1
|
Mishra D, Shekhar S, Subba P, Prasad TSK, Chakraborty S, Chakraborty N. Wheat TaNACα18 functions as a positive regulator of high-temperature adaptive responses and improves cell defense machinery. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38961633 DOI: 10.1111/tpj.16913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 07/05/2024]
Abstract
Global wheat production amounted to >780 MMT during 2022-2023 whose market size are valued at >$128 billion. Wheat is highly susceptible to high-temperature stress (HTS) throughout the life cycle and its yield declines 5-7% with the rise in each degree of temperature. Previously, we reported an array of HTS-response markers from a resilient wheat cv. Unnat Halna and described their putative role in heat acclimation. To complement our previous results and identify the key determinants of thermotolerance, here we examined the cytoplasmic proteome of a sensitive cv. PBW343. The HTS-triggered metabolite reprograming highlighted how proteostasis defects influence the formation of an integrated stress-adaptive response. The proteomic analysis identified several promising HTS-responsive proteins, including a NACα18 protein, designated TaNACα18, whose role in thermotolerance remains unknown. Dual localization of TaNACα18 suggests its crucial functions in the cytoplasm and nucleus. The homodimerization of TaNACα18 anticipated its function as a transcriptional coactivator. The complementation of TaNACα18 in yeast and overexpression in wheat demonstrated its role in thermotolerance across the kingdom. Altogether, our results suggest that TaNACα18 imparts tolerance through tight regulation of gene expression, cell wall remodeling and activation of cell defense responses.
Collapse
Affiliation(s)
- Divya Mishra
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shubhendu Shekhar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya, Mangalore, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya, Mangalore, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| |
Collapse
|
2
|
Li X, Tao N, Xu B, Xu J, Yang Z, Jiang C, Zhou Y, Deng M, Lv J, Zhao K. Establishment and application of a root wounding-immersion method for efficient virus-induced gene silencing in plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1336726. [PMID: 38708388 PMCID: PMC11066161 DOI: 10.3389/fpls.2024.1336726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/15/2024] [Indexed: 05/07/2024]
Abstract
In the post-genomic era, virus-induced gene silencing (VIGS) has played an important role in research on reverse genetics in plants. Commonly used Agrobacterium-mediated VIGS inoculation methods include stem scratching, leaf infiltration, use of agrodrench, and air-brush spraying. In this study, we developed a root wounding-immersion method in which 1/3 of the plant root (length) was cut and immersed in a tobacco rattle virus (TRV)1:TRV2 mixed solution for 30 min. We optimized the procedure in Nicotiana benthamiana and successfully silenced N. benthamiana, tomato (Solanum lycopersicum), pepper (Capsicum annuum L.), eggplant (Solanum melongena), and Arabidopsis thaliana phytoene desaturase (PDS), and we observed the movement of green fluorescent protein (GFP) from the roots to the stem and leaves. The silencing rate of PDS in N. benthamiana and tomato was 95-100%. In addition, we successfully silenced two disease-resistance genes, SITL5 and SITL6, to decrease disease resistance in tomatoes (CLN2037E). The root wounding-immersion method can be used to inoculate large batches of plants in a short time and with high efficiency, and fresh bacterial infusions can be reused several times. The most important aspect of the root wounding-immersion method is its application to plant species susceptible to root inoculation, as well as its ability to inoculate seedlings from early growth stages. This method offers a means to conduct large-scale functional genome screening in plants.
Collapse
Affiliation(s)
- Xinyun Li
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Na Tao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Bin Xu
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Junqiang Xu
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zhengan Yang
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Caiqian Jiang
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ying Zhou
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Minghua Deng
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Junheng Lv
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Kai Zhao
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| |
Collapse
|
3
|
Karunarathne S, Walker E, Sharma D, Li C, Han Y. Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance. J Zhejiang Univ Sci B 2023; 24:1069-1092. [PMID: 38057266 PMCID: PMC10710907 DOI: 10.1631/jzus.b2200552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/17/2023] [Indexed: 07/11/2023]
Abstract
Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern gene-editing platforms. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.
