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Ritonga FN, Gong Z, Zhang Y, Wang F, Gao J, Li C, Li J. Exploiting Brassica rapa L. subsp. pekinensis Genome Research. PLANTS (BASEL, SWITZERLAND) 2024; 13:2823. [PMID: 39409693 PMCID: PMC11478547 DOI: 10.3390/plants13192823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 10/01/2024] [Accepted: 10/02/2024] [Indexed: 10/20/2024]
Abstract
Chinese cabbage, Brassica rapa L. subsp. pekinensis is a crucial and extensively consumed vegetable in the world, especially Eastern Asia. The market demand for this leafy vegetable increases year by year, resulting in multiple challenges for agricultural researchers worldwide. Multi-omic approaches and the integration of functional genomics helps us understand the relationships between Chinese cabbage genomes and phenotypes under specific physiological and environmental conditions. However, challenges exist in integrating multi-omics for the functional analysis of genes and for developing potential traits for Chinese cabbage improvement. However, the panomics platform allows for the integration of complex omics, enhancing our understanding of molecular regulator networks in Chinese cabbage agricultural traits. In addition, the agronomic features of Chinese cabbage are significantly impacted by the environment. The expression of these agricultural features is tightly regulated by a combination of signals from both the internal regulatory network and the external growth environment. To comprehend the molecular process of these characteristics, it is necessary to have a prior understanding of molecular breeding for the objective of enhancing quality. While the use of various approaches in Chinese cabbage is still in its early stages, recent research has shown that it has the potential to uncover new regulators both rapidly and effectively, leading to updated regulatory networks. In addition, the utilization of the efficient transformation technique in conjunction with gene editing using CRISPR/Cas9 will result in a reduction in time requirements and facilitate a more precise understanding of the role of the regulators. Numerous studies about Chinese cabbage have been conducted in the past two decades, but a comprehensive review about its genome still limited. This review provides a concise summary of the latest discoveries in genomic research related to Brassica and explores the potential future developments for this species.
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Affiliation(s)
- Faujiah Nurhasanah Ritonga
- Shandong Key Laboratory of Bulk Open-field Vegetable Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Huang Huai Protected Horticulture Engineering, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (F.N.R.); (Y.Z.); (F.W.); (J.G.)
- Faculty of Forestry, Universitas Sumatera Utara, USU 2 Bekala Campus, Pancurbatu, Deli Serdang 20355, Indonesia
| | - Zeyu Gong
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan 250358, China;
| | - Yihui Zhang
- Shandong Key Laboratory of Bulk Open-field Vegetable Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Huang Huai Protected Horticulture Engineering, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (F.N.R.); (Y.Z.); (F.W.); (J.G.)
| | - Fengde Wang
- Shandong Key Laboratory of Bulk Open-field Vegetable Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Huang Huai Protected Horticulture Engineering, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (F.N.R.); (Y.Z.); (F.W.); (J.G.)
| | - Jianwei Gao
- Shandong Key Laboratory of Bulk Open-field Vegetable Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Huang Huai Protected Horticulture Engineering, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (F.N.R.); (Y.Z.); (F.W.); (J.G.)
| | - Cheng Li
- Shandong Key Laboratory of Bulk Open-field Vegetable Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Huang Huai Protected Horticulture Engineering, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (F.N.R.); (Y.Z.); (F.W.); (J.G.)
| | - Jingjuan Li
- Shandong Key Laboratory of Bulk Open-field Vegetable Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Huang Huai Protected Horticulture Engineering, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (F.N.R.); (Y.Z.); (F.W.); (J.G.)
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Nikhil PT, Faiz U, Sharma R, Mohapatra S. Modulation of plant polyamine and ethylene biosynthesis; and brassinosteroid signaling during Bacillus endophyticus J13-mediated salinity tolerance in Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2024; 301:154304. [PMID: 38991234 DOI: 10.1016/j.jplph.2024.154304] [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: 12/04/2023] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
Abstract
Salinity stress adversely impacts plant growth and development. Plant growth-promoting rhizobacteria (PGPR) are known to confer salinity stress tolerance in plants through several mechanisms. Here, we report the role of an abiotic stress-tolerant PGPR strain, Bacillus endophyticus J13, in promoting salinity stress tolerance in Arabidopsis thaliana, by elucidating its impact on physiological responses, polyamine (PA) and ethylene biosynthesis, and brassinosteroid signaling. Physiological analysis revealed that J13 can significantly improve the overall plant growth under salt stress by increasing the biomass, relative water content, and chlorophyll content, decreasing membrane damage and lipid peroxidation, and modulating proline homeostasis in plants. Evaluation of shoot polyamine levels upon J13 inoculation revealed an overall decrease in the levels of the three major PAs, putrescine (Put), spermidine (Spd), and spermine (Spm), under non-stressed conditions. Salt stress significantly increased the levels of Put and Spm, while decreasing the Spd levels in the plants. J13 inoculation under salt-stressed conditions, significantly decreased the Put levels, bringing them closer to those of the untreated control plants, whereas Spd and Spm levels did not change relative to the non-inoculated salt-stressed plants. The modulation of PA levels was accompanied by changes in the expressions of key PA biosynthetic genes under all treatments. Among the ethylene biosynthetic genes that we studied, ACS1 was induced by J13 inoculation under salt stress. J13 inoculation under salt stress resulted in the modulation of the expressions of BR-signaling genes, upregulating the expressions of the positive regulators of BR-signaling (BZR1 and BES2) and downregulating that of the negative regulator (BIN2). Our results provide a new avenue for J13-mediated salt stress amelioration in Arabidopsis, via tight control of polyamine and ethylene biosynthesis and enhanced brassinosteroid signaling.
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Affiliation(s)
- P T Nikhil
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, India
| | - Umema Faiz
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, India
| | - Raunak Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, India
| | - Sridev Mohapatra
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
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Sun H, Li C, Li S, Ma J, Li S, Li X, Gao C, Yang R, Ma N, Yang J, Yang P, He X, Hu T. Identification and validation of stable reference genes for RT-qPCR analyses of Kobresia littledalei seedlings. BMC PLANT BIOLOGY 2024; 24:389. [PMID: 38730341 PMCID: PMC11088182 DOI: 10.1186/s12870-024-04924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 03/18/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Kobreisa littledalei, belonging to the Cyperaceae family is the first Kobresia species with a reference genome and the most dominant species in Qinghai-Tibet Plateau alpine meadows. It has several resistance genes which could be used to breed improved crop varieties. Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) is a popular and accurate gene expression analysis method. Its reliability depends on the expression levels of reference genes, which vary by species, tissues and environments. However, K.littledalei lacks a stable and normalized reference gene for RT-qPCR analysis. RESULTS The stability of 13 potential reference genes was tested and the stable reference genes were selected for RT-qPCR normalization for the expression analysis in the different tissues of K. littledalei under two abiotic stresses (salt and drought) and two hormonal treatments (abscisic acid (ABA) and gibberellin (GA)). Five algorithms were used to assess the stability of putative reference genes. The results showed a variation amongst the methods, and the same reference genes showed tissue expression differences under the same conditions. The stability of combining two reference genes was better than a single one. The expression levels of ACTIN were stable in leaves and stems under normal conditions, in leaves under drought stress and in roots under ABA treatment. The expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression was stable in the roots under the control conditions and salt stress and in stems exposed to drought stress. Expression levels of superoxide dismutase (SOD) were stable in stems of ABA-treated plants and in the roots under drought stress. Moreover, RPL6 expression was stable in the leaves and stems under salt stress and in the stems of the GA-treated plants. EF1-alpha expression was stable in leaves under ABA and GA treatments. The expression levels of 28 S were stable in the roots under GA treatment. In general, ACTIN and GAPDH could be employed as housekeeping genes for K. littledalei under different treatments. CONCLUSION This study identified the best RT-qPCR reference genes for different K. littledalei tissues under five experimental conditions. ACTIN and GAPDH genes can be employed as the ideal housekeeping genes for expression analysis under different conditions. This is the first study to investigate the stable reference genes for normalized gene expression analysis of K. littledalei under different conditions. The results could aid molecular biology and gene function research on Kobresia and other related species.
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Affiliation(s)
- Haoyang Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Chunping Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Siyu Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jiaxin Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Shuo Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xin Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Cai Gao
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Rongchen Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Nan Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jing Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xueqing He
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
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Li C, Wang L, Su J, Li W, Tang Y, Zhao N, Lou L, Ou X, Jia D, Jiang J, Chen S, Chen F. A group VIIIa ethylene-responsive factor, CmERF4, negatively regulates waterlogging tolerance in chrysanthemum. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1479-1492. [PMID: 37952115 DOI: 10.1093/jxb/erad451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
Ethylene-responsive factors (ERF) play an important role in plant responses to waterlogging stress. However, the function and mechanism of action of ERFVIII in response to waterlogging stress remain poorly understood. In this study, we found that expression of the ERF VIIIa gene CmERF4 in chrysanthemum was induced by waterlogging stress. CmERF4 localized to the nucleus when expressed in tobacco leaves. Yeast two-hybrid and luciferase assays showed that CmERF4 is a transcriptional inhibitor. CmERF4 overexpression in chrysanthemum reduced plant waterlogging tolerance, whereas overexpression of the chimeric activator CmERF4-VP64 reversed its transcriptional activity, promoting higher waterlogging tolerance than that observed in wild-type plants, indicating that CmERF4 negatively regulates waterlogging tolerance. Transcriptome profiling showed that energy metabolism and reactive oxygen species (ROS) pathway-associated genes were differentially expressed between CmERF4-VP64 and wild-type plants. RT-qPCR analysis of selected energy metabolism and reactive oxygen species-related genes showed that the gene expression patterns were consistent with the expression levels obtained from RNA-seq analysis. Overall, we identified new functions of CmERF4 in negatively regulating chrysanthemum waterlogging tolerance by modulating energy metabolism and ROS pathway genes.
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Affiliation(s)
- Chuanwei Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Likai Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Jiangshuo Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Wenjie Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yun Tang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Nan Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - La Lou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xiaoli Ou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Diwen Jia
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration. College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
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Limbalkar OM, Vasisth P, Singh G, Jain P, Sharma M, Singh R, Dhanasekaran G, Kumar M, Meena ML, Iquebal MA, Jaiswal S, Rao M, Watts A, Bhattacharya R, Singh KH, Kumar D, Singh N. Dissection of QTLs conferring drought tolerance in B. carinata derived B. juncea introgression lines. BMC PLANT BIOLOGY 2023; 23:664. [PMID: 38129793 PMCID: PMC10740311 DOI: 10.1186/s12870-023-04614-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Drought is one of the important abiotic stresses that can significantly reduce crop yields. In India, about 24% of Brassica juncea (Indian mustard) cultivation is taken up under rainfed conditions, leading to low yields due to moisture deficit stress. Hence, there is an urgent need to improve the productivity of mustard under drought conditions. In the present study, a set of 87 B. carinata-derived B. juncea introgression lines (ILs) was developed with the goal of creating drought-tolerant genotypes. METHOD The experiment followed the augmented randomized complete block design with four blocks and three checks. ILs were evaluated for seed yield and its contributing traits under both rainfed and irrigated conditions in three different environments created by manipulating locations and years. To identify novel genes and alleles imparting drought tolerance, Quantitative Trait Loci (QTL) analysis was carried out. Genotyping-by-Sequencing (GBS) approach was used to construct the linkage map. RESULTS The linkage map consisted of 5,165 SNP markers distributed across 18 chromosomes and spanning a distance of 1,671.87 cM. On average, there was a 3.09 cM gap between adjoining markers. A total of 29 additive QTLs were identified for drought tolerance; among these, 17 (58.6% of total QTLs detected) were contributed by B. carinata (BC 4), suggesting a greater contribution of B. carinata towards improving drought tolerance in the ILs. Out of 17 QTLs, 11 (64.7%) were located on the B genome, indicating more introgression segments on the B genome of B. juncea. Eight QTL hotspots, containing two or more QTLs, governing seed yield contributing traits, water use efficiency, and drought tolerance under moisture deficit stress conditions were identified. Seventeen candidate genes related to biotic and abiotic stresses, viz., SOS2, SOS2 like, NPR1, FAE1-KCS, HOT5, DNAJA1, NIA1, BRI1, RF21, ycf2, WRKY33, PAL, SAMS2, orf147, MAPK3, WRR1 and SUS, were reported in the genomic regions of identified QTLs. CONCLUSIONS The significance of B. carinata in improving drought tolerance and WUE by introducing genomic segments in Indian mustard is well demonstrated. The findings also provide valuable insights into the genetic basis of drought tolerance in mustard and pave the way for the development of drought-tolerant varieties.
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Affiliation(s)
- Omkar Maharudra Limbalkar
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- Present Address: ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - Prashant Vasisth
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Guman Singh
- ICAR-Directorate of Rapeseed-Mustard Research, Sewar, Bharatpur, Rajasthan, India
| | - Priyanka Jain
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- Present Address: AIMMSCR, Amity University Uttar Pradesh, Sector 125, Noida, Uttar Pradesh, 201313, India
| | - Mohit Sharma
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Rajendra Singh
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gokulan Dhanasekaran
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Manish Kumar
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- Present Address: College of Agriculture, Navgaon, Alwar, Sri Karan Narendra Agriculture University, Jobner, Rajasthan, India
| | - Mohan Lal Meena
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mahesh Rao
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Anshul Watts
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Kunwar Harendra Singh
- ICAR-Directorate of Rapeseed-Mustard Research, Sewar, Bharatpur, Rajasthan, India
- Present Address: ICAR, Indian Institute of Soybean Research, Indore, Madhya Pradesh, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Naveen Singh
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India.
