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Martínez-Peña R, Vergara-Díaz O, Schlereth A, Höhne M, Morcuende R, Nieto-Taladriz MT, Araus JL, Aparicio N, Vicente R. Analysis of durum wheat photosynthetic organs during grain filling reveals the ear as a water stress-tolerant organ and the peduncle as the largest pool of primary metabolites. PLANTA 2023; 257:81. [PMID: 36917306 PMCID: PMC10014764 DOI: 10.1007/s00425-023-04115-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
The pool of carbon- and nitrogen-rich metabolites is quantitatively relevant in non-foliar photosynthetic organs during grain filling, which have a better response to water limitation than flag leaves. The response of durum wheat to contrasting water regimes has been extensively studied at leaf and agronomic level in previous studies, but the water stress effects on source-sink dynamics, particularly non-foliar photosynthetic organs, is more limited. Our study aims to investigate the response of different photosynthetic organs to water stress and to quantify the pool of carbon and nitrogen metabolites available for grain filling. Five durum wheat varieties were grown in field trials in the Spanish region of Castile and León under irrigated and rainfed conditions. Water stress led to a significant decrease in yield, biomass, and carbon and nitrogen assimilation, improved water use efficiency, and modified grain quality traits in the five varieties. The pool of carbon (glucose, glucose-6-phosphate, fructose, sucrose, starch, and malate) and nitrogen (glutamate, amino acids, proteins and chlorophylls) metabolites in leaf blades and sheaths, peduncles, awns, glumes and lemmas were also analysed. The results showed that the metabolism of the blades and peduncles was the most susceptible to water stress, while ear metabolism showed higher stability, particularly at mid-grain filling. Interestingly, the total metabolite content per organ highlighted that a large source of nutrients, which may be directly involved in grain filling, are found outside the blades, with the peduncles being quantitatively the most relevant. We conclude that yield improvements in our Mediterranean agro-ecosystem are highly linked to the success of shoots in producing ears and a higher number of grains, while grain filling is highly dependent on the capacity of non-foliar organs to fix CO2 and N. The ear organs show higher stress resilience than other organs, which deserves our attention in future breeding programmes.
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Affiliation(s)
- Raquel Martínez-Peña
- Cereals Group, Section of Herbaceous, Agro-Technological Institute of Castile and León, Junta de Castile and León, Valladolid, Spain
| | - Omar Vergara-Díaz
- Plant Ecophysiology and Metabolism Group, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Armin Schlereth
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Melanie Höhne
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Rosa Morcuende
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA), Consejo Superior de Investigaciones Científicas (CSIC), Salamanca, Spain
| | - María Teresa Nieto-Taladriz
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Luis Araus
- Integrative Crop Ecophysiology Group, Section of Plant Physiology, Faculty of Biology, University of Barcelona, Barcelona, and AGROTECNIO-CERCA Center, Lleida, Spain
| | - Nieves Aparicio
- Cereals Group, Section of Herbaceous, Agro-Technological Institute of Castile and León, Junta de Castile and León, Valladolid, Spain
| | - Rubén Vicente
- Plant Ecophysiology and Metabolism Group, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal.
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
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Tao J, Dong F, Wang Y, Chen H, Tang M. Arbuscular mycorrhizal fungi enhance photosynthesis and drought tolerance by regulating MAPK genes expressions of Populus simonii × P. nigra. PHYSIOLOGIA PLANTARUM 2022; 174:e13829. [PMID: 36437546 DOI: 10.1111/ppl.13829] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/29/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) promote plants to absorb more water and nutrients and improve their stress resistance. As the main signal transducer, the mitogen-activated protein kinase (MAPK) cascade plays a vital role in drought stress. However, how the MAPK family genes of mycorrhizal plants respond to stress is still not clear. Our study analyzed physiological indexes and expression profiles of MAPK family genes of Populus simonii × P. nigra under two inoculation treatments (inoculated with or without Rhizophagus irregularis) and two water conditions (well-watered or drought stress). The results showed that the stronger photosynthesis of mycorrhizal plants may be mediated by MAPK genes induced by AMF. Mycorrhizal plants showed lower oxidative damage and drought sensitivity. Mycorrhiza downregulated the expression of PsnMAPK7-2, PsnMAPK16-1, PsnMAPK19-2, and PsnMAPK20-2 which negatively regulate drought tolerance and induced specific PsnMAPKs in roots which activate transcription factors to regulate downstream gene expressions, enhancing drought tolerance. This is the first time to identify part of the MAPK gene family of P. simonii × P. nigra at the genome level and study MAPK genes in mycorrhizal forest trees. This is helpful to understand the function of the MAPK gene family in response to drought of mycorrhizal plants and lays a foundation for afforestation by using mycorrhizal saplings.
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Affiliation(s)
- Jing Tao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Fengxin Dong
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Yihan Wang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Ming Tang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, China
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Mapuranga J, Zhang N, Zhang L, Liu W, Chang J, Yang W. Harnessing genetic resistance to rusts in wheat and integrated rust management methods to develop more durable resistant cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:951095. [PMID: 36311120 PMCID: PMC9614308 DOI: 10.3389/fpls.2022.951095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Wheat is one of the most important staple foods on earth. Leaf rust, stem rust and stripe rust, caused by Puccini triticina, Puccinia f. sp. graminis and Puccinia f. sp. striiformis, respectively, continue to threaten wheat production worldwide. Utilization of resistant cultivars is the most effective and chemical-free strategy to control rust diseases. Convectional and molecular biology techniques identified more than 200 resistance genes and their associated markers from common wheat and wheat wild relatives, which can be used by breeders in resistance breeding programmes. However, there is continuous emergence of new races of rust pathogens with novel degrees of virulence, thus rendering wheat resistance genes ineffective. An integration of genomic selection, genome editing, molecular breeding and marker-assisted selection, and phenotypic evaluations is required in developing high quality wheat varieties with resistance to multiple pathogens. Although host genotype resistance and application of fungicides are the most generally utilized approaches for controlling wheat rusts, effective agronomic methods are required to reduce disease management costs and increase wheat production sustainability. This review gives a critical overview of the current knowledge of rust resistance, particularly race-specific and non-race specific resistance, the role of pathogenesis-related proteins, non-coding RNAs, and transcription factors in rust resistance, and the molecular basis of interactions between wheat and rust pathogens. It will also discuss the new advances on how integrated rust management methods can assist in developing more durable resistant cultivars in these pathosystems.
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Abstract
Drought is one of the major abiotic constraints on wheat yields and also for sustainability of production levels around the world. In the near future, the occurrence likelihood of droughts is predicted to become more common, due to changing climatic conditions, thereby posing a serious threat to the food security system. Heterogeneity, in its time of occurrence and severity levels, is likely to further augment the complexity of drought conditions. Although wheat crop growth has progressively risen to good levels, as evident by notable increases in both area and production, the expected wheat demand for the ever-growing population is quite high. Besides crop yield volatility in the era of climate change and dwindling resources, “trait-based” breeding programs are required, so as to develop high yielding, climate resilient and stable genotypes, at a faster pace. For this to happen, a broad genetic base and wider adaptability to suit varied agro-ecologies would provide enough scope for their quicker spread. The current review places emphasis on making distinct categories of the wheat cultivars/advanced breeding lines, as tolerant, moderately tolerant or susceptible to drought stresses, duly supported by an extensive up-to-date literature base and will be useful for wheat researchers, in order to choose the best potential donors as parents, coupled with the associated traits for the development of drought-tolerant wheat varieties, and also to facilitate molecular studies.
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Rabbi SMHA, Kumar A, Mohajeri Naraghi S, Simsek S, Sapkota S, Solanki S, Alamri MS, Elias EM, Kianian S, Missaoui A, Mergoum M. Genome-Wide Association Mapping for Yield and Related Traits Under Drought Stressed and Non-stressed Environments in Wheat. Front Genet 2021; 12:649988. [PMID: 34239537 PMCID: PMC8258415 DOI: 10.3389/fgene.2021.649988] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/28/2021] [Indexed: 12/02/2022] Open
Abstract
Understanding the genetics of drought tolerance in hard red spring wheat (HRSW) in northern USA is a prerequisite for developing drought-tolerant cultivars for this region. An association mapping (AM) study for drought tolerance in spring wheat in northern USA was undertaken using 361 wheat genotypes and Infinium 90K single-nucleotide polymorphism (SNP) assay. The genotypes were evaluated in nine different locations of North Dakota (ND) for plant height (PH), days to heading (DH), yield (YLD), test weight (TW), and thousand kernel weight (TKW) under rain-fed conditions. Rainfall data and soil type of the locations were used to assess drought conditions. A mixed linear model (MLM), which accounts for population structure and kinship (PC+K), was used for marker–trait association. A total of 69 consistent QTL involved with drought tolerance-related traits were identified, with p ≤ 0.001. Chromosomes 1A, 3A, 3B, 4B, 4D, 5B, 6A, and 6B were identified to harbor major QTL for drought tolerance. Six potential novel QTL were identified on chromosomes 3D, 4A, 5B, 7A, and 7B. The novel QTL were identified for DH, PH, and TKW. The findings of this study can be used in marker-assisted selection (MAS) for drought-tolerance breeding in spring wheat.
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Affiliation(s)
- S M Hisam A Rabbi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | | | - Senay Simsek
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Suraj Sapkota
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Mohammed S Alamri
- Department of Food Sciences and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Elias M Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Shahryar Kianian
- United States Department of Agriculture-The Agricultural Research Service (USDA-ARS) Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, United States
| | - Ali Missaoui
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
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Lin L, Wu J, Jiang M, Wang Y. Plant Mitogen-Activated Protein Kinase Cascades in Environmental Stresses. Int J Mol Sci 2021; 22:ijms22041543. [PMID: 33546499 PMCID: PMC7913722 DOI: 10.3390/ijms22041543] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
Due to global warming and population growth, plants need to rescue themselves, especially in unfavorable environments, to fulfill food requirements because they are sessile organisms. Stress signal sensing is a crucial step that determines the appropriate response which, ultimately, determines the survival of plants. As important signaling modules in eukaryotes, plant mitogen-activated protein kinase (MAPK) cascades play a key role in regulating responses to the following four major environmental stresses: high salinity, drought, extreme temperature and insect and pathogen infections. MAPK cascades are involved in responses to these environmental stresses by regulating the expression of related genes, plant hormone production and crosstalk with other environmental stresses. In this review, we describe recent major studies investigating MAPK-mediated environmental stress responses. We also highlight the diverse function of MAPK cascades in environmental stress. These findings help us understand the regulatory network of MAPKs under environmental stress and provide another strategy to improve stress resistance in crops to ensure food security.
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Affiliation(s)
- Li Lin
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225000, China;
| | - Jian Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225000, China;
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225000, China
- Correspondence: (J.W.); (Y.W.)
| | - Mingyi Jiang
- College of Life Sciences and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China;
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225000, China;
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225000, China
- Correspondence: (J.W.); (Y.W.)
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Kim MH, Cho JS, Park EJ, Lee H, Choi YI, Bae EK, Han KH, Ko JH. Overexpression of a Poplar RING-H2 Zinc Finger, Ptxerico, Confers Enhanced Drought Tolerance via Reduced Water Loss and Ion Leakage in Populus. Int J Mol Sci 2020; 21:E9454. [PMID: 33322558 PMCID: PMC7764267 DOI: 10.3390/ijms21249454] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 01/12/2023] Open
Abstract
Drought stress is one of the major environmental problems in the growth of crops and woody perennials, but it is getting worse due to the global climate crisis. XERICO, a RING (Really Interesting New Gene) zinc-finger E3 ubiquitin ligase, has been shown to be a positive regulator of drought tolerance in plants through the control of abscisic acid (ABA) homeostasis. We characterized a poplar (Populus trichocarpa) RING protein family and identified the closest homolog of XERICO called PtXERICO. Expression of PtXERICO is induced by both salt and drought stress, and by ABA treatment in poplars. Overexpression of PtXERICO in Arabidopsis confers salt and ABA hypersensitivity in young seedlings, and enhances drought tolerance by decreasing transpirational water loss. Consistently, transgenic hybrid poplars overexpressing PtXERICO demonstrate enhanced drought tolerance with reduced transpirational water loss and ion leakage. Subsequent upregulation of genes involved in the ABA homeostasis and drought response was confirmed in both transgenic Arabidopsis and poplars. Taken together, our results suggest that PtXERICO will serve as a focal point to improve drought tolerance of woody perennials.
