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Wang R, Wu X, Wang Z, Zhang X, Chen L, Duan Q, Huang J. Genome-Wide Identification and Expression Analysis of BrGeBP Genes Reveal Their Potential Roles in Cold and Drought Stress Tolerance in Brassica rapa. Int J Mol Sci 2023; 24:13597. [PMID: 37686403 PMCID: PMC10487926 DOI: 10.3390/ijms241713597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
The GLABROUS1 Enhancer Binding Protein (GeBP) gene family is pivotal in regulating plant growth, development, and stress responses. However, the role of GeBP in Brassica rapa remains unclear. This study identifies 20 BrGeBP genes distributed across 6 chromosomes, categorized into 4 subfamilies. Analysis of their promoter sequences reveals multiple stress-related elements, including those responding to drought, low temperature, methyl jasmonate (MeJA), and gibberellin (GA). Gene expression profiling demonstrates wide expression of BrGeBPs in callus, stem, silique, and flower tissues. Notably, BrGeBP5 expression significantly decreases under low-temperature treatment, while BrGeBP3 and BrGeBP14 show increased expression during drought stress, followed by a decrease. Protein interaction predictions suggest that BrGeBP14 homolog, At5g28040, can interact with DES1, a known stress-regulating protein. Additionally, microRNA172 targeting BrGeBP5 is upregulated under cold tolerance. These findings underscore the vital role of BrGeBPs in abiotic stress tolerance. Specifically, BrGeBP3, BrGeBP5, and BrGeBP14 show great potential for regulating abiotic stress. This study contributes to understanding the function of BrGeBPs and provides valuable insights for studying abiotic stress in B. rapa.
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Affiliation(s)
| | | | | | | | | | - Qiaohong Duan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China
| | - Jiabao Huang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China
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2
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Wu Y, Shi H, Yu H, Ma Y, Hu H, Han Z, Zhang Y, Zhen Z, Yi L, Hou J. Combined GWAS and Transcriptome Analyses Provide New Insights Into the Response Mechanisms of Sunflower Against Drought Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:847435. [PMID: 35592557 PMCID: PMC9111542 DOI: 10.3389/fpls.2022.847435] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/31/2022] [Indexed: 05/25/2023]
Abstract
Sunflower is one of the most important oil crops in the world, and drought stress can severely limit its production and quality. To understand the underlying mechanism of drought tolerance, and identify candidate genes for drought tolerance breeding, we conducted a combined genome-wide association studies (GWAS) and RNA-seq analysis. A total of 226 sunflower inbred lines were collected from different regions of China and other countries. Eight phenotypic traits were evaluated under control and drought stress conditions. Genotyping was performed using a Specific-Locus Amplified Fragment Sequencing (SLAF-seq) approach. A total of 934.08 M paired-end reads were generated, with an average Q30 of 91.97%. Based on the 243,291 polymorphic SLAF tags, a total of 94,162 high-quality SNPs were identified. Subsequent analysis of linkage disequilibrium (LD) and population structure in the 226 accessions was carried out based on the 94,162 high-quality SNPs. The average LD decay across the genome was 20 kb. Admixture analysis indicated that the entire population most likely originated from 11 ancestors. GWAS was performed using three methods (MLM, FarmCPU, and BLINK) simultaneously. A total of 80 SNPs showed significant associations with the 8 traits (p < 1.062 × 10-6). Next, a total of 118 candidate genes were found. To obtain more reliable candidate genes, RNA-seq analysis was subsequently performed. An inbred line with the highest drought tolerance was selected according to phenotypic traits. RNA was extracted from leaves at 0, 7, and 14 days of drought treatment. A total of 18,922 differentially expressed genes were obtained. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed up-regulated genes were mainly enriched in the branched-chain amino acid catabolic process, while the down-regulated genes were mainly enriched in the photosynthesis-related process. Six DEGs were randomly selected from all DEGs for validation; these genes showed similar patterns in RNA-seq and RT-qPCR analysis, with a correlation coefficient of 0.8167. Through the integration of the genome-wide association study and the RNA-sequencing, 14 candidate genes were identified. Four of them (LOC110885273, LOC110872899, LOC110891369, LOC110920644) were abscisic acid related protein kinases and transcription factors. These genes may play an important role in sunflower drought response and will be used for further study. Our findings provide new insights into the response mechanisms of sunflowers against drought stress and contribute to further genetic breeding.
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Affiliation(s)
- Yang Wu
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
| | - Huimin Shi
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
| | - Haifeng Yu
- Institute of Crop Breeding and Cultivation, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, China
| | - Yu Ma
- Institute of Crop Breeding and Cultivation, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, China
| | - Haibo Hu
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhigang Han
- Institute of Crop Breeding and Cultivation, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, China
| | - Yonghu Zhang
- Institute of Crop Breeding and Cultivation, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, China
| | - Zilong Zhen
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
| | - Liuxi Yi
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
| | - Jianhua Hou
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
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3
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Han Y, Wang Y, Zhai Y, Wen Z, Liu J, Xi C, Zhao H, Wang Y, Han S. OsOSCA1.1 Mediates Hyperosmolality and Salt Stress Sensing in Oryza sativa. BIOLOGY 2022; 11:biology11050678. [PMID: 35625406 PMCID: PMC9138581 DOI: 10.3390/biology11050678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/16/2022]
Abstract
OSCA (reduced hyperosmolality-induced [Ca2+]i increase) is a family of mechanosensitive calcium-permeable channels that play a role in osmosensing and stomatal immunity in plants. Oryza sativa has 11 OsOSCA genes; some of these were shown to complement hyperosmolality-induced [Ca2+]cyt increases (OICIcyt), salt stress-induced [Ca2+]cyt increases (SICIcyt), and the associated growth phenotype in the Arabidopsis thaliana mutant osca1. However, their biological functions in rice remain unclear. In this paper, we found that OsOSCA1.1 mediates OICIcyt and SICIcyt in rice roots, which are critical for stomatal closure, plant survival, and gene expression in shoots, in response to hyperosmolality and the salt stress treatment of roots. Compared with wild-type (Zhonghua11, ZH11) plants, OICIcyt and SICIcyt were abolished in the roots of 10-day-old ososca1.1 seedlings, in response to treatment with 250 mM of sorbitol and 100 mM of NaCl, respectively. Moreover, hyperosmolality- and salt stress-induced stomatal closure were also disrupted in a 30-day-old ososca1.1 mutant, resulting in lower stomatal resistance and survival rates than that in ZH11. However, overexpression of OsOSCA1.1 in ososca1.1 complemented stomatal movement and survival, in response to hyperosmolality and salt stress. The transcriptomic analysis further revealed the following three types of OsOSCA1.1-regulated genes in the shoots: 2416 sorbitol-responsive, 2349 NaCl-responsive and 1844 common osmotic stress-responsive genes after treated with 250 mM of sorbitol and 125 mM NaCl of in 30-day-old rice roots for 24 h. The Gene Ontology enrichment analysis showed that these OsOSCA1.1-regulated genes were relatively enriched in transcription regulation, hormone response, and phosphorylation terms of the biological processes category, which is consistent with the Cis-regulatory elements ABRE, ARE, MYB and MYC binding motifs that were overrepresented in 2000-bp promoter regions of these OsOSCA1.1-regulated genes. These results indicate that OsOSCA-mediated calcium signaling specifically regulates gene expression, in response to drought and salt stress in rice.
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Affiliation(s)
- Yang Han
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.H.); (Y.W.); (Y.Z.); (Z.W.); (J.L.); (C.X.); (H.Z.); (Y.W.)
| | - Yinxing Wang
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.H.); (Y.W.); (Y.Z.); (Z.W.); (J.L.); (C.X.); (H.Z.); (Y.W.)
| | - Yuanjun Zhai
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.H.); (Y.W.); (Y.Z.); (Z.W.); (J.L.); (C.X.); (H.Z.); (Y.W.)
| | - Zhaohong Wen
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.H.); (Y.W.); (Y.Z.); (Z.W.); (J.L.); (C.X.); (H.Z.); (Y.W.)
| | - Jin Liu
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.H.); (Y.W.); (Y.Z.); (Z.W.); (J.L.); (C.X.); (H.Z.); (Y.W.)
| | - Chao Xi
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.H.); (Y.W.); (Y.Z.); (Z.W.); (J.L.); (C.X.); (H.Z.); (Y.W.)
| | - Heping Zhao
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.H.); (Y.W.); (Y.Z.); (Z.W.); (J.L.); (C.X.); (H.Z.); (Y.W.)
| | - Yingdian Wang
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.H.); (Y.W.); (Y.Z.); (Z.W.); (J.L.); (C.X.); (H.Z.); (Y.W.)
- Academy of Plateau Science and Sustainability of the People’s Government of Qinghai Province & Beijing Normal University, Qinghai Normal University, Xining 810008, China
| | - Shengcheng Han
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.H.); (Y.W.); (Y.Z.); (Z.W.); (J.L.); (C.X.); (H.Z.); (Y.W.)
- Academy of Plateau Science and Sustainability of the People’s Government of Qinghai Province & Beijing Normal University, Qinghai Normal University, Xining 810008, China
- Correspondence:
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4
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Zhou H, Wang Y, Zhang Y, Xiao Y, Liu X, Deng H, Lu X, Tang W, Zhang G. Comparative Analysis of Heat-Tolerant and Heat-Susceptible Rice Highlights the Role of OsNCED1 Gene in Heat Stress Tolerance. PLANTS 2022; 11:plants11081062. [PMID: 35448790 PMCID: PMC9026844 DOI: 10.3390/plants11081062] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022]
Abstract
To elucidate the mechanism underlying the response of rice to heat stress (HS), the transcriptome profile of panicles was comparatively analyzed between the heat-tolerant line 252 (HTL252) and heat-susceptible line 082 (HSL082), two rice recombinant inbred lines (RILs). Our differentially expressed gene (DEG) analysis revealed that the DEGs are mainly associated with protein binding, catalysis, stress response, and cellular process. The MapMan analysis demonstrated that the heat-responsive (HR) genes for heat shock proteins, transcription factors, development, and phytohormones are specifically induced in HTL252 under HS. Based on the DEG analysis, the key gene OsNCED1 (Os02g0704000), which was induced under HS, was selected for further functional validation. Moreover, 9-cis-epoxycarotenoid dioxygenase (NCED) is a key rate-limiting enzyme in the ABA biosynthetic pathway. Overexpression of OsNCED1 improved the HS tolerance of rice at the heading and flowering stage. OsNCED1-overexpression plants exhibited significant increases in pollen viability, seed setting rate, superoxide dismutase (SOD) and peroxidase (POD) activities, while significantly lower electrolyte leakage and malondialdehyde (MDA) content relative to the wild type (WT). These results suggested that OsNCED1 overexpression can improve the heat tolerance of rice by enhancing the antioxidant capacity. Overall, this study lays a foundation for revealing the molecular regulatory mechanism underlying the response of rice to prolonged HS.