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Wirojsirasak W, Songsri P, Jongrungklang N, Tangphatsornruang S, Klomsa-ard P, Ukoskit K. A Large-Scale Candidate-Gene Association Mapping for Drought Tolerance and Agronomic Traits in Sugarcane. Int J Mol Sci 2023; 24:12801. [PMID: 37628982 PMCID: PMC10454574 DOI: 10.3390/ijms241612801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Dissection of the genetic loci controlling drought tolerance traits with a complex genetic inheritance is important for drought-tolerant sugarcane improvement. In this study, we conducted a large-scale candidate gene association study of 649 candidate genes in a sugarcane diversity panel to identify genetic variants underlying agronomic traits and drought tolerance indices evaluated in plant cane and ratoon cane under water-stressed (WS) and non-stressed (NS) environments. We identified 197 significant marker-trait associations (MTAs) in 141 candidate genes associated with 18 evaluated traits with the Bonferroni correction threshold (α = 0.05). Out of the total, 95 MTAs in 78 candidate genes and 62 MTAs in 58 candidate genes were detected under NS and WS conditions, respectively. Most MTAs were found only in specific water regimes and crop seasons. These MTAs explained 7.93-30.52% of phenotypic variation. Association mapping results revealed that 34, 59, and 104 MTAs involved physiological and molecular adaptation, phytohormone metabolism, and drought-inducible genes. They identified 19 pleiotropic genes associated with more than one trait and many genes related to drought tolerance indices. The genetic and genomic resources identified in this study will enable the combining of yield-related traits and sugar-related traits with agronomic value to optimize the yield of sugarcane cultivars grown under drought-stressed and non-stressed environments.
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Affiliation(s)
- Warodom Wirojsirasak
- Department of Biotechnology, Faculty of Science and Technology, Rangsit Campus, Thammasat University, Pathum Thani 12120, Thailand;
- Mitr Phol Innovation and Research Center, Chaiyaphum 36110, Thailand;
| | - Patcharin Songsri
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (P.S.); (N.J.)
- Northeast Thailand Cane and Sugar Research Center, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Nakorn Jongrungklang
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (P.S.); (N.J.)
- Northeast Thailand Cane and Sugar Research Center, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | | | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Rangsit Campus, Thammasat University, Pathum Thani 12120, Thailand;
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Kajla M, Roy A, Singh IK, Singh A. Regulation of the regulators: Transcription factors controlling biosynthesis of plant secondary metabolites during biotic stresses and their regulation by miRNAs. FRONTIERS IN PLANT SCIENCE 2023; 14:1126567. [PMID: 36938003 PMCID: PMC10017880 DOI: 10.3389/fpls.2023.1126567] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Biotic stresses threaten to destabilize global food security and cause major losses to crop yield worldwide. In response to pest and pathogen attacks, plants trigger many adaptive cellular, morphological, physiological, and metabolic changes. One of the crucial stress-induced adaptive responses is the synthesis and accumulation of plant secondary metabolites (PSMs). PSMs mitigate the adverse effects of stress by maintaining the normal physiological and metabolic functioning of the plants, thereby providing stress tolerance. This differential production of PSMs is tightly orchestrated by master regulatory elements, Transcription factors (TFs) express differentially or undergo transcriptional and translational modifications during stress conditions and influence the production of PSMs. Amongst others, microRNAs, a class of small, non-coding RNA molecules that regulate gene expression post-transcriptionally, also play a vital role in controlling the expression of many such TFs. The present review summarizes the role of stress-inducible TFs in synthesizing and accumulating secondary metabolites and also highlights how miRNAs fine-tune the differential expression of various stress-responsive transcription factors during biotic stress.
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Affiliation(s)
- Mohini Kajla
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Amit Roy
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Indrakant K. Singh
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Jagdish Chandra Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India
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8
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Ferreira-Neto JRC, de Araújo FC, de Oliveira Silva RL, de Melo NF, Pandolfi V, Frosi G, de Lima Morais DA, da Silva MD, Rivas R, Santos MG, de Tarso Aidar S, Morgante CV, Benko-Iseppon AM. Dehydration response in Stylosanthes scabra: Transcriptional, biochemical, and physiological modulations. PHYSIOLOGIA PLANTARUM 2022; 174:e13821. [PMID: 36345266 DOI: 10.1111/ppl.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Stylosanthes scabra, popularly known as stylo, is native to the Brazilian Caatinga semiarid region and stands out as a drought-tolerant shrub forage crop. This work provides information about the plant response during the first 48 h of water deficit, followed by a rehydration treatment. Besides root transcriptomics data, 13 physiological or biochemical parameters were scrutinized. Additionally, RNA-Seq annotated transcripts not associated with the "Viridiplantae" clade were taxonomically categorized. It was found that S. scabra quickly perceives and recovers from the oscillations of the imposed water regime. Physiologically, mechanisms that minimize evapotranspiration or protect the photosynthetic apparatus stood out. Biochemically, it was found that the root tissue invests in synthesizing compounds that can act as osmolytes (proline and sugars), emphasizing the importance of osmoregulation to water deficit acclimation. Consistently, transcriptome and qPCR analyses showed that a set of enriched biological processes with upregulated (UR) transcripts were involved in protective functions against reactive oxygen species or encoding enzymes of important metabolic pathways, which might contribute to S. scabra response to water deficit. Additionally, several UR kinases and transcription factors were identified. Finally, in an innovative approach, some naturally occurring microbial groups (such as Schizosaccharomyces, Bradyrhizobium, etc.) were identified in the S. scabra roots. This study reveals insights into the physiological, biochemical, and molecular mechanisms underlying the S. scabra response to water deficit and provides candidate genes that may be useful in developing drought-tolerant crop varieties through biotechnological applications.
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Affiliation(s)
- José Ribamar Costa Ferreira-Neto
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Flávia Czekalski de Araújo
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Roberta Lane de Oliveira Silva
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | | | - Valesca Pandolfi
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Gabriella Frosi
- Départament de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Manassés Daniel da Silva
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Rebeca Rivas
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Mauro Guida Santos
- Laboratório de Fisiologia Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Saulo de Tarso Aidar
- Empresa Brasileira de Pesquisa Agropecuária (SEMIÁRIDO), Petrolina, Pernambuco, Brazil
| | | | - Ana Maria Benko-Iseppon
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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9
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Wei N, Zhai Q, Li H, Zheng S, Zhang J, Liu W. Genome-Wide Identification of ERF Transcription Factor Family and Functional Analysis of the Drought Stress-Responsive Genes in Melilotus albus. Int J Mol Sci 2022; 23:ijms231912023. [PMID: 36233332 PMCID: PMC9570465 DOI: 10.3390/ijms231912023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
As an important forage legume with high values in feed and medicine, Melilotus albus has been widely cultivated. The AP2/ERF transcription factor has been shown to play an important regulatory role in plant drought resistance, but it has not been reported in the legume forage crop M. albus. To digger the genes of M. albus in response to drought stress, we identified and analyzed the ERF gene family of M. albus at the genome-wide level. A total of 100 MaERF genes containing a single AP2 domain sequence were identified in this study, named MaERF001 to MaERF100, and bioinformatics analysis was performed. Collinearity analysis indicated that segmental duplication may play a key role in the expansion of the M. albus ERF gene family. Cis-acting element predictions suggest that MaERF genes are involved in various hormonal responses and abiotic stresses. The expression patterns indicated that MaERFs responded to drought stress to varying degrees. Furthermore, four up-regulated ERFs (MaERF008, MaERF037, MaERF054 and MaERF058) under drought stress were overexpressed in yeast and indicated their biological functions to confer the tolerance to drought. This work will advance the understanding of the molecular mechanisms underlying the drought response in M. albus. Further study of the promising potential candidate genes identified in this study will provide a valuable resource as the next step in functional genomics studies and improve the possibility of improving drought tolerance in M. albus by transgenic approaches.
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10
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Zhang K, Lan Y, Wu M, Wang L, Liu H, Xiang Y. PhePLATZ1, a PLATZ transcription factor in moso bamboo (Phyllostachys edulis), improves drought resistance of transgenic Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 186:121-134. [PMID: 35835078 DOI: 10.1016/j.plaphy.2022.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/20/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Drought is one of the most serious environmental stresses. Plant AT-rich sequence and zinc-binding (PLATZ) proteins perform indispensable functions to regulate plant growth and development and to respond to environmental stress. In this present study, we identified PhePLATZ1 in moso bamboo and found that its expression was up-regulated in response to 20% PEG-6000 and abscisic acid (ABA) treatments. Next, transgenic PhePLATZ1-overexpressing Arabidopsis lines were generated. Overexpression of PhePLATZ1 improved drought stress resistance of transgenic plants by mediating osmotic regulation, enhancing water retention capacity and reducing membrane and oxidative damage. These findings were corroborated by analysing physiological indicators including chlorophyll, relative water content, leaf water loss rate, electrolyte leakage, H2O2, proline, malondialdehyde content and the enzyme activities of peroxidase and catalase. Subsequent seed germination and seedling root length experiments that included exposure to exogenous ABA treatments showed that ABA sensitivity decreased in transgenic plants relative to wild-type plants. Moreover, transgenic PhePLATZ1-overexpressing plants promoted stomatal closure in response to ABA treatment, suggesting that PhePLATZ1 might play a positive regulatory role in the drought resistance of plants via the ABA signaling pathway. In addition, the transgenic PhePLATZ1-OE plants showed altered expression of some stress-related genes when grown under drought conditions. Taken together, these findings improve our understanding of the drought response of moso bamboo and provide a key candidate gene for the molecular breeding of this species for drought tolerance.
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Affiliation(s)
- Kaimei Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Yangang Lan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Linna Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Hongxia Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
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11
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Zhang L, Zhang R, Ye X, Zheng X, Tan B, Wang W, Li Z, Li J, Cheng J, Feng J. Overexpressing VvWRKY18 from grapevine reduces the drought tolerance in Arabidopsis by increasing leaf stomatal density. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153741. [PMID: 35690029 DOI: 10.1016/j.jplph.2022.153741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 05/22/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
The growth of grapevine [Vitis vinifera L.] is commonly limited by drought stress. The mechanisms by which grapevine copes with drought stress have not yet been extensively clarified. In this study, the drought and abscisic acid (ABA)-induced gene VvWRKY18 was demonstrated to decreased drought tolerance of Arabidopsis thaliana overexpression (VvWRKY18-OE) lines. Compared to wild-type plants, VvWRKY18-OE lines showed increased levels of malonaldehyde (MDA) and the reactive oxygen species (ROS) H2O2 and O2- decreased levels of proline, weakened activity of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and decreased sensitivity to ABA with respect to stomatal closure.VvWRKY18-OE lines also showed an increase in stomatal density and a higher water loss rate. Negative regulators of stomatal development including SDD1, YDA, TMM, and MPK6, were downregulated in VvWRKY18-OE lines. Transcript levels of the stress-related genes DREB1A and CBF2 were significantly reduced in VvWRKY18-OE lines under drought stress. Taken together, these findings demonstrate that VvWRKY18 reduced drought tolerance in Arabidopsis. Our results contribute to understanding of the roles that WRKY genes play in drought stress and stomatal development.
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Affiliation(s)
- Langlang Zhang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Rui Zhang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Xia Ye
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Bin Tan
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Wei Wang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Zhiqian Li
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Jidong Li
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Jun Cheng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China.
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China.
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12
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Li L, Li X, Yang C, Cheng Y, Cai Z, Nian H, Ma Q. GsERF1 enhances Arabidopsis thaliana aluminum tolerance through an ethylene-mediated pathway. BMC PLANT BIOLOGY 2022; 22:258. [PMID: 35610574 PMCID: PMC9128276 DOI: 10.1186/s12870-022-03625-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 05/04/2022] [Indexed: 05/09/2023]
Abstract
Ethylene response factor (ERF) transcription factors constitute a subfamily of the AP2/ERF superfamily in plants and play multiple roles in plant growth and development as well as in stress responses. In this study, the GsERF1 gene from the wild soybean BW69 line (an Al-resistant Glycine soja line) was rapidly induced in response to aluminum stress. Quantitative real-time PCR (qRT-PCR) analysis showed that the GsERF1 gene maintained a constitutive expression pattern and was induced in soybean in response to aluminum stress, with increased amounts of transcripts detected in the roots. The putative GsERF1 protein, which contains an AP2 domain, was located in the nucleus and maintained transactivation activity. In addition, under AlCl3 treatment, GsERF1 overexpression increased the relative growth rate of the roots of Arabidopsis and weakened the hematoxylin staining of hairy roots. Ethylene synthesis-related genes such as ACS4, ACS5 and ACS6 were upregulated in GsERF1 transgenic lines compared with the wild type under AlCl3 treatment. Furthermore, the expression levels of stress/ABA-responsive marker genes, including ABI1, ABI2, ABI4, ABI5 and RD29B, in the GsERF1 transgenic lines were affected by AlCl3 treatment, unlike those in the wild type. Taken together, the results indicated that overexpression of GsERF1 may enhance aluminum tolerance of Arabidopsis through an ethylene-mediated pathway and/or ABA signaling pathway, the findings of which lay a foundation for breeding soybean plants tolerant to aluminum stress.