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Affiliation(s)
- Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 17104, Korea; (M.-H.K.); (J.-S.C.)
| | - Jin-Seong Cho
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 17104, Korea; (M.-H.K.); (J.-S.C.)
| | - Eung-Jun Park
- Division of Forest Biotechnology, National Institute of Forest Science, Suwon 16631, Korea; (E.-J.P.); (H.L.); (Y.-I.C.); (E.-K.B.)
| | - Hyoshin Lee
- Division of Forest Biotechnology, National Institute of Forest Science, Suwon 16631, Korea; (E.-J.P.); (H.L.); (Y.-I.C.); (E.-K.B.)
| | - Young-Im Choi
- Division of Forest Biotechnology, National Institute of Forest Science, Suwon 16631, Korea; (E.-J.P.); (H.L.); (Y.-I.C.); (E.-K.B.)
| | - Eun-Kyung Bae
- Division of Forest Biotechnology, National Institute of Forest Science, Suwon 16631, Korea; (E.-J.P.); (H.L.); (Y.-I.C.); (E.-K.B.)
| | - Kyung-Hwan Han
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA;
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 17104, Korea; (M.-H.K.); (J.-S.C.)
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Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat. PLoS One 2020; 15:e0236186. [PMID: 32866164 PMCID: PMC7458298 DOI: 10.1371/journal.pone.0236186] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/30/2020] [Indexed: 12/17/2022] Open
Abstract
AIM To establish a gene co-expression network for identifying principal modules and hub genes that are associated with drought resistance mechanisms, analyzing their mechanisms, and exploring candidate genes. METHODS AND FINDINGS 42 data sets including PRJNA380841 and PRJNA369686 were used to construct the co-expression network through weighted gene co-expression network analysis (WGCNA). A total of 1,896,897,901 (284.30 Gb) clean reads and 35,021 differentially expressed genes (DEGs) were obtained from 42 samples. Functional enrichment analysis indicated that photosynthesis, DNA replication, glycolysis/gluconeogenesis, starch and sucrose metabolism, arginine and proline metabolism, and cell cycle were significantly influenced by drought stress. Furthermore, the DEGs with similar expression patterns, detected by K-means clustering, were grouped into 29 clusters. Genes involved in the modules, such as dark turquoise, yellow, and brown, were found to be appreciably linked with drought resistance. Twelve central, greatly correlated genes in stage-specific modules were subsequently confirmed and validated at the transcription levels, including TraesCS7D01G417600.1 (PP2C), TraesCS5B01G565300.1 (ERF), TraesCS4A01G068200.1 (HSP), TraesCS2D01G033200.1 (HSP90), TraesCS6B01G425300.1 (RBD), TraesCS7A01G499200.1 (P450), TraesCS4A01G118400.1 (MYB), TraesCS2B01G415500.1 (STK), TraesCS1A01G129300.1 (MYB), TraesCS2D01G326900.1 (ALDH), TraesCS3D01G227400.1 (WRKY), and TraesCS3B01G144800.1 (GT). CONCLUSIONS Analyzing the response of wheat to drought stress during different growth stages, we have detected three modules and 12 hub genes that are associated with drought resistance mechanisms, and five of those genes are newly identified for drought resistance. The references provided by these modules will promote the understanding of the drought-resistance mechanism. In addition, the candidate genes can be used as a basis of transgenic or molecular marker-assisted selection for improving the drought resistance and increasing the yields of wheat.
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Proteomic profiling of developing wheat heads under water-stress. Funct Integr Genomics 2020; 20:695-710. [PMID: 32681185 DOI: 10.1007/s10142-020-00746-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 10/23/2022]
Abstract
A replicated iTRAQ (isobaric tags for relative and absolute quantification) study on developing wheat heads from two doubled haploid (DH) lines identified from a cross between cv Westonia x cv Kauz characterized the proteome changes influenced by reproductive stage water-stress. All lines were exposed to 10 days of water-stress from early booting (Zadok 40), with sample sets taken from five head developmental stages. Two sample groups (water-stressed and control) account for 120 samples that required 18 eight-plex iTRAQ runs. Based on the IWGSC RefSeq v1 wheat assembly, among the 4592 identified proteins, a total of 132 proteins showed a significant response to water-stress, including the down-regulation of a mitochondrial Rho GTPase, a regulator of intercellular fundamental biological processes (7.5 fold) and cell division protein FtsZ at anthesis (6.0 fold). Up-regulated proteins included inosine-5'-monophosphate dehydrogenase (3.83 fold) and glycerophosphodiester phosphodiesterase (4.05 fold). The Pre-FHE and FHE stages (full head emerged) of head development were differentiated by 391 proteins and 270 proteins differentiated the FHE and Post-FHE stages. Water-stress during meiosis affected seed setting with 27% and 6% reduction in the progeny DH105 and DH299 respectively. Among the 77 proteins that differentiated between the two DH lines, 7 proteins were significantly influenced by water-stress and correlated with the seed set phenotype response of the DH lines to water-stress (e.g. the up-regulation of a subtilisin-like protease in DH 299 relative to DH 105). This study provided unique insights into the biological changes in developing wheat head that occur during water-stress.
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Identification of Quantitative Trait Loci Relating to Flowering Time, Flag Leaf and Awn Characteristics in a Novel Triticum dicoccum Mapping Population. PLANTS 2020; 9:plants9070829. [PMID: 32630645 PMCID: PMC7412379 DOI: 10.3390/plants9070829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 06/25/2020] [Accepted: 06/30/2020] [Indexed: 12/01/2022]
Abstract
Tetraploid landraces of wheat harbour genetic diversity that could be introgressed into modern bread wheat with the aid of marker-assisted selection to address the genetic diversity bottleneck in the breeding genepool. A novel bi-parental Triticum turgidum ssp. dicoccum Schrank mapping population was created from a cross between two landrace accessions differing for multiple physiological traits. The population was phenotyped for traits hypothesised to be proxies for characteristics associated with improved photosynthesis or drought tolerance, including flowering time, awn length, flag leaf length and width, and stomatal and trichome density. The mapping individuals and parents were genotyped with the 35K Wheat Breeders’ single nucleotide polymorphism (SNP) array. A genetic linkage map was constructed from 104 F4 individuals, consisting of 2066 SNPs with a total length of 3295 cM and an average spacing of 1.6 cM. Using the population, 10 quantitative trait loci (QTLs) for five traits were identified in two years of trials. Three consistent QTLs were identified over both trials for awn length, flowering time and flag leaf width, on chromosomes 4A, 7B and 5B, respectively. The awn length and flowering time QTLs correspond with the major loci Hd and Vrn-B3, respectively. The identified marker-trait associations could be developed for marker-assisted selection, to aid the introgression of diversity from a tetraploid source into modern wheat for potential physiological trait improvement.
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Li X, Zhang X, Liu G, Tang Y, Zhou C, Zhang L, Lv J. The spike plays important roles in the drought tolerance as compared to the flag leaf through the phenylpropanoid pathway in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 152:100-111. [PMID: 32408177 DOI: 10.1016/j.plaphy.2020.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/22/2020] [Accepted: 05/01/2020] [Indexed: 05/27/2023]
Abstract
The spike photosynthesis plays a curial role in wheat photosynthesis under drought stress. However, the mechanism of drought tolerance in the spike is still unclear. Our study compared the gas exchange parameters, antioxidant system, and phenylpropanoid pathway between the wheat flag leaf and spike in response to drought stress. Compared with the flag leaf, the spike organs exhibited lower reductions in the net photosynthetic rate (Pn), relative water content (RWC), and chlorophyll content (Chl) under drought stress. The activities of phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), and 4-coumarate-coenzyme A ligase (4CL) enzymes, and the total contents of phenolics and flavonoids (TPC and TFC, respectively) were enhanced much more percentages in the spike organs than that in the flag leaf under drought stress. Drought also induced the expression of structural genes (TaPAL, TaC4H, Ta4CL, TaCHS, TaCHI, TaFNS, TaF3H, TaFLS, TaDFR, and TaANS) involved in the phenylpropanoid pathway of the spike organs during the middle and late grain filling periods. The spike organs also showed much smaller accumulations of O2.-, hydrogen peroxide (H2O2), and malondialdehyde (MDA) in treated wheat. Higher activities of antioxidant enzymes (superoxide dismutase, SOD; peroxidase, POD; and catalase, CAT) and more proline content were observed in the spike organs as compared to the flag leaf under drought stress. All these results indicated that the enhanced tolerance to drought stress in spike organs was related to the elevated phenylpropanoid pathway. It could make the spike maintain a better water status and further lead to the relatively higher photosynthesis and lower membrane damage.
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Affiliation(s)
- Xiaorui Li
- College of Life Sciences, Northwest A & F University, 712100, Yangling, China
| | - Xu Zhang
- College of Life Sciences, Northwest A & F University, 712100, Yangling, China
| | - Guangping Liu
- College of Chemistry & Pharmacy, Northwest A & F University, 712100, Yangling, China
| | - Yan Tang
- College of Life Sciences, Northwest A & F University, 712100, Yangling, China
| | - Chunju Zhou
- College of Life Sciences, Northwest A & F University, 712100, Yangling, China
| | - Lixin Zhang
- College of Life Sciences, Northwest A & F University, 712100, Yangling, China
| | - Jinyin Lv
- College of Life Sciences, Northwest A & F University, 712100, Yangling, China.
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Vergara-Diaz O, Vatter T, Vicente R, Obata T, Nieto-Taladriz MT, Aparicio N, Carlisle Kefauver S, Fernie A, Araus JL. Metabolome Profiling Supports the Key Role of the Spike in Wheat Yield Performance. Cells 2020; 9:E1025. [PMID: 32326207 PMCID: PMC7226616 DOI: 10.3390/cells9041025] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/07/2020] [Accepted: 04/15/2020] [Indexed: 11/30/2022] Open
Abstract
Although the relevance of spike bracts in stress acclimation and contribution to wheat yield was recently revealed, the metabolome of this organ and its response to water stress is still unknown. The metabolite profiles of flag leaves, glumes and lemmas were characterized under contrasting field water regimes in five durum wheat cultivars. Water conditions during growth were characterized through spectral vegetation indices, canopy temperature and isotope composition. Spike bracts exhibited better coordination of carbon and nitrogen metabolisms than the flag leaves in terms of photorespiration, nitrogen assimilation and respiration paths. This coordination facilitated an accumulation of organic and amino acids in spike bracts, especially under water stress. The metabolomic response to water stress also involved an accumulation of antioxidant and drought tolerance related sugars, particularly in the spikes. Furthermore, certain cell wall, respiratory and protective metabolites were associated with genotypic outperformance and yield stability. In addition, grain yield was strongly predicted by leaf and spike bracts metabolomes independently. This study supports the role of the spike as a key organ during wheat grain filling, particularly under stress conditions and provides relevant information to explore new ways to improve wheat productivity including potential biomarkers for yield prediction.
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Affiliation(s)
- Omar Vergara-Diaz
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (O.V.-D.); (T.V.); (R.V.); (S.C.K.)
- AGROTECNIO (Center of Research in Agrotechnology), 25198 Lleida, Spain
| | - Thomas Vatter
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (O.V.-D.); (T.V.); (R.V.); (S.C.K.)
- AGROTECNIO (Center of Research in Agrotechnology), 25198 Lleida, Spain
| | - Rubén Vicente
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (O.V.-D.); (T.V.); (R.V.); (S.C.K.)
- AGROTECNIO (Center of Research in Agrotechnology), 25198 Lleida, Spain
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (T.O.); (A.F.)
| | - Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (T.O.); (A.F.)
| | - Maria Teresa Nieto-Taladriz
- National Institute for Agricultural and Food Research and Technology (INIA), Ctra de la Coruña 7.5, 28040 Madrid, Spain;
| | - Nieves Aparicio
- Technological and Agrarian Institute of Castilla y León (ITACyL), Agricultural Research. Ctra Burgos km 119, 47041 Valladolid, Spain;
| | - Shawn Carlisle Kefauver
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (O.V.-D.); (T.V.); (R.V.); (S.C.K.)
