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Doolan O, Lewsey MG, Peirats-Llobet M, Bricklebank N, Aberdein N. Micro computed tomography analysis of barley during the first 24 hours of germination. PLANT METHODS 2024; 20:142. [PMID: 39285284 PMCID: PMC11406838 DOI: 10.1186/s13007-024-01266-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 09/02/2024] [Indexed: 09/19/2024]
Abstract
BACKGROUND Grains make up a large proportion of both human and animal diets. With threats to food production, such as climate change, growing sustainable and successful crops is essential to food security in the future. Germination is one of the most important stages in a plant's lifecycle and is key to the success of the resulting plant as the grain undergoes morphological changes and the development of specific organs. Micro-computed tomography is a non-destructive imaging technique based on the differing x-ray attenuations of materials which we have applied for the accurate analysis of grain morphology during the germination phase. RESULTS Micro Computed Tomography conditions and parameters were tested to establish an optimal protocol for the 3-dimensional analysis of barley grains. When comparing optimal scanning conditions, it was established that no filter, 0.4 degrees rotation step, 5 average frames, and 2016 × 1344 camera binning is optimal for imaging germinating grains. It was determined that the optimal protocol for scanning during the germination timeline was to scan individual grains at 0 h after imbibition (HAI) and then the same grain again at set time points (1, 3, 6, 24 HAI) to avoid any negative effects from X-ray radiation or disruption to growing conditions. CONCLUSION Here we sought to develop a method for the accurate analysis of grain morphology without the negative effects of possible radiation exposure. Several factors have been considered, such as the scanning conditions, reconstruction, and possible effects of X-ray radiation on the growth rate of the grains. The parameters chosen in this study give effective and reliable results for the 3-dimensional analysis of macro structures within barley grains while causing minimal disruption to grain development.
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Affiliation(s)
- Olivia Doolan
- Biomolecular Sciences Research Centre, Sheffield Hallam University, City Campus, Sheffield, S1 1WB, UK.
| | - Mathew G Lewsey
- La Trobe Institute for Sustainable Agriculture and Food, Department of Plant, Animal and Soil Sciences, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Centre of Excellence in Plants for Space, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Marta Peirats-Llobet
- La Trobe Institute for Sustainable Agriculture and Food, Department of Plant, Animal and Soil Sciences, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Neil Bricklebank
- Biomolecular Sciences Research Centre, Sheffield Hallam University, City Campus, Sheffield, S1 1WB, UK
| | - Nicola Aberdein
- Biomolecular Sciences Research Centre, Sheffield Hallam University, City Campus, Sheffield, S1 1WB, UK
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Sybilska E, Collin A, Sadat Haddadi B, Mur LAJ, Beckmann M, Guo W, Simpson CG, Daszkowska-Golec A. The cap-binding complex modulates ABA-responsive transcript splicing during germination in barley (Hordeum vulgare). Sci Rep 2024; 14:18278. [PMID: 39107424 PMCID: PMC11303550 DOI: 10.1038/s41598-024-69373-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024] Open
Abstract
To decipher the molecular bases governing seed germination, this study presents the pivotal role of the cap-binding complex (CBC), comprising CBP20 and CBP80, in modulating the inhibitory effects of abscisic acid (ABA) in barley. Using both single and double barley mutants in genes encoding the CBC, we revealed that the double mutant hvcbp20.ab/hvcbp80.b displays ABA insensitivity, in stark contrast to the hypersensitivity observed in single mutants during germination. Our comprehensive transcriptome and metabolome analysis not only identified significant alterations in gene expression and splicing patterns but also underscored the regulatory nexus among CBC, ABA, and brassinosteroid (BR) signaling pathways.
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Affiliation(s)
- Ewa Sybilska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | - Anna Collin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | | | - Luis A J Mur
- Department of Life Science, Aberystwyth University, Aberystwyth, UK
| | - Manfred Beckmann
- Department of Life Science, Aberystwyth University, Aberystwyth, UK
| | - Wenbin Guo
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Craig G Simpson
- Cell and Molecular Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland.
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3
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Kovacik M, Nowicka A, Zwyrtková J, Strejčková B, Vardanega I, Esteban E, Pasha A, Kaduchová K, Krautsova M, Červenková M, Šafář J, Provart NJ, Simon R, Pecinka A. The transcriptome landscape of developing barley seeds. THE PLANT CELL 2024; 36:2512-2530. [PMID: 38635902 PMCID: PMC11218782 DOI: 10.1093/plcell/koae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from grains 4-32 days after pollination. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes and transcription factors (TFs) potentially regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of TFs for functional studies of the pathways controlling barley grain development. Assessing selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely play a major role during barley endosperm development. The repressive H3K27me3 modification is globally reduced in endosperm tissues and at specific genes related to development and storage compounds. Altogether, this atlas uncovers the complexity of developmentally regulated gene expression in developing barley grains.
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Affiliation(s)
- Martin Kovacik
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Anna Nowicka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30 239 Kraków, Poland
| | - Jana Zwyrtková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Beáta Strejčková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Isaia Vardanega
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Kateřina Kaduchová
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Maryna Krautsova
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Marie Červenková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
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4
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Yan F, Wei T, Yang C, Yang Y, Luo Z, Jiang Y. Combined Analysis of Untargeted Metabolomics and Transcriptomics Revealed Seed Germination and Seedling Establishment in Zelkova schneideriana. Genes (Basel) 2024; 15:488. [PMID: 38674422 PMCID: PMC11050531 DOI: 10.3390/genes15040488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Zelkova schneideriana Hand.-Mazz is a valuable ornamental tree and timber source, whose seedling breeding and large-scale cultivation are restricted by low seed germination and seedling rates. The regulatory mechanisms underlying seed germination and seedling establishment in Z. schneideriana remain unknown. This study conducted metabolomic and transcriptomic analyses of seed germination and seedling establishment in Z. schneideriana. Regular expression of genes and metabolite levels has been observed in plant hormone signal transduction, starch and sucrose metabolism, linoleic acid metabolism, and phenylpropanoid biosynthesis. The reduction in abscisic acid during seed germination may lead to seed release from dormancy. After the seed is released from dormancy, the metabolic levels of auxin, cytokinins, brassinolide, and various sugars are elevated, and they are consumed in large quantities during the seedling establishment stage. Linoleic acid metabolism is gradually activated during seedling establishment. Transcriptome analysis showed that a large number of genes in different metabolic pathways are upregulated during plant establishment, and material metabolism may be accelerated during seedling establishment. Genes regulating carbohydrate metabolism are altered during seed germination and seedling establishment, which may have altered the efficiency of carbohydrate utilization. In addition, the syntheses of lignin monomers and cellulose have different characteristics at different stages. These results provide new insights into the complex mechanisms underlying seed germination and seedling establishment in Z. schneideriana and other woody plants.
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Affiliation(s)
- Fengxia Yan
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Academy of Forestry, Guiyang 550005, China; (F.Y.); (Y.Y.); (Y.J.)
| | - Tangmei Wei
- Xingyi Forestry Bureau, Qianxinan Prefecture Guizhou, Guiyang 562400, China;
| | - Chao Yang
- Institute for Forest Resources and Environment, Guizhou University, Guiyang 550025, China;
| | - Yanbing Yang
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Academy of Forestry, Guiyang 550005, China; (F.Y.); (Y.Y.); (Y.J.)
| | - Zaiqi Luo
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Academy of Forestry, Guiyang 550005, China; (F.Y.); (Y.Y.); (Y.J.)
| | - Yunli Jiang
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Academy of Forestry, Guiyang 550005, China; (F.Y.); (Y.Y.); (Y.J.)
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5
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Hong MJ, Ko CS, Kim JB, Kim DY. Identification and transcriptomic profiling of salinity stress response genes in colored wheat mutant. PeerJ 2024; 12:e17043. [PMID: 38464747 PMCID: PMC10924784 DOI: 10.7717/peerj.17043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
Background Salinity is a major abiotic stress that prevents normal plant growth and development, ultimately reducing crop productivity. This study investigated the effects of salinity stress on two wheat lines: PL1 (wild type) and PL6 (mutant line generated through gamma irradiation of PL1). Results The salinity treatment was carried out with a solution consisting of a total volume of 200 mL containing 150 mM NaCl. Salinity stress negatively impacted germination and plant growth in both lines, but PL6 exhibited higher tolerance. PL6 showed lower Na+ accumulation and higher K+ levels, indicating better ion homeostasis. Genome-wide transcriptomic analysis revealed distinct gene expression patterns between PL1 and PL6 under salt stress, resulting in notable phenotypic differences. Gene ontology analysis revealed positive correlations between salt stress and defense response, glutathione metabolism, peroxidase activity, and reactive oxygen species metabolic processes, highlighting the importance of antioxidant activities in salt tolerance. Additionally, hormone-related genes, transcription factors, and protein kinases showed differential expression, suggesting their roles in the differential salt stress response. Enrichment of pathways related to flavonoid biosynthesis and secondary metabolite biosynthesis in PL6 may contribute to its enhanced antioxidant activities. Furthermore, differentially expressed genes associated with the circadian clock system, cytoskeleton organization, and cell wall organization shed light on the plant's response to salt stress. Conclusions Understanding these mechanisms is crucial for developing stress-tolerant crop varieties, improving agricultural practices, and breeding salt-resistant crops to enhance global food production and address food security challenges.