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Grants
- 2016ZX08004002-007 the Major Project of New Varieties Cultivation of Genetically Modified Organisms
- 2016ZX08004002-007 the Major Project of New Varieties Cultivation of Genetically Modified Organisms
- 2016ZX08004002-007 the Major Project of New Varieties Cultivation of Genetically Modified Organisms
- 2016ZX08004002-007 the Major Project of New Varieties Cultivation of Genetically Modified Organisms
- 2016ZX08004002-007 the Major Project of New Varieties Cultivation of Genetically Modified Organisms
- 2016ZX08004002-007 the Major Project of New Varieties Cultivation of Genetically Modified Organisms
- 2016ZX08004002-007 the Major Project of New Varieties Cultivation of Genetically Modified Organisms
- 31771816, 31971965 the National Natural Science Foundation of China
- 31771816, 31971965 the National Natural Science Foundation of China
- 31771816, 31971965 the National Natural Science Foundation of China
- 31771816, 31971965 the National Natural Science Foundation of China
- 31771816, 31971965 the National Natural Science Foundation of China
- 31771816, 31971965 the National Natural Science Foundation of China
- 31771816, 31971965 the National Natural Science Foundation of China
- 4100-C17106, 21301091702101 the Special Supervision on Quality and Safety of Agricultural Products of the Ministry of Agriculture and Rural Areas
- 4100-C17106, 21301091702101 the Special Supervision on Quality and Safety of Agricultural Products of the Ministry of Agriculture and Rural Areas
- 4100-C17106, 21301091702101 the Special Supervision on Quality and Safety of Agricultural Products of the Ministry of Agriculture and Rural Areas
- 4100-C17106, 21301091702101 the Special Supervision on Quality and Safety of Agricultural Products of the Ministry of Agriculture and Rural Areas
- 4100-C17106, 21301091702101 the Special Supervision on Quality and Safety of Agricultural Products of the Ministry of Agriculture and Rural Areas
- 4100-C17106, 21301091702101 the Special Supervision on Quality and Safety of Agricultural Products of the Ministry of Agriculture and Rural Areas
- 4100-C17106, 21301091702101 the Special Supervision on Quality and Safety of Agricultural Products of the Ministry of Agriculture and Rural Areas
- 2018YFE0116900 the Key Projects of International Scientific and Technological Innovation Cooperation among Governments under National Key R & D Plan
- 2018YFE0116900 the Key Projects of International Scientific and Technological Innovation Cooperation among Governments under National Key R & D Plan
- 2018YFE0116900 the Key Projects of International Scientific and Technological Innovation Cooperation among Governments under National Key R & D Plan
- 2018YFE0116900 the Key Projects of International Scientific and Technological Innovation Cooperation among Governments under National Key R & D Plan
- 2018YFE0116900 the Key Projects of International Scientific and Technological Innovation Cooperation among Governments under National Key R & D Plan
- 2018YFE0116900 the Key Projects of International Scientific and Technological Innovation Cooperation among Governments under National Key R & D Plan
- 2018YFE0116900 the Key Projects of International Scientific and Technological Innovation Cooperation among Governments under National Key R & D Plan
- CARS-04-PS09 the China Agricultural Research System
- CARS-04-PS09 the China Agricultural Research System
- CARS-04-PS09 the China Agricultural Research System
- CARS-04-PS09 the China Agricultural Research System
- CARS-04-PS09 the China Agricultural Research System
- CARS-04-PS09 the China Agricultural Research System
- CARS-04-PS09 the China Agricultural Research System
- 2020B020220008 the Key-Area Research and Development Program of Guangdong Province
- 2020B020220008 the Key-Area Research and Development Program of Guangdong Province
- 2020B020220008 the Key-Area Research and Development Program of Guangdong Province
- 2020B020220008 the Key-Area Research and Development Program of Guangdong Province
- 2020B020220008 the Key-Area Research and Development Program of Guangdong Province
- 2020B020220008 the Key-Area Research and Development Program of Guangdong Province
- 2020B020220008 the Key-Area Research and Development Program of Guangdong Province
- 201804020015 the Project of Science and Technology of Guangzhou
- 201804020015 the Project of Science and Technology of Guangzhou
- 201804020015 the Project of Science and Technology of Guangzhou
- 201804020015 the Project of Science and Technology of Guangzhou
- 201804020015 the Project of Science and Technology of Guangzhou
- 201804020015 the Project of Science and Technology of Guangzhou
- 201804020015 the Project of Science and Technology of Guangzhou
- the Key Projects of International Scientific and Technological Innovation Cooperation among Governments under National Key R & D Plan
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Affiliation(s)
- Lu Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Zengcheng Teaching and Research Base, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Xingang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Zengcheng Teaching and Research Base, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Ce Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Zengcheng Teaching and Research Base, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Yanbo Cheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Zengcheng Teaching and Research Base, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Zhandong Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Zengcheng Teaching and Research Base, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Hai Nian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Zengcheng Teaching and Research Base, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
| | - Qibin Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Zengcheng Teaching and Research Base, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
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13
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Transcriptome and Physiological Analyses of a Navel Orange Mutant with Improved Drought Tolerance and Water Use Efficiency Caused by Increases of Cuticular Wax Accumulation and ROS Scavenging Capacity. Int J Mol Sci 2022; 23:ijms23105660. [PMID: 35628469 PMCID: PMC9145189 DOI: 10.3390/ijms23105660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 02/07/2023] Open
Abstract
Drought is one of the main abiotic stresses limiting the quality and yield of citrus. Cuticular waxes play an important role in regulating plant drought tolerance and water use efficiency (WUE). However, the contribution of cuticular waxes to drought tolerance, WUE and the underlying molecular mechanism is still largely unknown in citrus. 'Longhuihong' (MT) is a bud mutant of 'Newhall' navel orange with curly and bright leaves. In this study, significant increases in the amounts of total waxes and aliphatic wax compounds, including n-alkanes, n-primary alcohols and n-aldehydes, were overserved in MT leaves, which led to the decrease in cuticular permeability and finally resulted in the improvements in drought tolerance and WUE. Compared to WT leaves, MT leaves possessed much lower contents of malondialdehyde (MDA) and hydrogen peroxide (H2O2), significantly higher levels of proline and soluble sugar, and enhanced superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) activities under drought stress, which might reduce reactive oxygen species (ROS) damage, improve osmotic regulation and cell membrane stability, and finally, enhance MT tolerance to drought stress. Transcriptome sequencing results showed that seven structural genes were involved in wax biosynthesis and export, MAPK cascade, and ROS scavenging, and seven genes encoding transcription factors might play an important role in promoting cuticular wax accumulation, improving drought tolerance and WUE in MT plants. Our results not only confirmed the important role of cuticular waxes in regulating citrus drought resistance and WUE but also provided various candidate genes for improving citrus drought tolerance and WUE.
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14
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Zhang Q, Dai X, Wang H, Wang F, Tang D, Jiang C, Zhang X, Guo W, Lei Y, Ma C, Zhang H, Li P, Zhao Y, Wang Z. Transcriptomic Profiling Provides Molecular Insights Into Hydrogen Peroxide-Enhanced Arabidopsis Growth and Its Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:866063. [PMID: 35463436 PMCID: PMC9019583 DOI: 10.3389/fpls.2022.866063] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/28/2022] [Indexed: 05/05/2023]
Abstract
Salt stress is an important environmental factor limiting plant growth and crop production. Plant adaptation to salt stress can be improved by chemical pretreatment. This study aims to identify whether hydrogen peroxide (H2O2) pretreatment of seedlings affects the stress tolerance of Arabidopsis thaliana seedlings. The results show that pretreatment with H2O2 at appropriate concentrations enhances the salt tolerance ability of Arabidopsis seedlings, as revealed by lower Na+ levels, greater K+ levels, and improved K+/Na+ ratios in leaves. Furthermore, H2O2 pretreatment improves the membrane properties by reducing the relative membrane permeability (RMP) and malonaldehyde (MDA) content in addition to improving the activities of antioxidant enzymes, including superoxide dismutase, and glutathione peroxidase. Our transcription data show that exogenous H2O2 pretreatment leads to the induced expression of cell cycle, redox regulation, and cell wall organization-related genes in Arabidopsis, which may accelerate cell proliferation, enhance tolerance to osmotic stress, maintain the redox balance, and remodel the cell walls of plants in subsequent high-salt environments.
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Affiliation(s)
- Qikun Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiuru Dai
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai’an, China
| | - Huanpeng Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Fanhua Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Dongxue Tang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Chunyun Jiang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
- Linyi Center for Disease Control and Prevention, Linyi, China
| | - Xiaoyan Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Wenjing Guo
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yuanyuan Lei
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Changle Ma
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Hui Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Pinghua Li
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai’an, China
| | - Yanxiu Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zenglan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
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Abideen Z, Hanif M, Munir N, Nielsen BL. Impact of Nanomaterials on the Regulation of Gene Expression and Metabolomics of Plants under Salt Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050691. [PMID: 35270161 PMCID: PMC8912827 DOI: 10.3390/plants11050691] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 05/14/2023]
Abstract
Plant salinity resistance results from a combination of responses at the physiological, molecular, cellular, and metabolic levels. This article focuses on plant stress tolerance mechanisms for controlling ion homeostasis, stress signaling, hormone metabolism, anti-oxidative enzymes, and osmotic balance after nanoparticle applications. Nanoparticles are used as an emerging tool to stimulate specific biochemical reactions related to plant ecophysiological output because of their small size, increased surface area and absorption rate, efficient catalysis of reactions, and adequate reactive sites. Regulated ecophysiological control in saline environments could play a crucial role in plant growth promotion and survival of plants under suboptimal conditions. Plant biologists are seeking to develop a broad profile of genes and proteins that contribute to plant salt resistance. These plant metabolic profiles can be developed due to advancements in genomic, proteomic, metabolomic, and transcriptomic techniques. In order to quantify plant stress responses, transmembrane ion transport, sensors and receptors in signaling transduction, and metabolites involved in the energy supply require thorough study. In addition, more research is needed on the plant salinity stress response based on molecular interactions in response to nanoparticle treatment. The application of nanoparticles as an aspect of genetic engineering for the generation of salt-tolerant plants is a promising area of research. This review article addresses the use of nanoparticles in plant breeding and genetic engineering techniques to develop salt-tolerant crops.
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Affiliation(s)
- Zainul Abideen
- Dr. Muhammad Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi 75270, Pakistan;
| | - Maria Hanif
- Department of Biotechnology, Lahore College for Women University, Lahore 54000, Pakistan;
| | - Neelma Munir
- Department of Biotechnology, Lahore College for Women University, Lahore 54000, Pakistan;
- Correspondence: (N.M.); (B.L.N.)
| | - Brent L. Nielsen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
- Correspondence: (N.M.); (B.L.N.)
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16
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High-value pleiotropic genes for developing multiple stress-tolerant biofortified crops for 21st-century challenges. Heredity (Edinb) 2022; 128:460-472. [PMID: 35173311 PMCID: PMC8852949 DOI: 10.1038/s41437-022-00500-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 11/08/2022] Open
Abstract
The agriculture-based livelihood systems that are already vulnerable due to multiple challenges face immediate risk of increased crop failures due to weather vagaries. As breeders and biotechnologists, our strategy is to advance and innovate breeding for weather-proofing crops. Plant stress tolerance is a genetically complex trait. Additionally, crops rarely face a single type of stress in isolation, and it is difficult for plants to deal with multiple stresses simultaneously. One of the most helpful approaches to creating stress-resilient crops is genome editing and trans- or cis-genesis. Out of hundreds of stress-responsive genes, many have been used to impart tolerance against a particular stress factor, while a few used in combination for gene pyramiding against multiple stresses. However, a better approach would be to use multi-role pleiotropic genes that enable plants to adapt to numerous environmental stresses simultaneously. Herein we attempt to integrate and present the scattered information published in the past three decades about these pleiotropic genes for crop improvement and remodeling future cropping systems. Research articles validating functional roles of genes in transgenic plants were used to create groups of multi-role pleiotropic genes that could be candidate genes for developing weather-proof crop varieties. These biotech crop varieties will help create 'high-value farms' to meet the goal of a sustainable increase in global food productivity and stabilize food prices by ensuring a fluctuation-free assured food supply. It could also help create a gene repository through artificial gene synthesis for 'resilient high-value food production' for the 21st century.
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Combined Transcriptomics and Metabolomics Analysis Reveals the Molecular Mechanism of Salt Tolerance of Huayouza 62, an Elite Cultivar in Rapeseed ( Brassica napus L.). Int J Mol Sci 2022; 23:ijms23031279. [PMID: 35163202 PMCID: PMC8836002 DOI: 10.3390/ijms23031279] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/23/2023] Open
Abstract
Soil salinity is one of the most significant abiotic stresses affecting crop yield around the world. To explore the molecular mechanism of salt tolerance in rapeseed (Brassica napus L.), the transcriptome analysis and metabolomics analysis were used to dissect the differentially expressed genes and metabolites in two rapeseed varieties with significant differences in salt tolerance; one is an elite rapeseed cultivar, Huayouza 62. A total of 103 key differentially expressed metabolites (DEMs) and 53 key differentials expressed genes (DEGs) that might be related to salt stress were identified through metabolomics and transcriptomics analysis. GO and KEGG analysis revealed that the DEGs were mainly involved in ion transport, reactive oxygen scavenging, osmotic regulation substance synthesis, and macromolecular protein synthesis. The DEMs were involved in TCA cycle, proline metabolism, inositol metabolism, carbohydrate metabolic processes, and oxidation-reduction processes. In addition, overexpression of BnLTP3, which was one of the key DEGs, could increase tolerance to salt stress in Arabidopsis plants. This study reveals that the regulation mechanism of salt tolerance in rapeseed at the transcriptome and metabolism level and provides abundant data for further in-depth identification of essential salt tolerance genes.