Collapse
Affiliation(s)
- Sakura Karunarathne
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Darshan Sharma
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia.
| | - Yong Han
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia.
| |
Collapse
|
4
|
He M, Wang X, Bu Y, Yang X, Zhang L, Song X. Gibberellin confers to the expression of TaGA-6D and negatively regulates the fertility of wheat with Aegilops juvenalis cytoplasm. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023:111771. [PMID: 37328073 DOI: 10.1016/j.plantsci.2023.111771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 06/10/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
As the trace signal molecules widely existing in plants, plant hormones can regulate physiological responses of plants at low concentrations. At present, the effect of plant endogenous hormones on wheat male fertility has attracted attention, but the molecular mechanism underlying fertility regulation is unclear. Given this, the anthers of five isonuclear alloplasmic male sterile lines and their maintainer line were RNA-sequenced. A gene TaGA-6D encoding gibberellin (GA) regulated protein was isolated, which was located to the nucleus, cell wall and/or cell membrane, and predominantly highly expressed in the anther of Ju706A, a male sterile line with Aegilops juvenalis cytoplasm. By spraying assay of GA with different concentrations on fertility line Ju706R, it was found that with the increase of exogenous GA concentration, the content of endogenous GA and expression level of TaGA-6D in anther gradually increased, and the fertility decreased. However, silencing of TaGA-6D partially restore the fertility of Ju706R sprayed with 1000ng/μl GA, and indicating that gibberellin can promote the expression of TaGA-6D and negatively regulates the fertility of wheat with Aegilops juvenalis cytoplasm, which providing new insights for understanding hormone regulation of male fertility in wheat.
Collapse
Affiliation(s)
- Mengting He
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xiaoxia Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yaning Bu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xuetong Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
5
|
Geng X, Wang X, Wang J, Yang X, Zhang L, Song X. TaEXPB5 functions as a gene related to pollen development in thermo-sensitive male-sterility wheat with Aegilops kotschyi cytoplasm. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111377. [PMID: 35820549 DOI: 10.1016/j.plantsci.2022.111377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
The thermo-sensitive cytoplasmic male-sterility line with Aegilops kotschyi cytoplasm (K-TCMS) is completely male sterile under low temperature (< 18 ℃) during Zadoks growth stages 45-52, whereas its fertility can be restored under hot temperature (≥ 20 ℃). The K-TCMS line may facilitate hybrid breeding and hybrid wheat production. Therefore, to elucidate the molecular mechanisms of its male sterility/fertility conversion, we conducted the association analysis of proteins and transcript expression to screen fertility related genes using RNA-seq, iTRAQ, and PRM-based assay. A gene encoding expansin protein in wheat, TaEXPB5, was isolated in K-TCMS line KTM3315A, which upregulated expression in the fertility anthers. Subcellular localization analysis suggested that TaEXPB5 protein localized to nucleus and cell wall. The silencing of TaEXPB5 displayed pollen abortion and the declination of fertility. Further, cytological investigation indicated that the silencing of TaEXPB5 induced the early degradation of tapetum and abnormal development of pollen wall. These results implied that TaEXPB5 may be essential for anther or pollen development and male fertility of KTM3315A. These findings provide a novel insight into molecular mechanism of fertility conversion for thermo-sensitive cytoplasmic male-sterility wheat, and contribute to the molecular breeding of hybrid wheat in the future.
Collapse
Affiliation(s)
- Xingxia Geng
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xiaoxia Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jingchen Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xuetong Yang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| |
Collapse
|
6
|
Kumar J, Kumar A, Sen Gupta D, Kumar S, DePauw RM. Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops. Heredity (Edinb) 2022; 128:473-496. [PMID: 35249099 PMCID: PMC9178024 DOI: 10.1038/s41437-022-00513-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022] Open
Abstract
In the last decade, advancements in genomics tools and techniques have led to the discovery of many genes. Most of these genes still need to be characterized for their associated function and therefore, such genes remain underutilized for breeding the next generation of improved crop varieties. The recent developments in different reverse genetic approaches have made it possible to identify the function of genes controlling nutritional, biochemical, and metabolic traits imparting drought, heat, cold, salinity tolerance as well as diseases and insect-pests. This article focuses on reviewing the current status and prospects of using reverse genetic approaches to breed nutrient-rich and climate resilient cereal and food legume crops.
