hub regulatory genes, transcription factors, and functional modules having significant association with abiotic stress-related ontologies and cis-motifs. Out of the 6956 ASTR genes, 73 were co-located within the boundary of previously identified abiotic stress trait-related quantitative trait loci. Functional annotation of 14 uncharacterized ASTR genes is proposed using multiple computational methods. Around 65% of the top ASTR genes were found to be differentially expressed in at least one of the tolerant genotypes under different stress conditions (cold, salt, drought, or heat) from publicly available RNAseq data comparison. The candidate ASTR genes specifically associated with tolerance could be utilized for engineering rice and possibly other crops for broad-spectrum tolerance to abiotic stresses.
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Affiliation(s)
- Shuchi Smita
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amit Katiyar
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- ICMR-AIIMS Computational Genomics Center, Div. of I.S.R.M., Indian Council of Medical Research, Ansari Nagar, New Delhi, 110029, India
| | - Sangram Keshari Lenka
- TERI-Deakin Nanobiotechnology Center, The Energy and Resources Institute, Gurgaon, Haryana, 122001, India
| | - Monika Dalal
- ICAR-National Research Center on Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
| | - Amish Kumar
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjeet Kumar Mahtha
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Viswanathan Chinnusamy
- ICAR-Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Dev Mani Pandey
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kailash Chander Bansal
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India.
- TERI-Deakin Nanobiotechnology Center, The Energy and Resources Institute, Gurgaon, Haryana, 122001, India.
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Qi C, Lin X, Li S, Liu L, Wang Z, Li Y, Bai R, Xie Q, Zhang N, Ren S, Zhao B, Li X, Fan S, Guo YD. SoHSC70 positively regulates thermotolerance by alleviating cell membrane damage, reducing ROS accumulation, and improving activities of antioxidant enzymes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:385-395. [PMID: 31128709 DOI: 10.1016/j.plantsci.2019.03.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
High temperature is a major environmental factor affecting plant growth. Heat shock proteins (Hsps) are molecular chaperones that play important roles in improving plant thermotolerance during heat stress. Spinach (Spinacia oleracea) is very sensitive to high temperature; however, the specific function of Hsps in spinach is unclear. In this study, cytosolic heat shock 70 protein (SoHSC70), which was induced by heat stress, was cloned from spinach. Overexpressing SoHSC70 in spinach calli and Arabidopsis enhanced their thermotolerance. In contrast, spinach seedlings with silenced SoHSC70 by virus-induced gene silencing (VIGS) showed more sensitivity to heat stress. Further analysis revealed that overexpressing SoHSC70 altered relative electrical conductivity (REC), malondialdehyde (MDA) content, photosynthetic rate, reactive oxygen species (ROS) accumulation and the activities of antioxidant enzymes, such as superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), and catalase (CAT) after the heat treatment. Taken together, our results suggest that overexpressing SoHSC70 positively affects heat tolerance by reducing membrane damage and ROS accumulation and improving activities of antioxidant enzymes.
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Affiliation(s)
- Chuandong Qi
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xinpeng Lin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shuangtao Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Lun Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhirong Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yu Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ruyue Bai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Qian Xie
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Na Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shuxin Ren
- School of Agriculture, Virginia State University, Petersburg, USA
| | - Bing Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China.
| | - Xiangdong Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shuangxi Fan
- College of Plant Science & Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yang-Dong Guo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Horticulture, China Agricultural University, Beijing 100193, China.