- AGROTECNIO (Center of Research in Agrotechnology), 25198 Lleida, Spain
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (T.O.); (A.F.)
| | - José Luis Araus
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (O.V.-D.); (T.V.); (R.V.); (S.C.K.)
- AGROTECNIO (Center of Research in Agrotechnology), 25198 Lleida, Spain
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13
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Wu J, Jiang Y, Liang Y, Chen L, Chen W, Cheng B. Expression of the maize MYB transcription factor ZmMYB3R enhances drought and salt stress tolerance in transgenic plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 137:179-188. [PMID: 30798172 DOI: 10.1016/j.plaphy.2019.02.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 05/25/2023]
Abstract
MYB proteins are major transcription factors that play significant roles in plant defenses against various stresses. However, available information regarding stress-related MYB genes in maize is minimal. Herein, a maize MYB gene, ZmMYB3R, was cloned and functionally characterized. Subcellular localisation analysis showed that ZmMYB3R is localised to the nucleus. Yeast one-hybrid results revealed that ZmMYB3R has trans-activation activity, and a minimal activation domain at the C-terminus spanning residues 217-563. Gene expression analysis suggested that ZmMYB3R was induced by drought, salt and abscisic acid (ABA). Transgenic Arabidopsis plants overexpressing ZmMYB3R displayed enhanced growth performance and higher survival rates, elevated catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) enzyme activities, increased sensitivity to ABA, and regulation of the stomatal aperture, suggesting that ZmMYB3R enhances tolerance to drought and salt stress. qRT-PCR assays revealed elevated expression levels of stress/ABA genes in transgenic plants following stress treatments. Moreover, transgenic plants accumulated higher ABA content than wild-type plants under drought and salt stress conditions. Collectively, these results indicate that ZmMYB3R is a positive transcription factor that enhances tolerance to drought and salt stress via an ABA-dependent pathway. The findings may prove useful for engineering economically important crops.
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Affiliation(s)
- Jiandong Wu
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yingli Jiang
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yani Liang
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Long Chen
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Weijun Chen
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China.
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Agarwal P, Khurana P. Functional characterization of HSFs from wheat in response to heat and other abiotic stress conditions. Funct Integr Genomics 2019; 19:497-513. [PMID: 30868385 DOI: 10.1007/s10142-019-00666-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 10/27/2022]
Abstract
High temperature stress is known to be one of the major limiting factors for wheat productivity worldwide. HSFs are known to play a central role in heat stress response in plants. Hence, the current study is an attempt to explore an in-depth involvement of TaHSFs in stress responses mainly in heat and other abiotic responses like salinity, drought, and cold stress. Effort was made to understand as how the expression of HSF is able to define the differential robustness of wheat varieties. Subsequent studies were done to establish the involvement of any temporal or spatial cue on the behavior of these TaHSFs under heat stress conditions. A total of 53 HSFs have been reported until date and out of these, few TaHSFs including one identified in our library, i.e., TaHsfA2d (Traes_4AS_52EB860E7.2), were selected for the expression analysis studies. The expressions of these HSFs were found to differ in both magnitude and sensitivity to the heat as well as other abiotic stresses. Moreover, these TaHSFs displayed wide range of expression in different tissues like anther, ovary, lemma, palea, awn, glume, and different stages of seed development. Thus, TaHSFs appear to be under dynamic expression as they respond in a unique manner to spatial, temporal, and environmental cues. Therefore, these HSFs can be used as candidate genes for understanding the molecular mechanism under heat stress and can be utilized for improving crop yield by enhancing the tolerance and survival of the crop plants under adverse environment conditions.
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Affiliation(s)
- Preeti Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, 110021, India.
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15
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Marček T, Hamow KÁ, Végh B, Janda T, Darko E. Metabolic response to drought in six winter wheat genotypes. PLoS One 2019; 14:e0212411. [PMID: 30779775 PMCID: PMC6380608 DOI: 10.1371/journal.pone.0212411] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/02/2019] [Indexed: 12/13/2022] Open
Abstract
Wheat is one of the most important cereals, whose growth and development is strongly limited by drought. This study investigated the physiological and metabolic response of six winter wheat cultivars to drought with the emphasis on the induction of dominant metabolites affected by the treatment and genotypes or both. The plants were exposed to a moderate (non-lethal) drought stress, which was induced by withholding watering for six days under controlled greenhouse conditions. A decline in CO2 assimilation (Pn) and transpiration rate, stomata closure, a decrease in relative water content (RWC) and increase of malondialdehyde content were observed in drought-treated plants of all cultivars. These changes were most pronounced in Ellvis, while Soissons was able to retain the higher RWC and Pn. Among the studied metabolites, sugars (sucrose, glucose, fructose, several disaccharides), organic acids (malic acid, oxalic acids), amino acids (proline, threonine, gamma-aminobutyric acid (GABA), glutamine) and sugar alcohols such as myo-inositol accumulated to higher levels in the plants exposed to drought stress in comparison with the control. The accumulation of several metabolites in response to drought differed between the genotypes. Drought induced the production of sucrose, malic acid and oxalic acid, unknown organic acid 1, unknown disaccharide 1, 2 and 3, GABA, L-threonine, glutamic acid in four (Soissons, Žitarka, Antonija or Toborzó) out of six genotypes. In addition, Soissons, which was the most drought tolerant genotype, accumulated the highest amount of unknown disaccharide 5, galactonic and phosphoric acids. The two most drought sensitive cultivars, Srpanjka and Ellvis, demonstrated different metabolic adjustment in response to the stress treatment. Srpanjka responded to drought by increasing the amount of glucose and fructose originated from hydrolyses of sucrose and accumulating unidentified sugar alcohols 1 and 2. In Ellvis, drought caused inhibition of photosynthetic carbon metabolism, as evidence by the decreased Pn, gs, RWC and accumulation levels of sugar metabolites (sucrose, glucose and fructose). The results revealed the differences in metabolic response to drought among the genotypes, which drew attention on metabolites related with general response and on those metabolites which are part of specific response that may play an important role in drought tolerance.
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Affiliation(s)
- Tihana Marček
- Department of Food and Nutrition Research, Faculty of Food Technology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Kamirán Áron Hamow
- Department of Zoology, Plant Protection Institute, Centre for Agricultural Research of the Hungarian Academy of Sciences, Budapest, Hungary
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Balázs Végh
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Tibor Janda
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Eva Darko
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research of the Hungarian Academy of Sciences, Martonvásár, Hungary
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16
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Identification of Two Novel Wheat Drought Tolerance-Related Proteins by Comparative Proteomic Analysis Combined with Virus-Induced Gene Silencing. Int J Mol Sci 2018; 19:ijms19124020. [PMID: 30545152 PMCID: PMC6321273 DOI: 10.3390/ijms19124020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 02/06/2023] Open
Abstract
Drought is a major adversity that limits crop yields. Further exploration of wheat drought tolerance-related genes is critical for the genetic improvement of drought tolerance in this crop. Here, comparative proteomic analysis of two wheat varieties, XN979 and LA379, with contrasting drought tolerance was conducted to screen for drought tolerance-related proteins/genes. Virus-induced gene silencing (VIGS) technology was used to verify the functions of candidate proteins. A total of 335 differentially abundant proteins (DAPs) were exclusively identified in the drought-tolerant variety XN979. Most DAPs were mainly involved in photosynthesis, carbon fixation, glyoxylate and dicarboxylate metabolism, and several other pathways. Two DAPs (W5DYH0 and W5ERN8), dubbed TaDrSR1 and TaDrSR2, respectively, were selected for further functional analysis using VIGS. The relative electrolyte leakage rate and malonaldehyde content increased significantly, while the relative water content and proline content significantly decreased in the TaDrSR1- and TaDrSR2-knock-down plants compared to that in non-knocked-down plants under drought stress conditions. TaDrSR1- and TaDrSR2-knock-down plants exhibited more severe drooping and wilting phenotypes than non-knocked-down plants under drought stress conditions, suggesting that the former were more sensitive to drought stress. These results indicate that TaDrSR1 and TaDrSR2 potentially play vital roles in conferring drought tolerance in common wheat.
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Akpinar BA, Biyiklioglu S, Alptekin B, Havránková M, Vrána J, Doležel J, Distelfeld A, Hernandez P, Budak H. Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:2077-2087. [PMID: 29729062 PMCID: PMC6230948 DOI: 10.1111/pbi.12940] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/11/2018] [Accepted: 04/20/2018] [Indexed: 05/20/2023]
Abstract
Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization.
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Affiliation(s)
- Bala Ani Akpinar
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
| | - Sezgi Biyiklioglu
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
| | - Burcu Alptekin
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
| | - Miroslava Havránková
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Assaf Distelfeld
- Department of Molecular Biology and Ecology of PlantsFaculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS)Consejo Superior de Investigaciones Científicas (CSIC)CordobaSpain
| | - The IWGSC
- International Wheat Genome Sequencing ConsortiumBethesdaMDUSA
| | - Hikmet Budak
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
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18
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Zotova L, Kurishbayev A, Jatayev S, Khassanova G, Zhubatkanov A, Serikbay D, Sereda S, Sereda T, Shvidchenko V, Lopato S, Jenkins C, Soole K, Langridge P, Shavrukov Y. Genes Encoding Transcription Factors TaDREB5 and TaNFYC-A7 Are Differentially Expressed in Leaves of Bread Wheat in Response to Drought, Dehydration and ABA. FRONTIERS IN PLANT SCIENCE 2018; 9:1441. [PMID: 30319682 PMCID: PMC6171087 DOI: 10.3389/fpls.2018.01441] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/10/2018] [Indexed: 05/18/2023]
Abstract
Two groups of six spring bread wheat varieties with either high or low grain yield under the dry conditions of Central and Northern Kazakhstan were selected for analysis. Experiments were set up with the selected wheat varieties in controlled environments as follows: (1) slowly progressing drought imposed on plants in soil, (2) rapid dehydration of whole plants grown in hydroponics, (3) dehydration of detached leaves, and (4) ABA treatment of whole plants grown in hydroponics. Representatives of two different families of transcription factors (TFs), TaDREB5 and TaNFYC-A7, were found to be linked to yield-under-drought using polymorphic Amplifluor-like SNP marker assays. qRT-PCR revealed differing patterns of expression of these genes in the leaves of plants subjected to the above treatments. Under drought, TaDREB5 was significantly up-regulated in leaves of all high-yielding varieties tested and down-regulated in all low-yielding varieties, and the level of expression was independent of treatment type. In contrast, TaNFYC-A7 expression levels showed different responses in the high- and low-yield groups of wheat varieties. TaNFYC-A7 expression under dehydration (treatments 2 and 3) was higher than under drought (treatment 1) in all high-yielding varieties tested, while in all low-yielding varieties the opposite pattern was observed: the expression levels of this gene under drought were higher than under dehydration. Rapid dehydration of detached leaves and intact wheat plants grown in hydroponics produced similar changes in gene expression. ABA treatment of whole plants caused rapid stomatal closure and a rise in the transcript level of both genes during the first 30 min, which decreased 6 h after treatment. At this time-point, expression of TaNFYC-A7 was again significantly up-regulated compared to untreated controls, while TaDREB5 returned to its initial level of expression. These findings reveal significant differences in the transcriptional regulation of two drought-responsive and ABA-dependent TFs under slowly developing drought and rapid dehydration of wheat plants. The results obtained suggest that correlation between grain yield in dry conditions and TaNFYC-A7 expression levels in the examined wheat varieties is dependent on the length of drought development and/or strength of drought; while in the case of TaDREB5, no such dependence is observed.