Collapse
Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Ron M DePauw
- Advancing Wheat Technologies, 118 Strathcona Rd SW, Calgary, AB, T3H 1P3, Canada
| |
Collapse
|
7
|
Zhang Q, Yuan C, Wang F, Xu S, Li Y, Shi G, Ding Z. Roles of Small Subunits of Laccase (ssPOXA3a/b) in Laccase Production by Pleurotus eryngii var. ferulae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13113-13124. [PMID: 34696587 DOI: 10.1021/acs.jafc.1c04777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The small subunit, ssPOXA3a/b, and the large subunit, POXA3, are indispensable components of typical heterodimeric laccase (Lacc2) in white rot fungi. However, the enzymatic and biological functions of ssPOXA3a/b remain unclear. The present study revealed that neither ssPOXA3a nor ssPOXA3b per se has a catalytic ability, whereas their combination with POXA3 (and especially ssPOXA3b) enhances the activity, thermostability, and pH stability of POXA3. In Pleurotus eryngii var. ferulae, there was no regulatory relationship between ssPOXA3a/b and POXA3 at the transcriptional level. However, sspoxa3a/b overexpression had a negative feedback effect on lacc6 transcription. By contrast, poxa3 transcripts had no effect on any other laccase isoenzyme. Overexpression of sspoxa3a/b resulted in small fungal pellets, thin mycelial walls, and facilitated laccase secretion. However, poxa3 overexpression had no influence on pellet morphology. Collectively, this work elucidated the functions of ssPOXA3a/b and laid an empirical foundation for the development of high-yield laccase.
Collapse
Affiliation(s)
- Qi Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Chang Yuan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Feng Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Sha Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Youran Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Guiyang Shi
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zhongyang Ding
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| |
Collapse
|
8
|
Yang X, Ye J, Niu F, Feng Y, Song X. Identification and verification of genes related to pollen development and male sterility induced by high temperature in the thermo-sensitive genic male sterile wheat line. PLANTA 2021; 253:83. [PMID: 33770279 DOI: 10.1007/s00425-021-03601-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Bioinformatic analysis identified the function of genes regulating wheat fertility. Barley stripe mosaic virus-induced gene silencing verified that the genes TaMut11 and TaSF3 are involved in pollen development and related to fertility conversion. Environment-sensitive genic male sterility is of vital importance to hybrid vigor in crop production and breeding. Therefore, it is meaningful to study the function of the genes related to pollen development and male sterility, which is still not fully understand currently. In this study, YanZhan 4110S, a new thermo-sensitive genic male sterility wheat line, and its near-isogenic line YanZhan 4110 were analyzed. Through comparative transcriptome basic bioinformatics and weighted gene co-expression network to further identify some hub genes, the genes TaMut11 and TaSF3 associated with pollen development and male sterility induced by high-temperature were identified in YanZhan 4110S. Further verification through barley stripe mosaic virus-induced gene silencing elucidated that the silencing of TaMut11 and TaSF3 caused pollen abortion, finally resulting in the declination of fertility. These findings provided data on the abortive mechanism in environment-sensitive genic male sterility wheat.
Collapse
Affiliation(s)
- Xuetong Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jiali Ye
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fuqiang Niu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yi Feng
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
9
|
Zhang Q, Zhao L, Li Y, Wang F, Li S, Shi G, Ding Z. Comparative transcriptomics and transcriptional regulation analysis of enhanced laccase production induced by co-culture of Pleurotus eryngii var. ferulae with Rhodotorula mucilaginosa. Appl Microbiol Biotechnol 2019; 104:241-255. [PMID: 31735984 DOI: 10.1007/s00253-019-10228-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/09/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
The co-culturing of Pleurotus eryngii var. ferulae and Rhodotorula mucilaginosa was confirmed in our previous studies to be an efficient strategy to improve laccase production by submerged fermentation. To determine the possible regulation principles underlying this behaviour, comparative transcriptomic analysis was performed on P. eryngii var. ferulae to investigate the differential expression of genes in co-culture. RNA-seq analysis showed that genes concerning xenobiotic biodegradation and expenditure of energy were upregulated. However, genes related to oxidative stress were downregulated. In addition, the transcription levels of laccase isoenzymes were not consistent in the co-culture system: 3 laccase genes (lacc1, lacc2, lacc12) were upregulated, and 3 laccase genes (lacc4, lacc6, lacc9) were downregulated. The enhancement in laccase activity can be due to upregulation of a laccase heterodimer encoded by the genes lacc2 and ssPOXA3a (or ssPOXA3b), whose expression levels were increased by 459% and 769% (or 585% for ssPOXA3b) compared with those of a control, respectively. β-Carotene produced by R. mucilaginosa upregulated the transcription of lacc2 only. Combining these results with an analysis of cis-acting responsive elements indicated that four transcription factors (TFs) had potential regulatory effects on the transcription of laccase genes. It was supposed that TFa regulated lacc transcription by binding with methyl jasmonate and heat shock response elements. The expression of TFb, TFc, and TFd was regulated by β-carotene. However, β-carotene had no effect on TFa expression. These results provide a possible mechanism for the regulation of laccase gene transcription in the co-culture system and are also beneficial for the future intensification of fungal laccase production.