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Shukla PS, Mantin EG, Adil M, Bajpai S, Critchley AT, Prithiviraj B. Ascophyllum nodosum-Based Biostimulants: Sustainable Applications in Agriculture for the Stimulation of Plant Growth, Stress Tolerance, and Disease Management. FRONTIERS IN PLANT SCIENCE 2019; 10:655. [PMID: 31191576 PMCID: PMC6548832 DOI: 10.3389/fpls.2019.00655] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/01/2019] [Indexed: 05/06/2023]
Abstract
Abiotic and biotic stresses limit the growth and productivity of plants. In the current global scenario, in order to meet the requirements of the ever-increasing world population, chemical pesticides and synthetic fertilizers are used to boost agricultural production. These harmful chemicals pose a serious threat to the health of humans, animals, plants, and the entire biosphere. To minimize the agricultural chemical footprint, extracts of Ascophyllum nodosum (ANE) have been explored for their ability to improve plant growth and agricultural productivity. The scientific literature reviewed in this article attempts to explain how certain bioactive compounds present in extracts aid to improve plant tolerances to abiotic and/or biotic stresses, plant growth promotion, and their effects on root/microbe interactions. These reports have highlighted the use of various seaweed extracts in improving nutrient use efficiency in treated plants. These studies include investigations of physiological, biochemical, and molecular mechanisms as evidenced using model plants. However, the various modes of action of A. nodosum extracts have not been previously reviewed. The information presented in this review depicts the multiple, beneficial effects of A. nodosum-based biostimulant extracts on plant growth and their defense responses and suggests new opportunities for further applications for marked benefits in production and quality in the agriculture and horticultural sectors.
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Affiliation(s)
- Pushp Sheel Shukla
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Emily Grace Mantin
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Mohd Adil
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Sruti Bajpai
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Alan T. Critchley
- Research & Development, Acadian Seaplants Limited, Dartmouth, NS, Canada
| | - Balakrishnan Prithiviraj
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS, Canada
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Rana MM, Takamatsu T, Baslam M, Kaneko K, Itoh K, Harada N, Sugiyama T, Ohnishi T, Kinoshita T, Takagi H, Mitsui T. Salt Tolerance Improvement in Rice through Efficient SNP Marker-Assisted Selection Coupled with Speed-Breeding. Int J Mol Sci 2019; 20:ijms20102585. [PMID: 31130712 PMCID: PMC6567206 DOI: 10.3390/ijms20102585] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 12/30/2022] Open
Abstract
Salinity critically limits rice metabolism, growth, and productivity worldwide. Improvement of the salt resistance of locally grown high-yielding cultivars is a slow process. The objective of this study was to develop a new salt-tolerant rice germplasm using speed-breeding. Here, we precisely introgressed the hst1 gene, transferring salinity tolerance from “Kaijin” into high-yielding “Yukinko-mai” (WT) rice through single nucleotide polymorphism (SNP) marker-assisted selection. Using a biotron speed-breeding technique, we developed a BC3F3 population, named “YNU31-2-4”, in six generations and 17 months. High-resolution genotyping by whole-genome sequencing revealed that the BC3F2 genome had 93.5% similarity to the WT and fixed only 2.7% of donor parent alleles. Functional annotation of BC3F2 variants along with field assessment data indicated that “YNU31-2-4” plants carrying the hst1 gene had similar agronomic traits to the WT under normal growth condition. “YNU31-2-4” seedlings subjected to salt stress (125 mM NaCl) had a significantly higher survival rate and increased shoot and root biomasses than the WT. At the tissue level, quantitative and electron probe microanalyzer studies indicated that “YNU31-2-4” seedlings avoided Na+ accumulation in shoots under salt stress. The “YNU31-2-4” plants showed an improved phenotype with significantly higher net CO2 assimilation and lower yield decline than WT under salt stress at the reproductive stage. “YNU31-2-4” is a potential candidate for a new rice cultivar that is highly tolerant to salt stress at the seedling and reproductive stages, and which might maintain yields under a changing global climate.
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Affiliation(s)
- Md Masud Rana
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
- Agronomy Division, Bangladesh Rice Research Institute, Gazipur-1701, Bangladesh.
| | - Takeshi Takamatsu
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan.
| | - Marouane Baslam
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan.
| | - Kentaro Kaneko
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
| | - Kimiko Itoh
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan.
| | - Naoki Harada
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan.
| | - Toshie Sugiyama
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan.
| | - Takayuki Ohnishi
- Center for Education and Research of Community Collaboration, Utsunomiya University, Utsunomiya 321-8505, Japan.
| | - Tetsu Kinoshita
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan.
| | - Hiroki Takagi
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Ishikawa 921-8836, Japan.
| | - Toshiaki Mitsui
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan.