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Kumar S, Yadav A, Bano N, Dubey AK, Verma R, Pandey A, Kumar A, Bag S, Srivastava S, Sanyal I. Genome-wide profiling of drought-tolerant Arabidopsis plants over-expressing chickpea MT1 gene reveals transcription factors implicated in stress modulation. Funct Integr Genomics 2022; 22:153-170. [PMID: 34988675 DOI: 10.1007/s10142-021-00823-7] [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: 09/20/2021] [Revised: 11/12/2021] [Accepted: 11/23/2021] [Indexed: 11/24/2022]
Abstract
Drought, a major abiotic limiting factor, could be modulated with in-built reprogramming of plants at molecular level by regulating the activity of plant developmental processes, stress endurance and adaptation. The transgenic Arabidopsis thaliana over-expressing metallothionein 1 (MT1) gene of desi chickpea (Cicer arietinum L.) was subjected to transcriptome analysis. We evaluated drought tolerance of 7 days old plants of Arabidopsis thaliana in both wild-type (WT) as well as transgenic plants and performed transcriptome analysis. Our analysis revealed 24,737 transcripts representing 24,594 genes out of which 5,816 were differentially expressed genes (DEGs) under drought conditions and 841 genes were common in both genotypes. A total of 1251 DEGs in WT and 2099 in MT1 were identified in comparison with control. Out of the significant DEGs, 432 and 944 were upregulated, whereas 819 and 1155 were downregulated in WT and MT1 plants, respectively. The physiological and molecular parameters involving germination assay, root length measurements under different stress treatments and quantitative expression analysis of transgenic plants in comparison to wild-type were found to be enhanced. CarMT1 plants also demonstrated modulation of various other stress-responsive genes that reprogrammed themselves for stress adaptation. Amongst various drought-responsive genes, 24 DEGs showed similar quantitative expression as obtained through RNA sequencing data. Hence, these modulatory genes could be used as a genetic tool for understanding and delineating the mechanisms for fine-tuning of stress responses in crop plants.
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Affiliation(s)
- Sanoj Kumar
- Plant Transgenic Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Uttar Pradesh, Lucknow, 226001, India.,Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, India
| | - Ankita Yadav
- Plant Transgenic Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Uttar Pradesh, Lucknow, 226001, India.,Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Nasreen Bano
- Plant Transgenic Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Uttar Pradesh, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Arvind Kumar Dubey
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Be'er Sheva, Israel
| | - Rita Verma
- Plant Transgenic Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Uttar Pradesh, Lucknow, 226001, India.,Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Ankesh Pandey
- Plant Transgenic Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Uttar Pradesh, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anil Kumar
- Plant Transgenic Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Uttar Pradesh, Lucknow, 226001, India.,Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, 263136, India
| | - Sumit Bag
- Plant Transgenic Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Uttar Pradesh, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sudhakar Srivastava
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, India
| | - Indraneel Sanyal
- Plant Transgenic Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Uttar Pradesh, Lucknow, 226001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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19
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Chen H, Hu L, Wang L, Wang S, Cheng X. Genome-wide identification and expression profiles of AP2/ERF transcription factor family in mung bean (Vigna radiata L.). J Appl Genet 2022; 63:223-236. [PMID: 34989979 DOI: 10.1007/s13353-021-00675-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/28/2022]
Abstract
Mung bean (Vigna radiata L. Wilczek) is an economically important grain legume crop in Asia, with high nutritional quality and potential in other parts of the world particularly arid and semiarid regions. Considering the potential adverse effects of drought, high salt, and other abiotic stresses on crop yield, significant efforts have been made to understand the underlying molecular mechanisms of tolerance to these abiotic stresses in legumes. In this study, a total of 186 putative AP2/ERF genes were identified, which were named VrERF1-186. These VrERF genes were classified into four main subfamilies according to the number of AP2 domains and sequence similarity, including 24 AP2 gene members, 81 ERF gene members, 79 DREB gene members, and 2 RAV members. VrERF genes are scattered across all 11 chromosomes and form small gene clusters on chromosomes due to segmental or tandem duplication. Promoter analysis revealed various cis-acting elements related to light, hormones, and stress responsiveness processes. The expression profiles of the VrERF genes in tissues during development and in response to abiotic stresses were assessed by transcriptome sequencing, and the selected reference genes were validated by qRT-PCR. A total of 174 VrERF genes were expressed in at least one of five tissues, while others showed distinct expression patterns in different tissues or under specific abiotic stress treatments, which indicates that VrERF genes are involved in developmental and environmental stress responses in V. radiata. In conclusion, the genome localization, genome-wide characterization, gene duplication, phylogenetic relationships, and expression pattern of VrERF genes in V. radiata were analyzed, and these results will lay the foundation for further functional analysis of these genes and improve stress tolerance to adverse conditions in plants.
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Affiliation(s)
- Honglin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Liangliang Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixia Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Suhua Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuzhen Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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20
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Limbalkar OM, Singh R, Kumar P, Nanjundan J, Parihar CM, Vasisth P, Yadava DK, Chinnusamy V, Singh N. Deployment of Brassica carinata A. Braun Derived Brassica juncea (L.) Czern. Lines for Improving Heterosis and Water Use Efficiency Under Water Deficit Stress Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:765645. [PMID: 34899786 PMCID: PMC8655733 DOI: 10.3389/fpls.2021.765645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/13/2021] [Indexed: 05/14/2023]
Abstract
Among Brassica species, Ethiopian mustard (Brassica carinata A. Braun) is known to tolerate most abiotic stresses, including drought. Drought caused by low and erratic rainfall in semi-arid regions consistently challenges rapeseed mustard productivity. Development of B. carinata-derived lines (CDLs) in Brassica juncea (L.) Czern. nuclear background, carrying genomic segments from B. carinata, are expected to tolerate moisture deficit stress conditions. The present study was, thus, aimed to establish the phenomenon "heterosis" for drought tolerance and water use efficiency by evaluating 105 hybrids developed from intermating 15 CDLs in half diallel fashion. Data on 17 seed yield and yield contributing traits were recorded under two different environments, viz., irrigated and rainfed conditions. Traits under study were found to be governed by both additive and non-additive types of gene action. Average degree of dominance was higher (>2) for yield and yield contributing traits, viz., secondary branches/plant, point to first siliqua on main shoot, total siliquae/plant, 1,000-seed weight, seed yield/plant, biological yield, harvest index, and seed yield/hectare under rainfed conditions, clearly indicating that higher productivity under drought conditions can be realised through the development of hybrids. Out of 15, highly significant general combining ability (GCA) effects for seven CDLs were observed under rainfed condition. Furthermore, nine and six hybrids expressed highly significant specific combining ability (SCA) effects and > 50% heterobeltiosis for yield contributing traits under rainfed and irrigated conditions, respectively. Water use efficiency (WUE) of parental CDLs and hybrids varied from 2.05 to 2.57 kg m-3 under rainfed, while 1.10 to 1.28 kg m-3 under irrigated conditions. Hybrids expressed higher WUE than parental lines under both water regimes. Furthermore, selection indices such as drought tolerance index (DTI) and mean relative performance (MRP) were identified to be efficient in the selection of productive CDLs and hybrids under drought conditions. Nine hybrids, identified as highly productive in the present study, can further be exploited for improving the yield of Indian mustard in drought-prone areas. Usefulness of interspecific hybridisation in the development of B. carinata-derived B. juncea lines for improving heterosis and WUE is, thus, well demonstrated through the present study.
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Affiliation(s)
- Omkar Maharudra Limbalkar
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - Rajendra Singh
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - Parvesh Kumar
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - Joghee Nanjundan
- Indian Council of Agricultural Research-Indian Agricultural Research Institute Regional Station, Wellington, India
| | - Chiter Mal Parihar
- Division of Agronomy, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - Prashant Vasisth
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | | | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - Naveen Singh
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
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21
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Jogawat A, Yadav B, Lakra N, Singh AK, Narayan OP. Crosstalk between phytohormones and secondary metabolites in the drought stress tolerance of crop plants: A review. PHYSIOLOGIA PLANTARUM 2021; 172:1106-1132. [PMID: 33421146 DOI: 10.1111/ppl.13328] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/08/2020] [Accepted: 01/01/2021] [Indexed: 05/21/2023]
Abstract
Drought stress negatively affects crop performance and weakens global food security. It triggers the activation of downstream pathways, mainly through phytohormones homeostasis and their signaling networks, which further initiate the biosynthesis of secondary metabolites (SMs). Roots sense drought stress, the signal travels to the above-ground tissues to induce systemic phytohormones signaling. The systemic signals further trigger the biosynthesis of SMs and stomatal closure to prevent water loss. SMs primarily scavenge reactive oxygen species (ROS) to protect plants from lipid peroxidation and also perform additional defense-related functions. Moreover, drought-induced volatile SMs can alert the plant tissues to perform drought stress mitigating functions in plants. Other phytohormone-induced stress responses include cell wall and cuticle thickening, root and leaf morphology alteration, and anatomical changes of roots, stems, and leaves, which in turn minimize the oxidative stress, water loss, and other adverse effects of drought. Exogenous applications of phytohormones and genetic engineering of phytohormones signaling and biosynthesis pathways mitigate the drought stress effects. Direct modulation of the SMs biosynthetic pathway genes or indirect via phytohormones' regulation provides drought tolerance. Thus, phytohormones and SMs play key roles in plant development under the drought stress environment in crop plants.
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Affiliation(s)
| | - Bindu Yadav
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Nita Lakra
- Department of Biotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Amit Kumar Singh
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Om Prakash Narayan
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts, USA
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Nagamalla SS, Alaparthi MD, Mellacheruvu S, Gundeti R, Earrawandla JPS, Sagurthi SR. Morpho-Physiological and Proteomic Response of Bt-Cotton and Non-Bt Cotton to Drought Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:663576. [PMID: 34040622 PMCID: PMC8143030 DOI: 10.3389/fpls.2021.663576] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Drought stress impacts cotton plant growth and productivity across countries. Plants can initiate morphological, cellular, and proteomic changes to adapt to unfavorable conditions. However, our knowledge of how cotton plants respond to drought stress at the proteome level is limited. Herein, we elucidated the molecular coordination underlining the drought tolerance of two inbred cotton varieties, Bacillus thuringiensis-cotton [Bt-cotton + Cry1 Ac gene and Cry 2 Ab gene; NCS BG II BT (BTCS/BTDS)] and Hybrid cotton variety [Non-Bt-cotton; (HCS/HDS)]. Our morphological observations and biochemical experiments showed a different tolerance level between two inbred lines to drought stress. Our proteomic analysis using 2D-DIGE revealed that the changes among them were not obviously in respect to their controls apart from under drought stress, illustrating the differential expression of 509 and 337 proteins in BTDS and HDS compared to their controls. Among these, we identified eight sets of differentially expressed proteins (DEPs) and characterized them using MALDI-TOF/TOF mass spectrometry. Furthermore, the quantitative real-time PCR analysis was carried out with the identified drought-related proteins and confirmed differential expressions. In silico analysis of DEPs using Cytoscape network finds ATPB, NAT9, ERD, LEA, and EMB2001 to be functionally correlative to various drought-responsive genes LEA, AP2/ERF, WRKY, and NAC. These proteins play a vital role in transcriptomic regulation under stress conditions. The higher drought response in Bt cotton (BTCS/BTDS) attributed to the overexpression of photosynthetic proteins enhanced lipid metabolism, increased cellular detoxification and activation chaperones, and reduced synthesis of unwanted proteins. Thus, the Bt variety had enhanced photosynthesis, elevated water retention potential, balanced leaf stomata ultrastructure, and substantially increased antioxidant activity than the Non-Bt cotton. Our results may aid breeders and provide further insights into developing new drought-tolerant and high-yielding cotton hybrid varieties.
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Karamat U, Sun X, Li N, Zhao J. Genetic regulators of leaf size in Brassica crops. HORTICULTURE RESEARCH 2021; 8:91. [PMID: 33931619 PMCID: PMC8087820 DOI: 10.1038/s41438-021-00526-x] [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: 08/22/2020] [Revised: 01/03/2021] [Accepted: 02/24/2021] [Indexed: 05/06/2023]
Abstract
Leaf size influences plant development and biomass and is also an important agricultural trait in Brassica crops, in which leaves are the main organ produced for consumption. Leaf size is determined by the coordinated regulation of cell proliferation and cell expansion during leaf development, and these processes are strictly controlled by various integrated signals from the intrinsic regulatory network and the growth environment. Understanding the molecular mechanism of leaf size control is a prerequisite for molecular breeding for crop improvement purposes. Although research on leaf size control is just beginning in Brassica, recent studies have identified several genes and QTLs that are important in leaf size regulation. These genes have been proposed to influence leaf growth through different pathways and mechanisms, including phytohormone biosynthesis and signaling, transcription regulation, small RNAs, and others. In this review, we summarize the current findings regarding the genetic regulators of leaf size in Brassica and discuss future prospects for this research.