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Affiliation(s)
- Huang Zhou
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (Y.W.); (Y.Z.); (Y.X.); (X.L.); (H.D.); (X.L.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Hunan Agricultural University, Changsha 410128, China
| | - Yingfeng Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (Y.W.); (Y.Z.); (Y.X.); (X.L.); (H.D.); (X.L.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Hunan Agricultural University, Changsha 410128, China
| | - Yijin Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (Y.W.); (Y.Z.); (Y.X.); (X.L.); (H.D.); (X.L.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Hunan Agricultural University, Changsha 410128, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (Y.W.); (Y.Z.); (Y.X.); (X.L.); (H.D.); (X.L.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Hunan Agricultural University, Changsha 410128, China
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (Y.W.); (Y.Z.); (Y.X.); (X.L.); (H.D.); (X.L.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Hunan Agricultural University, Changsha 410128, China
| | - Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (Y.W.); (Y.Z.); (Y.X.); (X.L.); (H.D.); (X.L.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Hunan Agricultural University, Changsha 410128, China
| | - Xuedan Lu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (Y.W.); (Y.Z.); (Y.X.); (X.L.); (H.D.); (X.L.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Hunan Agricultural University, Changsha 410128, China
| | - Wenbang Tang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (Y.W.); (Y.Z.); (Y.X.); (X.L.); (H.D.); (X.L.)
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Centre, Changsha 410125, China
- Correspondence: (W.T.); (G.Z.)
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (Y.W.); (Y.Z.); (Y.X.); (X.L.); (H.D.); (X.L.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Hunan Agricultural University, Changsha 410128, China
- Correspondence: (W.T.); (G.Z.)
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5
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Tiwari S, Nutan KK, Deshmukh R, Sarsu F, Gupta KJ, Singh AK, Singla-Pareek SL, Pareek A. Seedling-stage salinity tolerance in rice: Decoding the role of transcription factors. PHYSIOLOGIA PLANTARUM 2022; 174:e13685. [PMID: 35419814 DOI: 10.1111/ppl.13685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/10/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Rice is an important staple food crop that feeds over half of the human population, particularly in developing countries. Increasing salinity is a major challenge for continuing rice production. Though rice is affected by salinity at all the developmental stages, it is most sensitive at the early seedling stage. The yield thus depends on how many seedlings can withstand saline water at the stage of transplantation, especially in coastal farms. The rapid development of "omics" approaches has assisted researchers in identifying biological molecules that are responsive to salt stress. Several salinity-responsive quantitative trait loci (QTL) contributing to salinity tolerance have been identified and validated, making it essential to narrow down the search for the key genes within QTLs. Owing to the impressive progress of molecular tools, it is now clear that the response of plants toward salinity is highly complex, involving multiple genes, with a specific role assigned to the repertoire of transcription factors (TF). Targeting the TFs for improving salinity tolerance can have an inbuilt advantage of influencing multiple downstream genes, which in turn can contribute toward tolerance to multiple stresses. This is the first comparative study for TF-driven salinity tolerance in contrasting rice cultivars at the seedling stage that shows how tolerant genotypes behave differently than sensitive ones in terms of stress tolerance. Understanding the complexity of salt-responsive TF networks at the seedling stage will be helpful to alleviate crop resilience and prevent crop damage at an early growth stage in rice.
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Affiliation(s)
- Shalini Tiwari
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Kamlesh Kant Nutan
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Sahibzada Ajit Singh Nagar, Punjab, India
| | - Fatma Sarsu
- General Directorate of Agricultural Research and Policies, Ministry of Agriculture and Forestry, Ankara, Turkey
| | | | - Anil K Singh
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, Delhi, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
- National Agri-Food Biotechnology Institute, Sahibzada Ajit Singh Nagar, Punjab, India
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6
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Zargar SM, Mir RA, Ebinezer LB, Masi A, Hami A, Manzoor M, Salgotra RK, Sofi NR, Mushtaq R, Rohila JS, Rakwal R. Physiological and Multi-Omics Approaches for Explaining Drought Stress Tolerance and Supporting Sustainable Production of Rice. FRONTIERS IN PLANT SCIENCE 2022; 12:803603. [PMID: 35154193 PMCID: PMC8829427 DOI: 10.3389/fpls.2021.803603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Drought differs from other natural disasters in several respects, largely because of the complexity of a crop's response to it and also because we have the least understanding of a crop's inductive mechanism for addressing drought tolerance among all abiotic stressors. Overall, the growth and productivity of crops at a global level is now thought to be an issue that is more severe and arises more frequently due to climatic change-induced drought stress. Among the major crops, rice is a frontline staple cereal crop of the developing world and is critical to sustaining populations on a daily basis. Worldwide, studies have reported a reduction in rice productivity over the years as a consequence of drought. Plants are evolutionarily primed to withstand a substantial number of environmental cues by undergoing a wide range of changes at the molecular level, involving gene, protein and metabolite interactions to protect the growing plant. Currently, an in-depth, precise and systemic understanding of fundamental biological and cellular mechanisms activated by crop plants during stress is accomplished by an umbrella of -omics technologies, such as transcriptomics, metabolomics and proteomics. This combination of multi-omics approaches provides a comprehensive understanding of cellular dynamics during drought or other stress conditions in comparison to a single -omics approach. Thus a greater need to utilize information (big-omics data) from various molecular pathways to develop drought-resilient crop varieties for cultivation in ever-changing climatic conditions. This review article is focused on assembling current peer-reviewed published knowledge on the use of multi-omics approaches toward expediting the development of drought-tolerant rice plants for sustainable rice production and realizing global food security.
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Affiliation(s)
- Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Leonard Barnabas Ebinezer
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Ammarah Hami
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Madhiya Manzoor
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Najeebul Rehman Sofi
- Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Roohi Mushtaq
- Department of Biotechnology and Bioinformatics, SP College, Cluster University Srinagar, Srinagar, India
| | - Jai Singh Rohila
- Dale Bumpers National Rice Research Center, United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Stuttgart, AR, United States
| | - Randeep Rakwal
- Faculty of Health and Sport Sciences, University of Tsukuba, Ibaraki, Japan
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7
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Gour P, Kansal S, Agarwal P, Mishra BS, Sharma D, Mathur S, Raghuvanshi S. Variety-specific transcript accumulation during reproductive stage in drought-stressed rice. PHYSIOLOGIA PLANTARUM 2022; 174:e13585. [PMID: 34652858 DOI: 10.1111/ppl.13585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/23/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
The divergence of natural stress tolerance mechanisms between species is an intriguing phenomenon. To study it in rice, a comparative transcriptome analysis was carried out in 'heading' stage tissue (flag leaf, panicles and roots) of Nagina 22 (N22; drought-tolerant) and IR64 (drought-sensitive) plants subjected to field drought. Interestingly, N22 showed almost double the number of differentially expressed genes (DEGs) than IR64. Many DEGs colocalized within drought-related QTLs responsible for grain yield and drought tolerance and also associated with drought tolerance and critical drought-related plant traits such as leaf rolling, trehalose content, sucrose and cellulose content. Besides, co-expression analysis of the DEGs revealed several 'hub' genes known to actively regulate drought stress response. Strikingly, 1366 DEGs, including 21 'hub' genes, showed a distinct opposite regulation in the two rice varieties under similar drought conditions. Annotation of these variety-specific DEGs (VS-DEGs) revealed that they are distributed in various biological pathways. Furthermore, 103 VS-DEGs were found to physically interact with over 1300 genes, including 32 that physically interact with other VS-DEGs as well. The promoter region of these genes has sequence variations among the two rice varieties, which might be in part responsible for their unique expression pattern.
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Affiliation(s)
- Pratibha Gour
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Shivani Kansal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Priyanka Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | | | - Deepika Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, New Delhi, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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8
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Yu RM, Suo YY, Yang R, Chang YN, Tian T, Song YJ, Wang HJ, Wang C, Yang RJ, Liu HL, Gao G. StMBF1c positively regulates disease resistance to Ralstonia solanacearum via it's primary and secondary upregulation combining expression of StTPS5 and resistance marker genes in potato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 307:110877. [PMID: 33902863 DOI: 10.1016/j.plantsci.2021.110877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Multiprotein bridging factor 1 (MBF1) is a transcription coactivator that has a general defense response to pathogens. However, the regulatory mechanisms of MBF1 resistance bacterial wilt remain largely unknown. Here, the role of StMBF1c in potato resistance to Ralstonia solanacearum infection was characterized. qRT-PCR assays indicated that StMBF1c could was elicited by SA, MJ and ABA and the time-course expression pattern of the StMBF1c gene induced by R. solanacearum was found to be twice significant upregulated expression during the early and middle stages of bacterial wilt. Combined with the co-expression analysis of disease-resistant marker genes, gain-of-function and loss-of-function assays demonstrated that StMBF1c was associated with defence priming. Overexpression or silencing the MBF1c could enhance plants resistance or sensitivity to R. solanacearum through inducing or reducing NPR and PR genes related to SA signal pathway. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) experiment results confirmed the interaction of StMBF1c with StTPS5 which played a key role in ABA signal pathway in potato. It is speculated that by combining StTPS5 and resistance marker genes, StMBF1c is activated twice to participate in potato bacterial wilt resistance, in which EPI, PTI involved.
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Affiliation(s)
- Rui-Min Yu
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Yan-Yun Suo
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Rui Yang
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Yan-Nan Chang
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Tian Tian
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Yan-Jie Song
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Huan-Jun Wang
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Cong Wang
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Ru-Jie Yang
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Hong-Liang Liu
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Gang Gao
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
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9
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A transcriptomic view to wounding response in young Scots pine stems. Sci Rep 2021; 11:3778. [PMID: 33580160 PMCID: PMC7881122 DOI: 10.1038/s41598-021-82848-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
We studied the stress response of five-year-old Scots pine xylem to mechanical wounding using RNA sequencing. In general, we observed a bimodal response in pine xylem after wounding. Transcripts associated with water deficit stress, defence, and cell wall modification were induced at the earliest time point of three hours; at the same time, growth-related processes were down-regulated. A second temporal wave was triggered either at the middle and/or at the late time points (one and four days). Secondary metabolism, such as stilbene and lignan biosynthesis started one day after wounding. Scots pine synthesises the stilbenes pinosylvin and its monomethyl ether both as constitutive and induced defence compounds. Stilbene biosynthesis is induced by wounding, pathogens and UV stress, but is also developmentally regulated when heartwood is formed. Comparison of wounding responses to heartwood formation shows that many induced processes (in addition to stilbene biosynthesis) are similar and relate to defence or desiccation stress, but often specific transcripts are up-regulated in the developmental and wounding induced contexts. Pine resin biosynthesis was not induced in response to wounding, at least not during the first four days.