Collapse
Affiliation(s)
- Qi Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Liting Zhao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - YouRan Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Feng Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Song Li
- School of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, 241000, China
| | - Guiyang Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Zhongyang Ding
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
10
|
Singh B, Kukreja S, Goutam U. Milestones achieved in response to drought stress through reverse genetic approaches. F1000Res 2018; 7:1311. [PMID: 30631439 PMCID: PMC6290974 DOI: 10.12688/f1000research.15606.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/20/2018] [Indexed: 01/07/2023] Open
Abstract
Drought stress is the most important abiotic stress that constrains crop production and reduces yield drastically. The germplasm of most of the cultivated crops possesses numerous unknown drought stress tolerant genes. Moreover, there are many reports suggesting that the wild species of most of the modern cultivars have abiotic stress tolerant genes. Due to climate change and population booms, food security has become a global issue. To develop drought tolerant crop varieties knowledge of various genes involved in drought stress is required. Different reverse genetic approaches such as virus-induced gene silencing (VIGS), clustered regularly interspace short palindromic repeat (CRISPR), targeting induced local lesions in genomes (TILLING) and expressed sequence tags (ESTs) have been used extensively to study the functionality of different genes involved in response to drought stress. In this review, we described the contributions of different techniques of functional genomics in the study of drought tolerant genes.
Collapse
Affiliation(s)
- Baljeet Singh
- Biotechnology, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Sarvjeet Kukreja
- Department of Botany, Ch. MRM Memorial College, Sriganganagar, Rajasthan, 335804, India
| | - Umesh Goutam
- Biotechnology, Lovely Professional University, Phagwara, Punjab, 144411, India
| |
Collapse
|
11
|
Tavakol E. Virus-Induced Gene Silencing (VIGS) in Aegilops tauschii and Its Use in Functional Analysis of AetDREB2. Mol Biotechnol 2017; 60:41-48. [PMID: 29196985 DOI: 10.1007/s12033-017-0042-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Among the available reverse genetic approaches for studying gene function, virus-induced gene silencing (VIGS) has several advantages. It allows rapid characterization of gene function independent of stable transformation, which is basically difficult to achieve in monocots, and offers the potential to silence individual or multiple genes of a gene family. In order to establish a VIGS system in Aegilops tauschii, modified vectors derived from Barley stripe mosaic virus (BSMV) were used for silencing a phytoene desaturase gene that provides a convenient visual reporter for silencing. The results demonstrated a high efficiency of BSMV-VIGS in A. tauschii. Moreover, the BSMV-VIGS system was used to target a 354 bp specific region of the Dehydration-responsive element-binding (AetDreb2) gene, resulting in successful silencing of the gene in A. tauschii plants, as verified by real-time qRT-PCR. Indeed, in comparison with plants that were inoculated with an empty vector (BSMV:00), a faster rate of wilting and a lower relative water content were observed in plants inoculated with BSMV:AetDreb2 when they were exposed to drought stress. Therefore, BSMV-VIGS can be efficiently employed as a novel tool for reverse genetics in A. tauschii. It can also be used to study the effects of polyploidization on the gene function by a comparative analysis between bread wheat and its diploid progenitor.