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Affiliation(s)
- Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk-do, Korea
| | - Chan Seop Ko
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk-do, Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk-do, Korea
| | - Dae Yeon Kim
- Plant Resources, Kongju National University, Yesan-eup, Chungnam, South Korea
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6
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Zhang Y, Yue S, Liu M, Wang X, Xu S, Zhang X, Zhou Y. Combined transcriptome and proteome analysis reveal the key physiological processes in seed germination stimulated by decreased salinity in the seagrass Zostera marina L. BMC PLANT BIOLOGY 2023; 23:605. [PMID: 38030999 PMCID: PMC10688091 DOI: 10.1186/s12870-023-04616-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Zostera marina L., or eelgrass, is the most widespread seagrass species throughout the temperate northern hemisphere. Unlike the dry seeds of terrestrial plants, eelgrass seeds must survive in water, and salinity is the key factor influencing eelgrass seed germination. In the present study, transcriptome and proteome analysis were combined to investigate the mechanisms via which eelgrass seed germination was stimulated by low salinity, in addition to the dynamics of key metabolic pathways under germination. RESULTS According to the results, low salinity stimulated the activation of Ca2+ signaling and phosphatidylinositol signaling, and further initiated various germination-related physiological processes through the MAPK transduction cascade. Starch, lipids, and storage proteins were mobilized actively to provide the energy and material basis for germination; abscisic acid synthesis and signal transduction were inhibited whereas gibberellin synthesis and signal transduction were activated, weakening seed dormancy and preparing for germination; cell wall weakening and remodeling processes were activated to provide protection for cotyledon protrusion; in addition, multiple antioxidant systems were activated to alleviate oxidative stress generated during the germination process; ERF transcription factor has the highest number in both stages suggested an active role in eelgrass seed germination. CONCLUSION In summary, for the first time, the present study investigated the mechanisms by which eelgrass seed germination was stimulated by low salinity and analyzed the transcriptomic and proteomic features during eelgrass seed germination comprehensively. The results of the present study enhanced our understanding of seagrass seed germination, especially the molecular ecology of seagrass seeds.
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Affiliation(s)
- Yu Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Shidong Yue
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Mingjie Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Xinhua Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Shaochun Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Xiaomei Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Yi Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China.
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7
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Bahmani M, Juhász A, Bose U, Nye-Wood MG, Blundell M, Howitt CA, Colgrave ML. Proteome Changes Resulting from Malting in Hordein-Reduced Barley Lines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14079-14091. [PMID: 37712129 PMCID: PMC10540200 DOI: 10.1021/acs.jafc.3c02292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/18/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
Hordeum vulgare L., commonly known as barley, is primarily used for animal feed and malting. The major storage proteins in barley are hordeins, known triggers of celiac disease (CD). Here, sequential window acquisition of all theoretical mass spectra (SWATH)-MS proteomics was employed to investigate the proteome profile of grain and malt samples from the malting barley cultivar Sloop and single-, double-, and triple hordein-reduced lines bred in a Sloop background. Using a discovery proteomics approach, 2688 and 3034 proteins were detected from the grain and malt samples, respectively. By utilizing label-free relative quantitation through SWATH-MS, a total of 2654 proteins have been quantified from grain and malt. The comparative analyses between the barley grain and malt samples revealed that the C-hordein-reduced lines have a more significant impact on proteome level changes due to malting than B- and D-hordein-reduced lines. Upregulated proteins in C-hordein-reduced lines were primarily involved in the tricarboxylic acid cycle and fatty acid peroxidation processes to provide more energy for seed germination during malting. By applying proteomics approaches after malting in hordein-reduced barley lines, we uncovered additional changes in the proteome driven by the genetic background that were not apparent in the sound grain. Our findings offer valuable insights for barley breeders and maltsters seeking to understand and optimize the performance of gluten-free grains in malt products.
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Affiliation(s)
- Mahya Bahmani
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Utpal Bose
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Mitchell G. Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | | | | | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
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8
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Tuan PA, Nguyen TN, Toora PK, Ayele BT. Temporal and spatial transcriptional regulation of phytohormone metabolism during seed development in barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1242913. [PMID: 37780505 PMCID: PMC10539596 DOI: 10.3389/fpls.2023.1242913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Plant hormones play important roles in seed development; however, transcriptional regulation of their metabolism and levels of the respective bioactive forms during barley seed development is poorly understood. To this end, this study performed a comprehensive analysis of changes in the expression patterns phytohormone metabolism genes and levels of the respective bioactive forms in the embryo and endosperm tissues. Our study showed the presence of elevated levels of abscisic acid (ABA), bioactive forms of gibberellins (GAs), jasmonate (JA) and cytokinins (CKs), auxin and salicylic acid (SA) in the endosperm and embryo tissues at early stage of seed filling (SF). The levels of all hormones in both tissues, except that of ABA, decreased to low levels during SF. In contrast, embryonic ABA level increased during SF and peaked at physiological maturity (PM) while the endospermic ABA was maintained at a similar level observed during SF. Although its level decreased high amount of ABA was still present in the embryo during post-PM. We detected low levels of ABA in the endosperm and all the other hormones in both tissues during post-PM phase except the relatively higher levels of jasmonoyl-isoleucine and SA detected at late stage of post-PM. Our data also showed that spatiotemporal changes in the levels of plant hormones during barley seed development are mediated by the expression of specific genes involved in their respective metabolic pathways. These results indicate that seed development in barley is mediated by spatiotemporal modulation in the metabolism and levels of plant hormones.
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Affiliation(s)
| | | | | | - Belay T. Ayele
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
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9
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Yi K, Yue J, Yang S, Jiang Y, Hong L, Zeng H, Wei K, Mao P, Sun Y, Dou L, Li M. Germination of aged oat seeds associated with changes in antioxidant enzyme activity and storage compounds mobilization. PHYSIOLOGIA PLANTARUM 2023; 175:e14020. [PMID: 37882312 DOI: 10.1111/ppl.14020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 10/27/2023]
Abstract
Germination of aged seeds may be associated with specific metabolic changes. The objective of this study was to examine physiological and metabolic alterations before and after germination of control and aged oat (Avena sativa) seeds. The activity of antioxidant enzymes and the level of storage compounds were measured in the embryo and endosperm at 0, 4, 16, and 32 h of imbibition for control seeds and 0, 4, 16, 32, and 60 h of imbibition for medium vigor seeds after artificially accelerated aging; metabolomic changes were determined in embryos at 16 and 32 h of seed imbibition. In aged oat seeds, superoxide dismutase activity and catalase activity increased in the late imbibition stage. The content of soluble sugars decreased significantly in the later stages of imbibition, while the content of proteins increased in 32 h of seed imbibition eventually producing mannitol and proline. The mobilization of fat in deteriorated seeds was mainly through the sphingolipid metabolic pathway generated by cell growth-promoting dihydrosphingosine-1-phosphate. Ascorbic acid, avenanthramide and proline levels increased significantly at 60 h of imbibition, playing an important role in the germination of aged oat seeds.
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Affiliation(s)
- Kun Yi
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Jiaming Yue
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Shuangfeng Yang
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, Indiana, USA
| | - Liu Hong
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Hanguo Zeng
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Kai Wei
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Peisheng Mao
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yan Sun
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Liru Dou
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Manli Li
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
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10
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Peirats-Llobet M, Yi C, Liew L, Berkowitz O, Narsai R, Lewsey M, Whelan J. Spatially resolved transcriptomic analysis of the germinating barley grain. Nucleic Acids Res 2023; 51:7798-7819. [PMID: 37351575 PMCID: PMC10450182 DOI: 10.1093/nar/gkad521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/26/2023] [Accepted: 06/03/2023] [Indexed: 06/24/2023] Open
Abstract
Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.
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Affiliation(s)
- Marta Peirats-Llobet
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Changyu Yi
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Lim Chee Liew
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Reena Narsai
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
- Research Centre for Engineering Biology, College of Life Science, Zhejiang University, 718 East Haizhou Road, Haining, Jiaxing, Zhejiang 314400, China
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11
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Ouellette L, Anh Tuan P, Toora PK, Yamaguchi S, Ayele BT. Heterologous functional analysis and expression patterns of gibberellin 2-oxidase genes of barley (Hordeum vulgare L.). Gene 2023; 861:147255. [PMID: 36746354 DOI: 10.1016/j.gene.2023.147255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/20/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
The level of bioactive gibberellins (GAs) in plants is regulated partly by their inactivation, mainly by the action of GA 2-oxidases (GA2oxs). This study identified three new GA2ox genes in barley: HvGA2ox1, HvGA2ox3 and HvGA2ox6. Analysis of their nucleotide and putative amino acid sequences revealed that they share high sequence identity with other plant GA2oxs and their corresponding proteins. Phylogenetic analysis revealed the HvGA2ox1, HvGA2ox3 and HvGA2ox6 belong to GA2ox structural classes II, I, and III, respectively. Feeding the HvGA2ox1 and HvGA2ox3 recombinant proteins with the C19-GAs, GA1 and GA20, resulted in the production of GA8 and GA29, respectively, with no product detected when they were fed with the C20-GA, GA12. Whereas the HvGA2ox6 recombinant protein was able to convert GA12 to GA110, and no product was detected when it was fed with GA1 or GA20. HvGA2ox1 and HvGA2ox3 were highly expressed in internodes and the endosperm of maturing seeds while HvGA2ox6 was predominantly expressed in the embryos. Salinity stress upregulated the expression of all three genes in seedling tissues. Our results indicate that HvGA2ox1, HvGA2ox3 and HvGA2ox6 encode functional GA2oxs that can regulate GA levels, and therefore growth and development of a barley plant, and its interaction with environment.
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Affiliation(s)
- Luc Ouellette
- Department of Plant Science, 222 Agriculture Building, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Pham Anh Tuan
- Department of Plant Science, 222 Agriculture Building, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Parneet K Toora
- Department of Plant Science, 222 Agriculture Building, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Shinjiro Yamaguchi
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Belay T Ayele
- Department of Plant Science, 222 Agriculture Building, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada.
