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Klaus A, Marcon C, Hochholdinger F. Spatiotemporal transcriptomic plasticity in barley roots: unravelling water deficit responses in distinct root zones. BMC Genomics 2024; 25:79. [PMID: 38243200 PMCID: PMC10799489 DOI: 10.1186/s12864-024-10002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/10/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Drought poses a major threat to agricultural production and thus food security. Understanding the processes shaping plant responses to water deficit is essential for global food safety. Though many studies examined the effect of water deficit on the whole-root level, the distinct functions of each root zone and their specific stress responses remain masked by this approach. RESULTS In this study, we investigated the effect of water deficit on root development of the spring barley (Hordeum vulgare L.) cultivar Morex and examined transcriptomic responses at the level of longitudinal root zones. Water deficit significantly reduced root growth rates after two days of treatment. RNA-sequencing revealed root zone and temporal gene expression changes depending on the duration of water deficit treatment. The majority of water deficit-regulated genes were unique for their respective root zone-by-treatment combination, though they were associated with commonly enriched gene ontology terms. Among these, we found terms associated with transport, detoxification, or cell wall formation affected by water deficit. Integration of weighted gene co-expression analyses identified differential hub genes, that highlighted the importance of modulating energy and protein metabolism and stress response. CONCLUSION Our findings provide new insights into the highly dynamic and spatiotemporal response cascade triggered by water deficit and the underlying genetic regulations on the level of root zones in the barley cultivar Morex, providing potential targets to enhance plant resilience against environmental constraints. This study further emphasizes the importance of considering spatial and temporal resolution when examining stress responses.
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Affiliation(s)
- Alina Klaus
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Caroline Marcon
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Frank Hochholdinger
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany.
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2
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Visser EA, Kampmann TP, Wegrzyn JL, Naidoo S. Multispecies comparison of host responses to Fusarium circinatum challenge in tropical pines show consistency in resistance mechanisms. PLANT, CELL & ENVIRONMENT 2023; 46:1705-1725. [PMID: 36541367 DOI: 10.1111/pce.14522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Fusarium circinatum poses a threat to both commercial and natural pine forests. Large variation in host resistance exists between species, with many economically important species being susceptible. Development of resistant genotypes could be expedited and optimised by investigating the molecular mechanisms underlying host resistance and susceptibility as well as increasing the available genetic resources. RNA-seq data, from F. circinatum inoculated and mock-inoculated ca. 6-month-old shoot tissue at 3- and 7-days postinoculation, was generated for three commercially important tropical pines, Pinus oocarpa, Pinus maximinoi and Pinus greggii. De novo transcriptomes were assembled and used to investigate the NLR and PR gene content within available pine references. Host responses to F. circinatum challenge were investigated in P. oocarpa (resistant) and P. greggii (susceptible), in comparison to previously generated expression profiles from Pinus tecunumanii (resistant) and Pinus patula (susceptible). Expression results indicated crosstalk between induced salicylate, jasmonate and ethylene signalling is involved in host resistance and compromised in susceptible hosts. Additionally, higher constitutive expression of sulfur metabolism and flavonoid biosynthesis in resistant hosts suggest involvement of these metabolites in resistance.
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Affiliation(s)
- Erik A Visser
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tamanique P Kampmann
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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3
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Ganther M, Lippold E, Bienert MD, Bouffaud ML, Bauer M, Baumann L, Bienert GP, Vetterlein D, Heintz-Buschart A, Tarkka MT. Plant Age and Soil Texture Rather Than the Presence of Root Hairs Cause Differences in Maize Resource Allocation and Root Gene Expression in the Field. PLANTS (BASEL, SWITZERLAND) 2022; 11:2883. [PMID: 36365336 PMCID: PMC9657941 DOI: 10.3390/plants11212883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Understanding the biological roles of root hairs is key to projecting their contributions to plant growth and to assess their relevance for plant breeding. The objective of this study was to assess the importance of root hairs for maize nutrition, carbon allocation and root gene expression in a field experiment. Applying wild type and root hairless rth3 maize grown on loam and sand, we examined the period of growth including 4-leaf, 9-leaf and tassel emergence stages, accompanied with a low precipitation rate. rth3 maize had lower shoot growth and lower total amounts of mineral nutrients than wild type, but the concentrations of mineral elements, root gene expression, or carbon allocation were largely unchanged. For these parameters, growth stage accounted for the main differences, followed by substrate. Substrate-related changes were pronounced during tassel emergence, where the concentrations of several elements in leaves as well as cell wall formation-related root gene expression and C allocation decreased. In conclusion, the presence of root hairs stimulated maize shoot growth and total nutrient uptake, but other parameters were more impacted by growth stage and soil texture. Further research should relate root hair functioning to the observed losses in maize productivity and growth efficiency.