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Upadhyay AK, Arora S, Pandey DK, Chaudhary B. Interspersed 5'cis-regulatory elements ascertain the spatio-temporal transcription of cytoskeletal profilin gene family in Arabidopsis. Comput Biol Chem 2019; 80:177-186. [PMID: 30974345 DOI: 10.1016/j.compbiolchem.2019.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/23/2019] [Accepted: 03/31/2019] [Indexed: 10/27/2022]
Abstract
Spatio-temporal expression patterns of cytoskeleton-associated profilin (PRF) family proteins in response to varied environmental stimuli are tightly regulated. Functional analyses of PRFs have revealed their crucial roles in varied developmental and stress related traits, but very little is implicit pertaining to cis-acting regulatory elements that regulate such intricate expression patterns. Here, we identified cis-elements with their varying distribution frequencies by scanning 1.5kbp upstream sequences of 5'regulatory regions of PRFs of dicot and monocot plant species. Predicted cis-elements in the regulatory sub-regions of Arabidopsis PRFs (AtPRFs) were predominantly associated with development-responsive motifs (DREs), light responsive elements (LREs), hormonal responsive elements (HREs), core motifs and stress-responsive elements (SREs). Interestingly, DREs, LREs and core promoter motifs, were extensively distributed up to the distal end of 5'regulatory regions on contrary to HREs present closer to the translational start site in Arabidopsis. The evolutionary footprints of predicted orthologous cis-elements were conserved, and preferably located in the proximal regions of 5'regulatory regions of evolutionarily diverged plant species. We also explored comprehensive tissue-specific global gene expression levels of PRFs under diverse hormonal and abiotic stress regimes. In response, the PRFs exhibited large transcriptional biases in a time- and organ-dependent manner. Further, the methodical elucidation of spatial expression analysis of predicted cis-elements binding transcription factors and relevant PRFs showed notable correlation. Results indicate that binding transcription factors' expression data is largely informative for envisaging their precise roles in the spatial regulation of target PRFs. These results highlight the importance of PRFs during plant development; and establish a relationship between their spatial expression patterns and presence of respective regulatory motifs in their promoter sequences. This information could be employed in future studies and field-utilization of cell wall structural genes.
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Affiliation(s)
- Arnav K Upadhyay
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201310, India
| | - Sakshi Arora
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201310, India
| | - Dhananjay K Pandey
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201310, India
| | - Bhupendra Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201310, India.
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Ganie SA, Molla KA, Henry RJ, Bhat KV, Mondal TK. Advances in understanding salt tolerance in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:851-870. [PMID: 30759266 DOI: 10.1007/s00122-019-03301-3308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/02/2019] [Indexed: 05/28/2023]
Abstract
This review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics. Salinity is one of the major constraints in rice cultivation globally. Traditionally, rice is a glycophyte except for a few genotypes that have been widely used in salinity tolerance breeding of rice. Both seedling and reproductive stages of rice are considered to be the salt-susceptible stages; however, research efforts have been biased towards improving the understanding of seedling-stage salt tolerance. An extensive literature survey indicated that there have been very few attempts to develop reproductive stage-specific salt tolerance in rice probably due to the lack of salt-tolerant phenotypes at the reproductive stage. Recently, the role of DNA methylation, genome duplication and codon usage bias in salinity tolerance of rice have been studied. Furthermore, the study of exogenous salt stress alleviants in rice has opened up another potential avenue for understanding and improving its salt tolerance. There is a need to not only generate additional genomic resources in the form of salt-responsive QTLs and molecular markers and to characterize the genes and their upstream regulatory regions, but also to use them to gain deep insights into the mechanisms useful for developing tolerant varieties. We analysed the genomic locations of diverse salt-responsive genomic resources and found that rice chromosomes 1-6 possess the majority of these salinity-responsive genomic resources. The review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics, which should help in understanding the molecular basis of salinity tolerance and its more effective improvement in rice.
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Affiliation(s)
- Showkat Ahmad Ganie
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India
| | - Kutubuddin Ali Molla
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - K V Bhat
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India
| | - Tapan Kumar Mondal
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India.
- ICAR-National Research Centre on Plant Biotechnology, IARI, Pusa, New Delhi, 110012, India.