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Affiliation(s)
- Umer Karamat
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xiaoxue Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Na Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
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Morpho-Physiological, Biochemical, and Genetic Responses to Salinity in Medicago truncatula. PLANTS 2021; 10:plants10040808. [PMID: 33924007 PMCID: PMC8072551 DOI: 10.3390/plants10040808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 02/08/2023]
Abstract
We used an integrated morpho-physiological, biochemical, and genetic approach to investigate the salt responses of four lines (TN1.11, TN6.18, JA17, and A10) of Medicago truncatula. Results showed that TN1.11 exhibited a high tolerance to salinity, compared with the other lines, recording a salinity induced an increase in soluble sugars and soluble proteins, a slight decrease in malondialdehyde (MDA) accumulation, and less reduction in plant biomass. TN6.18 was the most susceptible to salinity as it showed less plant weight, had elevated levels of MDA, and lower levels of soluble sugars and soluble proteins under salt stress. As transcription factors of the APETALA2/ethylene responsive factor (AP2/ERF) family play important roles in plant growth, development, and responses to biotic and abiotic stresses, we performed a functional characterization of MtERF1 gene. Real-time PCR analysis revealed that MtERF1 is mainly expressed in roots and is inducible by NaCl and low temperature. Additionally, under salt stress, a greater increase in the expression of MtERF1 was found in TN1.11 plants than that in TN6.18. Therefore, the MtERF1 pattern of expression may provide a useful marker for discriminating among lines of M. truncatula and can be used as a tool in breeding programs aiming at obtaining Medicago lines with improved salt tolerance.
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Balti I, Benny J, Perrone A, Caruso T, Abdallah D, Salhi-Hannachi A, Martinelli F. Identification of conserved genes linked to responses to abiotic stresses in leaves among different plant species. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 48:54-71. [PMID: 32727652 DOI: 10.1071/fp20028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
As a consequence of global climate change, certain stress factors that have a negative impact on crop productivity such as heat, cold, drought and salinity are becoming increasingly prevalent. We conducted a meta-analysis to identify genes conserved across plant species involved in (1) general abiotic stress conditions, and (2) specific and unique abiotic stress factors (drought, salinity, extreme temperature) in leaf tissues. We collected raw data and re-analysed eight RNA-Seq studies using our previously published bioinformatic pipeline. A total of 68 samples were analysed. Gene set enrichment analysis was performed using MapMan and PageMan whereas DAVID (Database for Annotation, Visualisation and Integrated Discovery) was used for metabolic process enrichment analysis. We identified of a total of 5122 differentially expressed genes when considering all abiotic stresses (3895 were upregulated and 1227 were downregulated). Jasmonate-related genes were more commonly upregulated by drought, whereas gibberellin downregulation was a key signal for drought and heat. In contrast, cold stress clearly upregulated genes involved in ABA (abscisic acid), cytokinin and gibberellins. A gene (non-phototrophic hypocotyl) involved in IAA (indoleacetic acid) response was induced by heat. Regarding secondary metabolism, as expected, MVA pathway (mevalonate pathway), terpenoids and alkaloids were generally upregulated by all different stresses. However, flavonoids, lignin and lignans were more repressed by heat (cinnamoyl coA reductase 1 and isopentenyl pyrophosphatase). Cold stress drastically modulated genes involved in terpenoid and alkaloids. Relating to transcription factors, AP2-EREBP, MADS-box, WRKY22, MYB, homoebox genes members were significantly modulated by drought stress whereas cold stress enhanced AP2-EREBPs, bZIP members, MYB7, BELL 1 and one bHLH member. C2C2-CO-LIKE, MADS-box and a homeobox (HOMEOBOX3) were mostly repressed in response to heat. Gene set enrichment analysis showed that ubiquitin-mediated protein degradation was enhanced by heat, which unexpectedly repressed glutaredoxin genes. Cold stress mostly upregulated MAP kinases (mitogen-activated protein kinase). Findings of this work will allow the identification of new molecular markers conserved across crops linked to major genes involved in quantitative agronomic traits affected by different abiotic stress.
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Affiliation(s)
- Imen Balti
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze ed. 4 Palermo, 90128, Italy; and Department of Biology, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Jubina Benny
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze ed. 4 Palermo, 90128, Italy
| | - Anna Perrone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Palermo, 90128, Italy
| | - Tiziano Caruso
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze ed. 4 Palermo, 90128, Italy
| | - Donia Abdallah
- Department of Biology, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Amel Salhi-Hannachi
- Department of Biology, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, 50019, Italy; and Corresponding author.
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Salt stress induces endoplasmic reticulum stress-responsive genes in a grapevine rootstock. PLoS One 2020; 15:e0236424. [PMID: 32730292 PMCID: PMC7392237 DOI: 10.1371/journal.pone.0236424] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/06/2020] [Indexed: 11/19/2022] Open
Abstract
Grapevines, although adapted to occasional drought or salt stress, are relatively sensitive to growth- and yield-limiting salinity stress. To understand the molecular mechanisms of salt tolerance and endoplasmic reticulum (ER) stress and identify genes commonly regulated by both stresses in grapevine, we investigated transcript profiles in leaves of the salt-tolerant grapevine rootstock 1616C under salt- and ER-stress. Among 1643 differentially expressed transcripts at 6 h post-treatment in leaves, 29 were unique to ER stress, 378 were unique to salt stress, and 16 were common to both stresses. At 24 h post-treatment, 243 transcripts were unique to ER stress, 1150 were unique to salt stress, and 168 were common to both stresses. GO term analysis identified genes in categories including ‘oxidative stress’, ‘protein folding’, ‘transmembrane transport’, ‘protein phosphorylation’, ‘lipid transport’, ‘proteolysis’, ‘photosynthesis’, and ‘regulation of transcription’. The expression of genes encoding transporters, transcription factors, and proteins involved in hormone biosynthesis increased in response to both ER and salt stresses. KEGG pathway analysis of differentially expressed genes for both ER and salt stress were divided into four main categories including; carbohydrate metabolism, amino acid metabolism, signal transduction and lipid metabolism. Differential expression of several genes was confirmed by qRT-PCR analysis, which validated our microarray results. We identified transcripts for genes that might be involved in salt tolerance and also many genes differentially expressed under both ER and salt stresses. Our results could provide new insights into the mechanisms of salt tolerance and ER stress in plants and should be useful for genetic improvement of salt tolerance in grapevine.
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Kumar M, Kesawat MS, Ali A, Lee SC, Gill SS, Kim HU. Integration of Abscisic Acid Signaling with Other Signaling Pathways in Plant Stress Responses and Development. PLANTS (BASEL, SWITZERLAND) 2019; 8:E592. [PMID: 31835863 PMCID: PMC6963649 DOI: 10.3390/plants8120592] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 11/26/2019] [Accepted: 12/10/2019] [Indexed: 12/30/2022]
Abstract
Plants are immobile and, to overcome harsh environmental conditions such as drought, salt, and cold, they have evolved complex signaling pathways. Abscisic acid (ABA), an isoprenoid phytohormone, is a critical signaling mediator that regulates diverse biological processes in various organisms. Significant progress has been made in the determination and characterization of key ABA-mediated molecular factors involved in different stress responses, including stomatal closure and developmental processes, such as seed germination and bud dormancy. Since ABA signaling is a complex signaling network that integrates with other signaling pathways, the dissection of its intricate regulatory network is necessary to understand the function of essential regulatory genes involved in ABA signaling. In the present review, we focus on two aspects of ABA signaling. First, we examine the perception of the stress signal (abiotic and biotic) and the response network of ABA signaling components that transduce the signal to the downstream pathway to respond to stress tolerance, regulation of stomata, and ABA signaling component ubiquitination. Second, ABA signaling in plant development processes, such as lateral root growth regulation, seed germination, and flowering time regulation is investigated. Examining such diverse signal integration dynamics could enhance our understanding of the underlying genetic, biochemical, and molecular mechanisms of ABA signaling networks in plants.
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Affiliation(s)
- Manu Kumar
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea
| | | | - Asjad Ali
- Southern Cross Plant Science, Southern Cross University, East Lismore NSW 2480, Australia;
| | | | - Sarvajeet Singh Gill
- Stress Physiology and Molecular Biology Lab, Centre for Biotechnology, MD University, Rohtak 124001, India;
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea
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Benny J, Pisciotta A, Caruso T, Martinelli F. Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data. BMC PLANT BIOLOGY 2019; 19:194. [PMID: 31077147 PMCID: PMC6511156 DOI: 10.1186/s12870-019-1794-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/22/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Our study is the first to provide RNA-Seq data analysis related to transcriptomic responses towards drought across different crops. The aim was to identify and map which genes play a key role in drought response on leaves across different crops. Forty-two RNA-seq samples were analyzed from 9 published studies in 7 plant species (Arabidopsis thaliana, Solanum lycopersicum, Zea mays, Vitis vinifera, Malus X domestica, Solanum tuberosum, Triticum aestivum). RESULTS Twenty-seven (16 up-regulated and 11 down-regulated) drought-regulated genes were commonly present in at least 7 of 9 studies, while 351 (147 up-regulated and 204 down-regulated) were commonly drought-regulated in 6 of 9 studies. Across all kind of leaves, the drought repressed gene-ontologies were related to the cell wall and membrane re-structuring such as wax biosynthesis, cell wall organization, fatty acid biosynthesis. On the other hand, drought-up-regulated biological processes were related to responses to osmotic stress, abscisic acid, water deprivation, abscisic-activated signalling pathway, salt stress, hydrogen peroxide treatment. A common metabolic feature linked to drought response in leaves is the repression of terpenoid pathways. There was an induction of AL1 (alfin-like), UGKYAH (trihelix), WRKY20, homeobox genes and members of the SET domain family in 6 of 9 studies. Several genes involved in detoxifying and antioxidant reactions, signalling pathways and cell protection were commonly modulated by drought across the 7 species. The chromosome (Chr) mapping of these key abiotic stress genes highlighted that Chr 4 in Arabidopsis thaliana, Chr 1 in Zea mays, Chr 2 and Chr 5 in Triticum aestivum contained a higher presence of drought-related genes compared to the other remaining chromosomes. In seedling studies, it is worth notice the up-regulation of ERF4 and ESE3 (ethylene), HVA22 (abscisic acid), TIR1 (auxin) and some transcription factors (MYB3, MYB94, MYB1, WRKY53 and WRKY20). In mature leaves, ERF1 and Alfin-like 1 were induced by drought while other transcription factors (YABBY5, ARR2, TRFL2) and genes involved phospholipid biosynthesis were repressed. CONCLUSIONS The identified and mapped genes might be potential targets of molecular breeding activities to develop cultivars with enhanced drought resistance and tolerance across different crops.
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Affiliation(s)
- Jubina Benny
- Dipartimento di Biologia, Università degli Studi di Firenze, Via Madonna del Piano 6, Sesto Fiorentino, FI 50019 Italy
| | - Antonino Pisciotta
- Dipartimento di Biologia, Università degli Studi di Firenze, Via Madonna del Piano 6, Sesto Fiorentino, FI 50019 Italy
| | - Tiziano Caruso
- Dipartimento di Biologia, Università degli Studi di Firenze, Via Madonna del Piano 6, Sesto Fiorentino, FI 50019 Italy
| | - Federico Martinelli
- Dipartimento di Biologia, Università degli Studi di Firenze, Via Madonna del Piano 6, Sesto Fiorentino, FI 50019 Italy
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Ma Q, Xia Z, Cai Z, Li L, Cheng Y, Liu J, Nian H. GmWRKY16 Enhances Drought and Salt Tolerance Through an ABA-Mediated Pathway in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 9:1979. [PMID: 30740122 PMCID: PMC6357947 DOI: 10.3389/fpls.2018.01979] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 12/20/2018] [Indexed: 05/19/2023]
Abstract
The WRKY transcription factors (TFs) are one of the largest families of TFs in plants and play multiple roles in plant development and stress response. In the present study, GmWRKY16 encoding a WRKY transcription factor in soybean was functionally characterized in Arabidopsis. GmWRKY16 is a nuclear protein that contains a highly conserved WRKY domain and a C2H2 zinc-finger structure, and has the characteristics of transcriptional activation ability, presenting a constitutive expression pattern with relative expression levels of over fourfold in the old leaves, flowers, seeds and roots of soybean. The results of quantitative real time polymerase chain reaction (qRT-PCR) showed that GmWRKY16 could be induced by salt, alkali, ABA, drought and PEG-6000. As compared with the control, overexpression of GmWRKY16 in Arabidopsis increased the seed germination rate and root growth of seedlings in transgenic lines under higher concentrations of mannitol, NaCl and ABA. In the meantime, GmWRKY16 transgenic lines showed over 75% survival rate after rehydration and enhanced Arabidopsis tolerance to salt and drought with higher proline and lower MDA accumulation, less water loss of the detached leaves, and accumulated more endogenous ABA than the control under stress conditions. Further studies showed that AtWRKY8, KIN1, and RD29A were induced in GmWRKY16 transgenic plants under NaCl treatment. The expressions of the ABA biosynthesis gene (NCED3), signaling genes (ABI1, ABI2, ABI4, and ABI5), responsive genes (RD29A, COR15A, COR15B, and RD22) and stress-related marker genes (KIN1, LEA14, LEA76, and CER3) were regulated in transgenic lines under drought stress. In summary, these results suggest that GmWRKY16 as a WRKY TF may promote tolerance to drought and salt stresses through an ABA-mediated pathway.