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Affiliation(s)
- Minh Ganther
- Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle, Germany
| | - Eva Lippold
- Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle, Germany
| | - Manuela Désirée Bienert
- TUM School of Life Sciences, Technical University of Munich, Alte Akademie 12, 85354 Freising, Germany
| | - Marie-Lara Bouffaud
- Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle, Germany
| | - Mario Bauer
- Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
| | - Louis Baumann
- Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle, Germany
| | - Gerd Patrick Bienert
- TUM School of Life Sciences, Technical University of Munich, Alte Akademie 12, 85354 Freising, Germany
| | - Doris Vetterlein
- Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle, Germany
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle/Saale, Germany
| | - Anna Heintz-Buschart
- Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle, Germany
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Mika Tapio Tarkka
- Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
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Nefissi Ouertani R, Arasappan D, Ruhlman TA, Ben Chikha M, Abid G, Mejri S, Ghorbel A, Jansen RK. Effects of Salt Stress on Transcriptional and Physiological Responses in Barley Leaves with Contrasting Salt Tolerance. Int J Mol Sci 2022; 23:5006. [PMID: 35563398 PMCID: PMC9103072 DOI: 10.3390/ijms23095006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 01/27/2023] Open
Abstract
Salt stress negatively impacts crop production worldwide. Genetic diversity among barley (Hordeum vulgare) landraces adapted to adverse conditions should provide a valuable reservoir of tolerance genes for breeding programs. To identify molecular and biochemical differences between barley genotypes, transcriptomic and antioxidant enzyme profiles along with several morpho-physiological features were compared between salt-tolerant (Boulifa) and salt-sensitive (Testour) genotypes subjected to salt stress. Decreases in biomass, photosynthetic parameters, and relative water content were low in Boulifa compared to Testour. Boulifa had better antioxidant protection against salt stress than Testour, with greater antioxidant enzymes activities including catalase, superoxide dismutase, and guaiacol peroxidase. Transcriptome assembly for both genotypes revealed greater accumulation of differentially expressed transcripts in Testour compared to Boulifa, emphasizing the elevated transcriptional response in Testour following salt exposure. Various salt-responsive genes, including the antioxidant catalase 3, the osmoprotectant betaine aldehyde dehydrogenase 2, and the transcription factors MYB20 and MYB41, were induced only in Boulifa. By contrast, several genes associated with photosystems I and II, and light receptor chlorophylls A and B, were more repressed in Testour. Co-expression network analysis identified specific gene modules correlating with differences in genotypes and morpho-physiological traits. Overall, salinity-induced differential transcript accumulation underlies the differential morpho-physiological response in both genotypes and could be important for breeding salt tolerance in barley.
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Affiliation(s)
- Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Dhivya Arasappan
- Center for Biomedical Research Support, University of Texas at Austin, Austin, TX 78712, USA;
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
| | - Mariem Ben Chikha
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia;
| | - Samiha Mejri
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Abdelwahed Ghorbel
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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Kaur B, Sandhu KS, Kamal R, Kaur K, Singh J, Röder MS, Muqaddasi QH. Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects. PLANTS 2021; 10:plants10101989. [PMID: 34685799 PMCID: PMC8541486 DOI: 10.3390/plants10101989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022]
Abstract
Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.
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Affiliation(s)
- Balwinder Kaur
- Everglades Research and Education Center, University of Florida, 3200 E. Palm Beach Rd., Belle Glade, FL 33430, USA;
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Kawalpreet Kaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
- Correspondence: or
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Nefissi Ouertani R, Arasappan D, Abid G, Ben Chikha M, Jardak R, Mahmoudi H, Mejri S, Ghorbel A, Ruhlman TA, Jansen RK. Transcriptomic Analysis of Salt-Stress-Responsive Genes in Barley Roots and Leaves. Int J Mol Sci 2021; 22:8155. [PMID: 34360920 PMCID: PMC8348758 DOI: 10.3390/ijms22158155] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
Barley is characterized by a rich genetic diversity, making it an important model for studies of salinity response with great potential for crop improvement. Moreover, salt stress severely affects barley growth and development, leading to substantial yield loss. Leaf and root transcriptomes of a salt-tolerant Tunisian landrace (Boulifa) exposed to 2, 8, and 24 h salt stress were compared with pre-exposure plants to identify candidate genes and pathways underlying barley's response. Expression of 3585 genes was upregulated and 5586 downregulated in leaves, while expression of 13,200 genes was upregulated and 10,575 downregulated in roots. Regulation of gene expression was severely impacted in roots, highlighting the complexity of salt stress response mechanisms in this tissue. Functional analyses in both tissues indicated that response to salt stress is mainly achieved through sensing and signaling pathways, strong transcriptional reprograming, hormone osmolyte and ion homeostasis stabilization, increased reactive oxygen scavenging, and activation of transport and photosynthesis systems. A number of candidate genes involved in hormone and kinase signaling pathways, as well as several transcription factor families and transporters, were identified. This study provides valuable information on early salt-stress-responsive genes in roots and leaves of barley and identifies several important players in salt tolerance.