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Tiwari P, Chakrabarty D. Dehydrin in the past four decades: From chaperones to transcription co-regulators in regulating abiotic stress response. CURRENT RESEARCH IN BIOTECHNOLOGY 2021. [DOI: 10.1016/j.crbiot.2021.07.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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11
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do Amaral MN, Auler PA, Rossatto T, Barros PM, Oliveira MM, Braga EJB. Long-term somatic memory of salinity unveiled from physiological, biochemical and epigenetic responses in two contrasting rice genotypes. PHYSIOLOGIA PLANTARUM 2020; 170:248-268. [PMID: 32515828 DOI: 10.1111/ppl.13149] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Plants are constantly exposed to environmental fluctuations, that may occur in a single day or over longer periods. In many cases, abiotic stresses are transient and recurrent, impacting how plants respond in subsequent adverse conditions. Adaptation mechanisms may occur at the physiological, biochemical and molecular level, modifying transcriptional response, regulatory proteins, epigenetic marks or metabolites. Here, we aimed to uncover the different strategies that rice uses to respond to recurrent stress. We tested varieties with contrasting behavior towards salinity (tolerance or sensitivity) and imposed salt stress (150 mM NaCl) during 48 h at vegetative and/or reproductive stages. After 48 h of stress in reproductive stage, leaves and roots were harvested separately or otherwise the plants were submitted to a 24 h recovery, prior to sample harvesting. Plants submitted to a recurrent stress responded differently from those suffering a single stress event. In the case of the sensitive genotype, recurrent stress led to lower Na/K ratio in roots and lower hydrogen peroxide accumulation and lipid peroxidation in leaves, but maintenance of global DNA methylation levels. In the tolerant genotype, recurrent stress did neither affect the Na/K ratio nor the stomatal conductance, although the levels of superoxide anion and hydrogen peroxide accumulation were lower, as also observed for global levels of DNA methylation. Our work shows that a short pre-exposure to salt stress may improve rice tolerance to subsequent stress, trough biochemical, physiological and epigenetic processes, with more significant changes visible in the tolerant genotype.
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Affiliation(s)
| | - Priscila Ariane Auler
- Department of Botany, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Tatiana Rossatto
- Department of Botany, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Pedro M Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress - Plant Functional Genomics Lab, Av. da República, Oeiras, 2780-157, Portugal
| | - Maria Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress - Plant Functional Genomics Lab, Av. da República, Oeiras, 2780-157, Portugal
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Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of qDTYs to Reproductive-Stage Drought Stress in Rice ( Oryza sativa L.). Genes (Basel) 2020; 11:genes11101124. [PMID: 32987927 PMCID: PMC7650634 DOI: 10.3390/genes11101124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022] Open
Abstract
Rice (Oryza sativa L.) is more sensitive to drought stress than other cereals. To dissect molecular mechanisms underlying drought-tolerant yield in rice, we applied differential expression and co-expression network approaches to transcriptomes from flag-leaf and emerging panicle tissues of a drought-tolerant yield introgression line, DTY-IL, and the recurrent parent Swarna, under moderate reproductive-stage drought stress. Protein turnover and efficient reactive oxygen species scavenging were found to be the driving factors in both tissues. In the flag-leaf, the responses further included maintenance of photosynthesis and cell wall reorganization, while in the panicle biosynthesis of secondary metabolites was found to play additional roles. Hub genes of importance in differential drought responses included an expansin in the flag-leaf and two peroxidases in the panicle. Overlaying differential expression data with allelic variation in DTY-IL quantitative trait loci allowed for the prioritization of candidate genes. They included a differentially regulated auxin-responsive protein, with DTY-IL-specific amino acid changes in conserved domains, as well as a protein kinase with a DTY-IL-specific frameshift in the C-terminal region. The approach highlights how the integration of differential expression and allelic variation can aid in the discovery of mechanism and putative causal contribution underlying quantitative trait loci for drought-tolerant yield.
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Jaimes-Miranda F, Chávez Montes RA. The plant MBF1 protein family: a bridge between stress and transcription. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1782-1791. [PMID: 32037452 PMCID: PMC7094072 DOI: 10.1093/jxb/erz525] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/06/2020] [Indexed: 05/20/2023]
Abstract
The Multiprotein Bridging Factor 1 (MBF1) proteins are transcription co-factors whose molecular function is to form a bridge between transcription factors and the basal machinery of transcription. MBF1s are present in most archaea and all eukaryotes, and numerous reports show that they are involved in developmental processes and in stress responses. In this review we summarize almost three decades of research on the plant MBF1 family, which has mainly focused on their role in abiotic stress responses, in particular the heat stress response. However, despite the amount of information available, there are still many questions that remain about how plant MBF1 genes, transcripts, and proteins respond to stress, and how they in turn modulate stress response transcriptional pathways.
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Affiliation(s)
- Fabiola Jaimes-Miranda
- CONACyT-Instituto Potosino de Investigación Científica y Tecnológica AC, División de Biología Molecular, San Luis Potosí, San Luis Potosí, México
- Correspondence:
| | - Ricardo A Chávez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
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Wu YS, Yang CY. Comprehensive Transcriptomic Analysis of Auxin Responses in Submerged Rice Coleoptile Growth. Int J Mol Sci 2020; 21:E1292. [PMID: 32075118 PMCID: PMC7072898 DOI: 10.3390/ijms21041292] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 11/16/2022] Open
Abstract
Cultivating rice in wet or water direct seeding systems is simple and time and labor efficient. Rice (Oryza sativa) seeds are a unique cereal that can germinate not only when submerged, but also in anoxic conditions. Many complicated hormone signals interact in submerged seed germination. Ethylene is involved in rice coleoptile elongation, but little is known regarding the role of auxin signaling under submergence. This study demonstrated that the coleoptile is shorter and curlier when submerged with 2,3,5-triiodobenzoic acid (TIBA). In transcriptomic analysis, 3448 of the 31,860 genes were upregulated, and 4360 genes were downregulated with submergence and TIBA treatment. The Gene Ontology function classification results demonstrated that upregulated differentially expressed genes (DEGs) were mainly involved in redox, stress, and signal transduction, whereas the down-regulated DEGs were mainly involved in RNA transcription, stress, and development. Furthermore, auxin signaling involved in the carbohydrate metabolism pathway was demonstrated while using transcriptomic analysis and confirmed in a quantitative real-time polymerase chain reaction. In addition, the transcript levels of development-related genes and mitochondria-electron- transport-related genes were regulated by auxin signaling under submergence. Auxin signaling was not only involved in regulating rice coleoptile elongation and development, but also regulated secondary metabolism, carbohydrate metabolism, and mitochondria electron transport under submergence. Our results presented that auxin signaling plays an important role during rice coleoptile elongation upon the submergence condition and improving the advance of research of direct rice seeding system.
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Affiliation(s)
- Yu-Sian Wu
- Department of Agronomy, National Chung Hsing University, Taichung 40227, Taiwan;
| | - Chin-Ying Yang
- Department of Agronomy, National Chung Hsing University, Taichung 40227, Taiwan;
- Pervasive AI Research (PAIR) Labs, Hsinchu 30010, Taiwan
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Harb A, Simpson C, Guo W, Govindan G, Kakani VG, Sunkar R. The Effect of Drought on Transcriptome and Hormonal Profiles in Barley Genotypes With Contrasting Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2020; 11:618491. [PMID: 33424910 PMCID: PMC7786106 DOI: 10.3389/fpls.2020.618491] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/27/2020] [Indexed: 05/21/2023]
Abstract
Like many cereal crops, barley is also negatively affected by drought stress. However, due to its simple genome as well as enhanced stress resilient nature compared to rice and wheat, barley has been considered as a model to decipher drought tolerance in cereals. In the present study, transcriptomic and hormonal profiles along with several biochemical features were compared between drought-tolerant (Otis) and drought-sensitive (Baronesse) barley genotypes subjected to drought to identify molecular and biochemical differences between the genotypes. The drought-induced decrease in the leaf relative water content, net photosynthesis, and biomass accumulation was relatively low in Otis compared to Baronesse. The hormonal profiles did not reveal significant differences for majority of the compounds other than the GA20 and the cis-zeatin-o-glucoside (c-ZOG), whose levels were greatly increased in Otis compared to Baronesse under drought. The major differences that emerged from the transcriptome analysis are; (1), the overall number of differentially expressed genes was relatively low in drought-tolerant Otis compared to drought-sensitive Baronesse; (2), a wax biosynthesis gene (CER1), and NAC transcription factors were specifically induced in Otis but not in Baronesse; (3), the degree of upregulation of betaine aldehyde dehydrogenase and a homeobox transcription factor (genes with proven roles in imparting drought tolerance), was greater in Otis compared to Baronesse; (4) the extent of downregulation of gene expression profiles for proteins of the reaction center photosystem II (PSII) (D1 and D2) was low in Otis compared to Baronesse; and, (5), alternative splicing (AS) was also found to differ between the genotypes under drought. Taken together, the overall transcriptional responses were low in drought-tolerant Otis but the genes that could confer drought tolerance were either specifically induced or greatly upregulated in the tolerant genotype and these differences could be important for drought tolerance in barley.
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Affiliation(s)
- Amal Harb
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid, Jordan
- *Correspondence: Amal Harb ;
| | - Craig Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Wenbin Guo
- Informatics and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Ganesan Govindan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
| | - Vijaya Gopal Kakani
- Department of Plant and Soil Science, Oklahoma State University, Stillwater, OK, United States
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Ramanjulu Sunkar
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Sharma E, Jain M, Khurana JP. Differential quantitative regulation of specific gene groups and pathways under drought stress in rice. Genomics 2019; 111:1699-1712. [DOI: 10.1016/j.ygeno.2018.11.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/10/2018] [Accepted: 11/21/2018] [Indexed: 10/27/2022]
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Antunes AC, Acunha TDS, Perin EC, Rombaldi CV, Galli V, Chaves FC. Untargeted metabolomics of strawberry (Fragaria x ananassa 'Camarosa') fruit from plants grown under osmotic stress conditions. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:6973-6980. [PMID: 31414485 DOI: 10.1002/jsfa.9986] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/08/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Plants activate defense mechanisms to cope with adverse environmental conditions, leading to the accumulation and / or depletion of general and specialized metabolites. In this study, a multiplatform untargeted metabolomics strategy was employed to evaluate metabolic changes in strawberry fruit of cv. Camarosa grown under osmotic stress conditions. Liquid chromatography-mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) data from strawberries grown under two water-deficit conditions, irrigated at 95% crop evapotranspiration (ETc) and 85% ETc, and one excess salt condition with a 80 mmol L-1 NaCl solution, were analyzed to determine treatment effects on fruit metabolism. RESULTS Multivariate principal component analysis, orthogonal projections to latent structures - discriminant analysis (OPLS-DA), and univariate statistical analyses were applied to the data set. While multivariate analyses showed group separation by treatment, T-tests and fold change revealed 12 metabolites differentially accumulated in strawberries from different treatments - among them phenolic compounds, glycerophospholipids, phytosterols, carbohydrates, and an aromatic amino acid. CONCLUSION Untargeted metabolomic analysis allowed for the annotation of compounds differentially accumulated in strawberry fruit from plants grown under osmotic stress and non-stressed plants. The metabolic disturbance in plants under stress involved metabolites associated with the inhibition of reactive oxygen species and cell-wall and membrane lipid biosynthesis, which might serve as osmotic stress biomarkers. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Ana Cn Antunes
- Graduate Program in Food Science and Technology, Department of Agroindustrial Science and Technology, School of Agronomy 'Eliseu Maciel', Federal University of Pelotas, Pelotas, Brazil
| | - Tanize Dos S Acunha
- Graduate Program in Food Science and Technology, Department of Agroindustrial Science and Technology, School of Agronomy 'Eliseu Maciel', Federal University of Pelotas, Pelotas, Brazil
- Graduate Program of the School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Ellen C Perin
- School of Food Technology, Federal University of Technology - Paraná, Francisco Beltrão, Brazil
| | - Cesar V Rombaldi
- Graduate Program in Food Science and Technology, Department of Agroindustrial Science and Technology, School of Agronomy 'Eliseu Maciel', Federal University of Pelotas, Pelotas, Brazil
| | - Vanessa Galli
- Graduate Program in Food Science and Technology, Department of Agroindustrial Science and Technology, School of Agronomy 'Eliseu Maciel', Federal University of Pelotas, Pelotas, Brazil
| | - Fabio C Chaves
- Graduate Program in Food Science and Technology, Department of Agroindustrial Science and Technology, School of Agronomy 'Eliseu Maciel', Federal University of Pelotas, Pelotas, Brazil
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Yan Q, Wu F, Yan Z, Li J, Ma T, Zhang Y, Zhao Y, Wang Y, Zhang J. Differential co-expression networks of long non-coding RNAs and mRNAs in Cleistogenes songorica under water stress and during recovery. BMC PLANT BIOLOGY 2019; 19:23. [PMID: 30634906 PMCID: PMC6330494 DOI: 10.1186/s12870-018-1626-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/28/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Water stress seriously constrains plant growth and yield. Long non-coding RNAs (lncRNAs) serve as versatile regulators in various biological regulatory processes. To date, the systematic screening and potential functions of lncRNA have not yet been characterized in Cleistogenes songorica, especially under water stress conditions. RESULTS In this study, we obtained the root and shoot transcriptomes of young C. songorica plants subjected to different degrees of water stress and recovery treatments by Illumina-based RNA-seq. A total of 3397 lncRNAs were identified through bioinformatics analysis. LncRNA differential expression analysis indicated that the higher response of roots compared to shoots during water stress and recovery. We further identified the 1644 transcription factors, 189 of which were corresponded to 163 lncRNAs in C. songorica. Though comparative analyses with major Poaceae species based on blast, 81 water stress-related orthologues regulated to lncRNAs were identified as a core of evolutionary conserved genes important to regulate water stress responses in the family. Among these target genes, two genes were found to be involved in the abscisic acid (ABA) signalling pathway, and four genes were enriched for starch and sucrose metabolism. Additionally, the 52 lncRNAs were predicted as target mimics for microRNAs (miRNAs) in C. songorica. RT-qPCR results suggested that MSTRG.43964.1 and MSTRG.4400.2 may regulate the expression of miRNA397 and miRNA166, respectively, as target mimics under water stress and during recovery. Finally, a co-expression network was constructed based on the lncRNAs, miRNAs, protein-coding genes (PCgenes) and transcription factors under water stress and during recovery in C. songorica. CONCLUSIONS In C. songorica, lncRNAs, miRNAs, PCgenes and transcription factors constitute a complex transcriptional regulatory network which lncRNAs can regulate PCgenes and miRNAs under water stress and recovery. This study provides fundamental resources to deepen our knowledge on lncRNAs during ubiquitous water stress.