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12
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Hu S, Qin Q, Liu J, Yin H, Meng Q, Yu J, Huang S, Ma Z. The Correlations of Barley Vitality and Storage Reserve Mobilization during Early Germination. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2023. [DOI: 10.1080/03610470.2022.2161270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Shumin Hu
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Qingqing Qin
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Jia Liu
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Hua Yin
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Qingshang Meng
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Junhong Yu
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Shuxia Huang
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Zengxin Ma
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, China
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13
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Zhang J, Ma H, Liu Y. Analysis on characteristics of female gametophyte and functional identification of genes related to inflorescences development of Kentucky bluegrass. PROTOPLASMA 2022; 259:1061-1079. [PMID: 34743240 DOI: 10.1007/s00709-021-01720-3] [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: 09/25/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
The inflorescence is composed of spikes, and the spike is the carrier of grass seed formation and development, so the development status of inflorescence implies grass seed yield and quality. So far, the systematic analysis of inflorescence development of Kentucky bluegrass has not been reported. The development process of the female gametophyte of wild germplasm materials of Kentucky bluegrass in Gannan, Gansu Province of China (KB-GN), was observed. Based on this, the key developmental stages of inflorescence in KB-GN were divided into premeiosis (GPreM), meiosis (GM), postmeiosis (GPostM), and anthesis (GA), and four stages of inflorescence were selected to analyze the transcriptome expression profile. We found that its sexual reproduction formed a polygonum-type embryo sac. Transcriptome analysis showed that 4256, 1125, 1699, and 3127 genes were highly expressed in GPreM, GM, GPostM, and GA, respectively. And a large number of transcription factors (TFs) such as MADS-box, MYB and NAC, AP2, C2H2, FAR1, B3, bHLH, WRKY, and TCP were highly expressed throughout the inflorescence development stages. KEGG enrichment and MapMan analysis showed that genes involved in plant hormone metabolism were also highly expressed at the entire stages of inflorescence development. However, a few TFs belong to stage-specific genes, such as TRAF proteins with unknown function in plants was screened firstly, which was specifically and highly expressed in the GPreM, indicating that TRAF may regulate the preparatory events of meiosis or be essential for the development of megaspore mother cell (MMC). The expression patterns of 15 MADS-box genes were analyzed by qRT-PCR, and the expression results were consistent with that of the transcriptome. The study on the inflorescence development of KB-GN will be great significant works and contribution to illustrate the basic mechanism of grass seeds formation and development.
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Affiliation(s)
- Jinqing Zhang
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu, 730070, China
| | - Huiling Ma
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu, 730070, China.
| | - Yan Liu
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu, 730070, China
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14
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Badoni S, Parween S, Henry RJ, Sreenivasulu N. Systems seed biology to understand and manipulate rice grain quality and nutrition. Crit Rev Biotechnol 2022:1-18. [PMID: 35723584 DOI: 10.1080/07388551.2022.2058460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
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Affiliation(s)
- Saurabh Badoni
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Sabiha Parween
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Robert J Henry
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Nese Sreenivasulu
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
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15
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Li Y, Liang Y, Liu M, Zhang Q, Wang Z, Fan J, Ruan Y, Zhang A, Dong X, Yue J, Li C. Genome-Wide Association Studies Provide Insights Into the Genetic Architecture of Seed Germination Traits in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:930438. [PMID: 35755688 PMCID: PMC9226777 DOI: 10.3389/fpls.2022.930438] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/25/2022] [Indexed: 06/01/2023]
Abstract
Seed germination is an important agronomic trait that affects crop yield and quality. Rapid and uniform seed germination traits are required in agricultural production. Although several genes are involved in seed germination and have been identified in Arabidopsis and rice, the genetic basis governing seed germination in maize remains unknown. Herein, we conducted a genome-wide association study to determine the genetic architecture of two germination traits, germination speed, and consistency, in a diverse panel. We genotyped 321 maize inbred populations with tropical, subtropical, or temperate origins using 1219401 single-nucleotide polymorphism markers. We identified 58 variants that were associated with the two traits, and 12 of these were shared between the two traits, indicating partial genetic similarity. Moreover, 36 candidate genes were involved in seed germination with functions including energy metabolism, signal transduction, and transcriptional regulation. We found that favorable variants had a greater effect on the tropical subpopulation than on the temperate. Accumulation of favorable variants shortened germination time and improved uniformity in maize inbred lines. These findings contribute significantly to understanding the genetic basis of maize seed germination and will contribute to the molecular breeding of maize seed germination.
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Affiliation(s)
- Yuntong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yameng Liang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Meiling Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Qiyuan Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Ziwei Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Jinjuan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Ao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Jing Yue
- College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang, China
| | - Cong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
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16
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Dong X, Sun L, Agarwal M, Maker G, Han Y, Yu X, Ren Y. The Effect of Ozone Treatment on Metabolite Profile of Germinating Barley. Foods 2022; 11:foods11091211. [PMID: 35563933 PMCID: PMC9104593 DOI: 10.3390/foods11091211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 12/25/2022] Open
Abstract
Ozone is widely used to control pests in grain and impacts seed germination, a crucial stage in crop establishment which involves metabolic alterations. In this study, dormancy was overcome through after-ripening (AR) in dry barley seed storage of more than 4 weeks; alternatively, a 15-min ozone treatment could break the dormancy of barley immediately after harvest, with accelerated germination efficiency remaining around 96% until 4 weeks. Headspace solid-phase microextraction (HS-SPME) and liquid absorption coupled with gas chromatography mass spectrometry (GC-MS) were utilized for metabolite profiling of 2-, 4- and 7-day germinating seeds. Metabolic changes during barley germination are reflected by time-dependent characteristics. Alcohols, fatty acids, and ketones were major contributors to time-driven changes during germination. In addition, greater fatty acids were released at the early germination stage when subjected to ozone treatment.
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Affiliation(s)
- Xue Dong
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Litao Sun
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
| | - Manjree Agarwal
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
| | - Garth Maker
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
| | - Yitao Han
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
| | - Xiangyang Yu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
- Correspondence: (X.Y.); (Y.R.); Tel.: +86-25-8439-1299 (X.Y.); +618-9360-1397 (Y.R.)
| | - Yonglin Ren
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
- Correspondence: (X.Y.); (Y.R.); Tel.: +86-25-8439-1299 (X.Y.); +618-9360-1397 (Y.R.)
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17
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Zaaboul F, Liu Y. Vitamin E in foodstuff: Nutritional, analytical, and food technology aspects. Compr Rev Food Sci Food Saf 2022; 21:964-998. [PMID: 35181987 DOI: 10.1111/1541-4337.12924] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 11/21/2021] [Accepted: 01/10/2022] [Indexed: 12/16/2022]
Abstract
Vitamin E is a group of isoprenoid chromanols with different biological activities. It comprises eight oil-soluble compounds: four tocopherols, namely, α-, β-, γ-, and δ-tocopherols; and four tocotrienols, namely, α-, β-, γ, and δ-tocotrienols. Vitamin E isomers are well-known for their antioxidant activity, gene-regulation effects, and anti-inflammatory and nephroprotective properties. Considering that vitamin E is exclusively synthesized by photosynthetic organisms, animals can only acquire it through their diet. Plant-based food is the primary source of vitamin E; hence, oils, nuts, fruits, and vegetables with high contents of vitamin E are mostly consumed after processing, including industrial processes and home-cooking, which involve vitamin E profile and content alteration during their preparation. Accordingly, it is essential to identify the vitamin E content and profile in foodstuff to match daily intake requirements. This review summarizes recent advances in vitamin E chemistry, metabolism and metabolites, current knowledge on their contents and profiles in raw and processed plant foods, and finally, their modern developments in analytical methods.
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Affiliation(s)
- Farah Zaaboul
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic China
| | - YuanFa Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic China
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18
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Zhang Y, Xu S, Yue S, Zhang X, Qiao Y, Liu M, Zhou Y. Reciprocal Field Transplant Experiment and Comparative Transcriptome Analysis Provide Insights Into Differences in Seed Germination Time of Two Populations From Different Geographic Regions of Zostera marina L. FRONTIERS IN PLANT SCIENCE 2022; 12:793060. [PMID: 35116049 PMCID: PMC8804501 DOI: 10.3389/fpls.2021.793060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Seagrasses are the only submerged marine higher plants, which can colonize the sea through sexual (via seeds) reproduction. The transition between seed dormancy and germination is an important ecological trait and a key stage in the life cycle of higher plants. According to our observations, the seeds of Zostera marina L. (eelgrass) in Swan Lake (SL) and Qingdao Bay (QB) in northern China have the same maturation time (summer) but different germination time. To investigate this phenomenon, we further carried out reciprocal transplantation experiment and transcriptome analysis. Results revealed that differences in the seed germination time between the two sites do exist and are determined by internal molecular mechanisms as opposed to environmental factors. Furthermore, we conducted comparative transcriptome analysis of seeds at the mature and early germination stages in both locations. The results that the number of genes related to energy, hormone and cell changes was higher in SL than in QB, could account for that the dormancy depth of seeds in SL was deeper than that in QB; consequently, the seeds in SL needed to mobilize more related genes to break dormancy and start germination. The results could have important practical implications for seagrass meadow restoration via seeds and provide in-depth and comprehensive data for understanding the molecular mechanisms related to seagrass seed germination.
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Affiliation(s)
- Yu Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Shaochun Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Shidong Yue
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Xiaomei Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Yongliang Qiao
- Qingdao University of Science and Technology, Qingdao, China
| | - Mingjie Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Yi Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
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19
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Sweeney DW, Kunze KH, Sorrells ME. QTL x environment modeling of malting barley preharvest sprouting. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:217-232. [PMID: 34633474 DOI: 10.1007/s00122-021-03961-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
HvMKK3 alleles are temperature sensitive and are major contributors to environmental stability of preharvest sprouting in barley. Preharvest sprouting (PHS) can severely damage barley (Hordeum vulgare L.) malting quality, but PHS resistance is often negatively correlated with malting quality. Seed dormancy is closely related to PHS. Increased temperature during grain fill can decrease seed dormancy in barley, but genetic components of seed dormancy temperature sensitivity are poorly understood. Six years of PHS data were used to fit quantitative trait locus (QTL) x environment mixed models incorporating marker data from seed dormancy genes HvAlaAT1, HvGA20ox1, and HvMKK3 and weather covariates in spring and winter two-row malting barley. Variation in winter barley PHS was best modeled by average temperature range during grain fill and spring barley PHS by total precipitation during grain fill. Average high temperature during grain fill also accurately modeled PHS for both datasets. A highly non-dormant HvMKK3 allele determined baseline PHS susceptibility and HvAlaAT1 interactions with multiple HvMKK3 alleles conferred environmental sensitivity. Polygenic variation for PHS within haplotype was detected. Residual genotype and QTL by environment interaction variance indicated additional environmental and genetic factors involved in PHS. These models provide insight into genotype and environmental regulation of barley seed dormancy, a method for PHS forecasting, and a tool for breeders to improve PHS resistance.
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Affiliation(s)
- Daniel W Sweeney
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Karl H Kunze
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA.