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Affiliation(s)
- Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhenglin Xia
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Lu Li
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jia Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, China
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Ku YS, Sintaha M, Cheung MY, Lam HM. Plant Hormone Signaling Crosstalks between Biotic and Abiotic Stress Responses. Int J Mol Sci 2018; 19:ijms19103206. [PMID: 30336563 PMCID: PMC6214094 DOI: 10.3390/ijms19103206] [Citation(s) in RCA: 269] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/13/2018] [Accepted: 10/14/2018] [Indexed: 01/01/2023] Open
Abstract
In the natural environment, plants are often bombarded by a combination of abiotic (such as drought, salt, heat or cold) and biotic (necrotrophic and biotrophic pathogens) stresses simultaneously. It is critical to understand how the various response pathways to these stresses interact with one another within the plants, and where the points of crosstalk occur which switch the responses from one pathway to another. Calcium sensors are often regarded as the first line of response to external stimuli to trigger downstream signaling. Abscisic acid (ABA) is a major phytohormone regulating stress responses, and it interacts with the jasmonic acid (JA) and salicylic acid (SA) signaling pathways to channel resources into mitigating the effects of abiotic stresses versus defending against pathogens. The signal transduction in these pathways are often carried out via GTP-binding proteins (G-proteins) which comprise of a large group of proteins that are varied in structures and functions. Deciphering the combined actions of these different signaling pathways in plants would greatly enhance the ability of breeders to develop food crops that can thrive in deteriorating environmental conditions under climate change, and that can maintain or even increase crop yield.
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Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Mariz Sintaha
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ming-Yan Cheung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Cheng Q, Dong L, Gao T, Liu T, Li N, Wang L, Chang X, Wu J, Xu P, Zhang S. The bHLH transcription factor GmPIB1 facilitates resistance to Phytophthora sojae in Glycine max. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2527-2541. [PMID: 29579245 PMCID: PMC5920285 DOI: 10.1093/jxb/ery103] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 03/16/2018] [Indexed: 05/07/2023]
Abstract
Phytophthora sojae Kaufmann and Gerdemann causes Phytophthora root rot, a destructive soybean disease worldwide. A basic helix-loop-helix (bHLH) transcription factor is thought to be involved in the response to P. sojae infection in soybean, as revealed by RNA sequencing (RNA-seq). However, the molecular mechanism underlying this response is currently unclear. Here, we explored the function and underlying mechanisms of a bHLH transcription factor in soybean, designated GmPIB1 (P. sojae-inducible bHLH transcription factor), during host responses to P. sojae. GmPIB1 was significantly induced by P. sojae in the resistant soybean cultivar 'L77-1863'. Analysis of transgenic soybean hairy roots with elevated or reduced expression of GmPIB1 demonstrated that GmPIB1 enhances resistance to P. sojae and reduces reactive oxygen species (ROS) accumulation. Quantitative reverse transcription PCR and chromatin immunoprecipitation-quantitative PCR assays revealed that GmPIB1 binds directly to the promoter of GmSPOD1 and represses its expression; this gene encodes a key enzyme in ROS production. Moreover, transgenic soybean hairy roots with GmSPOD1 silencing through RNA interference exhibited improved resistance to P. sojae and reduced ROS generation. These findings suggest that GmPIB1 enhances resistance to P. sojae by repressing the expression of GmSPOD1.
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Affiliation(s)
- Qun Cheng
- Soybean Research Institute/Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lidong Dong
- Soybean Research Institute/Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Tianjiao Gao
- Soybean Research Institute/Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Tengfei Liu
- Soybean Research Institute/Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Ninghui Li
- Soybean Research Institute/Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Le Wang
- Soybean Research Institute/Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Xin Chang
- Soybean Research Institute/Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Junjiang Wu
- Soybean Research Institute of Heilongjiang Academy of Agricultural Sciences, Key Laboratory of Soybean Cultivation of Ministry of Agriculture P. R. China, Harbin, China
| | - Pengfei Xu
- Soybean Research Institute/Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Shuzhen Zhang
- Soybean Research Institute/Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
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32
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Gupta R, Min CW, Kramer K, Agrawal GK, Rakwal R, Park KH, Wang Y, Finkemeier I, Kim ST. A Multi-Omics Analysis of Glycine max Leaves Reveals Alteration in Flavonoid and Isoflavonoid Metabolism Upon Ethylene and Abscisic Acid Treatment. Proteomics 2018; 18:e1700366. [PMID: 29457974 DOI: 10.1002/pmic.201700366] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/11/2018] [Indexed: 11/06/2022]
Abstract
Phytohormones are central to plant growth and development. Despite the advancement in our knowledge of hormone signaling, downstream targets, and their interactions upon hormones action remain largely fragmented, especially at the protein and metabolite levels. With an aim to get new insight into the effects of two hormones, ethylene (ET) and abscisic acid (ABA), this study utilizes an integrated proteomics and metabolomics approach to investigate their individual and combined (ABA+ET) signaling in soybean leaves. Targeting low-abundance proteins, our previously established protamine sulfate precipitation method was applied, followed by label-free quantification of identified proteins. A total of 4129 unique protein groups including 1083 differentially modulated in one (individual) or other (combined) treatments were discerned. Functional annotation of the identified proteins showed an increased abundance of proteins related to the flavonoid and isoflavonoid biosynthesis and MAPK signaling pathway in response to ET treatment. HPLC analysis showed an accumulation of isoflavones (genistin, daidzein, and genistein) upon ET treatment, in agreement with the proteomics results. A metabolome analysis assigned 79 metabolites and further confirmed the accumulation of flavonoids and isoflavonoids in response to ET. A potential cross-talk between ET and MAPK signaling, leading to the accumulation of flavonoids and isoflavonoids in soybean leaves is suggested.
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Affiliation(s)
- Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Katharina Kramer
- Plant Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, Kathmandu, Nepal
- GRADE Academy Private Limited, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry, Kathmandu, Nepal
- GRADE Academy Private Limited, Birgunj, Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan
- Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
| | - Ki-Hun Park
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Iris Finkemeier
- Plant Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
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Owji H, Hajiebrahimi A, Seradj H, Hemmati S. Identification and functional prediction of stress responsive AP2/ERF transcription factors in Brassica napus by genome-wide analysis. Comput Biol Chem 2017; 71:32-56. [PMID: 28961511 DOI: 10.1016/j.compbiolchem.2017.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 01/08/2023]
Abstract
Using homology and domain authentication, 321 putative AP2/ERF transcription factors were identified in Brassica napus, called BnAP2/ERF TFs. BnAP2/ERF TFs were classified into five major subfamilies, including DREB, ERF, AP2, RAV, and BnSoloist. This classification is based on phylogenetic analysis, motif identification, gene structure analysis, and physiochemical characterization. These TFs were annotated based on phylogenetic relationship with Brassica rapa. BnAP2/ERF TFs were located on 19 chromosomes of B. napus. Orthologs and paralogs were identified using synteny-based methods Ks calculation within B. napus genome and between B. napus with other species such as B. rapa, Brassica oleracea, and Arabidopsis thaliana indicated that BnAP2/ERF TFs were formed through duplication events occurred before B. napus formation. Kn/Ks values were between 0 and 1, suggesting the purifying selection among BnAP2/ERF TFs. Gene ontology annotation, cis-regulatory elements and functional interaction networks suggested that BnAP2/ERF TFs participate in response to stressors, including drought, high salinity, heat and cold as well as developmental processes particularly organ specification and embryogenesis. The identified cis-regulatory elements in the upstream of BnAP2/ERF TFs were responsive to abscisic acid. Analysis of the expression data derived from Illumina Hiseq 2000 RNA sequencing revealed that BnAP2/ERF genes were highly expressed in the roots comparing to flower buds, leaves, and stems. Also, the ERF subfamily was over-expressed under salt and fungal treatments. BnERF039 and BnERF245 are candidates for salt-tolerant B. napus. BnERF253-256 and BnERF260-277 are potential cytokinin response factors. BnERF227, BnERF228, BnERF234, BnERF134, BnERF132, BnERF176, and BnERF235 were suggested for resistance against Leptosphaeria maculan and Leptosphaeria biglobosa.
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Affiliation(s)
- Hajar Owji
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Hajiebrahimi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Seradj
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Li L, Mu S, Cheng Z, Cheng Y, Zhang Y, Miao Y, Hou C, Li X, Gao J. Characterization and expression analysis of the WRKY gene family in moso bamboo. Sci Rep 2017; 7:6675. [PMID: 28751687 PMCID: PMC5532226 DOI: 10.1038/s41598-017-06701-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 06/16/2017] [Indexed: 12/11/2022] Open
Abstract
The WRKY family of transcription factors (TFs) is one of the ten largest families of TFs in higher plants and has been implicated in multiple biological processes. Here, we identified 121 WRKY TFs in moso bamboo, including five novel members that were not annotated in the Phyllostachys edulis genomic database. Estimation of the divergence time of paralogous gene pairs revealed an important role of the recent whole-genome duplication in the expansion of the WRKY family. Expression analysis based on quantitative reverse-transcription polymerase chain reaction (qRT-PCR) data revealed that a large number of PheWRKY genes varied significantly under cold or drought stress treatments, which could be defined as abiotic stress-responsive genes. The overexpression of PheWRKY72-2 in Arabidopsis resulted in a decreased sensitivity to drought stress during early seedling growth. PheWRKY72-2 may enhance plant tolerance to stress by functioning as a positive regulator of stoma closure. Our study provides a theoretical foundation and some experimental evidence for further functional verification of the PheWRKY family of TFs.
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Affiliation(s)
- Long Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China.,College of Forestry, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shaohua Mu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China
| | - Zhanchao Cheng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China
| | - Yuanwen Cheng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China
| | - Ying Zhang
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China
| | - Ying Miao
- Center for Molecular Cell and Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Chenglin Hou
- Department of Microbiology, College of Life Science, Capital Normal University, Beijing, 100048, People's Republic of China
| | - Xueping Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China.
| | - Jian Gao
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China.
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35
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Shen X, Guo X, Guo X, Zhao D, Zhao W, Chen J, Li T. PacMYBA, a sweet cherry R2R3-MYB transcription factor, is a positive regulator of salt stress tolerance and pathogen resistance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 112:302-311. [PMID: 28126679 DOI: 10.1016/j.plaphy.2017.01.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/12/2017] [Accepted: 01/14/2017] [Indexed: 05/15/2023]
Abstract
Plant R2R3-MYB transcription factors play crucial roles in stress responses. We previously isolated a R2R3-MYB homolog from sweet cherry cv. Hong Deng, designated PacMYBA (GenBank accession No. KF974774). To explore the role of PacMYBA in the plant stress response, we heterologously expressed PacMYBA in transgenic Arabidopsis thaliana plants. In a previous study, we demonstrated that PacMYBA is mainly localized to the nucleus and could be induced by abscisic acid (ABA). Analysis of the promoter sequence of PacMYBA revealed that it contains several stress-related cis-elements. QPCR results showed that PacMYBA is induced by salt, salicylic (SA), and jasmonic acid (JA) in sweet cherry leaves. Transgenic Arabidopsis plants heterologously expressing PacMYBA exhibited enhanced salt-tolerance and increased resistance to Pseudomonas syringe pv. tomato (Pst) DC3000 infection. Overexpression of PacMYBA decreased the osmotic potential (OP), increased the free proline content, and increased the peroxidase content in transgenic Arabidopsis plants. Furthermore, overexpression of PacMYBA also affected the expression levels of salt stress- and pathogen defense-related genes in the transgenic plants. These results indicate that PacMYBA is a positive regulator of salt stress tolerance and pathogen resistance.
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Affiliation(s)
- Xinjie Shen
- Department of Fruit Science, College of Horticulture, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, People's Republic of China; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, People's Republic of China
| | - Xinwei Guo
- Department of Fruit Science, College of Horticulture, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, People's Republic of China
| | - Xiao Guo
- Department of Fruit Science, College of Horticulture, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, People's Republic of China
| | - Di Zhao
- Department of Fruit Science, College of Horticulture, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, People's Republic of China
| | - Wei Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, People's Republic of China
| | - Jingsheng Chen
- Daqing Branch, Heilongjiang Academy of Agricultural Sciences, Daqing 163316, Heilongjiang, People's Republic of China
| | - Tianhong Li
- Department of Fruit Science, College of Horticulture, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, People's Republic of China; Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit Trees, Beijing 102206, People's Republic of China.
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Cao Y, Luo Q, Tian Y, Meng F. Physiological and proteomic analyses of the drought stress response in Amygdalus Mira (Koehne) Yü et Lu roots. BMC PLANT BIOLOGY 2017; 17:53. [PMID: 28241796 PMCID: PMC5327565 DOI: 10.1186/s12870-017-1000-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/10/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Plants are oftentimes exposed to many types of abiotic stresses. Drought is one of the main environmental stresses which limits plant growth, distribution and crop yield worldwide. Amygdalus mira (Koehne) Yü et Lu is an important wild peach, and it is considered an ideal wild peach germplasm for improving cultivated peach plants. Because of the loss of genetic variation, cultivated peach plants are sensitive to biotic and abiotic stresses. Wild peach germplasm can offer many useful genes for peach improvement. Responses to drought by withholding water have been studied in Amygdalus mira (Koehne) Yü et Lu roots. In this study, plants were divided into well-watered (control) and water-stressed (treatment) groups, and the treatment group did not receive water until the recovery period (day 16). RESULTS Several physiological parameters, including root water content and root length, were reduced by drought stress and recovered after rewatering. In addition, the relative conductivity, the levels of proline, MDA and H2O2, and the activities of ROS scavenging enzymes (POD, APX and CAT) were increased, and none of these factors, except the level of proline, recovered after rewatering. In total, 95 differentially expressed proteins were revealed after drought. The identified proteins refer to a extensive range of biological processes, molecular functions and cellular components, including cytoskeleton dynamics (3.16% of the total 95 proteins), carbohydrate and nitrogen metabolism (6.33% of the total 95 proteins), energy metabolism (7.37% of the total 95 proteins), transcription and translation (18.95% of the total 95 proteins), transport (4.21% of the total 95 proteins), inducers (3.16% of the total 95 proteins), stress and defense (26.31% of the total 95 proteins), molecular chaperones (9.47% of the total 95 proteins), protein degradation (3.16% of the total 95 proteins), signal transduction (7.37% of the total 95 proteins), other materials metabolism (5.26% of the total 95 proteins) and unknown functions (5.26% of the total 95 proteins). Proteins related to defense, stress, transcription and translation play an important role in drought response. In addition, we also examined the correlation between protein and transcript levels. CONCLUSIONS The interaction between enzymatic and non-enzymatic antioxidants, the levels of proline, MDA, H2O2 and the relative conductivity, and the expression level of proteins in drought-treated plants all contribute to drought resistance in Amygdalus mira (Koehne) Yü et Lu.