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Affiliation(s)
- Qi Yan
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, People’s Republic of China
| | - Fan Wu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, People’s Republic of China
| | - Zhuanzhuan Yan
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, People’s Republic of China
| | - Jie Li
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, People’s Republic of China
| | - Tiantian Ma
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, People’s Republic of China
| | - Yufei Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, People’s Republic of China
| | - Yufeng Zhao
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, People’s Republic of China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, People’s Republic of China
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, People’s Republic of China
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Liu Y, Li L, Zhang L, Lv Q, Zhao Y, Li X. Isolation and identification of wheat gene TaDIS1 encoding a RING finger domain protein, which negatively regulates drought stress tolerance in transgenic Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 275:49-59. [PMID: 30107881 DOI: 10.1016/j.plantsci.2018.07.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 07/27/2018] [Accepted: 07/29/2018] [Indexed: 05/16/2023]
Abstract
Drought stress is a major factor that limits the yield and quality in wheat. In this study, we identified an orthologue of the rice gene OsDIS1 (Oryza sativa drought-induced SINA protein 1) in wheat (Triticum aestivum L.) called TaDIS1. TaDIS1 encodes a putative 301 amino acid protein with a C3HC4 RING finger conserved domain at the N-terminal and a SINA domain at the C-terminal. TaDIS1 contains three exons and two introns. qRT-PCR analysis showed that TaDIS1 expression was induced by PEG6000, NaCl, and abscisic acid (ABA) treatment. We generated TaDIS1-overexpressing transgenic Arabidopsis lines. Under drought stress conditions, the transgenic Arabidopsis plants had a lower germination rate, relative water content, and proline contents, with higher water loss, chlorophyll loss, relative electrical conductivity, and malondialdehyde contents compared with the wild type. The antioxidant enzyme (superoxide dismutase, peroxidase, and catalase) activity levels were lower in the transgenic plants. The TaDIS1-overexpressing plants had shorter roots with greater growth inhibition in response to mannitol treatment than the wild type, with increased hypersensitivity to ABA during seed germination and early seedling growth. The expression of stress-related genes in transgenic plants under drought stress suggests that TaDIS1 may function negatively in drought stress by regulating the stress response-related genes.
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Affiliation(s)
- Yan Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Liqun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Li Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Qian Lv
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yi Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Mackill DJ, Khush GS. IR64: a high-quality and high-yielding mega variety. RICE (NEW YORK, N.Y.) 2018; 11:18. [PMID: 29629479 PMCID: PMC5890005 DOI: 10.1186/s12284-018-0208-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/14/2018] [Indexed: 05/05/2023]
Abstract
High-yielding varieties developed in the 1960s and 1970s at the International Rice Research Institute (IRRI) and elsewhere benefited farmers and the public, ultimately increasing yields and reducing the cost of rice to consumers. Most of these varieties, however, did not have the optimum cooking quality that was possessed by many of the traditional varieties they replaced. In 1985, the IRRI-developed indica variety IR64 was released in the Philippines. In addition to its high yield, early maturity and disease resistance, it had excellent cooking quality, matching that of the best varieties available. These merits resulted in its rapid spread and cultivation on over 10 million ha in the two decades after it was released. It has intermediate amylose content and gelatinization temperature, and good taste. It is resistant to blast and bacterial blight diseases, and to brown planthopper. Because of its success as a variety, it has been used extensively in scientific studies and has been well-characterized genetically. Many valuable genes have been introduced into IR64 through backcross breeding and it has been used in thousands of crosses. Its area of cultivation has declined in the past 10 years, but it has been replaced by a new generation of high-quality varieties that are mostly its progeny or relatives. Continued basic studies on IR64 and related varieties should help in unraveling the complex genetic control of yield and other desirable traits that are prized by rice farmers and consumers.
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Affiliation(s)
- David J Mackill
- Mars, Inc. and Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Gurdev S Khush
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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21
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De Schutter K, Tsaneva M, Kulkarni SR, Rougé P, Vandepoele K, Van Damme EJM. Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa). RICE (NEW YORK, N.Y.) 2017; 10:26. [PMID: 28560587 PMCID: PMC5449364 DOI: 10.1186/s12284-017-0164-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/16/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Lectins, defined as 'Proteins that can recognize and bind specific carbohydrate structures', are widespread among all kingdoms of life and play an important role in various biological processes in the cell. Most plant lectins are involved in stress signaling and/or defense. The family of Euonymus-related lectins (EULs) represents a group of stress-related lectins composed of one or two EUL domains. The latter protein domain is unique in that it is ubiquitous in land plants, suggesting an important role for these proteins. RESULTS Despite the availability of multiple completely sequenced rice genomes, little is known on the occurrence of lectins in rice. We identified 329 putative lectin genes in the genome of Oryza sativa subsp. japonica belonging to nine out of 12 plant lectin families. In this paper, an in-depth molecular characterization of the EUL family of rice was performed. In addition, analyses of the promoter sequences and investigation of the transcript levels for these EUL genes enabled retrieval of important information related to the function and stress responsiveness of these lectins. Finally, a comparative analysis between rice cultivars and several monocot and dicot species revealed a high degree of sequence conservation within the EUL domain as well as in the domain organization of these lectins. CONCLUSIONS The presence of EULs throughout the plant kingdom and the high degree of sequence conservation in the EUL domain suggest that these proteins serve an important function in the plant cell. Analysis of the promoter region of the rice EUL genes revealed a diversity of stress responsive elements. Furthermore analysis of the expression profiles of the EUL genes confirmed that they are differentially regulated in response to several types of stress. These data suggest a potential role for the EULs in plant stress signaling and defense.
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Affiliation(s)
- Kristof De Schutter
- Laboratory Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Mariya Tsaneva
- Laboratory Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Shubhada R Kulkarni
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
| | - Pierre Rougé
- UMR 152 PHARMA-DEV, Université de Toulouse, IRD, UPS, Chemin des Maraîchers 35, 31400, Toulouse, France
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
| | - Els J M Van Damme
- Laboratory Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium.
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Quantitative Phosphoproteomic Analysis Provides Insight into the Response to Short-Term Drought Stress in Ammopiptanthus mongolicus Roots. Int J Mol Sci 2017; 18:ijms18102158. [PMID: 29039783 PMCID: PMC5666839 DOI: 10.3390/ijms18102158] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/11/2017] [Accepted: 10/14/2017] [Indexed: 01/12/2023] Open
Abstract
Drought is one of the major abiotic stresses that negatively affects plant growth and development. Ammopiptanthus mongolicus is an ecologically important shrub in the mid-Asia desert region and used as a model for abiotic tolerance research in trees. Protein phosphorylation participates in the regulation of various biological processes, however, phosphorylation events associated with drought stress signaling and response in plants is still limited. Here, we conducted a quantitative phosphoproteomic analysis of the response of A. mongolicus roots to short-term drought stress. Data are available via the iProx database with project ID IPX0000971000. In total, 7841 phosphorylation sites were found from the 2019 identified phosphopeptides, corresponding to 1060 phosphoproteins. Drought stress results in significant changes in the abundance of 103 phosphopeptides, corresponding to 90 differentially-phosphorylated phosphoproteins (DPPs). Motif-x analysis identified two motifs, including [pSP] and [RXXpS], from these DPPs. Functional enrichment and protein-protein interaction analysis showed that the DPPs were mainly involved in signal transduction and transcriptional regulation, osmotic adjustment, stress response and defense, RNA splicing and transport, protein synthesis, folding and degradation, and epigenetic regulation. These drought-corresponsive phosphoproteins, and the related signaling and metabolic pathways probably play important roles in drought stress signaling and response in A. mongolicus roots. Our results provide new information for understanding the molecular mechanism of the abiotic stress response in plants at the posttranslational level.
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Analysis of drought-responsive signalling network in two contrasting rice cultivars using transcriptome-based approach. Sci Rep 2017; 7:42131. [PMID: 28181537 PMCID: PMC5299611 DOI: 10.1038/srep42131] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/30/2016] [Indexed: 12/14/2022] Open
Abstract
Traditional cultivars of rice in India exhibit tolerance to drought stress due to their inherent genetic variations. Here we present comparative physiological and transcriptome analyses of two contrasting cultivars, drought tolerant Dhagaddeshi (DD) and susceptible IR20. Microarray analysis revealed several differentially expressed genes (DEGs) exclusively in DD as compared to IR20 seedlings exposed to 3 h drought stress. Physiologically, DD seedlings showed higher cell membrane stability and differential ABA accumulation in response to dehydration, coupled with rapid changes in gene expression. Detailed analyses of metabolic pathways enriched in expression data suggest interplay of ABA dependent along with secondary and redox metabolic networks that activate osmotic and detoxification signalling in DD. By co-localization of DEGs with QTLs from databases or published literature for physiological traits of DD and IR20, candidate genes were identified including those underlying major QTL qDTY1.1 in DD. Further, we identified previously uncharacterized genes from both DD and IR20 under drought conditions including OsWRKY51, OsVP1 and confirmed their expression by qPCR in multiple rice cultivars. OsFBK1 was also functionally validated in susceptible PB1 rice cultivar and Arabidopsis for providing drought tolerance. Some of the DEGs mapped to the known QTLs could thus, be of potential significance for marker-assisted breeding.