Collapse
Affiliation(s)
- Elahe Tavakol
- Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186, Shiraz, Iran.
| |
Collapse
|
12
|
Pruthvi V, Rama N, Parvathi MS, Nataraja KN. Transgenic tobacco plants constitutively expressing peanut BTF3 exhibit increased growth and tolerance to abiotic stresses. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:377-385. [PMID: 27981726 DOI: 10.1111/plb.12533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/11/2016] [Indexed: 06/06/2023]
Abstract
Abiotic stresses limit crop growth and productivity worldwide. Cellular tolerance, an important abiotic stress adaptive trait, involves coordinated activities of multiple proteins linked to signalling cascades, transcriptional regulation and other diverse processes. Basal transcriptional machinery is considered to be critical for maintaining transcription under stressful conditions. From this context, discovery of novel basal transcription regulators from stress adapted crops like peanut would be useful for improving tolerance of sensitive plant types. In this study, we prospected a basal transcription factor, BTF3 from peanut (Arachis hypogaea L) and studied its relevance in stress acclimation by over expression in tobacco. AhBTF3 was induced under PEG-, NaCl-, and methyl viologen-induced stresses in peanut. The constitutive expression of AhBTF3 in tobacco increased plant growth under non stress condition. The transgenic plants exhibited superior phenotype compared to wild type under mannitol- and NaCl-induced stresses at seedling level. The enhanced cellular tolerance of transgenic plants was evidenced by higher cell membrane stability, reactive oxygen species (ROS) scavenging activity, seedling survival and vigour than wild type. The transgenic lines showed better in vitro regeneration capacity on growth media supplemented with NaCl than wild type. Superior phenotype of transgenic plants under osmotic and salinity stresses seems to be due to constitutive activation of genes of multiple pathways linked to growth and stress adaptation. The study demonstrated that AhBTF3 is a positive regulator of growth and stress acclimation and hence can be considered as a potential candidate gene for crop improvement towards stress adaptation.
Collapse
Affiliation(s)
- V Pruthvi
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, Karnataka, India
| | - N Rama
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, Karnataka, India
| | - M S Parvathi
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, Karnataka, India
| | - K N Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, Karnataka, India
| |
Collapse
|
13
|
Shu S, Bai Y, Wang G, Xiao X, Fan Z, Zhang J, Zhao C, Zhao Y, Xia C, Zhang H. Differentially expressed serum proteins associated with calcium regulation and hypocalcemia in dairy cows. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:893-901. [PMID: 27809461 PMCID: PMC5411855 DOI: 10.5713/ajas.16.0615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/22/2016] [Accepted: 11/02/2016] [Indexed: 01/08/2023]
Abstract
Objective Hypocalcemia is an important metabolic disease of dairy cows during the transition period, although the effect of hypocalcemia on biological function in dairy cows remains unknown. Methods In this study, proteomic, mass spectrum, bioinformatics and western blotting were employed to identify differentially expressed proteins related to serum Ca concentration. Serum samples from dairy cows were collected at three time points: 3rd days before calving (day −3), the day of calving (day 0), and 3rd days after calving (day +3). According to the Ca concentration on day 0, a total of 27 dairy cows were assigned to one of three groups (clinical, subclinical, and healthy). Samples collected on day −3 were used for discovery of differentially expressed proteins, which were separated and identified via proteomic analysis and mass spectrometry. Bioinformatics analysis was performed to determine the function of the identified proteins (gene ontology and pathway analysis). The differentially expressed proteins were verified by western blot analysis. Results There were 57 differential spots separated and eight different proteins were identified. Vitamin D-binding protein precursor (group-specific component, GC), alpha-2-macroglobulin (A2M) protein, and apolipoprotein A-IV were related to hypocalcemia by bioinformatics analysis. Due to its specific expression (up-regulated in clinical hypocalcemia and down-regulated in subclinical hypocalcemia), A2M was selected for validation. The results were consistent with those of proteomic analysis. Conclusion A2M was as an early detection index for distinguishing clinical and subclinical hypocalcemia. The possible pathogenesis of clinical hypocalcemia caused by GC and apolipoprotein A-IV was speculated. The down-regulated expression of GC was a probable cause of the decrease in calcium concentration.