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Ganie SA, Molla KA, Henry RJ, Bhat KV, Mondal TK. Advances in understanding salt tolerance in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:851-870. [PMID: 30759266 DOI: 10.1007/s00122-019-03301-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/02/2019] [Indexed: 05/03/2023]
Abstract
This review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics. Salinity is one of the major constraints in rice cultivation globally. Traditionally, rice is a glycophyte except for a few genotypes that have been widely used in salinity tolerance breeding of rice. Both seedling and reproductive stages of rice are considered to be the salt-susceptible stages; however, research efforts have been biased towards improving the understanding of seedling-stage salt tolerance. An extensive literature survey indicated that there have been very few attempts to develop reproductive stage-specific salt tolerance in rice probably due to the lack of salt-tolerant phenotypes at the reproductive stage. Recently, the role of DNA methylation, genome duplication and codon usage bias in salinity tolerance of rice have been studied. Furthermore, the study of exogenous salt stress alleviants in rice has opened up another potential avenue for understanding and improving its salt tolerance. There is a need to not only generate additional genomic resources in the form of salt-responsive QTLs and molecular markers and to characterize the genes and their upstream regulatory regions, but also to use them to gain deep insights into the mechanisms useful for developing tolerant varieties. We analysed the genomic locations of diverse salt-responsive genomic resources and found that rice chromosomes 1-6 possess the majority of these salinity-responsive genomic resources. The review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics, which should help in understanding the molecular basis of salinity tolerance and its more effective improvement in rice.
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Affiliation(s)
- Showkat Ahmad Ganie
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India
| | - Kutubuddin Ali Molla
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - K V Bhat
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India
| | - Tapan Kumar Mondal
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India.
- ICAR-National Research Centre on Plant Biotechnology, IARI, Pusa, New Delhi, 110012, India.
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Li J, Gao Z, Zhou L, Li L, Zhang J, Liu Y, Chen H. Comparative transcriptome analysis reveals K + transporter gene contributing to salt tolerance in eggplant. BMC PLANT BIOLOGY 2019; 19:67. [PMID: 30744551 PMCID: PMC6371450 DOI: 10.1186/s12870-019-1663-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/25/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Soil salinization is one of the most crucial abiotic stresses that limit the growth and production of eggplant. The existing researches in eggplant were mostly focused on salt-induced morphological, biochemical and physiological changes, with only limited works centered on salt-response genes in eggplant at the transcriptomic level. RESULTS Our preliminary work found that Zhusiqie (No.118) is salt-tolerant and Hongqie (No.30) is salt-sensitive. Consequently, they were re-named as ST118 and SS30, respectively. ST118 showed less damaged on growth and higher K+/Na+ ratios in leaves than SS30. Comparative-transcriptome analysis was used as a powerful approach to understand the salt-response mechanisms in the leaves and roots of SS30 and ST118. And it revealed that genotype-specific and organ-specific manners exist in eggplant in response to salt stress. Strikingly, the genotype-specific differentially expressed genes (DEGs) in ST118 were considered crucial to its higher salt-tolerance, because the expression patterns of common DEGs in the leaves/roots of the two eggplant genotypes were almost the same. Among them, some transcription factors have been reported to be in response to elevated external salinity, including the members of C2C2-CO-like, WRKY, MYB and NAC family. In addition, the AKT1, KAT1 and SOS1 were up-regulated only in the leaves of ST118. Furthermore, the complementation assays demonstrated that the salt-tolerances of both yeast and Arabidopsis akt1 mutants were enhanced by heterologous expression of SmAKT1. CONCLUSION The comparative-transcriptome analysis indicated that the salt-tolerance can be increased by higher transcript level of some genotype-specific genes. This work revealed that eggplants seem to be more inclined to absorb K+ rather than to exclude Na+ under salt stress conditions because seven K+ transporters were significantly up-regulated, while only one Na+ transporter was similarly regulated. Finally, the complementation assays of SmAKT1, which is genotype-specific up-regulated in ST118, suggest that the other TFs and K+ transport genes were worthy of future investigation for their functions in salinity tolerance.