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Affiliation(s)
- Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Dhivya Arasappan
- Center for Biomedical Research Support, University of Texas at Austin, Austin, TX 78712, USA;
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia;
| | - Mariem Ben Chikha
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Rahma Jardak
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Henda Mahmoudi
- International Center for Biosaline Agriculture, Dubai 00000, United Arab Emirates;
| | - Samiha Mejri
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Abdelwahed Ghorbel
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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Kumar V, Singh D, Majee A, Singh S, Asif MH, Sane AP, Sane VA. Identification of tomato root growth regulatory genes and transcription factors through comparative transcriptomic profiling of different tissues. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1173-1189. [PMID: 34177143 PMCID: PMC8212336 DOI: 10.1007/s12298-021-01015-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 05/07/2021] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Tomato is an economically important vegetable crop and a model for development and stress response studies. Although studied extensively for understanding fruit ripening and pathogen responses, its role as a model for root development remains less explored. In this study, an Illumina-based comparative differential transcriptomic analysis of tomato root with different aerial tissues was carried out to identify genes that are predominantly expressed during root growth. Sequential comparisons revealed ~ 15,000 commonly expressed genes and ~ 3000 genes of several classes that were mainly expressed or regulated in roots. These included 1069 transcription factors (TFs) of which 100 were differentially regulated. Prominent amongst these were members of families encoding Zn finger, MYB, ARM, bHLH, AP2/ERF, WRKY and NAC proteins. A large number of kinases, phosphatases and F-box proteins were also expressed in the root transcriptome. The major hormones regulating root growth were represented by the auxin, ethylene, JA, ABA and GA pathways with root-specific expression of certain components. Genes encoding carbon metabolism and photosynthetic components showed reduced expression while several protease inhibitors were amongst the most highly expressed. Overall, the study sheds light on genes governing root growth in tomato and provides a resource for manipulation of root growth for plant improvement. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01015-0.
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Affiliation(s)
- Vinod Kumar
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Deepika Singh
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Integral University, Lucknow, 226026 India
| | - Adity Majee
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Shikha Singh
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Mehar Hasan Asif
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Aniruddha P. Sane
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Vidhu A. Sane
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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Hill CB, Angessa TT, Zhang XQ, Chen K, Zhou G, Tan C, Wang P, Westcott S, Li C. A global barley panel revealing genomic signatures of breeding in modern Australian cultivars. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:419-434. [PMID: 33506596 DOI: 10.1111/tpj.15173] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
The future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Today's gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact that breeding had on the genetic diversity of Hordeum vulgare (barley) released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a diverse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined data set and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.
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Affiliation(s)
- Camilla Beate Hill
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Tefera Tolera Angessa
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Xiao-Qi Zhang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Kefei Chen
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
- Statistics for the Australian Grains Industry (SAGI) West, Faculty of Science and Engineering, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Gaofeng Zhou
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
| | - Cong Tan
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Penghao Wang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Sharon Westcott
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
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Bonkowski M, Tarkka M, Razavi BS, Schmidt H, Blagodatskaya E, Koller R, Yu P, Knief C, Hochholdinger F, Vetterlein D. Spatiotemporal Dynamics of Maize ( Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota. Front Microbiol 2021; 12:619499. [PMID: 33815308 PMCID: PMC8010349 DOI: 10.3389/fmicb.2021.619499] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome.” Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Using maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.
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Affiliation(s)
- Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Mika Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bahar S Razavi
- Department of Soil and Plant Microbiome, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,Soil Science, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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10
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Chen X, Zhao B, Ji C, Zhu B, Wang R. Transcriptome profiling analysis of two contrasting barley genotypes in general combining ability for yield traits. BRAZILIAN JOURNAL OF BOTANY 2021; 44:117-123. [DOI: 10.1007/s40415-020-00696-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 09/01/2023]
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Modulation of Human Mesenchymal Stem Cells by Electrical Stimulation Using an Enzymatic Biofuel Cell. Catalysts 2021. [DOI: 10.3390/catal11010062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Enzymatic biofuel cells (EBFCs) have excellent potential as components in bioelectronic devices, especially as active biointerfaces to regulate stem cell behavior for regenerative medicine applications. However, it remains unclear to what extent EBFC-generated electrical stimulation can regulate the functional behavior of human adipose-derived mesenchymal stem cells (hAD-MSCs) at the morphological and gene expression levels. Herein, we investigated the effect of EBFC-generated electrical stimulation on hAD-MSC cell morphology and gene expression using next-generation RNA sequencing. We tested three different electrical currents, 127 ± 9, 248 ± 15, and 598 ± 75 nA/cm2, in mesenchymal stem cells. We performed transcriptome profiling to analyze the impact of EBFC-derived electrical current on gene expression using next generation sequencing (NGS). We also observed changes in cytoskeleton arrangement and analyzed gene expression that depends on the electrical stimulation. The electrical stimulation of EBFC changes cell morphology through cytoskeleton re-arrangement. In particular, the results of whole transcriptome NGS showed that specific gene clusters were up- or down-regulated depending on the magnitude of applied electrical current of EBFC. In conclusion, this study demonstrates that EBFC-generated electrical stimulation can influence the morphological and gene expression properties of stem cells; such capabilities can be useful for regenerative medicine applications such as bioelectronic devices.