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24
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An JP, Li R, Qu FJ, You CX, Wang XF, Hao YJ. Ectopic expression of an apple cytochrome P450 gene MdCYPM1 negatively regulates plant photomorphogenesis and stress response in Arabidopsis. Biochem Biophys Res Commun 2017; 483:1-9. [PMID: 28073698 DOI: 10.1016/j.bbrc.2017.01.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 11/29/2022]
Abstract
Cytochrome P450s play an important role in plant growth and are involved in multiple stresses response. However, little is known about the functions of cytochrome P450s in apple. Here, a Malus × domestica cytochrome P450 monooxygenase 1 gene, MdCYPM1, was identified and subsequently cloned from apple 'Gala' (Malus × domestica). To verify the functions of MdCYPM1, we generated transgenic Arabidopsis plants expressing the apple MdCYPM1 gene under the control of the Cauliflower mosaic virus 35S promoter. Four transgenic lines (#3, #5, #7 and #8) were selected for further study. The transgenic plants exhibited a series of skotomorphogenesis phenotypes relative to wild-type controls, such as reduction of the chlorophyll, anthocyanins content and hypocotyls elongation. In addition, overexpression of MdCYPM1 influenced auxin transport and flowering time in transgenic Arabidopsis. Furthermore, MdCYPM1 expression was induced by salt and mannitol treatments, and the transgenic plants were negatively regulated by salinity and osmotic stresses during germination. These results suggest that MdCYPM1 plays a vital role in plant growth and development.
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Affiliation(s)
- Jian-Ping An
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Rui Li
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Feng-Jia Qu
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Xiao-Fei Wang
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
| | - Yu-Jin Hao
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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25
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Bhattacharjee A, Sharma R, Jain M. Over-Expression of OsHOX24 Confers Enhanced Susceptibility to Abiotic Stresses in Transgenic Rice via Modulating Stress-Responsive Gene Expression. FRONTIERS IN PLANT SCIENCE 2017; 8:628. [PMID: 28484484 PMCID: PMC5399076 DOI: 10.3389/fpls.2017.00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/07/2017] [Indexed: 05/20/2023]
Abstract
Homeobox transcription factors play critical roles in plant development and abiotic stress responses. In the present study, we raised rice transgenics over-expressing stress-responsive OsHOX24 gene (rice homeodomain-leucine zipper I sub-family member) and analyzed their response to various abiotic stresses at different stages of development. At the seed germination stage, rice transgenics over-expressing OsHOX24 exhibited enhanced sensitivity to abiotic stress conditions and abscisic acid as compared to wild-type (WT). OsHOX24 over-expression rice seedlings showed reduced root and shoot growth under salinity and desiccation stress (DS) conditions. Various physiological and phenotypic assays confirmed higher susceptibility of rice transgenics toward abiotic stresses as compared to WT at mature and reproductive stages of rice development too. Global gene expression profiling revealed differential regulation of several genes in the transgenic plants under control and DS conditions. Many of these differentially expressed genes were found to be involved in transcriptional regulatory activities, besides carbohydrate, nucleic acid and lipid metabolic processes and response to abiotic stress and hormones. Taken together, our findings highlighted the role of OsHOX24 in regulation of abiotic stress responses via modulating the expression of stress-responsive genes in rice.
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Affiliation(s)
| | | | - Mukesh Jain
- National Institute of Plant Genome ResearchNew Delhi, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru UniversityNew Delhi, India
- *Correspondence: Mukesh Jain, ;
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26
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Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK. Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India. RICE (NEW YORK, N.Y.) 2016; 9:1. [PMID: 26743769 PMCID: PMC4705060 DOI: 10.1186/s12284-015-0073-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/22/2015] [Indexed: 05/05/2023]
Abstract
Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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27
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Srivastava R, Bajaj D, Malik A, Singh M, Parida SK. Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea. Sci Rep 2016; 6:33616. [PMID: 27680662 PMCID: PMC5041113 DOI: 10.1038/srep33616] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/26/2016] [Indexed: 01/03/2023] Open
Abstract
The RNA-sequencing followed by de-novo transcriptome assembly identified 11621 genes differentially xpressed in roots vs. shoots of a wild perennial Cicer microphyllum. Comparative analysis of transcriptomes between microphyllum and cultivated desi cv. ICC4958 detected 12772 including 3242 root- and 1639 shoot-specific microphyllum genes with 85% expression validation success rate. Transcriptional reprogramming of microphyllum root-specific genes implicates their possible role in regulating differential natural adaptive characteristics between wild and cultivated chickpea. The transcript-derived 5698 including 282 in-silico polymorphic SSR and 127038 SNP markers annotated at a genome-wide scale exhibited high amplification and polymorphic potential among cultivated (desi and kabuli) and wild accessions suggesting their utility in chickpea genomics-assisted breeding applications. The functional significance of markers was assessed based on their localization in non-synonymous coding and regulatory regions of microphyllum root-specific genes differentially expressed predominantly in ICC 4958 roots under drought stress. A high-density 490 genic SSR- and SNP markers-anchored genetic linkage map identified six major QTLs regulating drought tolerance-related traits, yield per plant and harvest-index in chickpea. The integration of high-resolution QTL mapping with comparative transcriptome profiling delineated five microphyllum root-specific genes with non-synonymous and regulatory SNPs governing drought-responsive yield traits. Multiple potential key regulators and functionally relevant molecular tags delineated can drive translational research and drought tolerance-mediated chickpea genetic enhancement.
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Affiliation(s)
- Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ayushi Malik
- Faculty of Science, Jamia Hamdard University, Hamdard Nagar, New Delhi 110062, India
| | - Mohar Singh
- National Bureau of Plant Genetic Resources Regional Station, Shimla, Himachal Pradesh 171004, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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28
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Galbiati F, Chiozzotto R, Locatelli F, Spada A, Genga A, Fornara F. Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice. PLANT, CELL & ENVIRONMENT 2016; 39:1982-93. [PMID: 27111837 DOI: 10.1111/pce.12760] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/10/2016] [Indexed: 05/20/2023]
Abstract
Plants show a high degree of developmental plasticity in response to external cues, including day length and environmental stress. Water scarcity in particular can interfere with photoperiodic flowering, resulting in the acceleration of the switch to reproductive growth in several species, a process called drought escape. However, other strategies are possible and drought stress can also delay flowering, albeit the underlying mechanisms have never been addressed at the molecular level. We investigated these interactions in rice, a short day species in which drought stress delays flowering. A protocol that allows the synchronization of drought with the floral transition was set up to profile the transcriptome of leaves subjected to stress under distinct photoperiods. We identified clusters of genes that responded to drought differently depending on day length. Exposure to drought stress under floral-inductive photoperiods strongly reduced transcription of EARLY HEADING DATE 1 (Ehd1), HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), primary integrators of day length signals, providing a molecular connection between stress and the photoperiodic pathway. However, phenotypic and transcriptional analyses suggested that OsGIGANTEA (OsGI) does not integrate drought and photoperiodic signals as in Arabidopsis, highlighting molecular differences between long and short day model species.
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Affiliation(s)
- Francesca Galbiati
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Remo Chiozzotto
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Franca Locatelli
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Alberto Spada
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Annamaria Genga
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
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29
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Nguyen Dinh S, Sai TZT, Nawaz G, Lee K, Kang H. Abiotic stresses affect differently the intron splicing and expression of chloroplast genes in coffee plants (Coffea arabica) and rice (Oryza sativa). JOURNAL OF PLANT PHYSIOLOGY 2016; 201:85-94. [PMID: 27448724 DOI: 10.1016/j.jplph.2016.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
Despite the increasing understanding of the regulation of chloroplast gene expression in plants, the importance of intron splicing and processing of chloroplast RNA transcripts under stress conditions is largely unknown. Here, to understand how abiotic stresses affect the intron splicing and expression patterns of chloroplast genes in dicots and monocots, we carried out a comprehensive analysis of the intron splicing and expression patterns of chloroplast genes in the coffee plant (Coffea arabica) as a dicot and rice (Oryza sativa) as a monocot under abiotic stresses, including drought, cold, or combined drought and heat stresses. The photosynthetic activity of both coffee plants and rice seedlings was significantly reduced under all stress conditions tested. Analysis of the transcript levels of chloroplast genes revealed that the splicing of tRNAs and mRNAs in coffee plants and rice seedlings were significantly affected by abiotic stresses. Notably, abiotic stresses affected differently the splicing of chloroplast tRNAs and mRNAs in coffee plants and rice seedlings. The transcript levels of most chloroplast genes were markedly downregulated in both coffee plants and rice seedlings upon stress treatment. Taken together, these results suggest that coffee and rice plants respond to abiotic stresses via regulating the intron splicing and expression of different sets of chloroplast genes.
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Affiliation(s)
- Sy Nguyen Dinh
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea; Institute of Environment and Biotechnology, Taynguyen University, 567 Le Duan Street, Buon Ma Thuot City, Daklak Province, Viet Nam
| | - Than Zaw Tun Sai
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Ghazala Nawaz
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Kwanuk Lee
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea.
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30
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Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses. Sci Rep 2016; 6:23719. [PMID: 27029818 PMCID: PMC4814823 DOI: 10.1038/srep23719] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/14/2016] [Indexed: 01/18/2023] Open
Abstract
Drought and salinity are the major environmental factors that affect rice productivity. Comparative transcriptome analysis between tolerant and sensitive rice cultivars can provide insights into the regulatory mechanisms involved in these stress responses. In this study, the comparison of transcriptomes of a drought-tolerant [Nagina 22 (N22)] and a salinity-tolerant (Pokkali) rice cultivar with IR64 (susceptible cultivar) revealed variable transcriptional responses under control and stress conditions. A total of 801 and 507 transcripts were exclusively differentially expressed in N22 and Pokkali rice cultivars, respectively, under stress conditions. Gene ontology analysis suggested the enrichment of transcripts involved in response to abiotic stress and regulation of gene expression in stress-tolerant rice cultivars. A larger number of transcripts encoding for members of NAC and DBP transcription factor (TF) families in N22 and members of bHLH and C2H2 TF families in Pokkali exhibited differential regulation under desiccation and salinity stresses, respectively. Transcripts encoding for thioredoxin and involved in phenylpropanoid metabolism were up-regulated in N22, whereas transcripts involved in wax and terpenoid metabolism were up-regulated in Pokkali. Overall, common and cultivar-specific stress-responsive transcripts identified in this study can serve as a helpful resource to explore novel candidate genes for abiotic stress tolerance in rice.