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Affiliation(s)
- Jing Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Zhen Gao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Lu Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Linzhi Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Junhao Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Yang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
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Lekklar C, Pongpanich M, Suriya-arunroj D, Chinpongpanich A, Tsai H, Comai L, Chadchawan S, Buaboocha T. Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand. BMC Genomics 2019; 20:76. [PMID: 30669971 PMCID: PMC6343365 DOI: 10.1186/s12864-018-5317-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Salt stress, a major plant environmental stress, is a critical constraint for rice productivity. Dissecting the genetic loci controlling salt tolerance in rice for improving productivity, especially at the flowering stage, remains challenging. Here, we conducted a genome-wide association study (GWAS) of salt tolerance based on exome sequencing of the Thai rice accessions. RESULTS Photosynthetic parameters and cell membrane stability under salt stress at the flowering stage; and yield-related traits of 104 Thai rice (Oryza sativa L.) accessions belonging to the indica subspecies were evaluated. The rice accessions were subjected to exome sequencing, resulting in 112,565 single nucleotide polymorphisms (SNPs) called with a minor allele frequency of at least 5%. LD decay analysis of the panel indicates that the average LD for SNPs at 20 kb distance from each other was 0.34 (r2), which decayed to its half value (~ 0.17) at around 80 kb. By GWAS performed using mixed linear model, two hundred loci containing 448 SNPs on exons were identified based on the salt susceptibility index of the net photosynthetic rate at day 6 after salt stress; and the number of panicles, filled grains and unfilled grains per plant. One hundred and forty six genes, which accounted for 73% of the identified loci, co-localized with the previously reported salt quantitative trait loci (QTLs). The top four regions that contained a high number of significant SNPs were found on chromosome 8, 12, 1 and 2. While many are novel, their annotation is consistent with potential involvement in plant salt tolerance and in related agronomic traits. These significant SNPs greatly help narrow down the region within these QTLs where the likely underlying candidate genes can be identified. CONCLUSIONS Insight into the contribution of potential genes controlling salt tolerance from this GWAS provides further understanding of salt tolerance mechanisms of rice at the flowering stage, which can help improve yield productivity under salinity via gene cloning and genomic selection.
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Affiliation(s)
- Chakkree Lekklar
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Duangjai Suriya-arunroj
- Nakhon Ratchasima Rice Research Center, Rice Department, Ministry of Agriculture and Cooperatives, Nakhon Ratchasima, Thailand
| | - Aumnart Chinpongpanich
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Helen Tsai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA USA
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA USA
| | - Supachitra Chadchawan
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Teerapong Buaboocha
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Lectin Sequence Distribution in QTLs from Rice (Oryza sativa) Suggest A Role in Morphological Traits and Stress Responses. Int J Mol Sci 2019; 20:ijms20020437. [PMID: 30669545 PMCID: PMC6359108 DOI: 10.3390/ijms20020437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/11/2022] Open
Abstract
Rice (Oryza sativa) is one of the main staple crops worldwide but suffers from important yield losses due to different abiotic and biotic stresses. Analysis of quantitative trait loci (QTL) is a classical genetic method which enables the creation of more resistant cultivars but does not yield information on the genes directly involved or responsible for the desired traits. Lectins are known as proteins with diverse functions in plants. Some of them are abundant proteins in seeds and are considered as storage/defense proteins while other lectins are known as stress-inducible proteins, implicated in stress perception and signal transduction as part of plant innate immunity. We investigated the distribution of lectin sequences in different QTL related to stress tolerance/resistance, morphology, and physiology through mapping of the lectin sequences and QTL regions on the chromosomes and subsequent statistical analysis. Furthermore, the domain structure and evolutionary relationships of the lectins in O. sativa spp. indica and japonica were investigated. Our results revealed that lectin sequences are statistically overrepresented in QTLs for (a)biotic resistance/tolerance as well as in QTLs related to economically important traits such as eating quality and sterility. These findings contribute to the characterization of the QTL sequences and can provide valuable information to the breeders.