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20
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Kan L, Liao Q, Chen Z, Wang S, Ma Y, Su Z, Zhang L. Dynamic Transcriptomic and Metabolomic Analyses of Madhuca pasquieri (Dubard) H. J. Lam During the Post-germination Stages. FRONTIERS IN PLANT SCIENCE 2021; 12:731203. [PMID: 34659296 PMCID: PMC8516028 DOI: 10.3389/fpls.2021.731203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/24/2021] [Indexed: 06/02/2023]
Abstract
The wild population of Madhuca pasquieri (Dubard) H. J. Lam is currently dwindling; its understory seedlings are rare, and there is a lack of molecular studies, which impedes the conservation of this species. This study exploited second-generation sequencing and widely targeted metabolomics analysis to uncover the dynamic changes in differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in five post-germination stages of M. pasquieri whole organism. Notably, the weighted gene co-expression network analysis (WGCNA), transcriptome, and metabolome association analyses all indicated significant enrichment of the flavonoid biosynthesis pathway in stage 4 (two-leaf), and an upregulation of the genes encoding flavonol biosynthesis in this stage. In stage 5 (nine-leaf), the flavonols were significantly accumulated, indicating that the changes in metabolites were driven at the transcript level. According to the significant changes in gene expression encoding auxin transport carriers and their correlation with flavonols during stage 5, the flavonols were speculated to have a direct inhibitory effect on the expression of PIN4 encoding gene, which may inhibit the process of polar auxin transport. The results provided important insights into the molecular network relationships between the transcription and metabolism of this rare and endangered species during the post-germination stages and explained the reasons for the slow growth of its seedlings at the molecular level.
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21
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Dermendjiev G, Schnurer M, Weiszmann J, Wilfinger S, Ott E, Gebert C, Weckwerth W, Ibl V. Tissue-Specific Proteome and Subcellular Microscopic Analyses Reveal the Effect of High Salt Concentration on Actin Cytoskeleton and Vacuolization in Aleurone Cells during Early Germination of Barley. Int J Mol Sci 2021; 22:ijms22179642. [PMID: 34502558 PMCID: PMC8431815 DOI: 10.3390/ijms22179642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 01/03/2023] Open
Abstract
Cereal grain germination provides the basis for crop production and requires a tissue-specific interplay between the embryo and endosperm during heterotrophic germination involving signalling, protein secretion, and nutrient uptake until autotrophic growth is possible. High salt concentrations in soil are one of the most severe constraints limiting the germination of crop plants, affecting the metabolism and redox status within the tissues of germinating seed. However, little is known about the effect of salt on seed storage protein mobilization, the endomembrane system, and protein trafficking within and between these tissues. Here, we used mass spectrometry analyses to investigate the protein dynamics of the embryo and endosperm of barley (Hordeum vulgare, L.) at five different early points during germination (0, 12, 24, 48, and 72 h after imbibition) in germinated grains subjected to salt stress. The expression of proteins in the embryo as well as in the endosperm was temporally regulated. Seed storage proteins (SSPs), peptidases, and starch-digesting enzymes were affected by salt. Additionally, microscopic analyses revealed an altered assembly of actin bundles and morphology of protein storage vacuoles (PSVs) in the aleurone layer. Our results suggest that besides the salt-induced protein expression, intracellular trafficking and actin cytoskeleton assembly are responsible for germination delay under salt stress conditions.
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Affiliation(s)
- Georgi Dermendjiev
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Madeleine Schnurer
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Jakob Weiszmann
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Sarah Wilfinger
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Emanuel Ott
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Claudia Gebert
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
- Vienna Metabolomics Center (VIME), University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
| | - Verena Ibl
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
- Correspondence:
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22
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Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins. Int J Mol Sci 2021; 22:ijms22158172. [PMID: 34360938 PMCID: PMC8347141 DOI: 10.3390/ijms22158172] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/22/2022] Open
Abstract
During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes in the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes in primary metabolites. Six metabolites in dry seeds known to be important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. Thermo-stable proteins were associated with a multitude of biological processes. In the heat-stable proteome, a relatively similar proportion of fully ordered and fully intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were found to be associated with functional categories development, protein, RNA and stress. As expected, the majority of LEA proteins decreased during germination and seedling establishment. However, four germination-specific dehydrins were identified, not present in dry seeds. A network analysis of proteins, metabolites and amino acids generated during the course of germination revealed a highly connected LEA protein network.
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Vinje MA, Henson CA, Duke SH, Simmons CH, Le K, Hall E, Hirsch CD. Description and functional analysis of the transcriptome from malting barley. Genomics 2021; 113:3310-3324. [PMID: 34273497 DOI: 10.1016/j.ygeno.2021.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022]
Abstract
The present study aimed to establish an early model of the malting barley transcriptome, which describes the expression of genes and their ontologies, identify the period during malting with the largest dynamic shift in gene expression for future investigation, and to determine the expression patterns of all starch degrading enzyme genes relevant to the malting and brewing industry. Large dynamic increases in gene expression occurred early in malting with differential expressed genes enriched for cell wall and starch hydrolases amongst many malting related categories. Twenty-five of forty starch degrading enzyme genes were differentially expressed in the malting barley transcriptome including eleven α-amylase genes, six β-amylase genes, three α-glucosidase genes, and all five starch debranching enzyme genes. Four new or novel α-amylase genes, one β-amylase gene (Bmy3), three α-glucosidase genes, and two isoamylase genes had appreciable expression that requires further exploration into their potential relevance to the malting and brewing industry.
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Affiliation(s)
- Marcus A Vinje
- USDA, Agricultural Research Service, Cereal Crops Research Unit, Madison, WI 53726, USA.
| | - Cynthia A Henson
- USDA, Agricultural Research Service, Cereal Crops Research Unit, Madison, WI 53726, USA; University of Wisconsin-Madison, Department of Agronomy, Madison, WI 53706, USA
| | - Stanley H Duke
- University of Wisconsin-Madison, Department of Agronomy, Madison, WI 53706, USA
| | - Carl H Simmons
- USDA, Agricultural Research Service, Cereal Crops Research Unit, Madison, WI 53726, USA
| | - Khoa Le
- University of Minnesota, Department of Plant Pathology, St. Paul, MN 55108, USA
| | - Evan Hall
- University of Minnesota, Department of Plant Pathology, St. Paul, MN 55108, USA
| | - Cory D Hirsch
- University of Minnesota, Department of Plant Pathology, St. Paul, MN 55108, USA
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24
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Bolortuya B, Kawabata S, Yamagami A, Davaapurev BO, Takahashi F, Inoue K, Kanatani A, Mochida K, Kumazawa M, Ifuku K, Jigjidsuren S, Battogtokh T, Udval G, Shinozaki K, Asami T, Batkhuu J, Nakano T. Transcriptome Analysis of Chloris virgata, Which Shows the Fastest Germination and Growth in the Major Mongolian Grassland Plant. FRONTIERS IN PLANT SCIENCE 2021; 12:684987. [PMID: 34262584 PMCID: PMC8275185 DOI: 10.3389/fpls.2021.684987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/26/2021] [Indexed: 06/13/2023]
Abstract
Plants in Mongolian grasslands are exposed to short, dry summers and long, cold winters. These plants should be prepared for fast germination and growth activity in response to the limited summer rainfall. The wild plant species adapted to the Mongolian grassland environment may allow us to explore useful genes, as a source of unique genetic codes for crop improvement. Here, we identified the Chloris virgata Dornogovi accession as the fastest germinating plant in major Mongolian grassland plants. It germinated just 5 h after treatment for germination initiation and showed rapid growth, especially in its early and young development stages. This indicates its high growth potential compared to grass crops such as rice and wheat. By assessing growth recovery after animal bite treatment (mimicked by cutting the leaves with scissors), we found that C. virgata could rapidly regenerate leaves after being damaged, suggesting high regeneration potential against grazing. To analyze the regulatory mechanism involved in the high growth potential of C. virgata, we performed RNA-seq-based transcriptome analysis and illustrated a comprehensive gene expression map of the species. Through de novo transcriptome assembly with the RNA-seq reads from whole organ samples of C. virgata at the germination stage (2 days after germination, DAG), early young development stage (8 DAG), young development stage (17 DAG), and adult development stage (28 DAG), we identified 21,589 unified transcripts (contigs) and found that 19,346 and 18,156 protein-coding transcripts were homologous to those in rice and Arabidopsis, respectively. The best-aligned sequences were annotated with gene ontology groups. When comparing the transcriptomes across developmental stages, we found an over-representation of genes involved in growth regulation in the early development stage in C. virgata. Plant development is tightly regulated by phytohormones such as brassinosteroids, gibberellic acid, abscisic acid, and strigolactones. Moreover, our transcriptome map demonstrated the expression profiles of orthologs involved in the biosynthesis of these phytohormones and their signaling networks. We discuss the possibility that C. virgata phytohormone signaling and biosynthesis genes regulate early germination and growth advantages. Comprehensive transcriptome information will provide a useful resource for gene discovery and facilitate a deeper understanding of the diversity of the regulatory systems that have evolved in C. virgata while adapting to severe environmental conditions.