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31
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Jangam AP, Pathak RR, Raghuram N. Microarray Analysis of Rice d1 (RGA1) Mutant Reveals the Potential Role of G-Protein Alpha Subunit in Regulating Multiple Abiotic Stresses Such as Drought, Salinity, Heat, and Cold. FRONTIERS IN PLANT SCIENCE 2016; 7:11. [PMID: 26858735 PMCID: PMC4729950 DOI: 10.3389/fpls.2016.00011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 01/07/2016] [Indexed: 05/18/2023]
Abstract
The genome-wide role of heterotrimeric G-proteins in abiotic stress response in rice has not been examined from a functional genomics perspective, despite the availability of mutants and evidences involving individual genes/processes/stresses. Our rice whole transcriptome microarray analysis (GSE 20925 at NCBI GEO) using the G-alpha subunit (RGA1) null mutant (Daikoku 1 or d1) and its corresponding wild type (Oryza sativa Japonica Nipponbare) identified 2270 unique differentially expressed genes (DEGs). Out of them, we mined for all the potentially abiotic stress-responsive genes using Gene Ontology terms, STIFDB2.0 and Rice DB. The first two approaches produced smaller subsets of the 1886 genes found at Rice DB. The GO approach revealed similar regulation of several families of stress-responsive genes in RGA1 mutant. The Genevestigator analysis of the stress-responsive subset of the RGA1-regulated genes from STIFDB revealed cold and drought-responsive clusters. Meta data analysis at Rice DB revealed large stress-response categories such as cold (878 up/810 down), drought (882 up/837 down), heat (913 up/777 down), and salt stress (889 up/841 down). One thousand four hundred ninety-eight of them are common to all the four abiotic stresses, followed by fewer genes common to smaller groups of stresses. The RGA1-regulated genes that uniquely respond to individual stresses include 111 in heat stress, eight each in cold only and drought only stresses, and two genes in salt stress only. The common DEGs (1498) belong to pathways such as the synthesis of polyamine, glycine-betaine, proline, and trehalose. Some of the common DEGs belong to abiotic stress signaling pathways such as calcium-dependent pathway, ABA independent and dependent pathway, and MAP kinase pathway in the RGA1 mutant. Gene ontology of the common stress responsive DEGs revealed 62 unique molecular functions such as transporters, enzyme regulators, transferases, hydrolases, carbon and protein metabolism, binding to nucleotides, carbohydrates, receptors and lipids, morphogenesis, flower development, and cell homeostasis. We also mined 63 miRNAs that bind to the stress responsive transcripts identified in this study, indicating their post-transcriptional regulation. Overall, these results indicate the potentially extensive role of RGA1 in the regulation of multiple abiotic stresses in rice for further validation.
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Fu Y, Poli M, Sablok G, Wang B, Liang Y, La Porta N, Velikova V, Loreto F, Li M, Varotto C. Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:54. [PMID: 26958077 PMCID: PMC4782572 DOI: 10.1186/s13068-016-0471-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 02/22/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND Arundo donax L. (Poaceae) is considered one of the most promising energy crops in the Mediterranean region because of its high biomass yield and low input requirements, but to date no information on its transcriptional responses to water stress is available. RESULTS We obtained by Illumina-based RNA-seq the whole root and shoot transcriptomes of young A. donax plants subjected to osmotic/water stress with 10 and 20 % polyethylene glycol (PEG; 3 biological replicates/organ/condition corresponding to 18 RNA-Seq libraries), and identified a total of 3034 differentially expressed genes. Blast-based mining of stress-related genes indicated the higher responsivity of roots compared to shoots at the early stages of water stress especially under the milder PEG treatment, with a majority of genes responsive to salt, oxidative, and dehydration stress. Analysis of gene ontology terms underlined the qualitatively different responses between root and shoot tissues. Among the most significantly enriched metabolic pathways identified using a Fisher's exact test with FDR correction, a crucial role was played in both shoots and roots by genes involved in the signaling cascade of abscisic acid. We further identified relatively large organ-specific differences in the patterns of drought-related transcription factor AP2-EREBP, AUX/IAA, MYB, bZIP, C2H2, and GRAS families, which may underlie the transcriptional reprogramming differences between organs. Through comparative analyses with major Poaceae species based on Blast, we finally identified a set of 53 orthologs that can be considered as a core of evolutionary conserved genes important to mediate water stress responses in the family. CONCLUSIONS This study provides the first characterization of A. donax transcriptome in response to water stress, thus shedding novel light at the molecular level on the mechanisms of stress response and adaptation in this emerging bioenergy species. The inventory of early-responsive genes to water stress identified could constitute useful markers of the physiological status of A. donax and be a basis for the improvement of its productivity under water limitation. The full water-stressed A. donax transcriptome is available for Blast-based homology searches through a dedicated web server (http://ecogenomics.fmach.it/arundo/).
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Affiliation(s)
- Yuan Fu
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
- />Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, Italy
| | - Michele Poli
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
- />Dipartimento di Scienze Agrarie, Università di Bologna, Bologna, Italy
| | - Gaurav Sablok
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
| | - Bo Wang
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
- />Centro di Biologia Integrata (CIBIO), University of Trento, Trento, Italy
| | - Yanchun Liang
- />College of Computer Science and Technology, Jilin University, Changchun, China
| | - Nicola La Porta
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
- />MOUNTFOR Project Centre, European Forest Institute, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
| | - Violeta Velikova
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
- />Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Francesco Loreto
- />The National Research Council of Italy (CNR), Department of Biology, Agriculture and Food Sciences, Rome, Italy
| | - Mingai Li
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
| | - Claudio Varotto
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
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Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response. Sci Rep 2015; 5:14922. [PMID: 26449881 PMCID: PMC4598828 DOI: 10.1038/srep14922] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/14/2015] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is an epigenetic mechanism that play an important role in gene regulation in response to environmental conditions. The understanding of DNA methylation at the whole genome level can provide insights into the regulatory mechanisms underlying abiotic stress response/adaptation. We report DNA methylation patterns and their influence on transcription in three rice (Oryza sativa) cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant; Pokkali, salinity-tolerant) via an integrated analysis of whole genome bisulphite sequencing and RNA sequencing. We discovered extensive DNA methylation at single-base resolution in rice cultivars, identified the sequence context and extent of methylation at each site. Overall, methylation levels were significantly different in the three rice cultivars. Numerous differentially methylated regions (DMRs) among different cultivars were identified and many of which were associated with differential expression of genes important for abiotic stress response. Transposon-associated DMRs were found coupled to the transcript abundance of nearby protein-coding gene(s). Small RNA (smRNA) abundance was found to be positively correlated with hypermethylated regions. These results provide insights into interplay among DNA methylation, gene expression and smRNA abundance, and suggest a role in abiotic stress adaptation in rice.
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Proteomics approach reveals mechanism underlying susceptibility of loquat fruit to sunburn during color changing period. Food Chem 2015; 176:388-95. [PMID: 25624247 DOI: 10.1016/j.foodchem.2014.12.076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/28/2014] [Accepted: 12/18/2014] [Indexed: 11/20/2022]
Abstract
The objective of this work was to investigate why loquat fruit peels are more sensitive to high temperature and strong sunlight, making them highly susceptible to sunburn, during the color changing period (CCP). Two dimensional gel electrophoresis (2-DE) of the fruit peel proteins was performed over three developmental periods, namely green fruit period (GFP), color changing period and yellow ripening period (YRP). Fifty-five protein spots with at least 2-fold differences in abundance were successfully identified by MALDI-TOF-TOF/MS. The identified proteins were divided into categories related to heat-shock response, stress response and defense, energy metabolism, photosynthesis and protein biosynthesis. The results showed that expression of proteins related to anaerobic respiration and photorespiration were increased while the proteins related to ROS scavenging, polyamine biosynthesis, defense pathogens and photosynthesis were decreased during CCP under heat stress. Our findings provide new insights into the molecular mechanism of loquat fruit susceptible to sunburn during CCP.
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Kujur A, Bajaj D, Upadhyaya HD, Das S, Ranjan R, Shree T, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea. FRONTIERS IN PLANT SCIENCE 2015; 6:162. [PMID: 25873920 PMCID: PMC4379880 DOI: 10.3389/fpls.2015.00162] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/01/2015] [Indexed: 05/19/2023]
Abstract
The genome-wide discovery and high-throughput genotyping of SNPs in chickpea natural germplasm lines is indispensable to extrapolate their natural allelic diversity, domestication, and linkage disequilibrium (LD) patterns leading to the genetic enhancement of this vital legume crop. We discovered 44,844 high-quality SNPs by sequencing of 93 diverse cultivated desi, kabuli, and wild chickpea accessions using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays that were physically mapped across eight chromosomes of desi and kabuli. Of these, 22,542 SNPs were structurally annotated in different coding and non-coding sequence components of genes. Genes with 3296 non-synonymous and 269 regulatory SNPs could functionally differentiate accessions based on their contrasting agronomic traits. A high experimental validation success rate (92%) and reproducibility (100%) along with strong sensitivity (93-96%) and specificity (99%) of GBS-based SNPs was observed. This infers the robustness of GBS as a high-throughput assay for rapid large-scale mining and genotyping of genome-wide SNPs in chickpea with sub-optimal use of resources. With 23,798 genome-wide SNPs, a relatively high intra-specific polymorphic potential (49.5%) and broader molecular diversity (13-89%)/functional allelic diversity (18-77%) was apparent among 93 chickpea accessions, suggesting their tremendous applicability in rapid selection of desirable diverse accessions/inter-specific hybrids in chickpea crossbred varietal improvement program. The genome-wide SNPs revealed complex admixed domestication pattern, extensive LD estimates (0.54-0.68) and extended LD decay (400-500 kb) in a structured population inclusive of 93 accessions. These findings reflect the utility of our identified SNPs for subsequent genome-wide association study (GWAS) and selective sweep-based domestication trait dissection analysis to identify potential genomic loci (gene-associated targets) specifically regulating important complex quantitative agronomic traits in chickpea. The numerous informative genome-wide SNPs, natural allelic diversity-led domestication pattern, and LD-based information generated in our study have got multidimensional applicability with respect to chickpea genomics-assisted breeding.
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Affiliation(s)
- Alice Kujur
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Rajeev Ranjan
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Tanima Shree
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | | | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB)New Delhi, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI)New Delhi, India
| | - C. L. L. Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | | | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
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Lima JM, Nath M, Dokku P, Raman KV, Kulkarni KP, Vishwakarma C, Sahoo SP, Mohapatra UB, Mithra SVA, Chinnusamy V, Robin S, Sarla N, Seshashayee M, Singh K, Singh AK, Singh NK, Sharma RP, Mohapatra T. Physiological, anatomical and transcriptional alterations in a rice mutant leading to enhanced water stress tolerance. AOB PLANTS 2015; 7:plv023. [PMID: 25818072 PMCID: PMC4482838 DOI: 10.1093/aobpla/plv023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 02/26/2015] [Indexed: 05/04/2023]
Abstract
Water stress is one of the most severe constraints to crop productivity. Plants display a variety of physiological and biochemical responses both at the cellular and whole organism level upon sensing water stress. Leaf rolling, stomatal closure, deeper root penetration, higher relative water content (RWC) and better osmotic adjustment are some of the mechanisms that plants employ to overcome water stress. In the current study, we report a mutant, enhanced water stress tolerant1 (ewst1) with enhanced water stress tolerance, identified from the ethyl methanesulfonate-induced mutant population of rice variety Nagina22 by field screening followed by withdrawal of irrigation in pots and hydroponics (PEG 6000). Though ewst1 was morphologically similar to the wild type (WT) for 35 of the 38 morphological descriptors (except chalky endosperm/expression of white core, decorticated grain colour and grain weight), it showed enhanced germination in polyethylene glycol-infused medium. It exhibited increase in maximum root length without any significant changes in its root weight, root volume and total root number on crown when compared with the WT under stress in PVC tube experiment. It also showed better performance for various physiological parameters such as RWC, cell membrane stability and chlorophyll concentration upon water stress in a pot experiment. Root anatomy and stomatal microscopic studies revealed changes in the number of xylem and phloem cells, size of central meta-xylem and number of closed stomata in ewst1. Comparative genome-wide transcriptome analysis identified genes related to exocytosis, secondary metabolites, tryptophan biosynthesis, protein phosphorylation and other signalling pathways to be playing a role in enhanced response to water stress in ewst1. The possible involvement of a candidate gene with respect to the observed morpho-physiological and transcriptional changes and its role in stress tolerance are discussed. The mutant identified and characterized in this study will be useful for further dissection of water stress tolerance in rice.