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Kruglova NN, Seldimirova OA, Zinatullina AE. In vitro Callus as a Model System for the Study of Plant Stress-Resistance to Abiotic Factors (on the Example of Cereals). ACTA ACUST UNITED AC 2018. [DOI: 10.1134/s2079086418060063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Chen HC, Cheng WH, Hong CY, Chang YS, Chang MC. The transcription factor OsbHLH035 mediates seed germination and enables seedling recovery from salt stress through ABA-dependent and ABA-independent pathways, respectively. RICE (NEW YORK, N.Y.) 2018; 11:50. [PMID: 30203325 PMCID: PMC6134479 DOI: 10.1186/s12284-018-0244-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/05/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Many transcription factors (TFs), such as those in the basic helix-loop-helix (bHLH) family, are important for regulating plant growth and plant responses to abiotic stress. The expression of OsbHLH035 is induced by drought and salinity. However, its functional role in rice growth, development, and the salt response is still unknown. RESULTS The bHLH TF OsbHLH035 is a salt-induced gene that is primarily expressed in germinating seeds and seedlings. Stable expression of GFP-fused OsbHLH035 in rice transgenic plants revealed that this protein is predominantly localized to the nucleus. Osbhlh035 mutants show delayed seed germination, particularly under salt-stress conditions. In parallel, abscisic acid (ABA) contents are over-accumulated, and the expression of the ABA biosynthetic genes OsABA2 and OsAAO3 is upregulated; furthermore, compared with that in wild-type (WT) seedlings, the salt-induced expression of OsABA8ox1, an ABA catabolic gene, in germinating Osbhlh035 mutant seeds is downregulated. Moreover, Osbhlh035 mutant seedlings are unable to recover from salt-stress treatment. Consistently, sodium is over-accumulated in aerial tissues but slightly reduced in terrestrial tissues from Osbhlh035 seedlings after salt treatment. Additionally, the expression of the sodium transporters OsHKT1;3 and 1;5 is reduced in Osbhlh035 aerial and terrestrial tissues, respectively. Furthermore, genetic complementation can restore both the delayed seed germination and the impaired recovery of salt-treated Osbhlh035 seedlings to normal growth. CONCLUSION OsbHLH035 mediates seed germination and seedling recovery after salt stress relief through the ABA-dependent and ABA-independent activation of OsHKT pathways, respectively.
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Affiliation(s)
- Hung-Chi Chen
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, Taiwan, Republic of China
| | - Wan-Hsing Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Chwan-Yang Hong
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Yu-Sen Chang
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Men-Chi Chang
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, Taiwan, Republic of China.
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Chowrasia S, Panda AK, Rawal HC, Kaur H, Mondal TK. Identification of jumonjiC domain containing gene family among the Oryza species and their expression analysis in FL478, a salt tolerant rice genotype. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:43-53. [PMID: 29960182 DOI: 10.1016/j.plaphy.2018.06.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 05/26/2023]
Abstract
The jumonji (JMJ)-C domain containing proteins belong to histone demethylases family with the ability to demethylate the tri-methylated histone residues. They act as chromatin regulators to regulate many physiological functions in plants. The present study deals with the characterization of JMJ-C gene family members in wild as well as cultivated rice species and their expression analysis in salt tolerant rice genotype, FL478. The genome wide study identified 151 members belonging to JMJ-C gene family in 11 different Oryza species. We also studied their structure, genomic location, gene duplication events, phylogenetic relationship, in silico expression analysis and identified cis elements in their promoters. We also found a few JMJ-C gene family members in rice which underwent duplication before the whole genome duplication event of the rice. The qRT-PCR based expression profiling revealed that out of the total 15 rice JMJ-C members, two were highly expressed in the flag leaf stage of FL478 under salt treatment. These two candidate JMJ-C members were also found to render salinity tolerance when over-expressed in yeast cells. Thus, the present study helps in further structural as well as functional characterization of JMJ-C genes under salinity stress in Oryza species.
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Affiliation(s)
- Soni Chowrasia
- ICAR-National Research Centre on Plant Biotechnology, Lal-Bahadur Shastri Centre, IARI, Pusa, New Delhi, 110012, India
| | - Alok Kumar Panda
- ICAR-National Research Centre on Plant Biotechnology, Lal-Bahadur Shastri Centre, IARI, Pusa, New Delhi, 110012, India
| | - Hukam C Rawal
- ICAR-National Research Centre on Plant Biotechnology, Lal-Bahadur Shastri Centre, IARI, Pusa, New Delhi, 110012, India
| | - Harmeet Kaur
- ICAR-National Research Centre on Plant Biotechnology, Lal-Bahadur Shastri Centre, IARI, Pusa, New Delhi, 110012, India
| | - Tapan Kumar Mondal
- ICAR-National Research Centre on Plant Biotechnology, Lal-Bahadur Shastri Centre, IARI, Pusa, New Delhi, 110012, India.