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Affiliation(s)
- Lyudmila Zotova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Akhylbek Kurishbayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Gulmira Khassanova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Askar Zhubatkanov
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergey Sereda
- Karaganda Research Institute of Plant Industry and Breeding, Karaganda, Kazakhstan
| | - Tatiana Sereda
- Karaganda Research Institute of Plant Industry and Breeding, Karaganda, Kazakhstan
| | - Vladimir Shvidchenko
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Colin Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
| | - Kathleen Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
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19
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Ye G, Ma Y, Feng Z, Zhang X. Transcriptomic analysis of drought stress responses of sea buckthorn (Hippophae rhamnoidessubsp. sinensis) by RNA-Seq. PLoS One 2018; 13:e0202213. [PMID: 30102736 PMCID: PMC6089444 DOI: 10.1371/journal.pone.0202213] [Citation(s) in RCA: 24] [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: 02/23/2018] [Accepted: 07/29/2018] [Indexed: 12/15/2022] Open
Abstract
Sea buckthorn is one of the most important eco-economic tree species in China due to its ability to grow and produce acceptable yields under limited water and fertilizer availability. In this study, the differentially expressed genes under drought stress (DS) of sea buckthorn were identified and compared with control (CK) by RNA-Seq. A total of 122,803 unigenes were identified in sea buckthorn, and 70,025 unigenes significantly matched a sequence in at least one of the seven databases. A total of 24,060 (19.59%) unigenes can be assigned to 19 KEGG pathways, and 1,644 unigenes were differentially expressed between DS and CK, of which 519 unigenes were up-regulated and 1,125 unigenes down-regulated. Of the 47 significantly enriched GO terms, 14, 7 and 26 items were related to BP, CC and MF, respectively. KEGG enrichment analysis showed 398 DEGs involved in 97 different pathways, of which 119 DEGs were up-regulated and 279 DEGs were down-regulated under drought stress. In addition, we found 4438 transcriptor factors (TFs) in sea buckthorn, of which 100 were differentially expressed between DS and CK. These results lay a first foundation for further investigations of the very specific functions of these unigenes in sea buckthorn in response to drought stress.
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Affiliation(s)
- Guisheng Ye
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Yuhua Ma
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
- * E-mail:
| | - Zhipeng Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Xiaofen Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
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20
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Abd El-Daim IA, Bejai S, Fridborg I, Meijer J. Identifying potential molecular factors involved in Bacillus amyloliquefaciens 5113 mediated abiotic stress tolerance in wheat. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:271-279. [PMID: 29247572 DOI: 10.1111/plb.12680] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 12/09/2017] [Indexed: 05/28/2023]
Abstract
Abiotic stressors are main limiting factors for agricultural production around the world. Plant growth-promoting bacteria have been successfully used to improve abiotic stress tolerance in several crops including wheat. However, the molecular changes involved in the improvement of stress management are poorly understood. The present investigation addressed some molecular factors involved in bacterially induced plant abiotic stress responses by identifying differentially expressed genes in wheat (Triticum aestivum) seedlings treated with the beneficial bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5113 prior to challenge with abiotic stress conditions such as heat, cold or drought. cDNA-AFLP analysis revealed differential expression of more than 200 transcript-derived fragments (TDFs) in wheat leaves. Expression of selected TDFs was confirmed using RT-PCR. DNA sequencing of 31 differentially expressed TDFs revealed significant homology with both known and unknown genes in database searches. Virus-induced gene silencing of two abscisic acid-related TDFs showed different effects upon heat and drought stress. We conclude that treatment with B. amyloliquefaciens 5113 caused molecular modifications in wheat in order to induce tolerance against heat, cold and drought stress. Bacillus treatment provides systemic effects that involve metabolic and regulatory functions supporting both growth and stress management.
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Affiliation(s)
- I A Abd El-Daim
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
- Department of Microbiology, Soils, Water and Environment Research Institute, Agricultural Research Centre, Giza, Egypt
| | - S Bejai
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
| | - I Fridborg
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
| | - J Meijer
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
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21
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Ullah N, Yüce M, Neslihan Öztürk Gökçe Z, Budak H. Comparative metabolite profiling of drought stress in roots and leaves of seven Triticeae species. BMC Genomics 2017; 18:969. [PMID: 29246190 PMCID: PMC5731210 DOI: 10.1186/s12864-017-4321-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/21/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Drought is a lifestyle disease. Plant metabolomics has been exercised for understanding the fine-tuning of the potential pathways to surmount the adverse effects of drought stress. A broad spectrum of morphological and metabolic responses from seven Triticeae species including wild types with different drought tolerance/susceptibility level was investigated under control and water scarcity conditions. RESULTS Significant morphological parameters measured were root length, surface area, average root diameter and overall root development. Principal Component Analysis, Partial Least-Squares-Discriminant Analysis and Hierarchical Cluster Analysis were applied to the metabolomic data obtained by Gas Chromatography-Mass Spectrometry technique in order to determine the important metabolites of the drought tolerance across seven different Triticeae species. The metabolites showing significant accumulation under the drought stress were considered as the key metabolites and correlated with potential biochemical pathways, enzymes or gene locations for a better understanding of the tolerance mechanisms. In all tested species, 45 significantly active metabolites with possible roles in drought stress were identified. Twenty-one metabolites out of forty-five including sugars, amino acids, organic acids and low molecular weight compounds increased in both leaf and root samples of TR39477, IG132864 and Bolal under the drought stress, contrasting to TTD-22, Tosunbey, Ligustica and Meyeri samples. Three metabolites including succinate, aspartate and trehalose were selected for further genome analysis due to their increased levels in TR39477, IG132864, and Bolal upon drought stress treatment as well as their significant role in energy producing biochemical pathways. CONCLUSION These results demonstrated that the genotypes with high drought tolerance skills, especially wild emmer wheat, have a great potential to be a genetic model system for experiments aiming to validate metabolomics-genomics networks.
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Affiliation(s)
- Naimat Ullah
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Meral Yüce
- Nanotechnology Research and Application Centre, Sabanci University, 34956, Istanbul, Turkey
| | - Z Neslihan Öztürk Gökçe
- Ayhan Sahenk Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240, Nigde, Turkey
| | - Hikmet Budak
- Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, USA.
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Kulkarni M, Soolanayakanahally R, Ogawa S, Uga Y, Selvaraj MG, Kagale S. Drought Response in Wheat: Key Genes and Regulatory Mechanisms Controlling Root System Architecture and Transpiration Efficiency. Front Chem 2017; 5:106. [PMID: 29259968 PMCID: PMC5723305 DOI: 10.3389/fchem.2017.00106] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/07/2017] [Indexed: 12/24/2022] Open
Abstract
Abiotic stresses such as, drought, heat, salinity, and flooding threaten global food security. Crop genetic improvement with increased resilience to abiotic stresses is a critical component of crop breeding strategies. Wheat is an important cereal crop and a staple food source globally. Enhanced drought tolerance in wheat is critical for sustainable food production and global food security. Recent advances in drought tolerance research have uncovered many key genes and transcription regulators governing morpho-physiological traits. Genes controlling root architecture and stomatal development play an important role in soil moisture extraction and its retention, and therefore have been targets of molecular breeding strategies for improving drought tolerance. In this systematic review, we have summarized evidence of beneficial contributions of root and stomatal traits to plant adaptation to drought stress. Specifically, we discuss a few key genes such as, DRO1 in rice and ERECTA in Arabidopsis and rice that were identified to be the enhancers of drought tolerance via regulation of root traits and transpiration efficiency. Additionally, we highlight several transcription factor families, such as, ERF (ethylene response factors), DREB (dehydration responsive element binding), ZFP (zinc finger proteins), WRKY, and MYB that were identified to be both positive and negative regulators of drought responses in wheat, rice, maize, and/or Arabidopsis. The overall aim of this review is to provide an overview of candidate genes that have been identified as regulators of drought response in plants. The lack of a reference genome sequence for wheat and non-transgenic approaches for manipulation of gene functions in wheat in the past had impeded high-resolution interrogation of functional elements, including genes and QTLs, and their application in cultivar improvement. The recent developments in wheat genomics and reverse genetics, including the availability of a gold-standard reference genome sequence and advent of genome editing technologies, are expected to aid in deciphering of the functional roles of genes and regulatory networks underlying adaptive phenological traits, and utilizing the outcomes of such studies in developing drought tolerant cultivars.
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Affiliation(s)
- Manoj Kulkarni
- Canadian Wheat Improvement Flagship Program, National Research Council Canada (NRC-CNRC), Saskatoon, SK, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Satoshi Ogawa
- Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusaku Uga
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Michael G. Selvaraj
- Agrobioversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Sateesh Kagale
- Canadian Wheat Improvement Flagship Program, National Research Council Canada (NRC-CNRC), Saskatoon, SK, Canada
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Liang J, Chen X, Deng G, Pan Z, Zhang H, Li Q, Yang K, Long H, Yu M. Dehydration induced transcriptomic responses in two Tibetan hulless barley (Hordeum vulgare var. nudum) accessions distinguished by drought tolerance. BMC Genomics 2017; 18:775. [PMID: 29020945 PMCID: PMC5637072 DOI: 10.1186/s12864-017-4152-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 10/02/2017] [Indexed: 12/21/2022] Open
Abstract
Background The harsh environment on the Qinghai-Tibetan Plateau gives Tibetan hulless barley (Hordeum vulgare var. nudum) great ability to resist adversities such as drought, salinity, and low temperature, and makes it a good subject for the analysis of drought tolerance mechanism. To elucidate the specific gene networks and pathways that contribute to its drought tolerance, and for identifying new candidate genes for breeding purposes, we performed a transcriptomic analysis using two accessions of Tibetan hulless barley, namely Z772 (drought-tolerant) and Z013 (drought-sensitive). Results There were more up-regulated genes of Z772 than Z013 under both mild (5439-VS-2604) and severe (7203-VS-3359) dehydration treatments. Under mild dehydration stress, the pathways exclusively enriched in drought-tolerance genotype Z772 included Protein processing in endoplasmic reticulum, tricarboxylic acid (TCA) cycle, Wax biosynthesis, and Spliceosome. Under severe dehydration stress, the pathways that were mainly enriched in Z772 included Carbon fixation in photosynthetic organisms, Pyruvate metabolism, Porphyrin and chlorophyll metabolism. The main differentially expressed genes (DEGs) in response to dehydration stress and genes whose expression was different between tolerant and sensitive genotypes were presented in this study, respectively. The candidate genes for drought tolerance were selected based on their expression patterns. Conclusions The RNA-Seq data obtained in this study provided an initial overview on global gene expression patterns and networks that related to dehydration shock in Tibetan hulless barley. Furthermore, these data provided pathways and a targeted set of candidate genes that might be essential for deep analyzing the molecular mechanisms of plant tolerance to drought stress. Electronic supplementary material The online version of this article (10.1186/s12864-017-4152-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China.,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China
| | - Xin Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China.,Center Laboratory Department, The General Hospital of Chengdu Army, Chengdu, 610083, People's Republic of China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China
| | - Qiao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China
| | - Kaijun Yang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China.,Ganzi Tibetan Autonomous Prefecture Institute of Agricultural Science, Kangding, 626000, People's Republic of China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China.
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China
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24
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Transcriptome and metabolome analysis of Ferula gummosa Boiss. to reveal major biosynthetic pathways of galbanum compounds. Funct Integr Genomics 2017; 17:725-737. [DOI: 10.1007/s10142-017-0567-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 02/06/2023]
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25
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Zang D, Wang L, Zhang Y, Zhao H, Wang Y. ThDof1.4 and ThZFP1 constitute a transcriptional regulatory cascade involved in salt or osmotic stress in Tamarix hispida. PLANT MOLECULAR BIOLOGY 2017; 94:495-507. [PMID: 28578496 DOI: 10.1007/s11103-017-0620-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/24/2017] [Indexed: 05/03/2023]
Abstract
Identification of the upstream regulators of a gene is important to characterize the transcriptional pathway and the function of the gene. Previously, we found that a zinc finger protein (ThZFP1) is involved in abiotic stress tolerance of Tamarix hispida. In the present study, we further investigated the transcriptional pathway of ThZFP1. Dof motifs are abundant in the ThZFP1 promoter; therefore, we used them to screen for transcriptional regulators of ThZFP1. A Dof protein, ThDof1.4, binds to the Dof motif specifically, and was hypothesized as the upstream regulator of ThZFP1. Further study showed that overexpression of ThDof1.4 in T. hispida activated the expression of GUS controlled by the ThZFP1 promoter. In T. hispida, transient overexpression of ThDof1.4 increased the transcripts of ThZFP1; conversely, transient RNAi-silencing of ThDof1.4 reduced the expression of ThZFP1. Chromatin immunoprecipitation indicated that ThDof1.4 binds to the ThZFP1 promoter. Additionally, ThDof1.4 and ThZFP1 share similar expression patterns in response to salt or drought stress. Furthermore, like ThZFP1, ThDof1.4 could increase the proline level and enhance ROS scavenging capability to improve salt and osmotic stress tolerance. Together, these results suggested that ThDof1.4 and ThZFP1 form a transcriptional regulatory cascade involved in abiotic stress resistance in T. hispida.