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12
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Mahmood K, Orabi J, Kristensen PS, Sarup P, Jørgensen LN, Jahoor A. De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea). Sci Rep 2020; 10:13475. [PMID: 32778722 PMCID: PMC7417550 DOI: 10.1038/s41598-020-70406-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/24/2020] [Indexed: 12/22/2022] Open
Abstract
Rye is used as food, feed, and for bioenergy production and remain an essential grain crop for cool temperate zones in marginal soils. Ergot is known to cause severe problems in cross-pollinated rye by contamination of harvested grains. The molecular response of the underlying mechanisms of this disease is still poorly understood due to the complex infection pattern. RNA sequencing can provide astonishing details about the transcriptional landscape, hence we employed a transcriptomic approach to identify genes in the underlying mechanism of ergot infection in rye. In this study, we generated de novo assemblies from twelve biological samples of two rye hybrids with identified contrasting phenotypic responses to ergot infection. The final transcriptome of ergot susceptible (DH372) and moderately ergot resistant (Helltop) hybrids contain 208,690 and 192,116 contigs, respectively. By applying the BUSCO pipeline, we confirmed that these transcriptome assemblies contain more than 90% of gene representation of the available orthologue groups at Virdiplantae odb10. We employed a de novo assembled and the draft reference genome of rye to count the differentially expressed genes (DEGs) between the two hybrids with and without inoculation. The gene expression comparisons revealed that 228 genes were linked to ergot infection in both hybrids. The genome ontology enrichment analysis of DEGs associated them with metabolic processes, hydrolase activity, pectinesterase activity, cell wall modification, pollen development and pollen wall assembly. In addition, gene set enrichment analysis of DEGs linked them to cell wall modification and pectinesterase activity. These results suggest that a combination of different pathways, particularly cell wall modification and pectinesterase activity contribute to the underlying mechanism that might lead to resistance against ergot in rye. Our results may pave the way to select genetic material to improve resistance against ergot through better understanding of the mechanism of ergot infection at molecular level. Furthermore, the sequence data and de novo assemblies are valuable as scientific resources for future studies in rye.
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Affiliation(s)
- Khalid Mahmood
- Nordic Seed A/S, Grindsnabevej 25, 8300, Odder, Denmark. .,Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, Flakkebjerg, 4200, Slagelse, Denmark.
| | - Jihad Orabi
- Nordic Seed A/S, Grindsnabevej 25, 8300, Odder, Denmark
| | | | | | - Lise Nistrup Jørgensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, Flakkebjerg, 4200, Slagelse, Denmark
| | - Ahmed Jahoor
- Nordic Seed A/S, Grindsnabevej 25, 8300, Odder, Denmark.,Department of Plant Breeding, The Swedish University of Agricultural Sciences, 23053, Alnarp, Sweden
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13
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Ho WWH, Hill CB, Doblin MS, Shelden MC, van de Meene A, Rupasinghe T, Bacic A, Roessner U. Integrative Multi-omics Analyses of Barley Rootzones under Salinity Stress Reveal Two Distinctive Salt Tolerance Mechanisms. PLANT COMMUNICATIONS 2020; 1:100031. [PMID: 33367236 PMCID: PMC7748018 DOI: 10.1016/j.xplc.2020.100031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/02/2020] [Accepted: 02/06/2020] [Indexed: 05/02/2023]
Abstract
The mechanisms underlying rootzone-localized responses to salinity during early stages of barley development remain elusive. In this study, we performed the analyses of multi-root-omes (transcriptomes, metabolomes, and lipidomes) of a domesticated barley cultivar (Clipper) and a landrace (Sahara) that maintain and restrict seedling root growth under salt stress, respectively. Novel generalized linear models were designed to determine differentially expressed genes (DEGs) and abundant metabolites (DAMs) specific to salt treatments, genotypes, or rootzones (meristematic Z1, elongation Z2, and maturation Z3). Based on pathway over-representation of the DEGs and DAMs, phenylpropanoid biosynthesis is the most statistically enriched biological pathway among all salinity responses observed. Together with histological evidence, an intense salt-induced lignin impregnation was found only at stelic cell wall of Clipper Z2, compared with a unique elevation of suberin deposition across Sahara Z2. This suggests two differential salt-induced modulations of apoplastic flow between the genotypes. Based on the global correlation network of the DEGs and DAMs, callose deposition that potentially adjusted symplastic flow in roots was almost independent of salinity in rootzones of Clipper, and was markedly decreased in Sahara. Taken together, we propose two distinctive salt tolerance mechanisms in Clipper (growth-sustaining) and Sahara (salt-shielding), providing important clues for improving crop plasticity to cope with deteriorating global soil salinization.
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Affiliation(s)
- William Wing Ho Ho
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Camilla B. Hill
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Monika S. Doblin
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Megan C. Shelden
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Allison van de Meene
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Thusitha Rupasinghe
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Antony Bacic
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Metabolomics Australia, The University of Melbourne, Parkville, VIC 3010, Australia
- Corresponding author
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14
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Sarabia LD, Boughton BA, Rupasinghe T, Callahan DL, Hill CB, Roessner U. Comparative spatial lipidomics analysis reveals cellular lipid remodelling in different developmental zones of barley roots in response to salinity. PLANT, CELL & ENVIRONMENT 2020; 43:327-343. [PMID: 31714612 PMCID: PMC7063987 DOI: 10.1111/pce.13653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/25/2019] [Accepted: 08/27/2019] [Indexed: 05/18/2023]
Abstract
Salinity-induced metabolic, ionic, and transcript modifications in plants have routinely been studied using whole plant tissues, which do not provide information on spatial tissue responses. The aim of this study was to assess the changes in the lipid profiles in a spatial manner and to quantify the changes in the elemental composition in roots of seedlings of four barley cultivars before and after a short-term salt stress. We used a combination of liquid chromatography-tandem mass spectrometry, inductively coupled plasma mass spectrometry, matrix-assisted laser desorption/ionization mass spectrometry imaging, and reverse transcription - quantitative real time polymerase chain reaction platforms to examine the molecular signatures of lipids, ions, and transcripts in three anatomically different seminal root tissues before and after salt stress. We found significant changes to the levels of major lipid classes including a decrease in the levels of lysoglycerophospholipids, ceramides, and hexosylceramides and an increase in the levels of glycerophospholipids, hydroxylated ceramides, and hexosylceramides. Our results revealed that modifications to lipid and transcript profiles in plant roots in response to a short-term salt stress may involve recycling of major lipid species, such as phosphatidylcholine, via resynthesis from glycerophosphocholine.