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Affiliation(s)
- John Milton Lima
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India Department of Botany, North Orissa University, Baripada, Odisha, India
| | - Manoj Nath
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - Prasad Dokku
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - K V Raman
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - K P Kulkarni
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - C Vishwakarma
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - S P Sahoo
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - U B Mohapatra
- Department of Botany, North Orissa University, Baripada, Odisha, India
| | - S V Amitha Mithra
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - V Chinnusamy
- Indian Agricultural Research Institute, New Delhi, India
| | - S Robin
- Tamil Nadu Agricultural University, Coimbatore, India
| | - N Sarla
- Directorate of Rice Research, Hyderabad, India
| | - M Seshashayee
- University of Agricultural Sciences, Bangalore, India
| | - K Singh
- Punjab Agricultural University, Ludhiana, India
| | - A K Singh
- Indian Agricultural Research Institute, New Delhi, India
| | - N K Singh
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - R P Sharma
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - T Mohapatra
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India Present address: Central Rice Research Institute, Cuttack, Odisha, India
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Fang H, Meng Q, Xu J, Tang H, Tang S, Zhang H, Huang J. Knock-down of stress inducible OsSRFP1 encoding an E3 ubiquitin ligase with transcriptional activation activity confers abiotic stress tolerance through enhancing antioxidant protection in rice. PLANT MOLECULAR BIOLOGY 2015; 87:441-58. [PMID: 25667045 DOI: 10.1007/s11103-015-0294-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 01/23/2015] [Indexed: 05/08/2023]
Abstract
E3 ubiquitin ligases are involved in a variety of physiological processes. This study demonstrated the function of a previously unknown rice RING finger E3 ligase, Oryza sativa Stress-related RING Finger Protein 1 (OsSRFP1) in stress responses in rice. OsSRFP1 was ubiquitously expressed in various rice organs, with the higher expression levels in roots, panicles and culm nodes. The transcript of OsSRFP1 was induced by cold, dehydration, salt, H2O2 and abscisic acid treatments. Interestingly, the OsSRFP1-overexpressing plants were less tolerant to salt, cold and oxidative stresses than wild type plants; while the RNA interference silencing of OsSRFP1 plants were more tolerant than wild type without yield penalty. Compared with the wild type, amounts of free proline and activities of antioxidant enzymes were increased in the RNAi plants but decreased in the overexpression plants under cold stress, which were inversely correlated with the malondialdehyde and hydrogen peroxide (H2O2) levels in the tested lines. Microarray analysis showed that expression of numerous genes involving in ROS homeostasis was altered in the OsSRFP1-overexpressing plants under normal and cold conditions. In vitro ubiquitination assays showed that OsSRFP1 possessed E3 ubiquitin ligase activity and the intact RING domain was essential for the activity. Moreover, OsSRFP1 might function in transcriptional regulation with nuclear localization. Taken together, our results demonstrate that OsSRFP1 may have dual functions in post-translational and transcriptional regulations in modulating abiotic stress responses in rice, at least in part, by negatively regulating antioxidant enzymes-mediated reactive oxygen species removal.
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Affiliation(s)
- Huimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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Todaka D, Shinozaki K, Yamaguchi-Shinozaki K. Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants. FRONTIERS IN PLANT SCIENCE 2015; 6:84. [PMID: 25741357 PMCID: PMC4332304 DOI: 10.3389/fpls.2015.00084] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/02/2015] [Indexed: 05/17/2023]
Abstract
Advances have been made in the development of drought-tolerant transgenic plants, including cereals. Rice, one of the most important cereals, is considered to be a critical target for improving drought tolerance, as present-day rice cultivation requires large quantities of water and as drought-tolerant rice plants should be able to grow in small amounts of water. Numerous transgenic rice plants showing enhanced drought tolerance have been developed to date. Such genetically engineered plants have generally been developed using genes encoding proteins that control drought regulatory networks. These proteins include transcription factors, protein kinases, receptor-like kinases, enzymes related to osmoprotectant or plant hormone synthesis, and other regulatory or functional proteins. Of the drought-tolerant transgenic rice plants described in this review, approximately one-third show decreased plant height under non-stressed conditions or in response to abscisic acid treatment. In cereal crops, plant height is a very important agronomic trait directly affecting yield, although the improvement of lodging resistance should also be taken into consideration. Understanding the regulatory mechanisms of plant growth reduction under drought stress conditions holds promise for developing transgenic plants that produce high yields under drought stress conditions. Plant growth rates are reduced more rapidly than photosynthetic activity under drought conditions, implying that plants actively reduce growth in response to drought stress. In this review, we summarize studies on molecular regulatory networks involved in response to drought stress. In a separate section, we highlight progress in the development of transgenic drought-tolerant rice plants, with special attention paid to field trial investigations.
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Affiliation(s)
- Daisuke Todaka
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, TokyoJapan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, YokohamaJapan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, TokyoJapan
- *Correspondence: Kazuko Yamaguchi-Shinozaki, Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan e-mail:
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Dansana PK, Kothari KS, Vij S, Tyagi AK. OsiSAP1 overexpression improves water-deficit stress tolerance in transgenic rice by affecting expression of endogenous stress-related genes. PLANT CELL REPORTS 2014; 33:1425-40. [PMID: 24965356 DOI: 10.1007/s00299-014-1626-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 03/21/2014] [Accepted: 04/22/2014] [Indexed: 05/19/2023]
Abstract
OsiSAP1, an A20/AN1 zinc-finger protein, confers water-deficit stress tolerance at different stages of growth by affecting expression of several endogenous genes in transgenic rice. Transgenic lines have been generated from rice constitutively expressing OsiSAP1, an A20/AN1 zinc-finger containing stress-associated protein gene from rice, driven by maize UBIQUITIN gene promoter and evaluated for water-deficit stress tolerance at different stages of growth. Their seeds show early germination and seedlings grow better under water-deficit stress compared to non-transgenic (NT) rice. Leaves from transgenic seedlings showed lesser membrane damage and lipid peroxidation under water-deficit stress. Relatively lower rate of leaf water loss has been observed in detached intact leaves from transgenic plants during late vegetative stage. Delayed leaf rolling and higher relative water content were also observed in transgenic plants under progressive water-deficit stress during reproductive developmental stage. Although reduction in grain yield is observed under unstressed condition, the relative water-deficit stress-induced yield losses are lower in transgenic rice vis-à-vis NT plants thereby resulting in yield loss protection. Transcriptome analysis suggests that overexpression of OsiSAP1 in transgenic rice results in altered expression of several endogenous genes including those coding for transcription factors, membrane transporters, signaling components and genes involved in metabolism, growth and development. A total of 150 genes were found to be more than twofold up-regulated in transgenic rice of which 43 genes are known to be involved in stress response. Our results suggest that OsiSAP1 is a positive regulator of water-deficit stress tolerance in rice.
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Affiliation(s)
- Prasant K Dansana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
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Mathur S, Agrawal D, Jajoo A. Photosynthesis: Response to high temperature stress. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 137:116-26. [DOI: 10.1016/j.jphotobiol.2014.01.010] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 01/10/2014] [Accepted: 01/10/2014] [Indexed: 01/06/2023]
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Shanker AK, Maheswari M, Yadav SK, Desai S, Bhanu D, Attal NB, Venkateswarlu B. Drought stress responses in crops. Funct Integr Genomics 2014; 14:11-22. [PMID: 24408129 DOI: 10.1007/s10142-013-0356-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/04/2013] [Accepted: 12/18/2013] [Indexed: 01/09/2023]
Abstract
Among the effects of impending climate change, drought will have a profound impact on crop productivity in the future. Response to drought stress has been studied widely, and the model plant Arabidopsis has guided the studies on crop plants with genome sequence information viz., rice, wheat, maize and sorghum. Since the value of functions of genes, dynamics of pathways and interaction of networks for drought tolerance in plants can only be judged by evidence from field performance, this mini-review provides a research update focussing on the current developments on the response to drought in crop plants. Studies in Arabidopsis provide the basis for interpreting the available information in a systems biology perspective. In particular, the elucidation of the mechanism of drought stress response in crops is considered from evidence-based outputs emerging from recent omic studies in crops.
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Affiliation(s)
- Arun K Shanker
- Division of Crop Sciences, Central Research Institute for Dryland Agriculture (CRIDA), Santoshnagar, Saidabad P.O, Hyderabad, 500-059, India,
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Abstract
Drought is one of the most important environmental stresses affecting the productivity of most field crops. Elucidation of the complex mechanisms underlying drought resistance in crops will accelerate the development of new varieties with enhanced drought resistance. Here, we provide a brief review on the progress in genetic, genomic, and molecular studies of drought resistance in major crops. Drought resistance is regulated by numerous small-effect loci and hundreds of genes that control various morphological and physiological responses to drought. This review focuses on recent studies of genes that have been well characterized as affecting drought resistance and genes that have been successfully engineered in staple crops. We propose that one significant challenge will be to unravel the complex mechanisms of drought resistance in crops through more intensive and integrative studies in order to find key functional components or machineries that can be used as tools for engineering and breeding drought-resistant crops.
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Affiliation(s)
- Honghong Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China; ,
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Kim SH, Hwang SG, Hwang JE, Jang CS, Velusamy V, Kim JB, Kim SH, Ha BK, Kang SY, Kim DS. The identification of candidate radio marker genes using a coexpression network analysis in gamma-irradiated rice. PHYSIOLOGIA PLANTARUM 2013; 149:554-570. [PMID: 23617399 DOI: 10.1111/ppl.12058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 02/28/2013] [Accepted: 03/25/2013] [Indexed: 06/02/2023]
Abstract
Plant physiological and biochemical processes are significantly affected by gamma irradiation stress. In addition, gamma-ray (GA) differentially affects gene expression across the whole genome. In this study, we identified radio marker genes (RMGs) responding only to GA stress compared with six abiotic stresses (chilling, cold, anoxia, heat, drought and salt) in rice. To analyze the expression patterns of differentially expressed genes (DEGs) in gamma-irradiated rice plants against six abiotic stresses, we conducted a hierarchical clustering analysis by using a complete linkage algorithm. The up- and downregulated DEGs were observed against six abiotic stresses in three and four clusters among a total of 31 clusters, respectively. The common gene ontology functions of upregulated DEGs in clusters 9 and 19 are associated with oxidative stress. In a Pearson's correlation coefficient analysis, GA stress showed highly negative correlation with salt stress. On the basis of specific data about the upregulated DEGs, we identified the 40 candidate RMGs that are induced by gamma irradiation. These candidate RMGs, except two genes, were more highly induced in rice roots than in other tissues. In addition, we obtained other 38 root-induced genes by using a coexpression network analysis of the specific upregulated candidate RMGs in an ARACNE algorithm. Among these genes, we selected 16 RMGs and 11 genes coexpressed with three RMGs to validate coexpression network results. RT-PCR assay confirmed that these genes were highly upregulated in GA treatment. All 76 genes (38 root-induced genes and 38 candidate RMGs) might be useful for the detection of GA sensitivity in rice roots.