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Affiliation(s)
- Dandan Zang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Lina Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yiming Zhang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Huimin Zhao
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yucheng Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, Xinjiang, China.
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26
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Transcriptome analysis of drought-responsive genes regulated by hydrogen sulfide in wheat (Triticum aestivum L.) leaves. Mol Genet Genomics 2017. [DOI: 10.1007/s00438-017-1330-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Song J, Liu Q, Hu B, Wu W. Photoreceptor PhyB Involved in Arabidopsis Temperature Perception and Heat-Tolerance Formation. Int J Mol Sci 2017; 18:ijms18061194. [PMID: 28587227 PMCID: PMC5486017 DOI: 10.3390/ijms18061194] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 01/02/2023] Open
Abstract
The influence of temperature on plants is essential. However, our knowledge on the intricate regulation process underlying heat stress (HS) response in plants is limited. Recently, information about thermal sensors in vivo has begun to emerge. In this study, another primary environmental stimulus, light, was verified once again to work with temperature synergistically on plants, through the modulation of numerous biological processes. With the application of transcriptomic analysis, a substantial number of heat-responsive genes were detected involved in both light- and phytohormone-mediated pathways in Arabidopsis. During this process, phytoreceptor phyB acts as a molecular switch to turn on or turn off several other genes HS response, under different light conditions. Furthermore, a morphological study showed the afunction of phyB enhanced plants thermal tolerance, confirming the important role of this phytochrome in temperature perception and response in plants. This study adds data to the picture of light and temperature signaling cross-talk in plants, which is important for the exploration of complicated HS responses or light-mediated mechanisms. Furthermore, based on its influence on Arabidopsis thermal response in both morphological and physiological levels, phyB is a photoreceptor, as revealed before, as well as an essential thermal sensor in plants.
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Affiliation(s)
- Junyi Song
- College of Science, National University of Defense Technology, Changsha 410073, China.
| | - Qijun Liu
- College of Science, National University of Defense Technology, Changsha 410073, China.
| | - Biru Hu
- College of Science, National University of Defense Technology, Changsha 410073, China.
| | - Wenjian Wu
- College of Science, National University of Defense Technology, Changsha 410073, China.
- State Key Lab of Nuclear, Biological and Chemical Protection for Civilian, Beijing 102205, China.
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28
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Lee D, Chung PJ, Jeong JS, Jang G, Bang SW, Jung H, Kim YS, Ha S, Choi YD, Kim J. The rice OsNAC6 transcription factor orchestrates multiple molecular mechanisms involving root structural adaptions and nicotianamine biosynthesis for drought tolerance. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:754-764. [PMID: 27892643 PMCID: PMC5425393 DOI: 10.1111/pbi.12673] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 11/16/2016] [Accepted: 11/23/2016] [Indexed: 05/02/2023]
Abstract
Drought has a serious impact on agriculture worldwide. A plant's ability to adapt to rhizosphere drought stress requires reprogramming of root growth and development. Although physiological studies have documented the root adaption for tolerance to the drought stress, underlying molecular mechanisms is still incomplete, which is essential for crop engineering. Here, we identified OsNAC6-mediated root structural adaptations, including increased root number and root diameter, which enhanced drought tolerance. Multiyear drought field tests demonstrated that the grain yield of OsNAC6 root-specific overexpressing transgenic rice lines was less affected by drought stress than were nontransgenic controls. Genome-wide analyses of loss- and gain-of-function mutants revealed that OsNAC6 up-regulates the expression of direct target genes involved in membrane modification, nicotianamine (NA) biosynthesis, glutathione relocation, 3'-phophoadenosine 5'-phosphosulphate accumulation and glycosylation, which represent multiple drought tolerance pathways. Moreover, overexpression of NICOTIANAMINE SYNTHASE genes, direct targets of OsNAC6, promoted the accumulation of the metal chelator NA and, consequently, drought tolerance. Collectively, OsNAC6 orchestrates novel molecular drought tolerance mechanisms and has potential for the biotechnological development of high-yielding crops under water-limiting conditions.
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Affiliation(s)
- Dong‐Keun Lee
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Pil Joong Chung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Jin Seo Jeong
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Geupil Jang
- Department of Agricultural BiotechnologySeoul National UniversitySeoulKorea
| | - Seung Woon Bang
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Harin Jung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Sun‐Hwa Ha
- Department of Genetic Engineering and Graduate School of BiotechnologyKyung Hee UniversityYonginKorea
| | - Yang Do Choi
- Department of Agricultural BiotechnologySeoul National UniversitySeoulKorea
| | - Ju‐Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
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29
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Exploring the heat-responsive chaperones and microsatellite markers associated with terminal heat stress tolerance in developing wheat. Funct Integr Genomics 2017; 17:621-640. [PMID: 28573536 DOI: 10.1007/s10142-017-0560-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 04/06/2017] [Accepted: 04/17/2017] [Indexed: 10/19/2022]
Abstract
Global warming is a major threat for agriculture and food security, and in many cases the negative impacts are already apparent. Wheat is one of the most important staple food crops and is highly sensitive to the heat stress (HS) during reproductive and grain-filling stages. Here, whole transcriptome analysis of thermotolerant wheat cv. HD2985 was carried out at the post-anthesis stage under control (22 ± 3 °C) and HS-treated (42 °C, 2 h) conditions using Illumina Hiseq and Roche GS-FLX 454 platforms. We assembled ~24 million (control) and ~23 million (HS-treated) high-quality trimmed reads using different assemblers with optimal parameters. De novo assembly yielded 52,567 (control) and 59,658 (HS-treated) unigenes. We observed 785 transcripts to be upregulated and 431 transcripts to be downregulated under HS; 78 transcripts showed >10-fold upregulation such as HSPs, metabolic pathway-related genes, etc. Maximum number of upregulated genes was observed to be associated with processes such as HS-response, protein-folding, oxidation-reduction and photosynthesis. We identified 2008 and 2483 simple sequence repeats (SSRs) markers from control and HS-treated samples; 243 SSRs were observed to be overlying on stress-associated genes. Polymorphic study validated four SSRs to be heat-responsive in nature. Expression analysis of identified differentially expressed transcripts (DETs) showed very high fold increase in the expression of catalytic chaperones (HSP26, HSP17, and Rca) in contrasting wheat cvs. HD2985 and HD2329 under HS. We observed positive correlation between RNA-seq and qRT-PCR expression data. The present study culminated in greater understanding of the heat-response of tolerant genotype and has provided good candidate genes for the marker development and screening of wheat germplasm for thermotolerance.
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30
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Lucas SJ, Salantur A, Yazar S, Budak H. High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis. Funct Integr Genomics 2017; 17:667-685. [PMID: 28550605 DOI: 10.1007/s10142-017-0563-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 11/24/2022]
Abstract
Durum wheat (Triticum turgidum var. durum Desf.) is a major world crop that is grown primarily in areas of the world that experience periodic drought, and therefore, breeding climate-resilient durum wheat is a priority. High-throughput single nucleotide polymorphism (SNP) genotyping techniques have greatly increased the power of linkage and association mapping analyses for bread wheat, but as yet there is no durum wheat-specific platform available. In this study, we evaluate the new 384HT Wheat Breeders Array for its usefulness in tetraploid wheat breeding by genotyping a breeding population of F6 hybrids, derived from multiple crosses between T. durum cultivars and wild and cultivated emmer wheat accessions. Using a combined linkage and association mapping approach, we generated a genetic map including 1345 SNP markers, and identified markers linked to 6 QTLs for coleoptile length (2), heading date (1), anthocyanin accumulation (1) and osmotic stress tolerance (2). We also developed a straightforward approach for combining genetic data from multiple families of limited size that will be useful for evaluating and mapping pre-existing breeding material.
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Affiliation(s)
- Stuart J Lucas
- SU Nanotechnology Research and Application Centre, Sabanci University, 34956, Tuzla, İstanbul, Turkey.
| | - Ayten Salantur
- Breeding and Genetics, Field Crops Central Research Institute, Ankara, Turkey
| | - Selami Yazar
- Breeding and Genetics, Field Crops Central Research Institute, Ankara, Turkey
| | - Hikmet Budak
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey. .,412 Leon Johnson Hall, Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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31
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Alptekin B, Langridge P, Budak H. Abiotic stress miRNomes in the Triticeae. Funct Integr Genomics 2017; 17:145-170. [PMID: 27665284 PMCID: PMC5383695 DOI: 10.1007/s10142-016-0525-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/02/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage. The negative effects of abiotic stresses have increased at an alarming rate in recent years and are predicted to further deteriorate due to climate change, land degradation, and declining water supply. New technologies have provided an important tool with great potential for improving crop tolerance to the abiotic stresses: microRNAs (miRNAs). miRNAs are small regulators of gene expression that act on many different molecular and biochemical processes such as development, environmental adaptation, and stress tolerance. miRNAs can act at both the transcriptional and post-transcriptional levels, although post-transcriptional regulation is the most common in plants where miRNAs can inhibit the translation of their mRNA targets via complementary binding and cleavage. To date, expression of several miRNA families such as miR156, miR159, and miR398 has been detected as responsive to environmental conditions to regulate stress-associated molecular mechanisms individually and/or together with their various miRNA partners. Manipulation of these miRNAs and their targets may pave the way to improve crop performance under several abiotic stresses. Here, we summarize the current status of our knowledge on abiotic stress-associated miRNAs in members of the Triticeae tribe, specifically in wheat and barley, and the miRNA-based regulatory mechanisms triggered by stress conditions. Exploration of further miRNA families together with their functions under stress will improve our knowledge and provide opportunities to enhance plant performance to help us meet global food demand.
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Affiliation(s)
- Burcu Alptekin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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32
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Exploring drought stress-regulated genes in senna (Cassia angustifolia Vahl.): a transcriptomic approach. Funct Integr Genomics 2016; 17:1-25. [PMID: 27709374 DOI: 10.1007/s10142-016-0523-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 09/02/2016] [Accepted: 09/05/2016] [Indexed: 01/08/2023]
Abstract
De novo assembly of reads produced by next-generation sequencing (NGS) technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Senna (Cassia angustifolia Vahl.) is a drought-tolerant annual undershrub of Caesalpiniaceae, a subfamily of Fabaceae. There are insufficient transcriptomic and genomic data in public databases for understanding the molecular mechanism underlying the drought tolerance of senna. Therefore, the main purpose of this study was to know the transcriptome profile of senna, with special reference to drought stress. RNA from two different stages of leaf development was extracted and sequenced separately using the Illumina technology. A total of 200 million reads were generated, and a de novo assembly of processed reads in the pooled transcriptome using Trinity yielded 43,413 transcripts which were further annotated using NCBI BLAST with "green plant database (txid 33090)," Swiss Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Out of the total transcripts, 42,280 (95.0 %) were annotated by BLASTX against the green plant database of NCBI. Senna transcriptome showed the highest similarity to Glycine max (41 %), followed by Phaseolus vulgaris (16 %), Cicer arietinum (15 %), and Medicago trancatula (5 %). The highest number of GO terms were enriched for the molecular functions category; of these "catalytic activity" (GO: 0003824) (25.10 %) and "binding activity" (GO: 0005488) (20.10 %) were most abundantly represented. We used InterProscan to see protein similarity at domain level; a total of 33,256 transcripts were annotated against the Pfam domains. The transcripts were assigned with various KEGG pathways. Coding DNA sequences (CDS) encoding various drought stress-regulated pathways such as signaling factors, protein-modifying/degrading enzymes, biosynthesis of phytohormone, phytohormone signaling, osmotically active compounds, free radical scavengers, chlorophyll metabolism, leaf cuticular wax, polyamines, and protective proteins were identified through BLASTX search. The lucine-rich repeat kinase family was the most abundantly found group of protein kinases. Orphan, bHLH, and bZIP family TFs were the most abundantly found in senna. Six genes encoding MYC2 transcription factor, 9-cis-epoxycarotenoid dioxygenase (NCED), l -ascorbate peroxidase (APX), aminocyclopropane carboxylate oxidase (ACO), abscisic acid 8'-hydroxylase (ABA), and WRKY transcription factor were confirmed through reverse transcriptase-PCR (RT-PCR) and Sanger sequencing for the first time in senna. The potential drought stress-related transcripts identified in this study provide a good start for further investigation into the drought adaptation in senna. Additionally, our transcriptome sequences are the valuable resource for accelerated genomics-assisted genetic improvement programs and facilitate manipulation of biochemical pathways for developing drought-tolerant genotypes of crop plants.