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Affiliation(s)
- Lenin D. Sarabia
- School of BioSciences and Metabolomics AustraliaUniversity of MelbourneParkvilleVIC3010Australia
| | | | | | - Damien L. Callahan
- School of Life and Environmental Sciences, Centre for Chemistry and Biotechnology, (Burwood Campus)Deakin University, Geelong, Australia221 Burwood HighwayBurwoodVIC3125Australia
| | - Camilla B. Hill
- School of Veterinary and Life SciencesMurdoch UniversityMurdochWA6150Australia
| | - Ute Roessner
- School of BioSciences and Metabolomics AustraliaUniversity of MelbourneParkvilleVIC3010Australia
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15
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Zhang L, Wang Y, Zhang Q, Jiang Y, Zhang H, Li R. Overexpression of HbMBF1a, encoding multiprotein bridging factor 1 from the halophyte Hordeum brevisubulatum, confers salinity tolerance and ABA insensitivity to transgenic Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2020; 102:1-17. [PMID: 31655970 PMCID: PMC6976555 DOI: 10.1007/s11103-019-00926-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/13/2019] [Indexed: 05/11/2023]
Abstract
HbMBF1a was isolated and characterized in H. brevisubulatum, and overexpressed HbMBF1a could enhance the salt tolerance and ABA insensitivity in Arabidopsis thaliana. The transcript levels of stress-responsive genes were significantly increased in the transgenic lines under salt and ABA conditions. Salinity is an abiotic stress that considerably affects plant growth, yield, and distribution. Hordeum brevisubulatum is a halophyte that evolved to become highly tolerant to salinity. Multiprotein bridging factor 1 (MBF1) is a transcriptional coactivator and an important regulator of stress tolerance. In this study, we isolated and characterized HbMBF1a based on the transcriptome data of H. brevisubulatum grown under saline conditions. We overexpressed HbMBF1a in Arabidopsis thaliana and compared the phenotypes of the transgenic lines and the wild-type in response to stresses. The results indicated that HbMBF1a expression was induced by salt and ABA treatments during the middle and late stages. The overexpression of HbMBF1a in A. thaliana resulted in enhanced salt tolerance and ABA insensitivity. More specifically, the enhanced salt tolerance manifested as the increased seed germination and seedling growth and development. Similarly, under ABA treatments, the cotyledon greening rate and seedling root length were higher in the HbMBF1a-overexpressing lines, suggesting the transgenic plants were better adapted to high exogenous ABA levels. Furthermore, the transcript levels of stress-responsive genes were significantly increased in the transgenic lines under salt and ABA conditions. Thus, HbMBF1a is a positive regulator of salt and ABA responses, and the corresponding gene may be useful for producing transgenic plants that are salt tolerant and/or ABA insensitive, with few adverse effects. This study involved a comprehensive analysis of HbMBF1a. The results may provide the basis and insight for the application of MBF1 family genes for developing stress-tolerant crops.
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Affiliation(s)
- Lili Zhang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Yunxiao Wang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Qike Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024 China
| | - Ying Jiang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Haiwen Zhang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Ruifen Li
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
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16
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Huang Y, Cao H, Yang L, Chen C, Shabala L, Xiong M, Niu M, Liu J, Zheng Z, Zhou L, Peng Z, Bie Z, Shabala S. Tissue-specific respiratory burst oxidase homolog-dependent H2O2 signaling to the plasma membrane H+-ATPase confers potassium uptake and salinity tolerance in Cucurbitaceae. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5879-5893. [PMID: 31290978 PMCID: PMC6812723 DOI: 10.1093/jxb/erz328] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/03/2019] [Indexed: 05/02/2023]
Abstract
Potassium (K+) is a critical determinant of salinity tolerance, and H2O2 has been recognized as an important signaling molecule that mediates many physiological responses. However, the details of how H2O2 signaling regulates K+ uptake in the root under salt stress remain elusive. In this study, salt-sensitive cucumber and salt-tolerant pumpkin which belong to the same family, Cucurbitaceae, were used to answer the above question. We show that higher salt tolerance in pumpkin was related to its superior ability for K+ uptake and higher H2O2 accumulation in the root apex. Transcriptome analysis showed that salinity induced 5816 (3005 up- and 2811 down-) and 4679 (3965 up- and 714 down-) differentially expressed genes (DEGs) in cucumber and pumpkin, respectively. DEGs encoding NADPH oxidase (respiratory burst oxidase homolog D; RBOHD), 14-3-3 protein (GRF12), plasma membrane H+-ATPase (AHA1), and potassium transporter (HAK5) showed higher expression in pumpkin than in cucumber under salinity stress. Treatment with the NADPH oxidase inhibitor diphenylene iodonium resulted in lower RBOHD, GRF12, AHA1, and HAK5 expression, reduced plasma membrane H+-ATPase activity, and lower K+ uptake, leading to a loss of the salinity tolerance trait in pumpkin. The opposite results were obtained when the plants were pre-treated with exogenous H2O2. Knocking out of RBOHD in pumpkin by CRISPR/Cas9 [clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9] editing of coding sequences resulted in lower root apex H2O2 and K+ content and GRF12, AHA1, and HAK5 expression, ultimately resulting in a salt-sensitive phenotype. However, ectopic expression of pumpkin RBOHD in Arabidopsis led to the opposite effect. Taken together, this study shows that RBOHD-dependent H2O2 signaling in the root apex is important for pumpkin salt tolerance and suggests a novel mechanism that confers this trait, namely RBOHD-mediated transcriptional and post-translational activation of plasma membrane H+-ATPase operating upstream of HAK5 K+ uptake transporters.