Collapse
Affiliation(s)
- Shi Shu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Yunlong Bai
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Gang Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xinhuan Xiao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Ziling Fan
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Jiang Zhang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Chang Zhao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Yang Zhao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Cheng Xia
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Hongyou Zhang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| |
Collapse
|
14
|
Massange-Sánchez JA, Palmeros-Suárez PA, Espitia-Rangel E, Rodríguez-Arévalo I, Sánchez-Segura L, Martínez-Gallardo NA, Alatorre-Cobos F, Tiessen A, Délano-Frier JP. Overexpression of Grain Amaranth (Amaranthus hypochondriacus) AhERF or AhDOF Transcription Factors in Arabidopsis thaliana Increases Water Deficit- and Salt-Stress Tolerance, Respectively, via Contrasting Stress-Amelioration Mechanisms. PLoS One 2016; 11:e0164280. [PMID: 27749893 PMCID: PMC5066980 DOI: 10.1371/journal.pone.0164280] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/22/2016] [Indexed: 11/19/2022] Open
Abstract
Two grain amaranth transcription factor (TF) genes were overexpressed in Arabidopsis plants. The first, coding for a group VII ethylene response factor TF (i.e., AhERF-VII) conferred tolerance to water-deficit stress (WS) in transgenic Arabidopsis without affecting vegetative or reproductive growth. A significantly lower water-loss rate in detached leaves coupled to a reduced stomatal opening in leaves of plants subjected to WS was associated with this trait. WS tolerance was also associated with an increased antioxidant enzyme activity and the accumulation of putative stress-related secondary metabolites. However, microarray and GO data did not indicate an obvious correlation between WS tolerance, stomatal closure, and abscisic acid (ABA)-related signaling. This scenario suggested that stomatal closure during WS in these plants involved ABA-independent mechanisms, possibly involving reactive oxygen species (ROS). WS tolerance may have also involved other protective processes, such as those employed for methyl glyoxal detoxification. The second, coding for a class A and cluster I DNA binding with one finger TF (i.e., AhDof-AI) provided salt-stress (SS) tolerance with no evident fitness penalties. The lack of an obvious development-related phenotype contrasted with microarray and GO data showing an enrichment of categories and genes related to developmental processes, particularly flowering. SS tolerance also correlated with increased superoxide dismutase activity but not with augmented stomatal closure. Additionally, microarray and GO data indicated that, contrary to AhERF-VII, SS tolerance conferred by AhDof-AI in Arabidopsis involved ABA-dependent and ABA-independent stress amelioration mechanisms.
Collapse
Affiliation(s)
- Julio A. Massange-Sánchez
- Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, C.P. 36821, Irapuato, Gto., México
| | - Paola A. Palmeros-Suárez
- Laboratorio de Biología Molecular, Instituto Tecnológico de Tlajomulco, Jalisco, km 10 Carretera a San Miguel Cuyutlán, CP 45640 Tlajomulco de Zúñiga, Jalisco, Mexico
| | - Eduardo Espitia-Rangel
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Km 13.5 Carrretera Los Reyes-Texcoco, C.P. 56250, Coatlinchán Texcoco, Estado de México, México
| | - Isaac Rodríguez-Arévalo
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato, Gto., Mexico
| | - Lino Sánchez-Segura
- Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, C.P. 36821, Irapuato, Gto., México
| | - Norma A. Martínez-Gallardo
- Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, C.P. 36821, Irapuato, Gto., México
| | - Fulgencio Alatorre-Cobos
- Conacyt Research Fellow-Colegio de Postgraduados, Campus Campeche. Carretera Haltunchen-Edzna Km 17.5, Sihochac, Champoton, 24450, Campeche, México
| | - Axel Tiessen
- Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, C.P. 36821, Irapuato, Gto., México
| | - John P. Délano-Frier
- Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, C.P. 36821, Irapuato, Gto., México
| |
Collapse
|
15
|
Jamil M, Wang W, Xu M, Tu J. Exploring the roles of basal transcription factor 3 in eukaryotic growth and development. Biotechnol Genet Eng Rev 2015; 31:21-45. [PMID: 26428578 DOI: 10.1080/02648725.2015.1080064] [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] [Indexed: 10/23/2022]
Abstract
Basal transcription factor 3 (BTF3) has been reported to play a significant part in the transcriptional regulation linking with eukaryotes growth and development. Alteration in the BTF3 gene expression patterns or variation in their activities adds to the explanation of different signaling pathways and regulatory networks. Moreover, BTF3s often respond to numerous stresses, and subsequently they are involved in regulation of various mechanisms. BTF3 proteins also function through protein-protein contact, which can assist us to identify the multifaceted processes of signaling and transcriptional regulation controlled by BTF3 proteins. In this review, we discuss current advances made in starting to explore the roles of BTF3 transcription factors in eukaryotes especially in plant growth and development.