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Poersch-Bortolon LB, Pereira JF, Nhani A, Gonzáles HHS, Torres GAM, Consoli L, Arenhart RA, Bodanese-Zanettini MH, Margis-Pinheiro M. Gene expression analysis reveals important pathways for drought response in leaves and roots of a wheat cultivar adapted to rainfed cropping in the Cerrado biome. Genet Mol Biol 2016; 39:629-645. [PMID: 27768155 PMCID: PMC5127152 DOI: 10.1590/1678-4685-gmb-2015-0327] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/27/2016] [Indexed: 01/22/2023] Open
Abstract
Drought limits wheat production in the Brazilian Cerrado biome. In order to search for candidate genes associated to the response to water deficit, we analyzed the gene expression profiles, under severe drought stress, in roots and leaves of the cultivar MGS1 Aliança, a well-adapted cultivar to the Cerrado. A set of 4,422 candidate genes was found in roots and leaves. The number of down-regulated transcripts in roots was higher than the up-regulated transcripts, while the opposite occurred in leaves. The number of common transcripts between the two tissues was 1,249, while 2,124 were specific to roots and 1,049 specific to leaves. Quantitative RT-PCR analysis revealed a 0.78 correlation with the expression data. The candidate genes were distributed across all chromosomes and component genomes, but a greater number was mapped on the B genome, particularly on chromosomes 3B, 5B and 2B. When considering both tissues, 116 different pathways were induced. One common pathway, among the top three activated pathways in both tissues, was starch and sucrose metabolism. These results pave the way for future marker development and selection of important genes and are useful for understanding the metabolic pathways involved in wheat drought response.
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Affiliation(s)
| | | | | | - Hebert Hernán Soto Gonzáles
- Embrapa Trigo, Passo Fundo, RS, Brazil
- Programa de Pós-Graduação em Recursos Naturais, Universidade Federal
de Roraima, Boa Vista, RR, Brazil
| | | | | | - Rafael Augusto Arenhart
- Departamento de Genética, Instituto de Biociências, Universidade
Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Márcia Margis-Pinheiro
- Departamento de Genética, Instituto de Biociências, Universidade
Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Cheng L, Wang Y, He Q, Li H, Zhang X, Zhang F. Comparative proteomics illustrates the complexity of drought resistance mechanisms in two wheat (Triticum aestivum L.) cultivars under dehydration and rehydration. BMC PLANT BIOLOGY 2016; 16:188. [PMID: 27576435 PMCID: PMC5006382 DOI: 10.1186/s12870-016-0871-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 08/10/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Drought stress is one of the most adverse environmental constraints to plant growth and productivity. Comparative proteomics of drought-tolerant and sensitive wheat genotypes is a strategy to understand the complexity of molecular mechanism of wheat in response to drought. This study attempted to extend findings regarding the potential proteomic dynamics in wheat under drought stress and to enrich the research content of drought tolerance mechanism. RESULTS A comparative proteomics approach was applied to analyze proteome change of Xihan No. 2 (a drought-tolerant cultivar) and Longchun 23 (a drought-sensitive cultivar) subjected to a range of dehydration treatments (18 h, 24 h and 48 h) and rehydration treatment (R24 h) using 2-DE, respectively. Quantitative image analysis showed a total of 172 protein spots in Xihan No. 2 and 215 spots from Longchun 23 with their abundance significantly altered (p < 0.05) more than 2.5-fold. Out of these spots, a total of 84 and 64 differentially abundant proteins were identified by MALDI-TOF/TOF MS in Xihan No. 2 and Longchun 23, respectively. Most of these identified proteins were involved in metabolism, photosynthesis, defence and protein translation/processing/degradation in both two cultivars. In addition, the proteins involved in redox homeostasis, energy, transcription, cellular structure, signalling and transport were also identified. Furthermore, the comparative analysis of drought-responsive proteome allowed for the general elucidation of the major mechanisms associated with differential responses to drought of both two cultivars. These cellular processes work more cooperatively to re-establish homeostasis in Xihan No. 2 than Longchun 23. The resistance mechanisms of Xihan No. 2 mainly included changes in the metabolism of carbohydrates and amino acids as well as in the activation of more antioxidation and defense systems and in the levels of proteins involved in ATP synthesis and protein degradation/refolding. CONCLUSIONS This study revealed that the levels of a number of proteins involved in various cellular processes were affected by drought stress in two wheat cultivars with different drought tolerance. The results showed that there exist specific responses to drought in Xihan No. 2 and Longchun 23. The proposed hypothetical model would explain the interaction of these identified proteins that are associated with drought-responses in two cultivars, and help in developing strategies to improve drought tolerance in wheat.
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Affiliation(s)
- Lixiang Cheng
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Yuping Wang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Qiang He
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Huijun Li
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
- Wuwei Agricultural and Animal Husbandry Bureau, Wuwei, China
| | - Xiaojing Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
- Gansu Dingxi Academy of Agricultural Science, Dingxi, China
| | - Feng Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
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Huang L, Raats D, Sela H, Klymiuk V, Lidzbarsky G, Feng L, Krugman T, Fahima T. Evolution and Adaptation of Wild Emmer Wheat Populations to Biotic and Abiotic Stresses. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:279-301. [PMID: 27296141 DOI: 10.1146/annurev-phyto-080614-120254] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The genetic bottlenecks associated with plant domestication and subsequent selection in man-made agroecosystems have limited the genetic diversity of modern crops and increased their vulnerability to environmental stresses. Wild emmer wheat, the tetraploid progenitor of domesticated wheat, distributed along a wide range of ecogeographical conditions in the Fertile Crescent, has valuable "left behind" adaptive diversity to multiple diseases and environmental stresses. The biotic and abiotic stress responses are conferred by series of genes and quantitative trait loci (QTLs) that control complex resistance pathways. The study of genetic diversity, genomic organization, expression profiles, protein structure and function of biotic and abiotic stress-resistance genes, and QTLs could shed light on the evolutionary history and adaptation mechanisms of wild emmer populations for their natural habitats. The continuous evolution and adaptation of wild emmer to the changing environment provide novel solutions that can contribute to safeguarding food for the rapidly growing human population.
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Affiliation(s)
- Lin Huang
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Dina Raats
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Hanan Sela
- The Institute for Cereal Crops Improvement, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Valentina Klymiuk
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Gabriel Lidzbarsky
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Lihua Feng
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Tamar Krugman
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
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Shavrukov Y, Zhumalin A, Serikbay D, Botayeva M, Otemisova A, Absattarova A, Sereda G, Sereda S, Shvidchenko V, Turbekova A, Jatayev S, Lopato S, Soole K, Langridge P. Expression Level of the DREB2-Type Gene, Identified with Amplifluor SNP Markers, Correlates with Performance, and Tolerance to Dehydration in Bread Wheat Cultivars from Northern Kazakhstan. FRONTIERS IN PLANT SCIENCE 2016; 7:1736. [PMID: 27917186 PMCID: PMC5114286 DOI: 10.3389/fpls.2016.01736] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/03/2016] [Indexed: 05/18/2023]
Abstract
A panel of 89 local commercial cultivars of bread wheat was tested in field trials in the dry conditions of Northern Kazakhstan. Two distinct groups of cultivars (six cultivars in each group), which had the highest and the lowest grain yield under drought were selected for further experiments. A dehydration test conducted on detached leaves indicated a strong association between rates of water loss in plants from the first group with highest grain yield production in the dry environment relative to the second group. Modern high-throughput Amplifluor Single Nucleotide Polymorphism (SNP) technology was applied to study allelic variations in a series of drought-responsive genes using 19 SNP markers. Genotyping of an SNP in the TaDREB5 (DREB2-type) gene using the Amplifluor SNP marker KATU48 revealed clear allele distribution across the entire panel of wheat accessions, and distinguished between the two groups of cultivars with high and low yield under drought. Significant differences in expression levels of TaDREB5 were revealed by qRT-PCR. Most wheat plants from the first group of cultivars with high grain yield showed slight up-regulation in the TaDREB5 transcript in dehydrated leaves. In contrast, expression of TaDREB5 in plants from the second group of cultivars with low grain yield was significantly down-regulated. It was found that SNPs did not alter the amino acid sequence of TaDREB5 protein. Thus, a possible explanation is that alternative splicing and up-stream regulation of TaDREB5 may be affected by SNP, but these hypotheses require additional analysis (and will be the focus of future studies).
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Affiliation(s)
- Yuri Shavrukov
- School of Agriculture, Food and Wine, Faculty of Sciences, University of AdelaideUrrbrae, SA, Australia
- School of Biological Sciences, Flinders University, Bedford ParkSA, Australia
- *Correspondence: Yuri Shavrukov, ;
| | - Aibek Zhumalin
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Makpal Botayeva
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Ainur Otemisova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | | | - Grigoriy Sereda
- Karaganda Research Institute of Plant Industry and BreedingKaraganda, Kazakhstan
| | - Sergey Sereda
- Karaganda Research Institute of Plant Industry and BreedingKaraganda, Kazakhstan
| | - Vladimir Shvidchenko
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Arysgul Turbekova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, Faculty of Sciences, University of AdelaideUrrbrae, SA, Australia
| | - Kathleen Soole
- School of Biological Sciences, Flinders University, Bedford ParkSA, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, Faculty of Sciences, University of AdelaideUrrbrae, SA, Australia
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Akpinar BA, Budak H. Dissecting miRNAs in Wheat D Genome Progenitor, Aegilops tauschii. FRONTIERS IN PLANT SCIENCE 2016; 7:606. [PMID: 27200073 PMCID: PMC4855405 DOI: 10.3389/fpls.2016.00606] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/20/2016] [Indexed: 05/09/2023]
Abstract
As the post-transcriptional regulators of gene expression, microRNAs or miRNAs comprise an integral part of understanding how genomes function. Although miRNAs have been a major focus of recent efforts, miRNA research is still in its infancy in most plant species. Aegilops tauschii, the D genome progenitor of bread wheat, is a wild diploid grass exhibiting remarkable population diversity. Due to the direct ancestry and the diverse gene pool, A. tauschii is a promising source for bread wheat improvement. In this study, a total of 87 Aegilops miRNA families, including 51 previously unknown, were computationally identified both at the subgenomic level, using flow-sorted A. tauschii 5D chromosome, and at the whole genome level. Predictions at the genomic and subgenomic levels suggested A. tauschii 5D chromosome as rich in pre-miRNAs that are highly associated with Class II DNA transposons. In order to gain insights into miRNA evolution, putative 5D chromosome miRNAs were compared to its modern ortholog, Triticum aestivum 5D chromosome, revealing that 48 of the 58 A. tauschii 5D miRNAs were conserved in orthologous T. aestivum 5D chromosome. The expression profiles of selected miRNAs (miR167, miR5205, miR5175, miR5523) provided the first experimental evidence for miR5175, miR5205 and miR5523, and revealed differential expressional changes in response to drought in different genetic backgrounds for miR167 and miR5175. Interestingly, while miR5523 coding regions were present and expressed as pre-miR5523 in both T. aestivum and A. tauschii, the expression of mature miR5523 was observed only in A. tauschii under normal conditions, pointing out to an interference at the downstream processing of pre-miR5523 in T. aestivum. Overall, this study expands our knowledge on the miRNA catalog of A. tauschii, locating a subset specifically to the 5D chromosome, with ample functional and comparative insight which should contribute to and complement efforts to develop drought tolerant wheat varieties.