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Affiliation(s)
- Yuan Huang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, PR China
- Tasmanian Institute for Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Haishun Cao
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, PR China
| | - Li Yang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, PR China
| | - Chen Chen
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, PR China
| | - Lana Shabala
- Tasmanian Institute for Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Mu Xiong
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, PR China
| | - Mengliang Niu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, PR China
| | - Juan Liu
- Tasmanian Institute for Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Zuhua Zheng
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, PR China
| | - Lijian Zhou
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, PR China
| | - Zhaowen Peng
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, PR China
| | - Zhilong Bie
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, PR China
| | - Sergey Shabala
- Tasmanian Institute for Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, PR China
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17
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Ma Y, Liu M, Stiller J, Liu C. A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication. BMC Genomics 2019; 20:12. [PMID: 30616511 PMCID: PMC6323845 DOI: 10.1186/s12864-018-5357-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/09/2018] [Indexed: 11/12/2022] Open
Abstract
Background It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications. Results In this study we constructed a pan-transcriptome for barley by de novo assembling 288 sets of RNA-seq data from 32 cultivated barley genotypes and 31 wild barley genotypes. The pan-transcriptome consists of 756,632 transcripts with an average N50 length of 1240 bp. Of these, 289,697 (38.2%) were not found in the genome of the international reference genotype Morex. The novel transcripts are enriched with genes associated with responses to different stresses and stimuli. At the pan-transcriptome level, genotypes of wild barley have a higher proportion of disease resistance genes than cultivated ones. Conclusions We demonstrate that the use of the pan-transcriptome dramatically improved the efficiency in detecting variation in barley. Analysing the pan-transcriptome also found that, compared with those in other categories, disease resistance genes have gone through stronger selective pressures during domestication. Electronic supplementary material The online version of this article (10.1186/s12864-018-5357-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanling Ma
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Miao Liu
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia.,Crop Research Institute of Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Jiri Stiller
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Chunji Liu
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
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18
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Visser EA, Wegrzyn JL, Myburg AA, Naidoo S. Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation). BMC Genomics 2018; 19:632. [PMID: 30139335 PMCID: PMC6108113 DOI: 10.1186/s12864-018-5015-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 08/14/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Fusarium circinatum is a pressing threat to the cultivation of many economically important pine tree species. Efforts to develop effective disease management strategies can be aided by investigating the molecular mechanisms involved in the host-pathogen interaction between F. circinatum and pine species. Pinus tecunumanii and Pinus patula are two closely related tropical pine species that differ widely in their resistance to F. circinatum challenge, being resistant and susceptible respectively, providing the potential for a useful pathosystem to investigate the molecular responses underlying resistance to F. circinatum. However, no genomic resources are available for P. tecunumanii. Pathogenesis-related proteins are classes of proteins that play important roles in plant-microbe interactions, e.g. chitinases; proteins that break down the major structural component of fungal cell walls. Generating a reference sequence for P. tecunumanii and characterizing pathogenesis related gene families in these two pine species is an important step towards unravelling the pine-F. circinatum interaction. RESULTS Eight reference based and 12 de novo assembled transcriptomes were produced, for juvenile shoot tissue from both species. EvidentialGene pipeline redundancy reduction, expression filtering, protein clustering and taxonomic filtering produced a 50 Mb shoot transcriptome consisting of 28,621 contigs for P. tecunumanii and a 72 Mb shoot transcriptome consisting of 52,735 contigs for P. patula. Predicted protein sequences encoded by the assembled transcriptomes were clustered with reference proteomes from 92 other species to identify pathogenesis related gene families in P. patula, P. tecunumanii and other pine species. CONCLUSIONS The P. tecunumanii transcriptome is the first gene catalogue for the species, representing an important resource for studying resistance to the pitch canker pathogen, F. circinatum. This study also constitutes, to our knowledge, the largest index of gymnosperm PR-genes to date.
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Affiliation(s)
- Erik A. Visser
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028 South Africa
| | - Jill L. Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269 USA
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028 South Africa
| | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028 South Africa
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19
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Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare). EPIGENOMES 2018. [DOI: 10.3390/epigenomes2020012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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20
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Variable Levels of Tolerance to Water Stress (Drought) and Associated Biochemical Markers in Tunisian Barley Landraces. Molecules 2018. [PMID: 29518035 PMCID: PMC6017546 DOI: 10.3390/molecules23030613] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Due to its high tolerance to abiotic stress, barley (Hordeum vulgare) is cultivated in many arid areas of the world. In the present study, we evaluate the tolerance to water stress (drought) in nine accessions of “Ardhaoui” barley landraces from different regions of Tunisia. The genetic diversity of the accessions is evaluated with six SSR markers. Seedlings from the nine accessions are subjected to water stress by completely stopping irrigation for three weeks. A high genetic diversity is detected among the nine accessions, with no relationships between genetic distance and geographical or ecogeographical zone. The analysis of growth parameters and biochemical markers in the water stress-treated plants in comparison to their respective controls indicated great variability among the studied accessions. Accession 2, from El May Island, displayed high tolerance to drought. Increased amounts of proline in water-stressed plants could not be correlated with a better response to drought, as the most tolerant accessions contained lower levels of this osmolyte. A good correlation was established between the reduction of growth and degradation of chlorophylls and increased levels of malondialdehyde and total phenolics. These biochemical markers may be useful for identifying drought tolerant materials in barley.