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Affiliation(s)
- Byambajav Bolortuya
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | | | - Ayumi Yamagami
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Bekh-Ochir Davaapurev
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Asaka Kanatani
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Minoru Kumazawa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kentaro Ifuku
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Sodnomdarjaa Jigjidsuren
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Tugsjargal Battogtokh
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Gombosuren Udval
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Tadao Asami
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
| | - Javzan Batkhuu
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Takeshi Nakano
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
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25
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Huang X, Tian T, Chen J, Wang D, Tong B, Liu J. Transcriptome analysis of Cinnamomum migao seed germination in medicinal plants of Southwest China. BMC PLANT BIOLOGY 2021; 21:270. [PMID: 34116632 PMCID: PMC8194011 DOI: 10.1186/s12870-021-03020-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Cinnamomum migao is an endangered evergreen woody plant species endemic to China. Its fruit is used as a traditional medicine by the Miao nationality of China and has a high commercial value. However, its seed germination rate is extremely low under natural and artificial conditions. As the foundation of plant propagation, seed germination involves a series of physiological, cellular, and molecular changes; however, the molecular events and systematic changes occurring during C. migao seed germination remain unclear. RESULTS In this study, combined with the changes in physiological indexes and transcription levels, we revealed the regulation characteristics of cell structures, storage substances, and antioxidant capacity during seed germination. Electron microscopy analysis revealed that abundant smooth and full oil bodies were present in the cotyledons of the seeds. With seed germination, oil bodies and other substances gradually degraded to supply energy; this was consistent with the content of storage substances. In parallel to electron microscopy and physiological analyses, transcriptome analysis showed that 80-90 % of differentially expressed genes (DEGs) appeared after seed imbibition, reflecting important development and physiological changes. The unigenes involved in material metabolism (glycerolipid metabolism, fatty acid degradation, and starch and sucrose metabolism) and energy supply pathways (pentose phosphate pathway, glycolysis pathway, pyruvate metabolism, tricarboxylic acid cycle, and oxidative phosphorylation) were differentially expressed in the four germination stages. Among these DEGs, a small number of genes in the energy supply pathway at the initial stage of germination maintained high level of expression to maintain seed vigor and germination ability. Genes involved in lipid metabolism were firstly activated at a large scale in the LK (seed coat fissure) stage, and then genes involved in carbohydrates (CHO) metabolism were activated, which had their own species specificity. CONCLUSIONS Our study revealed the transcriptional levels of genes and the sequence of their corresponding metabolic pathways during seed germination. The changes in cell structure and physiological indexes also confirmed these events. Our findings provide a foundation for determining the molecular mechanisms underlying seed germination.
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Affiliation(s)
- Xiaolong Huang
- Department of Ecology, College of Forestry, Guizhou University, 550025, Guiyang, China
- Forest Ecology Research Center of Guizhou University, 550025, Guiyang, China
| | - Tian Tian
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, 550025, Guiyang, China
| | - Jingzhong Chen
- Department of Ecology, College of Forestry, Guizhou University, 550025, Guiyang, China
- Forest Ecology Research Center of Guizhou University, 550025, Guiyang, China
| | - Deng Wang
- Department of Ecology, College of Forestry, Guizhou University, 550025, Guiyang, China
- Forest Ecology Research Center of Guizhou University, 550025, Guiyang, China
| | - Bingli Tong
- Department of Ecology, College of Forestry, Guizhou University, 550025, Guiyang, China
- Forest Ecology Research Center of Guizhou University, 550025, Guiyang, China
| | - Jiming Liu
- Department of Ecology, College of Forestry, Guizhou University, 550025, Guiyang, China.
- Forest Ecology Research Center of Guizhou University, 550025, Guiyang, China.
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26
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Transcriptome and metabolome analyses revealing the potential mechanism of seed germination in Polygonatum cyrtonema. Sci Rep 2021; 11:12161. [PMID: 34108536 PMCID: PMC8190097 DOI: 10.1038/s41598-021-91598-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/27/2021] [Indexed: 12/02/2022] Open
Abstract
Polygonatum cyrtonema Hua (Huangjing, HJ) has medicinal and edible value in China. However, the seeds of this plant are naturally difficult to germinate. Therefore, to elucidate the mechanism underlying the germination of this plant in order to meet the market demand, the metabolomic and transcriptomic analyses were performed in this study. We observed that plant hormones and α-amylase activity were differentially regulated when comparing germinated and un-germinated seeds. In addition, the metabolites related to phenylpropanoid and flavonoid biosynthesis were significantly up-accumulated in germinated seeds. Hydroxycinnamoyl derivatives and organic acids were observed to be significantly decreased during germination. The results of this study suggested that compared to un-germinated seeds, germinated seeds promote flavonoid synthesis and inhibit lignin synthesis which could be beneficial to the germination of HJ seeds. Furthermore, these results suggested that starch if hydrolyzed into glucose, which could provide the necessary energy for germination. Our results may help to establish a foundation for further research investigating the regulatory networks of seed germination and may facilitate the propagation of HJ seeds.
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27
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Endopolyploidy Variation in Wild Barley Seeds across Environmental Gradients in Israel. Genes (Basel) 2021; 12:genes12050711. [PMID: 34068721 PMCID: PMC8151103 DOI: 10.3390/genes12050711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 12/21/2022] Open
Abstract
Wild barley is abundant, occupying large diversity of sites, ranging from the northern mesic Mediterranean meadows to the southern xeric deserts in Israel. This is also reflected in its wide phenotypic heterogeneity. We investigated the dynamics of DNA content changes in seed tissues in ten wild barley accessions that originated from an environmental gradient in Israel. The flow cytometric measurements were done from the time shortly after pollination up to the dry seeds. We show variation in mitotic cell cycle and endoreduplication dynamics in both diploid seed tissues (represented by seed maternal tissues and embryo) and in the triploid endosperm. We found that wild barley accessions collected at harsher xeric environmental conditions produce higher proportion of endoreduplicated nuclei in endosperm tissues. Also, a comparison of wild and cultivated barley strains revealed a higher endopolyploidy level in the endosperm of wild barley, that is accompanied by temporal changes in the timing of the major developmental phases. In summary, we present a new direction of research focusing on connecting spatiotemporal patterns of endoreduplication in barley seeds and possibly buffering for stress conditions.
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28
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Gomez-Sanchez A, Santamaria ME, Gonzalez-Melendi P, Muszynska A, Matthess C, Martinez M, Diaz I. Repression of barley cathepsins, HvPap-19 and HvPap-1, differentially alters grain composition and delays germination. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3474-3485. [PMID: 33454762 DOI: 10.1093/jxb/erab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
During barley germination, cysteine proteases are essential in the mobilization of storage compounds providing peptides and amino acids to sustain embryo growth until photosynthesis is completely established. Knockdown barley plants, generated by artificial miRNA, for the cathepsins B- and F-like HvPap-19 and HvPap-1 genes, respectively, showed less cysteine protease activities and consequently lower protein degradation. The functional redundancy between proteases triggered an enzymatic compensation associated with an increase in serine protease activities in both knockdown lines, which was not sufficient to maintain germination rates and behaviour. Concomitantly, these transgenic lines showed alterations in the accumulation of protein and carbohydrates in the grain. While the total amount of protein increased in both transgenic lines, the starch content decreased in HvPap-1 knockdown lines and the sucrose concentration was reduced in silenced HvPap-19 grains. Consequently, phenotypes of HvPap-1 and HvPap-19 artificial miRNA lines showed a delay in the grain germination process. These data demonstrate the potential of exploring the properties of barley proteases for selective modification and use in brewing or in the livestock feeding industry.
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Affiliation(s)
- Andrea Gomez-Sanchez
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid (UPM), Spain
| | - M Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid (UPM), Spain
| | - Pablo Gonzalez-Melendi
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid (UPM), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
| | - Aleksandra Muszynska
- Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse, Gatersleben, Germany
| | - Christiane Matthess
- Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse, Gatersleben, Germany
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid (UPM), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid (UPM), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
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29
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Tai L, Wang HJ, Xu XJ, Sun WH, Ju L, Liu WT, Li WQ, Sun J, Chen KM. Pre-harvest sprouting in cereals: genetic and biochemical mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2857-2876. [PMID: 33471899 DOI: 10.1093/jxb/erab024] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/18/2021] [Indexed: 05/22/2023]
Abstract
With the growth of the global population and the increasing frequency of natural disasters, crop yields must be steadily increased to enhance human adaptability to risks. Pre-harvest sprouting (PHS), a term mainly used to describe the phenomenon in which grains germinate on the mother plant directly before harvest, is a serious global problem for agricultural production. After domestication, the dormancy level of cultivated crops was generally lower than that of their wild ancestors. Although the shortened dormancy period likely improved the industrial performance of cereals such as wheat, barley, rice, and maize, the excessive germination rate has caused frequent PHS in areas with higher rainfall, resulting in great economic losses. Here, we systematically review the causes of PHS and its consequences, the major indicators and methods for PHS assessment, and emphasize the biological significance of PHS in crop production. Wheat quantitative trait loci functioning in the control of PHS are also comprehensively summarized in a meta-analysis. Finally, we use Arabidopsis as a model plant to develop more complete PHS regulatory networks for wheat. The integration of this information is conducive to the development of custom-made cultivated lines suitable for different demands and regions, and is of great significance for improving crop yields and economic benefits.
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Affiliation(s)
- Li Tai
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hong-Jin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiao-Jing Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wei-Hang Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lan Ju
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
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30
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Mohanty B. Promoter Architecture and Transcriptional Regulation of Genes Upregulated in Germination and Coleoptile Elongation of Diverse Rice Genotypes Tolerant to Submergence. Front Genet 2021; 12:639654. [PMID: 33796132 PMCID: PMC8008075 DOI: 10.3389/fgene.2021.639654] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/08/2021] [Indexed: 12/24/2022] Open
Abstract
Rice has the natural morphological adaptation to germinate and elongate its coleoptile under submerged flooding conditions. The phenotypic deviation associated with the tolerance to submergence at the germination stage could be due to natural variation. However, the molecular basis of this variation is still largely unknown. A comprehensive understanding of gene regulation of different genotypes that have diverse rates of coleoptile elongation can provide significant insights into improved rice varieties. To do so, publicly available transcriptome data of five rice genotypes, which have different lengths of coleoptile elongation under submergence tolerance, were analyzed. The aim was to identify the correlation between promoter architecture, associated with transcriptional and hormonal regulation, in diverse genotype groups of rice that have different rates of coleoptile elongation. This was achieved by identifying the putative cis-elements present in the promoter sequences of genes upregulated in each group of genotypes (tolerant, highly tolerant, and extremely tolerant genotypes). Promoter analysis identified transcription factors (TFs) that are common and unique to each group of genotypes. The candidate TFs that are common in all genotypes are MYB, bZIP, AP2/ERF, ARF, WRKY, ZnF, MADS-box, NAC, AS2, DOF, E2F, ARR-B, and HSF. However, the highly tolerant genotypes interestingly possess binding sites associated with HY5 (bZIP), GBF3, GBF4 and GBF5 (bZIP), DPBF-3 (bZIP), ABF2, ABI5, bHLH, and BES/BZR, in addition to the common TFs. Besides, the extremely tolerant genotypes possess binding sites associated with bHLH TFs such as BEE2, BIM1, BIM3, BM8 and BAM8, and ABF1, in addition to the TFs identified in the tolerant and highly tolerant genotypes. The transcriptional regulation of these TFs could be linked to phenotypic variation in coleoptile elongation in response to submergence tolerance. Moreover, the results indicate a cross-talk between the key TFs and phytohormones such as gibberellic acid, abscisic acid, ethylene, auxin, jasmonic acid, and brassinosteroids, for an altered transcriptional regulation leading to differences in germination and coleoptile elongation under submergence. The information derived from the current in silico analysis can potentially assist in developing new rice breeding targets for direct seeding.