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Affiliation(s)
- Bala A. Akpinar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
- Department of Plant Sciences and Plant Pathology, Montana State UniversityBozeman, MT, USA
- *Correspondence: Hikmet Budak,
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Muthusamy SK, Dalal M, Chinnusamy V, Bansal KC. Differential Regulation of Genes Coding for Organelle and Cytosolic ClpATPases under Biotic and Abiotic Stresses in Wheat. FRONTIERS IN PLANT SCIENCE 2016; 7:929. [PMID: 27446158 PMCID: PMC4923199 DOI: 10.3389/fpls.2016.00929] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/10/2016] [Indexed: 05/06/2023]
Abstract
A sub-group of class I Caseinolytic proteases (Clps) function as molecular chaperone and confer thermotolerance to plants. We identified class I Clp family consisting of five ClpB/HSP100, two ClpC, and two ClpD genes from bread wheat. Phylogenetic analysis showed that these genes were highly conserved across grass genomes. Subcellular localization prediction revealed that TaClpC and TaClpD subgroup proteins and TaClpB1 proteins are potentially targeted to chloroplast, while TaClpB5 to mitochondria, and TaClpB2, TaClpB3, and TaClpB4 to cytoplasm. Spatio-temporal expression pattern analysis revealed that four TaClpB and TaClpD2 genes are expressed in majority of all tissues and developmental stages of wheat. Real-time RT-PCR analysis of expression levels of Clp genes in seven wheat genotypes under different abiotic stresses revealed that genes coding for the cytosolic Clps namely TaClpB2 and TaClpB3 were upregulated under heat, salt and oxidative stress but were downregulated by cold stress in most genotypes. In contrast, genes coding for the chloroplastic Clps TaClpC1, TaClpC2, and TaClpD1 genes were significantly upregulated by mainly by cold stress in most genotypes, while TaClpD2 gene was upregulated >2 fold by salt stress in DBW16. The TaClpB5 gene coding for mitochondrial Clp was upregulated in all genotypes under heat, salt and oxidative stresses. In addition, we found that biotic stresses also upregulated TaClpB4 and TaClpD1. Among biotic stresses, Tilletia caries induced TaClpB2, TaClpB3, TaClpC1, and TaClpD1. Differential expression pattern under different abiotic and biotic stresses and predicted differential cellular localization of Clps suggest their non-redundant organelle and stress-specific roles. Our results also suggest the potential role of Clps in cold, salt and biotic stress responses in addition to the previously established role in thermotolerance of wheat.
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Affiliation(s)
- Senthilkumar K. Muthusamy
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
- Division of Crop Improvement, ICAR-Indian Institute of Wheat and Barley ResearchKarnal, India
| | - Monika Dalal
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Kailash C. Bansal
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
- ICAR-National Bureau of Plant Genetic ResourcesNew Delhi, India
- *Correspondence: Kailash C. Bansal
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Zou H, Tzarfati R, Hübner S, Krugman T, Fahima T, Abbo S, Saranga Y, Korol AB. Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars. BMC Genomics 2015; 16:777. [PMID: 26462652 PMCID: PMC4603339 DOI: 10.1186/s12864-015-1996-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/03/2015] [Indexed: 12/02/2022] Open
Abstract
Background Wheat domestication is considered as one of the most important events in the development of human civilization. Wheat spikelets have undergone significant changes during evolution under domestication, resulting in soft glumes and larger kernels that are released easily upon threshing. Our main goal was to explore changes in transcriptome expression in glumes that accompanied wheat evolution under domestication. Methods A total of six tetraploid wheat accessions were selected for transcriptome profiling based on their rachis brittleness and glumes toughness. RNA pools from glumes of the central spikelet at heading time were used to construct cDNA libraries for sequencing. The trimmed reads from each library were separately aligned to the reference sub-genomes A and B, which were extracted from wheat survey sequence. Differentially expression analysis and functional annotation were performed between wild and domesticated wheat, to identity candidate genes associated with evolution under domestication. Selected candidate genes were validated using real time PCR. Results Transcriptome profiles of wild emmer wheat, wheat landraces, and wheat cultivars were compared using next generation sequencing (RNA-seq). We have found a total of 194,893 transcripts, of which 73,150 were shared between wild, landraces, and cultivars. From 781 differentially expressed genes (DEGs), 336 were down-regulated and 445 were up-regulated in the domesticated compared to wild wheat genotypes. Gene Ontology (GO) annotation assigned 293 DEGs (37.5 %) to GO term groups, of which 134 (17.1 %) were down-regulated and 159 (20.4 %) up-regulated in the domesticated wheat. Some of the down-regulated DEGs in domesticated wheat are related to the biosynthetic pathways that eventually define the mechanical strength of the glumes, such as cell wall, lignin, pectin and wax biosynthesis. The reduction in gene expression of such genes, may explain the softness of the glumes in the domesticated forms. In addition, we have identified genes involved in nutrient remobilization that may affect grain size and other agronomic traits evolved under domestication. Conclusions The comparison of RNA-seq profiles between glumes of wheat groups differing in glumes toughness and rachis brittleness revealed a few DEGs that may be involved in glumes toughness and nutrient remobilization. These genes may be involved in processes of wheat improvement under domestication. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1996-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongda Zou
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Raanan Tzarfati
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Sariel Hübner
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Tamar Krugman
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Shahal Abbo
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Yehoshua Saranga
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Abraham B Korol
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
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Achieving Crop Stress Tolerance and Improvement—an Overview of Genomic Techniques. Appl Biochem Biotechnol 2015; 177:1395-408. [DOI: 10.1007/s12010-015-1830-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 09/02/2015] [Indexed: 01/09/2023]
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Gregorová Z, Kováčik J, Klejdus B, Maglovski M, Kuna R, Hauptvogel P, Matušíková I. Drought-Induced Responses of Physiology, Metabolites, and PR Proteins in Triticum aestivum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:8125-33. [PMID: 26330002 DOI: 10.1021/acs.jafc.5b02951] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The impact of severe drought stress (13% soil moisture) on the physiological responses, metabolic profile, and pathogenesis-related (PR) proteins in wheat above- and below-ground biomass after 20 days of treatment was studied. Drought depleted growth, assimilation pigments, and majority of free amino acids in the shoots (but proline increased considerably, +160%). On the contrary, root growth parameters were elevated, and free amino acids did not decrease, indicating investment of metabolites into the growth of roots under water deficiency. Mineral nutrients were only slightly influenced. Profiling of pathogenesis-related (PR) proteins revealed that chitinases (EC 3.2.1.14) and glucanases (EC 3.2.1.39) were activated in wheat by drought. Individual isoforms and their activity were rather stimulated under drought, especially in shoots. The expression of selected genes is in agreement with enzymatic data and suggests an organ (tissue) specific- and opposing behavior of these two types of defense components in drought-stressed wheat. Metabolic analyses at the level of phenolics showed an increase in the free and bound fraction of phenolic acids almost exclusively in the shoots and flavonoid isoorientin increased considerably: protective action against oxidative stress and dehydration of the leaves seems to be the main reason for this finding. The role of PR proteins and phenolics in drought-stressed tissue is discussed.
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Affiliation(s)
- Zuzana Gregorová
- Faculty of Natural Sciences, Department of Botany and Genetics, Constantine the Philosopher University , Nábrežie mládeže 91, 949 74 Nitra, Slovak Republic
| | | | | | - Marína Maglovski
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences , Akademická 2, P.O. Box 39A, 950 07 Nitra, Slovak Republic
| | - Roman Kuna
- Faculty of Natural Sciences, Department of Botany and Genetics, Constantine the Philosopher University , Nábrežie mládeže 91, 949 74 Nitra, Slovak Republic
| | - Pavol Hauptvogel
- National Agricultural and Food Centre - Research Institute of Plant Production, Bratislavská cesta 122, 921 68 Piešt'any, Slovak Republic
| | - Ildikó Matušíková
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences , Akademická 2, P.O. Box 39A, 950 07 Nitra, Slovak Republic
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Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress. Funct Integr Genomics 2015; 15:587-98. [PMID: 26174050 DOI: 10.1007/s10142-015-0453-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/26/2015] [Accepted: 07/01/2015] [Indexed: 01/09/2023]
Abstract
MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identify miRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype- and/or stress-specific miRNAs provide insights into our understanding of the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties.
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Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides. Sci Rep 2015; 5:10763. [PMID: 26084265 PMCID: PMC4471722 DOI: 10.1038/srep10763] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/28/2015] [Indexed: 12/13/2022] Open
Abstract
Wild emmer wheat, Triticum turgidum ssp. dicoccoides is the wild relative of Triticum turgidum, the progenitor of durum and bread wheat, and maintains a rich allelic diversity among its wild populations. The lack of adequate genetic and genomic resources, however, restricts its exploitation in wheat improvement. Here, we report next-generation sequencing of the flow-sorted chromosome 5B of T. dicoccoides to shed light into its genome structure, function and organization by exploring the repetitive elements, protein-encoding genes and putative microRNA and tRNA coding sequences. Comparative analyses with its counterparts in modern and wild wheats suggest clues into the B-genome evolution. Syntenic relationships of chromosome 5B with the model grasses can facilitate further efforts for fine-mapping of traits of interest. Mapping of 5B sequences onto the root transcriptomes of two additional T. dicoccoides genotypes, with contrasting drought tolerances, revealed several thousands of single nucleotide polymorphisms, of which 584 shared polymorphisms on 228 transcripts were specific to the drought-tolerant genotype. To our knowledge, this study presents the largest genomics resource currently available for T. dicoccoides, which, we believe, will encourage the exploitation of its genetic and genomic potential for wheat improvement to meet the increasing demand to feed the world.
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Cheng Z, Dong K, Ge P, Bian Y, Dong L, Deng X, Li X, Yan Y. Identification of Leaf Proteins Differentially Accumulated between Wheat Cultivars Distinct in Their Levels of Drought Tolerance. PLoS One 2015; 10:e0125302. [PMID: 25984726 PMCID: PMC4436182 DOI: 10.1371/journal.pone.0125302] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/12/2015] [Indexed: 12/27/2022] Open
Abstract
The drought-tolerant ‘Ningchun 47’ (NC47) and drought-sensitive ‘Chinese Spring’ (CS) wheat (Triticum aestivum L.) cultivars were treated with different PEG6000 concentrations at the three-leaf stage. An analysis on the physiological and proteomic changes of wheat seedling in response to drought stress was performed. In total, 146 differentially accumulated protein (DAP) spots were separated and recognised using two-dimensional gel electrophoresis. In total, 101 DAP spots representing 77 unique proteins were identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. These proteins were allocated to 10 groups according to putative functions, which were mainly involved in carbon metabolism (23.4%), photosynthesis/respiration (22.1%) and stress/defence/detoxification (18.2%). Some drought stress-related proteins in NC47, such as enolase, 6-phosphogluconate dehydrogenase, Oxygen-evolving enhancer protein 2, fibrillin-like protein, 2-Cys peroxiredoxin BAS1 and 70-kDa heat shock protein, were more upregulated than those in CS. Multivariate principal components analysis revealed obvious differences between the control and treatments in both NC47 and CS, while cluster analysis showed that the DAPs displayed five and six accumulation patterns in NC47 and CS, respectively. Protein–protein interaction network analysis showed that some key DAPs, such as 2-Cys peroxiredoxin BAS1, RuBisCO large subunit-binding protein, 50S ribosomal protein L1, 6-phosphogluconate dehydrogenase, glyceraldehyde 3-phosphate dehydrogenase isoenzyme and 70-kDa heat shock protein, with upregulated accumulation in NC47, had complex interactions with other proteins related to amino acid metabolism, carbon metabolism, energy pathway, signal transduction, stress/defence/detoxification, protein folding and nucleotide metabolism. These proteins could play important roles in drought-stress tolerance and contribute to the relatively stronger drought tolerance of NC47.