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21
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Sarabia LD, Boughton BA, Rupasinghe T, van de Meene AML, Callahan DL, Hill CB, Roessner U. High-mass-resolution MALDI mass spectrometry imaging reveals detailed spatial distribution of metabolites and lipids in roots of barley seedlings in response to salinity stress. Metabolomics 2018; 14:63. [PMID: 29681790 PMCID: PMC5907631 DOI: 10.1007/s11306-018-1359-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/09/2018] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Mass spectrometry imaging (MSI) is a technology that enables the visualization of the spatial distribution of hundreds to thousands of metabolites in the same tissue section simultaneously. Roots are below-ground plant organs that anchor plants to the soil, take up water and nutrients, and sense and respond to external stresses. Physiological responses to salinity are multifaceted and have predominantly been studied using whole plant tissues that cannot resolve plant salinity responses spatially. OBJECTIVES This study aimed to use a comprehensive approach to study the spatial distribution and profiles of metabolites, and to quantify the changes in the elemental content in young developing barley seminal roots before and after salinity stress. METHODS Here, we used a combination of liquid chromatography-mass spectrometry (LC-MS), inductively coupled plasma mass spectrometry (ICP-MS), and matrix-assisted laser desorption/ionization (MALDI-MSI) platforms to profile and analyze the spatial distribution of ions, metabolites and lipids across three anatomically different barley root zones before and after a short-term salinity stress (150 mM NaCl). RESULTS We localized, visualized and discriminated compounds in fine detail along longitudinal root sections and compared ion, metabolite, and lipid composition before and after salt stress. Large changes in the phosphatidylcholine (PC) profiles were observed as a response to salt stress with PC 34:n showing an overall reduction in salt treated roots. ICP-MS analysis quantified changes in the elemental content of roots with increases of Na+ and decreases of K+ content. CONCLUSION Our results established the suitability of combining three mass spectrometry platforms to analyze and map ionic and metabolic responses to salinity stress in plant roots and to elucidate tolerance mechanisms in response to abiotic stress, such as salinity stress.
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Affiliation(s)
- Lenin D Sarabia
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Berin A Boughton
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Thusitha Rupasinghe
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Damien L Callahan
- School of Life and Environmental Sciences, Centre for Chemistry and Biotechnology, Deakin University, 221 Burwood Highway, Burwood, VIC, 3125, Australia
| | - Camilla B Hill
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
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Wu Q, Bai X, Zhao W, Xiang D, Wan Y, Yan J, Zou L, Zhao G. De Novo Assembly and Analysis of Tartary Buckwheat (Fagopyrum tataricum Garetn.) Transcriptome Discloses Key Regulators Involved in Salt-Stress Response. Genes (Basel) 2017; 8:genes8100255. [PMID: 28972562 PMCID: PMC5664105 DOI: 10.3390/genes8100255] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 11/24/2022] Open
Abstract
Soil salinization has been a tremendous obstacle for agriculture production. The regulatory networks underlying salinity adaption in model plants have been extensively explored. However, limited understanding of the salt response mechanisms has hindered the planting and production in Fagopyrum tataricum, an economic and health-beneficial plant mainly distributing in southwest China. In this study, we performed physiological analysis and found that salt stress of 200 mM NaCl solution significantly affected the relative water content (RWC), electrolyte leakage (EL), malondialdehyde (MDA) content, peroxidase (POD) and superoxide dismutase (SOD) activities in tartary buckwheat seedlings. Further, we conducted transcriptome comparison between control and salt treatment to identify potential regulatory components involved in F. tataricum salt responses. A total of 53.15 million clean reads from control and salt-treated libraries were produced via an Illumina sequencing approach. Then we de novo assembled these reads into a transcriptome dataset containing 57,921 unigenes with N50 length of 1400 bp and total length of 44.5 Mb. A total of 36,688 unigenes could find matches in public databases. GO, KEGG and KOG classification suggested the enrichment of these unigenes in 56 sub-categories, 25 KOG, and 273 pathways, respectively. Comparison of the transcriptome expression patterns between control and salt treatment unveiled 455 differentially expressed genes (DEGs). Further, we found the genes encoding for protein kinases, phosphatases, heat shock proteins (HSPs), ATP-binding cassette (ABC) transporters, glutathione S-transferases (GSTs), abiotic-related transcription factors and circadian clock might be relevant to the salinity adaption of this species. Thus, this study offers an insight into salt tolerance mechanisms, and will serve as useful genetic information for tolerant elite breeding programs in future.
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Affiliation(s)
- Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, Chengdu 610106, China.
- National Research and Development Center for Coarse Cereal Processing, Chengdu 610106, China.
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China.
| | - Xue Bai
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, Chengdu 610106, China.
- National Research and Development Center for Coarse Cereal Processing, Chengdu 610106, China.
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China.
| | - Wei Zhao
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China.
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, Chengdu 610106, China.