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Affiliation(s)
- Bijayalaxmi Mohanty
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
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Bitarishvili SV, Bondarenko VS, Geras’kin SA. Expression of Gibberelline Biosynthesis and Catabolism Genes in the Embryos of γ-Irradiated Barley Seeds. BIOL BULL+ 2021. [DOI: 10.1134/s1062359020110059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhang G, Zhang G, Zeng X, Xu Q, Wang Y, Yuan H, Zhang Y, Nyima T. Quantitative Proteome Profiling Provides Insight into the Proteins Associated with β-Glucan Accumulation in Hull-less Barley Grains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:568-583. [PMID: 33371680 DOI: 10.1021/acs.jafc.0c05284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The hull-less barley (Qingke) is widely planted as a staple food crop in the Tibetan area, China, and the grains contains high content of β-glucan (BG). The mechanisms of BG synthesis and accumulation in qingke has not been studied at the protein level. This study characterized the proteins associated with BG synthesis and accumulation during qingke seed development. The proteome profiles of qingke seeds taken at 20, 30, and 40 days after flowering were compared using the TMT-based quantitative proteomics. A total of 4283 proteins were identified, with 759 being differentially expressed (DEPs) throughout seed development. Comparisons of protein expression pattern, functions, and pathway enrichment tests highlight cell wall modification, carbon and energy metabolism, polysaccharide metabolism, post-transcriptional modifications, and vesicular transport as critical biological processes related to qingke BG accumulation. Furthermore, induction of starch synthase, starch branching enzyme, pectin acetyl esterases, beta-glucosidases, beta-amylases, 1,4-beta-xylan, xyloglucan, α-amylase inhibitors, and glycosyltransferases underpinned BG synthesis. The results also indicated that the proteins involved in glycolytic, gluconeogenesis, and glyoxylate bypass pathways provided energy and reducing power for BG storage. Parallel reaction monitoring (PRM) and quantitative real-time PCR (qPCR) analyses confirmed the expression profile of the proteins obtained by TMT-based proteomics. The current results provided an insight into the mechanisms of BG synthesis and accumulation during qingke seed development.
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Affiliation(s)
- Guoqiang Zhang
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Guoping Zhang
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | - Xingquan Zeng
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Qijun Xu
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Yulin Wang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Hongjun Yuan
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Yuhong Zhang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Tashi Nyima
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
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Xie D, Yu Y, Dai Z, Sun J, Su J. Identification and characterization of miRNAs and target genes in developing flax seeds by multigroup analysis. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1903337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Dongwei Xie
- Department of Biotechnology, School of Life Science, Nantong University, Jiangsu, Nantong, PR China
| | - Yue Yu
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
| | - Zhigang Dai
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
| | - Jian Sun
- Department of Biotechnology, School of Life Science, Nantong University, Jiangsu, Nantong, PR China
| | - Jianguang Su
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
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Proteomics analysis of Cyclobalanopsis gilva provides new insights of low seed germination. Biochimie 2020; 180:68-78. [PMID: 33250447 DOI: 10.1016/j.biochi.2020.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 12/27/2022]
Abstract
A valuable plant, Cyclobalanopsis gilva, (C. gilva) has a low germination rate (below 50%) under its natural habitations. In order to examine the reasons for the low germination rate, the seeds of C. gilva (germinated and non-germinated) were evaluated using comparative proteomics analysis. A total of 3078 differentially abundant proteins (DAPs) were identified through a label-free method; most DAPs up-accumulated in germinated seeds were related to carbohydrates metabolism. Furthermore the proteins related to the signals, stress, and protein metabolism showed up-accumulation in germinated and no abundance or down-accumulation in non-germinated seeds. Enzyme activity of HK, PGK, PFK, and PK from glycolysis in SG-Control samples were 1.7-, 1.1-, 1.4-, and 1.3-times higher compared with those in control ones while CS, NAD-MDH, α-KGDH, and ICDH from the TCA cycle in SG-Control samples were 3, 1.1, 1.2, and 1.2 times higher than those in NG-Control ones. The β-amylase activity was 4-fold higher in successfully germinated seeds compared to non-germinated seeds. Interestingly, α-amylase did not show significant changes in protein abundance and enzyme activity among the three samples. The present findings reveal that unsuccessful germination of C. gilva seeds is due to lack of energy.
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Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana. Int J Mol Sci 2020; 21:ijms21197404. [PMID: 33036486 PMCID: PMC7584043 DOI: 10.3390/ijms21197404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 11/16/2022] Open
Abstract
Seed germination is a critical process for completion of the plant life cycle and for global food production. Comparing the germination transcriptomes of barley (Hordeum vulgare) to Arabidopsis thaliana revealed the overall pattern was conserved in terms of functional gene ontology; however, many oppositely responsive orthologous genes were identified. Conserved processes included a set of approximately 6000 genes that peaked early in germination and were enriched in processes associated with RNA metabolism, e.g., pentatricopeptide repeat (PPR)-containing proteins. Comparison of orthologous genes revealed more than 3000 orthogroups containing almost 4000 genes that displayed similar expression patterns including functions associated with mitochondrial tricarboxylic acid (TCA) cycle, carbohydrate and RNA/DNA metabolism, autophagy, protein modifications, and organellar function. Biochemical and proteomic analyses indicated mitochondrial biogenesis occurred early in germination, but detailed analyses revealed the timing involved in mitochondrial biogenesis may vary between species. More than 1800 orthogroups representing 2000 genes displayed opposite patterns in transcript abundance, representing functions of energy (carbohydrate) metabolism, photosynthesis, protein synthesis and degradation, and gene regulation. Differences in expression of basic-leucine zippers (bZIPs) and Apetala 2 (AP2)/ethylene-responsive element binding proteins (EREBPs) point to differences in regulatory processes at a high level, which provide opportunities to modify processes in order to enhance grain quality, germination, and storage as needed for different uses.
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Dolui AK, Vijayaraj P. Functional Omics Identifies Serine Hydrolases That Mobilize Storage Lipids during Rice Seed Germination. PLANT PHYSIOLOGY 2020; 184:693-708. [PMID: 32817194 PMCID: PMC7536657 DOI: 10.1104/pp.20.00268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/04/2020] [Indexed: 05/10/2023]
Abstract
Elucidating proteolipidome dynamics is crucial for understanding the roles of these molecules in plant physiology and disease. Sequence-based functional annotation of the protein is inadequate, since protein activities depend on posttranslational modification. In this study, we applied a gel-free activity-based protein profiling approach to unravel the active lipases, including other Serine hydrolases (SHs), expressed during seed germination in rice (Oryza sativa). We successfully mapped the active sites of 43 active SHs encompassing lipases/esterases, GDSL lipases, proteases, Ser carboxypeptidases, ABHD protein, pectin acetylesterase, and other SHs. The mRNA expression levels of those genes encoding the identified SHs were monitored using microarray analysis. The lipidome analysis revealed distinct patterns of molecular species distribution in individual lipid classes and displayed the metabolic connections between lipid mobilization and rice seedling growth. Changes in the mobilization of storage lipids and their molecular species remodeling were correlated with the expression of the identified lipases and their lipase activity in a time-dependent manner. The physiological significance of the identified SHs was explored during biotic stress with Fusarium verticillioides infection. The fungal infection significantly reduced lipase activity and lipid mobilization, thus impairing the rice seedling. Collectively, our data demonstrate application of the functional proteome strategy along with the shotgun lipidome approach for the identification of active SHs, and thus for deciphering the role of lipid homeostasis during rice seed germination.
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Affiliation(s)
- Achintya Kumar Dolui
- Lipid and Nutrition Laboratory, Department of Lipid Science, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore, Karnataka, 570020, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, Uttar Pradesh, India
| | - Panneerselvam Vijayaraj
- Lipid and Nutrition Laboratory, Department of Lipid Science, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore, Karnataka, 570020, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, Uttar Pradesh, India
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Wu TY, Müller M, Gruissem W, Bhullar NK. Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains. RICE (NEW YORK, N.Y.) 2020; 13:62. [PMID: 32894395 PMCID: PMC7477059 DOI: 10.1186/s12284-020-00421-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/20/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. MAIN TEXT Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development. CONCLUSION Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.
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Affiliation(s)
- Ting-Ying Wu
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Present address: Temasek Life Science Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Marlen Müller
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Present address: Roche Glycart AG, Wagistrasse 10, 8952, Schlieren, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Advanced Plant Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
| | - Navreet K Bhullar
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland.
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Yang J, Su L, Li D, Luo L, Sun K, Yang M, Gu F, Xia A, Liu Y, Wang H, Chen Z, Guo T. Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages. BMC Genomics 2020; 21:603. [PMID: 32867689 PMCID: PMC7460786 DOI: 10.1186/s12864-020-07024-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 08/25/2020] [Indexed: 11/10/2022] Open
Abstract
Background Seed germination and young seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice. Previous studies have focused on the identification of QTLs. However, there are few studies on the metabolome or transcriptome of germination and young seedling growth in rice. Results Here, an indica rice and a japonica rice were used as materials, and the transcripts and metabolites were detected during the germination and young seedling growth periods on a large scale by using RNA sequencing and a widely targeted metabolomics method, respectively. Fourteen shared transcripts and 15 shared metabolites that were continuously differentially expressed in the two materials were identified and may be essential for seed germination and young seedling growth. Enrichment analysis of differentially expressed genes in transcriptome expression profiles at different stages indicated that cell wall metabolism, lipid metabolism, nucleotide degradation, amino acid, etc., were enriched at 0–2 days, and most of the results are consistent with those of previous reports. Specifically, phenylpropanoid biosynthesis and glutathione metabolism were continuously enriched during the seed germination and young seedling growth stages. Next, KO enrichment analysis was conducted by using the differentially expressed genes of the two materials at 2, 3 and 4 days. Fourteen pathways were enriched. Additionally, 44 differentially expressed metabolites at 2, 3 and 4 days were identified. These metabolites may be responsible for the differences in germination and young seedling growth between the two materials. Further attention was focused on the ascorbate–glutathione pathway, and it was found that differences in ROS-scavenging abilities mediated by some APX, GPX and GST genes may be directly involved in mediating differences in the germination and young seedling growth speed of the two materials. Conclusions In summary, these results may enhance the understanding of the overall mechanism of seed germination and young seedling growth, and the outcome of this study is expected to facilitate rice breeding for direct seeding.