Collapse
Affiliation(s)
- Muhammad Jamil
- a College of Agriculture and Biotechnology, Institute of Crop Science , Zhejiang University , Yu-Hang-Tang Rd. 866, Hangzhou 310058 , China.,b Department of Biotechnology and Genetic Engineering , Kohat University of Science and Technology , Kohat 26000 , Pakistan
| | - Wenyi Wang
- a College of Agriculture and Biotechnology, Institute of Crop Science , Zhejiang University , Yu-Hang-Tang Rd. 866, Hangzhou 310058 , China
| | - Mengyun Xu
- a College of Agriculture and Biotechnology, Institute of Crop Science , Zhejiang University , Yu-Hang-Tang Rd. 866, Hangzhou 310058 , China
| | - Jumin Tu
- a College of Agriculture and Biotechnology, Institute of Crop Science , Zhejiang University , Yu-Hang-Tang Rd. 866, Hangzhou 310058 , China
| |
Collapse
|
16
|
Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, Haynes PA, Mirzaei M, Komatsu S. Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives. J Proteome Res 2015; 14:2723-44. [DOI: 10.1021/acs.jproteome.5b00211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | | | - Pingfang Yang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Sun Hee Woo
- Chungbuk National University, Cheongju 362-763, Korea
| | - Chiew Foan Chin
- University of Nottingham Malaysia Campus, 43500 Semenyih, Selangor, Malaysia
| | - Chris Gehring
- King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | | | - Setsuko Komatsu
- National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan
| |
Collapse
|
17
|
Chen ZY, Guo XJ, Chen ZX, Chen WY, Liu DC, Zheng YL, Liu YX, Wei YM, Wang JR. Genome-wide characterization of developmental stage- and tissue-specific transcription factors in wheat. BMC Genomics 2015; 16:125. [PMID: 25766308 PMCID: PMC4344791 DOI: 10.1186/s12864-015-1313-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 02/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat (Triticum aestivum) is one of the most important cereal crops, providing food for humans and feed for other animals. However, its productivity is challenged by various biotic and abiotic stresses such as fungal diseases, insects, drought, salinity, and cold. Transcription factors (TFs) regulate gene expression in different tissues and at various developmental stages in plants and animals, and they can be identified and classified into families according to their structural and specialized DNA-binding domains (DBDs). Transcription factors are important regulatory components of the genome, and are the main targets for engineering stress tolerance. RESULTS In total, 2407 putative TFs were identified from wheat expressed sequence tags, and then classified into 63 families by using Hmm searches against hidden Markov model (HMM) profiles. In this study, 2407 TFs represented approximately 2.22% of all genes in the wheat genome, a smaller proportion than those reported for other cereals in PlantTFDB V3.0 (3.33%-5.86%) and PlnTFDB (4.30%-6.46%). We assembled information from the various databases for individual TFs, including annotations and details of their developmental stage- and tissue-specific expression patterns. Based on this information, we identified 1257 developmental stage-specific TFs and 1104 tissue-specific TFs, accounting for 52.22% and 45.87% of the 2407 wheat TFs, respectively. We identified 338, 269, 262, 175, 49, and 18 tissue-specific TFs in the flower, seed, root, leaf, stem, and crown, respectively. There were 100, 6, 342, 141, 390, and 278 TFs specifically expressed at the dormant seed, germinating seed, reproductive, ripening, seedling, and vegetative stages, respectively. We constructed a comprehensive database of wheat TFs, designated as WheatTFDB ( http://xms.sicau.edu.cn/wheatTFDB/ ). CONCLUSIONS Approximately 2.22% (2407 genes) of all genes in the wheat genome were identified as TFs, and were clustered into 63 TF families. We identified 1257 developmental stage-specific TFs and 1104 tissue-specific TFs, based on information about their developmental- and tissue-specific expression patterns obtained from publicly available gene expression databases. The 2407 wheat TFs and their annotations are summarized in our database, WheatTFDB. These data will be useful identifying target TFs involved in the stress response at a particular stage of development.