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Affiliation(s)
- Yuan Cao
- College of Life Science, Northeast Forestry University, Harbin, 150040 China
| | - Qiuxiang Luo
- Key Laboratory of Saline-Alkaline Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Yan Tian
- College of Life Science, Northeast Forestry University, Harbin, 150040 China
| | - Fanjuan Meng
- College of Life Science, Northeast Forestry University, Harbin, 150040 China
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Li H, Wang Y, Wu M, Li L, Li C, Han Z, Yuan J, Chen C, Song W, Wang C. Genome-Wide Identification of AP2/ERF Transcription Factors in Cauliflower and Expression Profiling of the ERF Family under Salt and Drought Stresses. FRONTIERS IN PLANT SCIENCE 2017; 8:946. [PMID: 28642765 PMCID: PMC5462956 DOI: 10.3389/fpls.2017.00946] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/22/2017] [Indexed: 05/18/2023]
Abstract
The AP2/ERF transcription factors (TFs) comprise one of the largest gene superfamilies in plants. These TFs perform vital roles in plant growth, development, and responses to biotic and abiotic stresses. In this study, 171 AP2/ERF TFs were identified in cauliflower (Brassica oleracea L. var. botrytis), one of the most important horticultural crops in Brassica. Among these TFs, 15, 9, and 1 TFs were classified into the AP2, RAV, and Soloist family, respectively. The other 146 TFs belong to ERF family, which were further divided into the ERF and DREB subfamilies. The ERF subfamily contained 91 TFs, while the DREB subfamily contained 55 TFs. Phylogenetic analysis results indicated that the AP2/ERF TFs can be classified into 13 groups, in which 25 conserved motifs were confirmed. Some motifs were group- or subgroup- specific, implying that they are significant to the functions of the AP2/ERF TFs of these clades. In addition, 35 AP2/ERF TFs from the 13 groups were selected randomly and then used for expression pattern analysis under salt and drought stresses. The majority of these AP2/ERF TFs exhibited positive responses to these stress conditions. In specific, Bra-botrytis-ERF054a, Bra-botrytis-ERF056, and Bra-botrytis-CRF2a demonstrated rapid responses. By contrast, six AP2/ERF TFs were showed to delay responses to both stresses. The AP2/ERF TFs exhibiting specific expression patterns under salt or drought stresses were also confirmed. Further functional analysis indicated that ectopic overexpression of Bra-botrytis-ERF056 could increase tolerance to both salt and drought treatments. These findings provide new insights into the AP2/ERF TFs present in cauliflower, and offer candidate AP2/ERF TFs for further studies on their roles in salt and drought stress tolerance.
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Affiliation(s)
- Hui Li
- College of Life Sciences, Nankai UniversityTianjin, China
- College of Horticulture and Landscape, Tianjin Agricultural UniversityTianjin, China
| | - Yu Wang
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Mei Wu
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Lihong Li
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Cong Li
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Zhanpin Han
- College of Horticulture and Landscape, Tianjin Agricultural UniversityTianjin, China
| | - Jiye Yuan
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Chengbin Chen
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Wenqin Song
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Chunguo Wang
- College of Life Sciences, Nankai UniversityTianjin, China
- *Correspondence: Chunguo Wang
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Yao W, Wang S, Zhou B, Jiang T. Transgenic poplar overexpressing the endogenous transcription factor ERF76 gene improves salinity tolerance. TREE PHYSIOLOGY 2016; 36:896-908. [PMID: 26941290 DOI: 10.1093/treephys/tpw004] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 01/08/2016] [Indexed: 05/19/2023]
Abstract
The ethylene response factor (ERF) family is one of the largest plant-specific transcription factor families, playing an important role in plant development and response to stresses. The ERF76 gene is a member of the poplar ERF transcription factor gene family. First, we validated that the ERF76 gene expressed in leaf and root tissues is responsive to salinity stress. We then successfully cloned the ERF76 cDNA fragment containing an open reading frame from di-haploid Populus simonii × Populus nigra and proved that ERF76 protein is targeted to the nucleus. Finally, we transferred the gene into the same poplar clone by the Agrobacterium-mediated leaf disc method. Using both RNA-Seq and reverse transcription-quantitative polymerase chain reaction, we validated that expression level of ERF76 is significantly higher in transgenic plants than that in the nontransgenic control. Using RNA-Seq data, we have identified 375 genes that are differentially expressed between the transgenic plants and the control under salt treatment. Among the differentially expressed genes, 16 are transcription factor genes and 45 are stress-related genes, both of which are upregulated significantly in transgenic plants, compared with the control. Under salt stress, the transgenic plants showed significant increases in plant height, root length, fresh weight, and abscisic acid (ABA) and gibberellin (GA) concentration compared with the control, suggesting that overexpression of ERF76 in transgenic poplar upregulated the expression of stress-related genes and increased the ability of ABA and GA biosynthesis, which resulted in stronger tolerance to salt stress.
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Affiliation(s)
- Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
| | - Shengji Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
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Zhu M, Monroe JG, Suhail Y, Villiers F, Mullen J, Pater D, Hauser F, Jeon BW, Bader JS, Kwak JM, Schroeder JI, McKay JK, Assmann SM. Molecular and systems approaches towards drought-tolerant canola crops. THE NEW PHYTOLOGIST 2016; 210:1169-1189. [PMID: 26879345 DOI: 10.1111/nph.13866] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 12/14/2015] [Indexed: 06/05/2023]
Abstract
1169 I. 1170 II. 1170 III. 1172 IV. 1176 V. 1181 VI. 1182 1183 References 1183 SUMMARY: Modern agriculture is facing multiple challenges including the necessity for a substantial increase in production to meet the needs of a burgeoning human population. Water shortage is a deleterious consequence of both population growth and climate change and is one of the most severe factors limiting global crop productivity. Brassica species, particularly canola varieties, are cultivated worldwide for edible oil, animal feed, and biodiesel, and suffer dramatic yield loss upon drought stress. The recent release of the Brassica napus genome supplies essential genetic information to facilitate identification of drought-related genes and provides new information for agricultural improvement in this species. Here we summarize current knowledge regarding drought responses of canola, including physiological and -omics effects of drought. We further discuss knowledge gained through translational biology based on discoveries in the closely related reference species Arabidopsis thaliana and through genetic strategies such as genome-wide association studies and analysis of natural variation. Knowledge of drought tolerance/resistance responses in canola together with research outcomes arising from new technologies and methodologies will inform novel strategies for improvement of drought tolerance and yield in this and other important crop species.
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Affiliation(s)
- Mengmeng Zhu
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
| | - J Grey Monroe
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Yasir Suhail
- Department of Biomedical Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Florent Villiers
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20740, USA
| | - Jack Mullen
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Dianne Pater
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - Felix Hauser
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - Byeong Wook Jeon
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
| | - Joel S Bader
- Department of Biomedical Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205, USA
| | - June M Kwak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20740, USA
- Center for Plant Aging Research, Institute for Basic Science, Department of New Biology, DGIST, Daegu, 42988, Korea
| | - Julian I Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - John K McKay
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Sarah M Assmann
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
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Solis J, Baisakh N, Brandt SR, Villordon A, La Bonte D. Transcriptome Profiling of Beach Morning Glory (Ipomoea imperati) under Salinity and Its Comparative Analysis with Sweetpotato. PLoS One 2016; 11:e0147398. [PMID: 26848754 PMCID: PMC4743971 DOI: 10.1371/journal.pone.0147398] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 01/04/2016] [Indexed: 01/23/2023] Open
Abstract
The response and adaption to salt remains poorly understood for beach morning glory [Ipomoea imperati (Vahl) Griseb], one of a few relatives of sweetpotato, known to thrive under salty and extreme drought conditions. In order to understand the genetic mechanisms underlying salt tolerance of a Convolvulaceae member, a genome-wide transcriptome study was carried out in beach morning glory by 454 pyrosequencing. A total of 286,584 filtered reads from both salt stressed and unstressed (control) root and shoot tissues were assembled into 95,790 unigenes with an average length of 667 base pairs (bp) and N50 of 706 bp. Putative differentially expressed genes (DEGs) were identified as transcripts overrepresented under salt stressed tissues compared to the control, and were placed into metabolic pathways. Most of these DEGs were involved in stress response, membrane transport, signal transduction, transcription activity and other cellular and molecular processes. We further analyzed the gene expression of 14 candidate genes of interest for salt tolerance through quantitative reverse transcription PCR (qRT-PCR) and confirmed their differential expression under salt stress in both beach morning glory and sweetpotato. The results comparing transcripts of I. imperati against the transcriptome of other Ipomoea species, including sweetpotato are also presented in this study. In addition, 6,233 SSR markers were identified, and an in silico analysis predicted that 434 primer pairs out of 4,897 target an identifiable homologous sequence in other Ipomoea transcriptomes, including sweetpotato. The data generated in this study will help in understanding the basics of salt tolerance of beach morning glory and the SSR resources generated will be useful for comparative genomics studies and further enhance the path to the marker-assisted breeding of sweetpotato for salt tolerance.
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Affiliation(s)
- Julio Solis
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States of America
| | - Niranjan Baisakh
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States of America
- * E-mail: (NB); (DL)
| | - Steven R. Brandt
- Louisiana Digital Media Center, Louisiana State University, Baton Rouge, LA, United States of America
| | - Arthur Villordon
- Sweet Potato Research Station, Louisiana State University Agricultural Center, Chase, LA, United States of America
| | - Don La Bonte
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States of America
- * E-mail: (NB); (DL)
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41
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Gao S, Yang L, Zeng HQ, Zhou ZS, Yang ZM, Li H, Sun D, Xie F, Zhang B. A cotton miRNA is involved in regulation of plant response to salt stress. Sci Rep 2016; 6:19736. [PMID: 26813144 PMCID: PMC4728436 DOI: 10.1038/srep19736] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/15/2015] [Indexed: 11/09/2022] Open
Abstract
The present study functionally identified a new microRNA (microRNA ovual line 5, miRNVL5) with its target gene GhCHR from cotton (Gossypium hirsutum). The sequence of miRNVL5 precursor is 104 nt long, with a well developed secondary structure. GhCHR contains two DC1 and three PHD Cys/His-rich domains, suggesting that GhCHR encodes a zinc-finger domain-containing transcription factor. miRNVL5 and GhCHR express at various developmental stages of cotton. Under salt stress (50-400 mM NaCl), miRNVL5 expression was repressed, with concomitant high expression of GhCHR in cotton seedlings. Ectopic expression of GhCHR in Arabidopsis conferred salt stress tolerance by reducing Na(+) accumulation in plants and improving primary root growth and biomass. Interestingly, Arabidopsis constitutively expressing miRNVL5 showed hypersensitivity to salt stress. A GhCHR orthorlous gene At2g44380 from Arabidopsis that can be cleaved by miRNVL5 was identified by degradome sequencing, but no confidential miRNVL5 homologs in Arabidopsis have been identified. Microarray analysis of miRNVL5 transgenic Arabidopsis showed six downstream genes (CBF1, CBF2, CBF3, ERF4, AT3G22920, and AT3G49200), which were induced by salt stress in wild-type but repressed in miRNVL5-expressing Arabidopsis. These results indicate that miRNVL5 is involved in regulation of plant response to salt stress.