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Affiliation(s)
- Jing Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Ling Su
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Dandan Li
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Lixin Luo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Kai Sun
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Meng Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Fengwei Gu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Aoyun Xia
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
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Kim H, Kim OW, Ahn JH, Kim BM, Oh J, Kim HJ. Metabolomic Analysis of Germinated Brown Rice at Different Germination Stages. Foods 2020; 9:E1130. [PMID: 32824423 PMCID: PMC7491196 DOI: 10.3390/foods9081130] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022] Open
Abstract
Brown rice (BR) is unpolished rice containing many bioactive compounds in addition to the basic nutrients of the rice grain. Herein, BR was germinated for up to 48 h to prepare germinated brown rice (GBR). The physiological and chemical changes in the GBR during germination were analyzed. GBR samples germinated for 48 h were in the radicle-emergence stage, but root formation was not observed. The change in the GBR metabolite profile during germination was analyzed to determine the effect of germination on the chemical profiles of the GBR samples. Twenty-five metabolites including acidic compounds, amino acids, sugars, lipid metabolites, and secondary metabolites were identified as the components that contributed to the variations in the GBR groups germinated for different time periods. Among the metabolites, the carbohydrates associated with energy production and lipid metabolites changed significantly. Based on the identified metabolites, a metabolomic pathway was proposed. Carbohydrate metabolism, citric acid cycle, and lipid metabolism were the main processes that were affected during germination. Although further studies on the relationship between the metabolite profile and nutritional quality of the GBR are needed, these results are useful for understanding the effect of germination on the physiological and chemical changes in BR.
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Affiliation(s)
- Hoon Kim
- Korea Food Research Institute, Research Group of Consumer Safety, 245 Nongsaengmyeong-ro, Iseo-myeon, Wanju-Gun, Jeollabuk-do 55365, Korea; (H.K.); (O.-W.K.); (J.-H.A.)
| | - Oui-Woung Kim
- Korea Food Research Institute, Research Group of Consumer Safety, 245 Nongsaengmyeong-ro, Iseo-myeon, Wanju-Gun, Jeollabuk-do 55365, Korea; (H.K.); (O.-W.K.); (J.-H.A.)
| | - Jae-Hwan Ahn
- Korea Food Research Institute, Research Group of Consumer Safety, 245 Nongsaengmyeong-ro, Iseo-myeon, Wanju-Gun, Jeollabuk-do 55365, Korea; (H.K.); (O.-W.K.); (J.-H.A.)
| | - Bo-Min Kim
- EZmass.Co. Ltd., 501 Jinjudaero, Jinju, Gyeongsangnam-do 52828, Korea; (B.-M.K.); (J.O.)
| | - Juhong Oh
- EZmass.Co. Ltd., 501 Jinjudaero, Jinju, Gyeongsangnam-do 52828, Korea; (B.-M.K.); (J.O.)
| | - Hyun-Jin Kim
- EZmass.Co. Ltd., 501 Jinjudaero, Jinju, Gyeongsangnam-do 52828, Korea; (B.-M.K.); (J.O.)
- Division of Applied Life Sciences (BK21 plus), Department of Food Science and Technology, and Institute of Agriculture and Life Science, Gyeongsang National University, 501 Jinjudaero, Jinju, Gyeongsangnam-do 52828, Korea
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Ma JJ, Liu SW, Han FX, Li W, Li Y, Niu SH. Comparative transcriptome analyses reveal two distinct transcriptional modules associated with pollen shedding time in pine. BMC Genomics 2020; 21:504. [PMID: 32698817 PMCID: PMC7374968 DOI: 10.1186/s12864-020-06880-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/02/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Seasonal flowering time is an ecologically and economically important trait in temperate trees. Previous studies have shown that temperature in many tree species plays a pivotal role in regulating flowering time. However, genetic control of flowering time is not synchronised in different individual trees under comparable temperature conditions, the underlying molecular mechanism is mainly to be investigated. RESULTS In the present study, we analysed the transcript abundance in male cones and needles from six early pollen-shedding trees (EPs) and six neighbouring late pollen-shedding trees (LPs) in Pinus tabuliformis at three consecutive time points in early spring. We found that the EPs and LPs had distinct preferred transcriptional modules in their male cones and, interestingly, the expression pattern was also consistently maintained in needles even during the winter dormancy period. Additionally, the preferred pattern in EPs was also adopted by other fast-growing tissues, such as elongating new shoots. Enhancement of nucleic acid synthesis and stress resistance pathways under cold conditions can facilitate rapid growth and maintain higher transcriptional activity. CONCLUSIONS During the cold winter and early spring seasons, the EPs were more sensitive to relatively warmer temperatures and showed higher transcriptomic activity than the LPs, indicating that EPs required less heat accumulation for pollen shedding than LPs. These results provided a transcriptomic-wide understanding of the temporal regulation of pollen shedding in pines.
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Affiliation(s)
- Jing-Jing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Shuang-Wei Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Fang-Xu Han
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Wei Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Yue Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Shi-Hui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
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Sánchez-Camargo VA, Suárez-Espinoza C, Romero-Rodríguez S, Garza-Aguilar SM, Stam M, García-Ramírez E, Lara-Núñez A, Vázquez-Ramos JM. Maize E2F transcription factors. Expression, association to promoters of S-phase genes and interaction with the RBR1 protein in chromatin during seed germination. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 296:110491. [PMID: 32540010 DOI: 10.1016/j.plantsci.2020.110491] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
For seed germination, it is necessary to restart the cell cycle, a process regulated at multiple levels including transcriptional control, that is executed by the E2F family of transcription factors. We identified 12 genes of the E2F family in maize that are expressed differentially during the first 28 h post imbibition (HAI). E2Fa/b1;1 and E2Fc proteins were characterized as an activator and a putative repressor respectively, both forming heterodimers with DPb2 that bind differentially to consensus E2F response elements in promoters of E2F target genes. Transcripts of target genes for these transcription factors accumulate during germination; in dry seeds E2Fc protein is enriched in the target promoters and is replaced by E2Fa/b1;1 as germination advances. RBR1 is found in the same promoters in non-imbibed and 28 HAI seeds, when DNA replication has concluded, and transcription of the E2F targets should stop. During germination promoters of these target genes seem to be decorated with histone marks related to relaxed chromatin structure. Therefore, E2Fs appear to occupy their target genes in a context of open chromatin, with RBR1 fine tuning the progression between the phases.
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Affiliation(s)
- Víctor A Sánchez-Camargo
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Av. Universidad y Copilco, Ciudad de México 04510, Mexico
| | - Cassandra Suárez-Espinoza
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Av. Universidad y Copilco, Ciudad de México 04510, Mexico
| | - Samantha Romero-Rodríguez
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Av. Universidad y Copilco, Ciudad de México 04510, Mexico
| | - Sara M Garza-Aguilar
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Av. Universidad y Copilco, Ciudad de México 04510, Mexico
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Elpidio García-Ramírez
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Av. Universidad y Copilco, Ciudad de México 04510, Mexico
| | - Aurora Lara-Núñez
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Av. Universidad y Copilco, Ciudad de México 04510, Mexico
| | - Jorge M Vázquez-Ramos
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Av. Universidad y Copilco, Ciudad de México 04510, Mexico.
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Zafari S, Hebelstrup KH, Igamberdiev AU. Transcriptional and Metabolic Changes Associated with Phytoglobin Expression during Germination of Barley Seeds. Int J Mol Sci 2020; 21:ijms21082796. [PMID: 32316536 PMCID: PMC7215281 DOI: 10.3390/ijms21082796] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 12/17/2022] Open
Abstract
To understand how the class 1 phytoglobin is involved in germination process via the modulation of the nitric oxide (NO) metabolism, we performed the analysis of physiological and molecular parameters in the embryos of transgenic barley (Hordeum vulgare L. cv Golden Promise) plants differing in expression levels of the phytoglobin (Pgb1) gene during the first 48 h of germination. Overexpression of Pgb1 resulted in a higher rate of germination, higher protein content and higher ATP/ADP ratios. This was accompanied by a lower rate of NO emission after radicle protrusion, as compared to the wild type and downregulating line, and a lower rate of S-nitrosylation of proteins in the first hours postimbibition. The rate of fermentation estimated by the expression and activity of alcohol dehydrogenase was significantly higher in the Pgb1 downregulating line, the same tendency was observed for nitrate reductase expression. The genes encoding succinate dehydrogenase and pyruvate dehydrogenase complex subunits were more actively expressed in embryos of the seeds overexpressing Pgb1. It is concluded that Pgb1 expression in embryo is essential for the maintenance of redox and energy balance before radicle protrusion, when seeds experience low internal oxygen concentration and exerts the effect on metabolism during the initial development of seedlings.