Collapse
Affiliation(s)
- Zhen-Yong Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
- College of Life Science, China West Normal University, Nanchong, 637009, China.
| | - Xiao-Jiang Guo
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Zhong-Xu Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Wei-Ying Chen
- College of Life Science, China West Normal University, Nanchong, 637009, China.
| | - Deng-Cai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - You-Liang Zheng
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Yaan, Sichuan, 625014, China.
| | - Ya-Xi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Ji-Rui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| |
Collapse
|
18
|
Zhao Y, Zhao C, Li Y, Chang Y, Zhang J, Zeng Z, Lu X, Xu G. Study of metabolite differences of flue-cured tobacco from different regions using a pseudotargeted gas chromatography with mass spectrometry selected-ion monitoring method. J Sep Sci 2014; 37:2177-84. [PMID: 24865655 DOI: 10.1002/jssc.201400097] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 04/02/2014] [Accepted: 05/17/2014] [Indexed: 12/16/2023]
Abstract
A pseudotargeted method based on gas chromatography and mass spectrometry with selected-ion monitoring was established to investigate the metabolite differences of flue-cured tobacco from three different growing regions. The mixed solvent of acetonitrile/isopropanol/water (3:3:2, v/v/v) was chosen as the optimal extraction system based on the good repeatability and extraction efficiency. A self-developed software coupled with commercial software was used to establish the pseudotargeted method including 289 peaks and 47 groups. Multivariable statistical analysis indicated that tobacco samples can be obviously separated based on the geographical origins. On the basis of a Mann-Whitney U test, organic acids, phenols, and alkaloids had higher levels in Hunan province. In contrast, a large proportion of amino acids (including L-tyrosine, L-proline, and serine), sucrose, and linoleic acid were the highest in Yunnan province. Meanwhile, multiple metabolic pathways (including carbohydrate metabolism, tricarboxylic acid cycle, and nitrogen metabolism) were influenced by growing regions. Twenty-eight differential metabolites, which had great contributions to the classification of tobacco samples of three growing regions, were further defined. The results demonstrated that the developed pseudotargeted method was a powerful tool to investigate the metabolic profiling of tobacco leaves and discriminate tobacco leaves of different growing regions.
Collapse
Affiliation(s)
- Yanni Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Ramegowda V, Mysore KS, Senthil-Kumar M. Virus-induced gene silencing is a versatile tool for unraveling the functional relevance of multiple abiotic-stress-responsive genes in crop plants. FRONTIERS IN PLANT SCIENCE 2014; 5:323. [PMID: 25071806 PMCID: PMC4085877 DOI: 10.3389/fpls.2014.00323] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/19/2014] [Indexed: 05/03/2023]
Abstract
Virus-induced gene silencing (VIGS) is an effective tool for gene function analysis in plants. Over the last decade, VIGS has been successfully used as both a forward and reverse genetics technique for gene function analysis in various model plants, as well as crop plants. With the increased identification of differentially expressed genes under various abiotic stresses through high-throughput transcript profiling, the application of VIGS is expected to be important in the future for functional characterization of a large number of genes. In the recent past, VIGS was proven to be an elegant tool for functional characterization of genes associated with abiotic stress responses. In this review, we provide an overview of how VIGS is used in different crop species to characterize genes associated with drought-, salt-, oxidative- and nutrient-deficiency-stresses. We describe the examples from studies where abiotic stress related genes are characterized using VIGS. In addition, we describe the major advantages of VIGS over other currently available functional genomics tools. We also summarize the recent improvements, limitations and future prospects of using VIGS as a tool for studying plant responses to abiotic stresses.
Collapse
Affiliation(s)
- Venkategowda Ramegowda
- Department of Crop Physiology, University of Agricultural Sciences, GKVKBangalore, India
| | | | | |
Collapse
|