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Affiliation(s)
- Shuai Gao
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Lu Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Hou Qing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhao Sheng Zhou
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Hua Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China.,Department of Plant Science, College of Life Science, Henan Agricultural University, Henan 450002, China
| | - Di Sun
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China.,Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, TA 77843, USA
| | - Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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Wang F, Chen HW, Li QT, Wei W, Li W, Zhang WK, Ma B, Bi YD, Lai YC, Liu XL, Man WQ, Zhang JS, Chen SY. GmWRKY27 interacts with GmMYB174 to reduce expression of GmNAC29 for stress tolerance in soybean plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:224-36. [PMID: 25990284 DOI: 10.1111/tpj.12879] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/15/2015] [Accepted: 04/27/2015] [Indexed: 05/19/2023]
Abstract
Soybean (Glycine max) is an important crop for oil and protein resources worldwide. The molecular mechanism of the abiotic stress response in soybean is largely unclear. We previously identified multiple stress-responsive WRKY genes from soybean. Here, we further characterized the roles of one of these genes, GmWRKY27, in abiotic stress tolerance using a transgenic hairy root assay. GmWRKY27 expression was increased by various abiotic stresses. Over-expression and RNAi analysis demonstrated that GmWRKY27 improves salt and drought tolerance in transgenic soybean hairy roots. Measurement of physiological parameters, including reactive oxygen species and proline contents, supported this conclusion. GmWRKY27 inhibits expression of a downstream gene GmNAC29 by binding to the W-boxes in its promoter region. The GmNAC29 is a negative factor of stress tolerance as indicated by the performance of transgenic hairy roots under stress. GmWRKY27 interacts with GmMYB174, which also suppresses GmNAC29 expression and enhances drought stress tolerance. The GmWRKY27 and GmMYB174 may have evolved to bind to neighbouring cis elements in the GmNAC29 promoter to co-reduce promoter activity and gene expression. Our study discloses a valuable mechanism in soybean for regulation of the stress response by two associated transcription factors. Manipulation of these genes should facilitate improvements in stress tolerance in soybean and other crops.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao-Wei Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing-Tian Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Li
- Institute of Crop Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang Province, China
| | - Wan-Ke Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Biao Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying-Dong Bi
- Institute of Crop Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang Province, China
| | - Yong-Cai Lai
- Institute of Crop Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang Province, China
| | - Xin-Lei Liu
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, 368 Xuefu Road, Harbin, 150086, China
| | - Wei-Qun Man
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, 368 Xuefu Road, Harbin, 150086, China
| | - Jin-Song Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shou-Yi Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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Ransbotyn V, Yeger-Lotem E, Basha O, Acuna T, Verduyn C, Gordon M, Chalifa-Caspi V, Hannah MA, Barak S. A combination of gene expression ranking and co-expression network analysis increases discovery rate in large-scale mutant screens for novel Arabidopsis thaliana abiotic stress genes. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:501-13. [PMID: 25370817 DOI: 10.1111/pbi.12274] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/29/2014] [Accepted: 08/28/2014] [Indexed: 05/20/2023]
Abstract
As challenges to food security increase, the demand for lead genes for improving crop production is growing. However, genetic screens of plant mutants typically yield very low frequencies of desired phenotypes. Here, we present a powerful computational approach for selecting candidate genes for screening insertion mutants. We combined ranking of Arabidopsis thaliana regulatory genes according to their expression in response to multiple abiotic stresses (Multiple Stress [MST] score), with stress-responsive RNA co-expression network analysis to select candidate multiple stress regulatory (MSTR) genes. Screening of 62 T-DNA insertion mutants defective in candidate MSTR genes, for abiotic stress germination phenotypes yielded a remarkable hit rate of up to 62%; this gene discovery rate is 48-fold greater than that of other large-scale insertional mutant screens. Moreover, the MST score of these genes could be used to prioritize them for screening. To evaluate the contribution of the co-expression analysis, we screened 64 additional mutant lines of MST-scored genes that did not appear in the RNA co-expression network. The screening of these MST-scored genes yielded a gene discovery rate of 36%, which is much higher than that of classic mutant screens but not as high as when picking candidate genes from the co-expression network. The MSTR co-expression network that we created, AraSTressRegNet is publicly available at http://netbio.bgu.ac.il/arnet. This systems biology-based screening approach combining gene ranking and network analysis could be generally applicable to enhancing identification of genes regulating additional processes in plants and other organisms provided that suitable transcriptome data are available.
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Affiliation(s)
- Vanessa Ransbotyn
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
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Kazan K. Diverse roles of jasmonates and ethylene in abiotic stress tolerance. TRENDS IN PLANT SCIENCE 2015; 20:219-29. [PMID: 25731753 DOI: 10.1016/j.tplants.2015.02.001] [Citation(s) in RCA: 410] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/25/2015] [Accepted: 02/01/2015] [Indexed: 05/18/2023]
Abstract
Jasmonates (JAs) and ethylene (ET), often acting cooperatively, play essential roles in regulating plant defense against pests and pathogens. Recent research reviewed here has revealed mechanistic new insights into the mode of action of these hormones in plant abiotic stress tolerance. During cold stress, JAs and ET differentially regulate the C-repeat binding factor (CBF) pathway. Major JA and ET signaling hubs such as JAZ proteins, CTR1, MYC2, components of the mediator complex, EIN2, EIN3, and several members of the AP2/ERF transcription factor gene family all have complex regulatory roles during abiotic stress adaptation. Better understanding the roles of these phytohormones in plant abiotic stress tolerance will contribute to the development of crop plants tolerant to a wide range of stressful environments.
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Affiliation(s)
- Kemal Kazan
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, Queensland, Australia; The Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Queensland Bioscience Precinct, Brisbane, Queensland, Australia.
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Tan FQ, Tu H, Liang WJ, Long JM, Wu XM, Zhang HY, Guo WW. Comparative metabolic and transcriptional analysis of a doubled diploid and its diploid citrus rootstock (C. junos cv. Ziyang xiangcheng) suggests its potential value for stress resistance improvement. BMC PLANT BIOLOGY 2015; 15:89. [PMID: 25848687 PMCID: PMC4374211 DOI: 10.1186/s12870-015-0450-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/05/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Polyploidy has often been considered to confer plants a better adaptation to environmental stresses. Tetraploid citrus rootstocks are expected to have stronger stress tolerance than diploid. Plenty of doubled diploid citrus plants were exploited from diploid species for citrus rootstock improvement. However, limited metabolic and molecular information related to tetraploidization is currently available at a systemic biological level. This study aimed to evaluate the occurrence and extent of metabolic and transcriptional changes induced by tetraploidization in Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka), which is a special citrus germplasm native to China and widely used as an iron deficiency tolerant citrus rootstock. RESULTS Doubled diploid Ziyang xiangcheng has typical morphological and anatomical features such as shorter plant height, larger and thicker leaves, bigger stomata and lower stomatal density, compared to its diploid parent. GC-MS (Gas chromatography coupled to mass spectrometry) analysis revealed that tetraploidization has an activation effect on the accumulation of primary metabolites in leaves; many stress-related metabolites such as sucrose, proline and γ-aminobutyric acid (GABA) was remarkably up-regulated in doubled diploid. However, LC-QTOF-MS (Liquid chromatography quadrupole time-of-flight mass spectrometry) analysis demonstrated that tetraploidization has an inhibition effect on the accumulation of secondary metabolites in leaves; all the 33 flavones were down-regulated while all the 6 flavanones were up-regulated in 4x. By RNA-seq analysis, only 212 genes (0.8% of detected genes) are found significantly differentially expressed between 2x and 4x leaves. Notably, those genes were highly related to stress-response functions, including responses to salt stress, water and abscisic acid. Interestingly, the transcriptional divergence could not explain the metabolic changes, probably due to post-transcriptional regulation. CONCLUSION Taken together, tetraploidization induced considerable changes in leaf primary and secondary metabolite accumulation in Ziyang xiangcheng. However, the effect of tetraploidization on transcriptome is limited. Compared to diploid, higher expression level of stress related genes and higher content of stress related metabolites in doubled diploid could be beneficial for its stress tolerance.
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Affiliation(s)
- Feng-Quan Tan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Hong Tu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wu-Jun Liang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jian-Mei Long
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Hong-Yan Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
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Chen D, Ma X, Li C, Zhang W, Xia G, Wang M. A wheat aminocyclopropane-1-carboxylate oxidase gene, TaACO1, negatively regulates salinity stress in Arabidopsis thaliana. PLANT CELL REPORTS 2014; 33:1815-27. [PMID: 25048023 DOI: 10.1007/s00299-014-1659-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/23/2014] [Accepted: 07/14/2014] [Indexed: 05/23/2023]
Abstract
TaACO1 could catalyze ACC into ethylene in vitro. Constitutive expression of TaACO1 in Arabidopsis conferred salt sensitivity, and TaACO1 regulates salt stress mainly via the DREB1/CBF signal transduction pathway. Ethylene signaling plays essential roles in mediating plant responses to biotic and abiotic stresses, besides regulating plant growth and development. The roles of ethylene biosynthesis in abiotic stress, however, remain elusive. In this study, an aminocyclopropane-1-carboxylate oxidase gene, TaACO1, affecting the terminal step in ethylene biosynthesis, was isolated from a salt-tolerant bread wheat introgression line Shanrong No. 3 (SR3) and its effect on salt-stress response was examined. Purified recombinant protein of TaACO1 heterogenously expressed in Escherchia coli could catalyze ACC into ethylene in vitro. TaACO1 transcripts were down-regulated by salt, drought, oxidative stress and ABA. TaACO1-transgenic plants conferred salt sensitivity as judged from the seed germination, cotyledon greening and the relative root growth under salt stress. Constitutive expression of TaACO1 in Arabidopsis increased AtMYB15 expression and suppressed the expression of stress-responsive genes AtRAB18, AtCBF1 and AtCBF3. These findings are helpful in understanding the roles of ethylene biosynthesis in plant salt-stress response.
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Affiliation(s)
- Donghua Chen
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, People's Republic of China
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Wan L, Wu Y, Huang J, Dai X, Lei Y, Yan L, Jiang H, Zhang J, Varshney RK, Liao B. Identification of ERF genes in peanuts and functional analysis of AhERF008 and AhERF019 in abiotic stress response. Funct Integr Genomics 2014; 14:467-77. [PMID: 24902799 DOI: 10.1007/s10142-014-0381-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 05/13/2014] [Accepted: 05/26/2014] [Indexed: 12/24/2022]
Abstract
Ethylene-responsive factor (ERF) play an important role in regulating gene expression in plant development and response to stresses. In peanuts (Arachis hypogaea L.), which produce flowers aerially and pods underground, only a few ERF genes have been identified so far. This study identifies 63 ERF unigenes from 247,313 peanut EST sequences available in the NCBI database. The phylogeny, gene structures, and putative conserved motifs in the peanut ERF proteins were analysed. Comparative analysis revealed the absence of two subgroups (A1 and A3) of the ERF family in peanuts; only 10 subgroups were identified in peanuts compared to 12 subgroups in Arabidopsis and soybeans. AP2/ERF domains were found to be conserved among peanuts, Arabidopsis, and soybeans. Outside the AP2/ERF domain, many soybean-specific conserved motifs were also detected in peanuts. The expression analysis of ERF family genes representing each clade revealed differential expression patterns in response to biotic and abiotic stresses. Overexpression of AhERF008 influenced the root gravity of Arabidopsis, whereas overexpression of AhERF019 enhanced tolerance to drought, heat, and salt stresses in Arabidopsis. The information generated in this study will be helpful to further investigate the function of ERFs in plant development and stress response.
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Affiliation(s)
- Liyun Wan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China,
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Zhang X, Lu G, Long W, Zou X, Li F, Nishio T. Recent progress in drought and salt tolerance studies in Brassica crops. BREEDING SCIENCE 2014; 64:60-73. [PMID: 24987291 PMCID: PMC4031111 DOI: 10.1270/jsbbs.64.60] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 03/19/2014] [Indexed: 05/19/2023]
Abstract
Water deficit imposed by either drought or salinity brings about severe growth retardation and yield loss of crops. Since Brassica crops are important contributors to total oilseed production, it is urgently needed to develop tolerant cultivars to ensure yields under such adverse conditions. There are various physiochemical mechanisms for dealing with drought and salinity in plants at different developmental stages. Accordingly, different indicators of tolerance to drought or salinity at the germination, seedling, flowering and mature stages have been developed and used for germplasm screening and selection in breeding practices. Classical genetic and modern genomic approaches coupled with precise phenotyping have boosted the unravelling of genes and metabolic pathways conferring drought or salt tolerance in crops. QTL mapping of drought and salt tolerance has provided several dozen target QTLs in Brassica and the closely related Arabidopsis. Many drought- or salt-tolerant genes have also been isolated, some of which have been confirmed to have great potential for genetic improvement of plant tolerance. It has been suggested that molecular breeding approaches, such as marker-assisted selection and gene transformation, that will enhance oil product security under a changing climate be integrated in the development of drought- and salt-tolerant Brassica crops.
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Affiliation(s)
- Xuekun Zhang
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute,
CAAS, Wuhan 430062,
China
| | - Guangyuan Lu
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute,
CAAS, Wuhan 430062,
China
| | - Weihua Long
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute,
CAAS, Wuhan 430062,
China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences,
Nanjing 210014,
China
| | - Xiling Zou
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute,
CAAS, Wuhan 430062,
China
| | - Feng Li
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute,
CAAS, Wuhan 430062,
China
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University,
Sendai, Miyagi 981-8555,
Japan
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A systematic exploration of high-temperature stress-responsive genes in potato using large-scale yeast functional screening. Mol Genet Genomics 2013; 289:185-201. [DOI: 10.1007/s00438-013-0795-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/18/2013] [Indexed: 11/25/2022]
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Licausi F, Ohme-Takagi M, Perata P. APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs. THE NEW PHYTOLOGIST 2013; 199:639-49. [PMID: 24010138 DOI: 10.1111/nph.12291] [Citation(s) in RCA: 590] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Transcription factors belonging to the APETALA2/Ethylene Responsive Factor (AP2/ERF) family are conservatively widespread in the plant kingdom. These regulatory proteins are involved in the control of primary and secondary metabolism, growth and developmental programs, as well as responses to environmental stimuli. Due to their plasticity and to the specificity of individual members of this family, AP2/ERF transcription factors represent valuable targets for genetic engineering and breeding of crops. In this review, we integrate the evidence collected from functional and structural studies to describe their different mechanisms of action and the regulatory pathways that affect their activity.
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