- National Research and Development Center for Coarse Cereal Processing, Chengdu 610106, China.
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China.
| | - Yan Wan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, Chengdu 610106, China.
- National Research and Development Center for Coarse Cereal Processing, Chengdu 610106, China.
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China.
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, Chengdu 610106, China.
- National Research and Development Center for Coarse Cereal Processing, Chengdu 610106, China.
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China.
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, Chengdu 610106, China.
- National Research and Development Center for Coarse Cereal Processing, Chengdu 610106, China.
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China.
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, Chengdu 610106, China.
- National Research and Development Center for Coarse Cereal Processing, Chengdu 610106, China.
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China.
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Li Q, Wu Y, Chen W, Jin R, Kong F, Ke Y, Shi H, Yuan J. Cultivar Differences in Root Nitrogen Uptake Ability of Maize Hybrids. FRONTIERS IN PLANT SCIENCE 2017; 8:1060. [PMID: 28676812 PMCID: PMC5476776 DOI: 10.3389/fpls.2017.01060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/01/2017] [Indexed: 05/23/2023]
Abstract
Although, considerable differences in root size in response to nitrogen (N) application among crop species and cultivars have been widely reported, there has been limited focus on the differences in root N uptake ability. In this study, two maize (Zea mays L.) hybrids, Zhenghong 311 (ZH 311, N-efficient) and Xianyu 508 (XY 508, N-inefficient), were used to compare differences in root N uptake ability. The two cultivars were grown in field pots Experiment I (Exp. I) and hydroponic cultures Experiment II (Exp. II) supplemented with different concentrations of N fertilizer. In both experiments, the levels of accumulated N were higher in ZH 311 than in XY 508 under low- and high-N supply, and the increment in accumulated N was greater under N deficiency. The maximum N uptake rate (Vm) and average N uptake rate (Va) in Exp. I, the root N kinetic parameter maximum uptake rate (Vmax) per fresh weight (FW) and Vmax per plant in Exp. II, and the root N uptake rate in both experiments were significantly higher for ZH 311 than for XY 508. In contrast, the root-to-shoot N ratio in both experiments and the root N kinetic parameter Michaelis constant (Km) in in Exp. II were markedly higher in XY 508 than in ZH 311, particularly under N-deficient conditions. Higher root N kinetic parameters Vmax per FW and Vmax per plant and lower Km values contributed to higher N affinity and uptake potential, more coordinated N distribution in the root and shoot, and higher root N uptake rates throughout the growth stages, thus enhancing the N accumulation and yield of the N-efficient maize cultivar. We conclude that the N uptake ability of roots in the N-efficient cultivar ZH 311 is significantly greater than that in the N-inefficient cultivar XY 508, and that this advantage is more pronounced under N-deficient conditions. The efficient N acquisition in ZH 311 is due to higher N uptake rate per root FW under optimal N conditions and the comprehensive effects of root size and N uptake rate per root FW under N deficiency.
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Cao D, Lutz A, Hill CB, Callahan DL, Roessner U. A Quantitative Profiling Method of Phytohormones and Other Metabolites Applied to Barley Roots Subjected to Salinity Stress. FRONTIERS IN PLANT SCIENCE 2017; 7:2070. [PMID: 28119732 PMCID: PMC5222860 DOI: 10.3389/fpls.2016.02070] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/27/2016] [Indexed: 05/22/2023]
Abstract
As integral parts of plant signaling networks, phytohormones are involved in the regulation of plant metabolism and growth under adverse environmental conditions, including salinity. Globally, salinity is one of the most severe abiotic stressors with an estimated 800 million hectares of arable land affected. Roots are the first plant organ to sense salinity in the soil, and are the initial site of sodium (Na+) exposure. However, the quantification of phytohormones in roots is challenging, as they are often present at extremely low levels compared to other plant tissues. To overcome this challenge, we developed a high-throughput LC-MS method to quantify ten endogenous phytohormones and their metabolites of diverse chemical classes in roots of barley. This method was validated in a salinity stress experiment with six barley varieties grown hydroponically with and without salinity. In addition to phytohormones, we quantified 52 polar primary metabolites, including some phytohormone precursors, using established GC-MS and LC-MS methods. Phytohormone and metabolite data were correlated with physiological measurements including biomass, plant size and chlorophyll content. Root and leaf elemental analysis was performed to determine Na+ exclusion and K+ retention ability in the studied barley varieties. We identified distinct phytohormone and metabolite signatures as a response to salinity stress in different barley varieties. Abscisic acid increased in the roots of all varieties under salinity stress, and elevated root salicylic acid levels were associated with an increase in leaf chlorophyll content. Furthermore, the landrace Sahara maintained better growth, had lower Na+ levels and maintained high levels of the salinity stress linked metabolite putrescine as well as the phytohormone metabolite cinnamic acid, which has been shown to increase putrescine concentrations in previous studies. This study highlights the importance of root phytohormones under salinity stress and the multi-variety analysis provides an important update to analytical methodology, and adds to the current knowledge of salinity stress responses in plants at the molecular level.
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Affiliation(s)
- Da Cao
- School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
| | - Adrian Lutz
- Metabolomics Australia, School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
| | - Camilla B. Hill
- School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
- School of Veterinary and Life Sciences, Murdoch University, MurdochWA, Australia
| | - Damien L. Callahan
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, BurwoodVIC, Australia
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
- Metabolomics Australia, School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
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