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Affiliation(s)
- Sun-Hee Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Sun-Goo Hwang
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Jung Eun Hwang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Cheol Seong Jang
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Vijayanand Velusamy
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Bo-Keun Ha
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Dong Sub Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
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Zhang X, Rerksiri W, Liu A, Zhou X, Xiong H, Xiang J, Chen X, Xiong X. Transcriptome profile reveals heat response mechanism at molecular and metabolic levels in rice flag leaf. Gene 2013; 530:185-92. [PMID: 23994682 DOI: 10.1016/j.gene.2013.08.048] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/30/2013] [Accepted: 08/13/2013] [Indexed: 10/26/2022]
Abstract
Flag leaf is one of the key photosynthesis organs during rice reproductive stage. A time course microarray analysis of rice flag leaf was done after 40°C treatment for 0 min, 20 min, 60 min, 2h, 4h, and 8h. The identified significant heat responsive genes were mainly involved in transcriptional regulation, transport, protein binding, antioxidant, and stress response. KMC analysis discovered the time-dependent gene expression pattern under heat. MapMan analysis demonstrated that, under heat treatment, Hsp genes and genes involved in glycolysis and ubiquitin-proteasome were enhanced, and genes involved in TCA, carotenoid, dihydroflavonol and anthocyanin metabolisms and light-reaction in the photosynthesis were widely repressed. Meanwhile, some rate-limiting enzyme genes in shikimate, lignin, and mevalonic acid metabolisms were up-regulated, revealing the importance of maintaining specific secondary metabolites under heat stress. The present study increased our understanding of heat response in rice flag leaf and provided good candidate genes for crop improvement.
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Affiliation(s)
- Xianwen Zhang
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China; College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
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Priya P, Jain M. RiceSRTFDB: a database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat027. [PMID: 23660286 PMCID: PMC3649641 DOI: 10.1093/database/bat027] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Rice is one of the most important crop plants, representing the staple food for more than half the world’s population. However, its productivity is challenged by various stresses, including drought and salinity. Transcription factors (TFs) represent a regulatory component of the genome and are the most important targets for engineering stress tolerance. Here, we constructed a database, RiceSRTFDB, which provides comprehensive expression information for rice TFs during drought and salinity stress conditions and various stages of development. This information will be useful to identify the target TF(s) involved in stress response at a particular stage of development. The curated information for cis-regulatory elements present in their promoters has also been provided, which will be important to study the binding proteins. In addition, we have provided the available mutants and their phenotype information for rice TFs. All these information have been integrated in the database to facilitate the selection of target TFs of interest for functional analysis. This database aims to accelerate functional genomics research of rice TFs and understand the regulatory mechanisms underlying abiotic stress responses. Database URL:http://www.nipgr.res.in/RiceSRTFDB.html
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Affiliation(s)
- Pushp Priya
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Qu AL, Ding YF, Jiang Q, Zhu C. Molecular mechanisms of the plant heat stress response. Biochem Biophys Res Commun 2013; 432:203-7. [PMID: 23395681 DOI: 10.1016/j.bbrc.2013.01.104] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 01/24/2013] [Indexed: 11/30/2022]
Abstract
High temperature has become a global concern, which seriously affects the growth and production of plants, particularly crops. Thus, the molecular mechanism of the heat stress response and breeding of heat-tolerant plants is necessary to protect food production and ensure crop safety. This review elaborates on the response networks of heat stress in plants, including the Hsf and Hsp response pathways, the response of ROS and the network of the hormones. In addition, the production of heat stress response elements during particular physiological periods of the plant is described. We also discuss the existing problems and future prospects concerning the molecular mechanisms of the heat stress response in plants.
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Affiliation(s)
- Ai-Li Qu
- China Jiliang University, Xueyuan Road 258, Hangzhou 310018, China
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Zhang X, Li J, Liu A, Zou J, Zhou X, Xiang J, Rerksiri W, Peng Y, Xiong X, Chen X. Expression profile in rice panicle: insights into heat response mechanism at reproductive stage. PLoS One 2012; 7:e49652. [PMID: 23155476 PMCID: PMC3498232 DOI: 10.1371/journal.pone.0049652] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/11/2012] [Indexed: 12/20/2022] Open
Abstract
Rice at reproductive stage is more sensitive to environmental changes, and little is known about the mechanism of heat response in rice panicle. Here, using rice microarray, we provided a time course gene expression profile of rice panicle at anther developmental stage 8 after 40°C treatment for 0 min, 20 min, 60 min, 2 h, 4 h, and 8 h. The identified differentially expressed genes were mainly involved in transcriptional regulation, transport, cellular homeostasis, and stress response. The predominant transcription factor gene families responsive to heat stress were Hsf, NAC, AP2/ERF, WRKY, MYB, and C2H2. KMC analysis discovered the time-dependent gene expression pattern under heat stress. The motif co-occurrence analysis on the promoters of genes from an early up-regulated cluster showed the important roles of GCC box, HSE, ABRE, and CE3 in response to heat stress. The regulation model central to ROS combined with transcriptome and ROS quantification data in rice panicle indicated the great importance to maintain ROS balance and the existence of wide cross-talk in heat response. The present study increased our understanding of the heat response in rice panicle and provided good candidate genes for crop improvement.
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Affiliation(s)
- Xianwen Zhang
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jiaping Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Ailing Liu
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jie Zou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Xiaoyun Zhou
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jianhua Xiang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Wirat Rerksiri
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yan Peng
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Xingyao Xiong
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
- * E-mail: (XX); (XC)
| | - Xinbo Chen
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- * E-mail: (XX); (XC)
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48
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Shaik R, Ramakrishna W. Bioinformatic analysis of epigenetic and microRNA mediated regulation of drought responsive genes in rice. PLoS One 2012; 7:e49331. [PMID: 23145152 PMCID: PMC3493535 DOI: 10.1371/journal.pone.0049331] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/09/2012] [Indexed: 12/02/2022] Open
Abstract
Drought stress response is a complex trait regulated at multiple levels. Changes in the epigenetic and miRNA regulatory landscape can dramatically alter the outcome of a stress response. However, little is known about the scope and extent of these regulatory factors on drought related cellular processes and functions. To this end, we selected a list of 5468 drought responsive genes (DRGs) of rice identified in multiple microarray studies and mapped the DNA methylation regions found in a genome wide methylcytosine immunoprecipitation and sequencing (mCIP-Seq) study to their genic and promoter regions, identified the chromatin remodeling genes and the genes that are targets of miRNAs. We found statistically significant enrichment of DNA methylation reads and miRNA target sequences in DRGs compared to a random set of genes. About 75% of the DRGs annotated to be involved in chromatin remodeling were downregulated. We found one-third of the DRGs are targeted by two-thirds of all known/predicted miRNAs in rice which include many transcription factors targeted by more than five miRNAs. Clustering analysis of the DRGs with epigenetic and miRNA features revealed, upregulated cluster was enriched in drought tolerance mechanisms while the downregulated cluster was enriched in drought resistance mechanisms evident by their unique gene ontologies (GOs), protein-protein interactions (PPIs), specific transcription factors, protein domains and metabolic pathways. Further, we analyzed the proteome of two weeks old young rice plants treated with a global demethylating agent, 5-azacytidine (5-azaC), subjected to drought stress and identified 56 protein spots that are differentially expressed. Out of the 56 spots, 35 were differently expressed in the sample with both demethylation and drought stress treatments and 28 (50%) were part of DRGs considered in the bioinformatic analysis.
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Affiliation(s)
- Rafi Shaik
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Wusirika Ramakrishna
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
- * E-mail:
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49
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Sharma R, Agarwal P, Ray S, Deveshwar P, Sharma P, Sharma N, Nijhawan A, Jain M, Singh AK, Singh VP, Khurana JP, Tyagi AK, Kapoor S. Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Funct Integr Genomics 2012. [PMID: 22466020 DOI: 10.1007/s10142‐012‐0274‐3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22,980 genes in at least one of the tissues. Differential expression analysis with respect to five vegetative tissues and preceding stages of development revealed reproductive stage-preferential/-specific genes. By using subtractive logic, we identified 354 and 456 genes expressing specifically during panicle and seed development, respectively. The metabolic/hormonal pathways and transcription factor families playing key role in reproductive development were elucidated after overlaying the expression data on the public databases and manually curated list of transcription factors, respectively. During floral meristem differentiation (P1) and male meiosis (P3), the genes involved in jasmonic acid and phenylpropanoid biosynthesis were significantly upregulated. P6 stage of panicle, containing mature gametophytes, exhibited enrichment of transcripts involved in homogalacturonon degradation. Genes regulating auxin biosynthesis were induced during early seed development. We validated the stage-specificity of regulatory regions of three panicle-specific genes, OsAGO3, OsSub42, and RTS, and an early seed-specific gene, XYH, in transgenic rice. The data generated here provides a snapshot of the underlying complexity of the gene networks regulating rice reproductive development.
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Affiliation(s)
- Rita Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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50
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Sharma R, Agarwal P, Ray S, Deveshwar P, Sharma P, Sharma N, Nijhawan A, Jain M, Singh AK, Singh VP, Khurana JP, Tyagi AK, Kapoor S. Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Funct Integr Genomics 2012; 12:229-48. [PMID: 22466020 DOI: 10.1007/s10142-012-0274-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 03/02/2012] [Accepted: 03/06/2012] [Indexed: 12/20/2022]
Abstract
Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22,980 genes in at least one of the tissues. Differential expression analysis with respect to five vegetative tissues and preceding stages of development revealed reproductive stage-preferential/-specific genes. By using subtractive logic, we identified 354 and 456 genes expressing specifically during panicle and seed development, respectively. The metabolic/hormonal pathways and transcription factor families playing key role in reproductive development were elucidated after overlaying the expression data on the public databases and manually curated list of transcription factors, respectively. During floral meristem differentiation (P1) and male meiosis (P3), the genes involved in jasmonic acid and phenylpropanoid biosynthesis were significantly upregulated. P6 stage of panicle, containing mature gametophytes, exhibited enrichment of transcripts involved in homogalacturonon degradation. Genes regulating auxin biosynthesis were induced during early seed development. We validated the stage-specificity of regulatory regions of three panicle-specific genes, OsAGO3, OsSub42, and RTS, and an early seed-specific gene, XYH, in transgenic rice. The data generated here provides a snapshot of the underlying complexity of the gene networks regulating rice reproductive development.
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Affiliation(s)
- Rita Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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