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Li J, Guo X, Zhang M, Wang X, Zhao Y, Yin Z, Zhang Z, Wang Y, Xiong H, Zhang H, Todorovska E, Li Z. OsERF71 confers drought tolerance via modulating ABA signaling and proline biosynthesis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:131-139. [PMID: 29576066 DOI: 10.1016/j.plantsci.2018.01.017] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 01/19/2018] [Accepted: 01/31/2018] [Indexed: 05/05/2023]
Abstract
Plants have evolved multiple protective strategies to adapt to adverse environmental conditions. Upland rice (UR) has evolved as a "drought-resistant type". However, little is known about genes or mechanisms in UR that underlying drought tolerance at the molecular level. Here we report isolation and functional characterization of the ERF gene, OsERF71, from the UR variety, IRAT109. The expression of OsERF71 was induced by abscisic acid (ABA) and various abiotic stresses preferentially in IRAT109 under ABA, dehydration, and polyethyleneglycol (PEG) treatments. OsERF71 was verified as a nuclear-localized protein and had transcriptional activity in yeast cells. Overexpression of the OsERF71 in Nipponbare demonstrated a significant increase in tolerance to drought stress and a reduced rate of water loss. In contrast, OsERF71 interference lines were sensitive to drought stress and exhibited a higher rate of water loss. OsERF71-overexpressing lines also showed enhanced tolerance to high salinity. Moreover, OsERF71 regulated the expression of several ABA- responsive and proline biosynthesis genes under drought stress, resulting in enhanced sensitivity to exogenous ABA treatment and proline accumulation. Accordingly, we suggest that OsERF71 plays a positive role in drought stress tolerance by increasing the expression of genes associated with ABA signaling and proline biosynthesis under stress.
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Affiliation(s)
- Jinjie Li
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, People's Republic of China
| | - Xiao Guo
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, People's Republic of China
| | - Minghui Zhang
- College of Life Science, Northeast Agricultural University, Harbin, People's Republic of China
| | - Xin Wang
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, People's Republic of China
| | - Yan Zhao
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, People's Republic of China
| | - Zhigang Yin
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, People's Republic of China
| | - Zhanying Zhang
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, People's Republic of China
| | - Yanming Wang
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, People's Republic of China
| | - Haiyan Xiong
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, People's Republic of China
| | - Hongliang Zhang
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, People's Republic of China
| | | | - Zichao Li
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, People's Republic of China.
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Ashoub A, Müller N, Jiménez-Gómez JM, Brüggemann W. Prominent alterations of wild barley leaf transcriptome in response to individual and combined drought acclimation and heat shock conditions. PHYSIOLOGIA PLANTARUM 2018; 163:18-29. [PMID: 29111595 DOI: 10.1111/ppl.12667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/19/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
Under field conditions, drought and heat stress typically happen simultaneously and their negative impact on the agricultural production is expected to increase worldwide under the climate change scenario. In this study, we performed RNA-sequencing analysis on leaves of wild barley (Hordeum spontaneum) originated from the northern coastal region of Egypt following individual drought acclimation (DA) and heat shock (HS) treatments and their combination (CS, combined stresses) to distinguish the unique and shared differentially expressed genes (DEG). Results indicated that the number of unique genes that were differentially expressed following HS treatment exceeded the number of those expressed following DA. In addition, the number of genes that were uniquely differentially expressed in response to CS treatment exceeded the number of those of shared responses to individual DA and HS treatments. These results indicate a better adaptation of the Mediterranean wild barley to drought conditions when compared with heat stress. It also manifests that the wild barley response to CS tends to be unique rather than common. Annotation of DEG showed that metabolic processes were the most influenced biological function in response to the applied stresses.
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Affiliation(s)
- Ahmed Ashoub
- Institute of Ecology, Evolution, and Diversity, Johann Wolfgang Goethe-University Frankfurt, Frankfurt am Main, Germany
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Niels Müller
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - José M Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Wolfgang Brüggemann
- Institute of Ecology, Evolution, and Diversity, Johann Wolfgang Goethe-University Frankfurt, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
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