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Affiliation(s)
- Zhiwei Cheng
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Kun Dong
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Pei Ge
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Yanwei Bian
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Liwei Dong
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xiong Deng
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xiaohui Li
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Yueming Yan
- College of Life Science, Capital Normal University, 100048 Beijing, China
- Hubei Collaborative Innovation Center for Grain Industry (HCICGI), 434025 Jingzhou, China
- * E-mail:
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Liu H, Sultan MARF, Liu XL, Zhang J, Yu F, Zhao HX. Physiological and comparative proteomic analysis reveals different drought responses in roots and leaves of drought-tolerant wild wheat (Triticum boeoticum). PLoS One 2015; 10:e0121852. [PMID: 25859656 PMCID: PMC4393031 DOI: 10.1371/journal.pone.0121852] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/16/2015] [Indexed: 11/18/2022] Open
Abstract
To determine the proteomic-level responses of drought tolerant wild wheat (Triticum boeoticum), physiological and comparative proteomic analyses were conducted using the roots and the leaves of control and short term drought-stressed plants. Drought stress was imposed by transferring hydroponically grown seedlings at the 3-leaf stage into 1/2 Hoagland solution containing 20% PEG-6000 for 48 h. Root and leaf samples were separately collected at 0 (control), 24, and 48 h of drought treatment for analysis. Physiological analysis indicated that abscisic acid (ABA) level was greatly increased in the drought-treated plants, but the increase was greater and more rapid in the leaves than in the roots. The net photosynthetic rate of the wild wheat leaves was significantly decreased under short-term drought stress. The deleterious effects of drought on the studied traits mainly targeted photosynthesis. Comparative proteomic analysis identified 98 and 85 differently changed protein spots (DEPs) (corresponding to 87 and 80 unique proteins, respectively) in the leaves and the roots, respectively, with only 6 mutual unique proteins in the both organs. An impressive 86% of the DEPs were implicated in detoxification and defense, carbon metabolism, amino acid and nitrogen metabolism, proteins metabolism, chaperones, transcription and translation, photosynthesis, nucleotide metabolism, and signal transduction. Further analysis revealed some mutual and tissue-specific responses to short-term drought in the leaves and the roots. The differences of drought-response between the roots and the leaves mainly included that signal sensing and transduction-associated proteins were greatly up-regulated in the roots. Photosynthesis and carbon fixation ability were decreased in the leaves. Glycolysis was down-regulated but PPP pathway enhanced in the roots, resulting in occurrence of complex changes in energy metabolism and establishment of a new homeostasis. Protein metabolism was down-regulated in the roots, but enhanced in the leaves. These results will contribute to the existing knowledge on the complexity of root and leaf protein changes that occur in response to drought, and also provide a framework for further functional studies on the identified proteins.
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Affiliation(s)
- Hui Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | | | - Xiang li Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Yu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hui xian Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
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Kong D, Li M, Dong Z, Ji H, Li X. Identification of TaWD40D, a wheat WD40 repeat-containing protein that is associated with plant tolerance to abiotic stresses. PLANT CELL REPORTS 2015; 34:395-410. [PMID: 25447637 DOI: 10.1007/s00299-014-1717-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/11/2014] [Accepted: 11/20/2014] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE TaWD40D that encodes a member of WD40 family proteins is a novel gene involved in the wheat response to abiotic stress. TaWD40D functions as a positive regulator of plant responses to salt stress and osmotic stress in plant. Abiotic stresses can severely affect plant growth and crop productivity. WD40 repeat-containing proteins play a key role in protein-protein or protein-DNA interactions by acting as scaffolding molecules and promoting protein activity. In this study, a stress-inducible gene, TaWD40D, was identified from Chinese spring wheat (Triticum aestivum L.). TaWD40D encodes a protein containing seven WD40 domains. Subcellular localization in Nicotiana benthamiana mesophyll cells and Arabidopsis root cells showed the presence of TaWD40D in the cytoplasm and nucleus. Heterologous overexpression of TaWD40D in Arabidopsis greatly increased plant tolerance to abscisic acid (ABA), salt stress, and osmotic stress during seed germination and seedling development. The expression patterns of two genes from the SOS pathway (SOS2 and SOS3) and three ABA genes (ABI2, RAB18 and DREB2A) functioning in ABA-dependent and ABA-independent pathways were altered in the transgenic lines overexpressing TaWD40D under the treatments. Notably, the basal level of the ABI2 expression was substantially increased in the TaWD40D overexpression lines. The down-regulation of TaWD40D in wheat by virus-induced gene silencing resulted in a decreased relative water content and less vigorous growth compared to non-silenced lines. Our results suggest that TaWD40D functions as a positive regulator of plant responses to salt stress and osmotic stress that could be utilized for the genetic improvement of stress tolerance in crop plants.
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Affiliation(s)
- Dejing Kong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, Hebei, China
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Cloning and analysis of expression patterns and transcriptional regulation of RghBNG in response to plant growth regulators and abiotic stresses in Rehmannia glutinosa. SPRINGERPLUS 2015; 4:60. [PMID: 25674509 PMCID: PMC4320158 DOI: 10.1186/s40064-015-0830-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/16/2015] [Indexed: 01/23/2023]
Abstract
RghBNG, a gene of unknown function, was cloned from Rehmannia glutinosa by reverse transcription PCR and rapid amplification of cDNA ends. The full-length cDNA of RghBNG was 548 bp with a282-bp open reading frame. It encoded a polypeptide of 93 amino acids with a predicted molecular weight of 10.5 kDa and a theoretical isoelectric point of 9.25. Bioinformatics analysis indicated that RghBNG had no homology to any known plant genes, whereas the RghBNG polypeptide was highly similar to other plant proteins and possessed one conserved B12D protein family functional domain. Phylogenetic analysis revealed that RghBNG encoded for a dicot protein. RghBNG spatial and temporal expression patterns and responses to abiotic stresses and plant growth regulators were investigated by qRT-PCR. RghBNG transcripts were detected in roots, stems, leaves, petals, receptacles, stamens and pistils with the highest and lowest levels respectively observed in petals and leaves of mature plants. Additionally, RghBNG transcripts were detected at three developmental stages of roots, stems and leaves; the highest levels were observed in roots at seedling stage; Transcript levels changed to varying degrees in different tissues and stages; We also studied the effects of abiotic stress and plant growth regulators in roots and leaves. RghBNG expression was significantly increased (p < 0.01) by chromium, gibberellic acid and NaCl, with the highest levels induced by chromium stress; In contrast, 6-benzyladenine reduced expression. These results strongly suggest that RghBNG is involved in R. glutinosa growth, development and response to plant growth regulators and abiotic stresses.
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Pingault L, Choulet F, Alberti A, Glover N, Wincker P, Feuillet C, Paux E. Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome. Genome Biol 2015; 16:29. [PMID: 25853487 PMCID: PMC4355351 DOI: 10.1186/s13059-015-0601-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 01/28/2015] [Indexed: 12/19/2022] Open
Abstract
Background Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before. Results By combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level. Conclusions Our analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0601-9) contains supplementary material, which is available to authorized users.
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Budak H, Hussain B, Khan Z, Ozturk NZ, Ullah N. From Genetics to Functional Genomics: Improvement in Drought Signaling and Tolerance in Wheat. FRONTIERS IN PLANT SCIENCE 2015; 6:1012. [PMID: 26635838 PMCID: PMC4652017 DOI: 10.3389/fpls.2015.01012] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 11/02/2015] [Indexed: 05/18/2023]
Abstract
Drought being a yield limiting factor has become a major threat to international food security. It is a complex trait and drought tolerance response is carried out by various genes, transcription factors (TFs), microRNAs (miRNAs), hormones, proteins, co-factors, ions, and metabolites. This complexity has limited the development of wheat cultivars for drought tolerance by classical breeding. However, attempts have been made to fill the lost genetic diversity by crossing wheat with wild wheat relatives. In recent years, several molecular markers including single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs) associated with genes for drought signaling pathways have been reported. Screening of large wheat collections by marker assisted selection (MAS) and transformation of wheat with different genes/TFs has improved drought signaling pathways and tolerance. Several miRNAs also provide drought tolerance to wheat by regulating various TFs/genes. Emergence of OMICS techniques including transcriptomics, proteomics, metabolomics, and ionomics has helped to identify and characterize the genes, proteins, metabolites, and ions involved in drought signaling pathways. Together, all these efforts helped in understanding the complex drought tolerance mechanism. Here, we have reviewed the advances in wide hybridization, MAS, QTL mapping, miRNAs, transgenic technique, genome editing system, and above mentioned functional genomics tools for identification and utility of signaling molecules for improvement in wheat drought tolerance.
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Affiliation(s)
- Hikmet Budak
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
- *Correspondence: Hikmet Budak,
| | - Babar Hussain
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Zaeema Khan
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Neslihan Z. Ozturk
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niǧde UniversityNiǧde, Turkey
| | - Naimat Ullah
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
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Melloul M, Iraqi D, El Alaoui M, Erba G, Alaoui S, Ibriz M, Elfahime E. Identification of Differentially Expressed Genes by
cDNA-AFLP Technique in Response to Drought Stress
in Triticum durum. Food Technol Biotechnol 2014; 52:479-488. [PMID: 27904321 PMCID: PMC5079143 DOI: 10.17113/ftb.52.04.14.3701] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 08/12/2014] [Indexed: 12/27/2022] Open
Abstract
Drought is the single largest abiotic stress factor leading to reduced crop yields. The identification of differentially expressed genes and the understanding of their functions in environmentally stressful conditions are essential to improve drought tolerance. Transcriptomics is a powerful approach for the global analysis of molecular mechanisms under abiotic stress. To identify genes that are important for drought tolerance, we analyzed mRNA populations from untreated and drought-stressed leaves of Triticum durum by cDNA- -amplified fragment length polymorphism (cDNA-AFLP) technique. Overall, 76 transcript- -derived fragments corresponding to differentially induced transcripts were successfully sequenced. Most of the transcripts identified here, using basic local alignment search tool (BLAST) database, were genes belonging to different functional categories related to metabolism, energy, cellular biosynthesis, cell defense, signal transduction, transcription regulation, protein degradation and transport. The expression patterns of these genes were confirmed by quantitative reverse transcriptase real-time polymerase chain reaction (qRT- -PCR) based on ten selected genes representing different patterns. These results could facilitate the understanding of cellular mechanisms involving groups of genes that act in coordination in response to stimuli of water deficit. The identification of novel stress-responsive genes will provide useful data that could help develop breeding strategies aimed at improving durum wheat tolerance to field stress.
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Affiliation(s)
- Marouane Melloul
- Genetic and Biometry Laboratory, Faculty of Sciences, University Ibn Tofail, BP 133,
14000 Kenitra, Morocco
- Functional Genomic Platform, Technical Unit (UATRS), National Center for Scientific and Technical Research (CNRST), Angle Allal Fassi, Avenue des FAR, Hay Riad, BP 8027, 10102 Rabat, Morocco
| | - Driss Iraqi
- National Institute of Agronomical Research, Avenue de la Victoire, BP 415, Rabat, Morocco
| | - MyAbdelaziz El Alaoui
- Genetic and Biometry Laboratory, Faculty of Sciences, University Ibn Tofail, BP 133,
14000 Kenitra, Morocco
- Functional Genomic Platform, Technical Unit (UATRS), National Center for Scientific and Technical Research (CNRST), Angle Allal Fassi, Avenue des FAR, Hay Riad, BP 8027, 10102 Rabat, Morocco
| | - Gilles Erba
- Labgene Scientific Instruments, Athens Building, Business Park, 74160 Archamps, France
| | - Sanaa Alaoui
- Functional Genomic Platform, Technical Unit (UATRS), National Center for Scientific and Technical Research (CNRST), Angle Allal Fassi, Avenue des FAR, Hay Riad, BP 8027, 10102 Rabat, Morocco
| | - Mohammed Ibriz
- Genetic and Biometry Laboratory, Faculty of Sciences, University Ibn Tofail, BP 133,
14000 Kenitra, Morocco
| | - Elmostafa Elfahime
- Functional Genomic Platform, Technical Unit (UATRS), National Center for Scientific and Technical Research (CNRST), Angle Allal Fassi, Avenue des FAR, Hay Riad, BP 8027, 10102 Rabat, Morocco
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