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Affiliation(s)
- Somaieh Zafari
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada;
| | - Kim H. Hebelstrup
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, DK-4200 Slagelse, Denmark;
| | - Abir U. Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada;
- Correspondence:
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43
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Wang H, Guo X, Li Q, Lu Y, Huang W, Zhang F, Chen L, Liu RH, Yan S. Integrated Transcriptomic and Metabolic Framework for Carbon Metabolism and Plant Hormones Regulation in Vigna radiata during Post-Germination Seedling Growth. Sci Rep 2020; 10:3745. [PMID: 32111951 PMCID: PMC7048927 DOI: 10.1038/s41598-020-60771-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 02/17/2020] [Indexed: 11/09/2022] Open
Abstract
During mung bean post-germination seedling growth, various metabolic and physiological changes occurred, leading to the improvement of its nutritional values. Here, transcriptomic and metabolomic analyses of mung bean samples from 6-hour, 3-day and 6-day after imbibition (6-HAI, 3-DAI, and 6-DAI) were performed to characterize the regulatory mechanism of the primary metabolites during the post-germination seedling growth. From 6-HAI to 3-DAI, rapid changes in transcript level occurred, including starch and sucrose metabolism, glycolysis, citrate cycle, amino acids synthesis, and plant hormones regulation. Later changes in the metabolites, including carbohydrates and amino acids, appeared to be driven by increases in transcript levels. During this process, most amino acids and monosaccharides kept increasing, and accumulated in 6-day germinated sprouts. These processes were also accompanied with changes in hormones including abscisic acid, gibberellin, jasmonic acid, indole-3-acetic acid, etc. Overall, these results will provide insights into molecular mechanisms underlying the primary metabolic regulation in mung bean during post-germination seedling growth.
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Affiliation(s)
- Hong Wang
- School of Food Science and Engineering, Ministry of Education Engineering Research Centre of Starch & Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, 510640, China
| | - Xinbo Guo
- School of Food Science and Engineering, Ministry of Education Engineering Research Centre of Starch & Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, 510640, China.
| | - Quan Li
- School of Food Science and Engineering, Ministry of Education Engineering Research Centre of Starch & Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, 510640, China
| | - Yanyan Lu
- School of Food Science and Engineering, Ministry of Education Engineering Research Centre of Starch & Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, 510640, China
| | - Wenjie Huang
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Fangyuan Zhang
- School of Life Science, Southwest University, Chongqing, 400715, China
| | - Ling Chen
- School of Food Science and Engineering, Ministry of Education Engineering Research Centre of Starch & Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, 510640, China
| | - Rui Hai Liu
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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44
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Vinje MA, Duke SH, Henson CA. De novo Expression of β-amylase2 (Bmy2) in Barley Grains During Micromalting. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2020. [DOI: 10.1080/03610470.2019.1705104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Marcus A. Vinje
- Agricultural Research Service, Cereal Crops Research Unit, USDA, Madison, WI, U.S.A.
| | - Stanley H. Duke
- Department of Agronomy, University of Wisconsin- Madison, Madison, WI, U.S.A
| | - Cynthia A. Henson
- Agricultural Research Service, Cereal Crops Research Unit, USDA, Madison, WI, U.S.A.
- Department of Agronomy, University of Wisconsin- Madison, Madison, WI, U.S.A
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45
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Bai B, van der Horst S, Cordewener JHG, America TAHP, Hanson J, Bentsink L. Seed-Stored mRNAs that Are Specifically Associated to Monosomes Are Translationally Regulated during Germination. PLANT PHYSIOLOGY 2020; 182:378-392. [PMID: 31527088 PMCID: PMC6945870 DOI: 10.1104/pp.19.00644] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/01/2019] [Indexed: 05/20/2023]
Abstract
The life cycle of many organisms includes a quiescent stage, such as bacterial or fungal spores, insect larvae, or plant seeds. Common to these stages is their low water content and high survivability during harsh conditions. Upon rehydration, organisms need to reactivate metabolism and protein synthesis. Plant seeds contain many mRNAs that are transcribed during seed development. Translation of these mRNAs occurs during early seed germination, even before the requirement of transcription. Therefore, stored mRNAs are postulated to be important for germination. How these mRNAs are stored and protected during long-term storage is unknown. The aim of this study was to investigate how mRNAs are stored in dry seeds and whether they are indeed translated during seed germination. We investigated seed polysome profiles and the mRNAs and protein complexes that are associated with these ribosomes in seeds of the model organism Arabidopsis (Arabidopsis thaliana). We showed that most stored mRNAs are associated with monosomes in dry seeds; therefore, we focus on monosomes in this study. Seed ribosome complexes are associated with mRNA-binding proteins, stress granule, and P-body proteins, which suggests regulated packing of seed mRNAs. Interestingly, ∼17% of the mRNAs that are specifically associated with monosomes are translationally up-regulated during seed germination. These mRNAs are transcribed during seed maturation, suggesting a role for this developmental stage in determining the translational fate of mRNAs during early germination.
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Affiliation(s)
- Bing Bai
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Sjors van der Horst
- Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Jan H G Cordewener
- BU Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
- Centre for BioSystems Genomics, 6700 AB Wageningen, The Netherlands
- Netherlands Proteomics Centre, 3508 TB Utrecht, The Netherlands
| | - Twan A H P America
- BU Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
- Centre for BioSystems Genomics, 6700 AB Wageningen, The Netherlands
- Netherlands Proteomics Centre, 3508 TB Utrecht, The Netherlands
| | - Johannes Hanson
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Leónie Bentsink
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
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46
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Ju C, Kong D, Lee Y, Ge G, Song Y, Liu J, Kwak JM. Methionine synthase 1 provides methionine for activation of the GLR3.5 Ca2+ channel and regulation of germination in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:178-187. [PMID: 31563952 PMCID: PMC6913737 DOI: 10.1093/jxb/erz431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 09/11/2019] [Indexed: 05/09/2023]
Abstract
Seed germination is a developmental process regulated by numerous internal and external cues. Our previous studies have shown that calcium influx mediated by the Arabidopsis glutamate receptor homolog 3.5 (AtGLR3.5) modulates the expression of the ABSCISIC ACID INSENSITIVE 4 (ABI4) transcription factor during germination and that L-methionine (L-Met) activates AtGLR3.1/3.5 Ca2+ channels in guard cells. However, it is not known whether L-Met participates in regulation of germination and what cellular mechanism is responsible for Met production during germination. Here, we describe Arabidopsis methionine synthase 1 (AtMS1), which acts in the final step of Met biosynthesis, synthesizes the Met required for the activation of AtGLR3.5 Ca2+ channels whose expression is up-regulated during germination, leading to the regulation of seed germination. We show that exogenous L-Met promotes germination in an AtGRL3.5-dependent manner. We also demonstrate that L-Met directly regulates the AtGLR3.5-mediated increase in cytosolic Ca2+ level in seedlings. We provide pharmacological and genetic evidence that Met synthesized via AtMS1 acts upstream of the AtGLR3.5-mediated Ca2+ signal and regulates the expression of ABI4, a major regulator in the abscisic acid response in seeds. Overall, our results link AtMS1, L-Met, the AtGLR3.5 Ca2+ channel, Ca2+ signals, and ABI4, and shed light on the physiological role and molecular mechanism of L-Met in germination.
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Affiliation(s)
- Chuanli Ju
- College of Life Sciences, Capital Normal University, Beijing, China
- Correspondence: or
| | - Dongdong Kong
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Yuree Lee
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Gege Ge
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Yanan Song
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Jiawen Liu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - June M Kwak
- Department of New Biology, DGIST, Daegu, Republic of Korea
- Correspondence: or
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Han Z, Wang B, Tian L, Wang S, Zhang J, Guo S, Zhang H, Xu L, Chen Y. Comprehensive dynamic transcriptome analysis at two seed germination stages in maize (Zea mays L.). PHYSIOLOGIA PLANTARUM 2020; 168:205-217. [PMID: 30767243 DOI: 10.1111/ppl.12944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
Seed germination, as an integral stage of crop production, directly affects Zea mays (maize) yield and grain quality. However, the molecular mechanisms of seed germination remain unclear in maize. We performed comparative transcriptome analysis of two maize inbred lines, Yu82 and Yu537A, at two stages of seed germination. Expression profile analysis during seed germination revealed that a total of 3381 and 4560 differentially expressed genes (DEGs) were identified in Yu82 and Yu537A at the two stages. Transcription factors were detected from several families, such as the bZIP, ERF, WRKY, MYB and bHLH families, which indicated that these transcription factor families might be involved in driving seed germination in maize. Prominent DEGs were submitted for KEGG enrichment analysis, which included plant hormones, amino acid mechanism, nutrient reservoir, metabolic pathways and ribosome. Of these pathways, genes associated with plant hormones, especially gibberellins, abscisic acid and auxin may be important for early germination in Yu82. In addition, DEGs involved in amino acid mechanism showed significantly higher expression levels in Yu82 than in Yu537A, which indicated that energy supply from soluble sugars and amino acid metabolism may contribute to early germination in Yu82. This results provide novel insights into transcriptional changes and gene interactions in maize during seed germination.
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Affiliation(s)
- Zanping Han
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471003, China
| | - Bin Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471003, China
| | - Lei Tian
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shunxi Wang
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jun Zhang
- Henan Academy of Agricultural Science/Henan Provincial Key Laboratory of Maize Biology, Cereal Institute, Zhengzhou, 450002, China
| | - ShuLei Guo
- Henan Academy of Agricultural Science/Henan Provincial Key Laboratory of Maize Biology, Cereal Institute, Zhengzhou, 450002, China
| | - Hengchao Zhang
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471003, China
| | - Lengrui Xu
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471003, China
| | - Yanhui Chen
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
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48
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Qu C, Zhao H, Chen J, Zuo Z, Sun X, Huang J, Yang C, Zhang X, Zhang P, Quan X, Xu Z, Liu G. The transcriptional events and their relationship to physiological changes during poplar seed germination and post-germination. BMC Genomics 2019; 20:801. [PMID: 31684868 PMCID: PMC6829952 DOI: 10.1186/s12864-019-6180-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background Seed germination, the foundation of plant propagation, involves a series of changes at the molecular level. Poplar is a model woody plant, but the molecular events occurring during seed germination in this species are unclear. Results In this study, we investigated changes in gene transcriptional levels during different germination periods in poplar by high-throughput sequencing technology. Analysis of genes expressed at specific germination stages indicated that these genes are distributed in many metabolic pathways. Enrichment analysis of significantly differentially expressed genes based on hypergeometric testing revealed that multiple pathways, such as pathways related to glycolysis, lipid, amino acid, protein and ATP synthesis metabolism, changed significantly at the transcriptional level during seed germination. A comparison of ΣZ values uncovered a series of transcriptional changes in biological processes related to primary metabolism during poplar seed germination. Among these changes, genes related to CHO metabolism were the first to be activated, with subsequent expression of genes involved in lipid metabolism and then those associated with protein metabolism. The pattern of metabolomic and physiological index changes further verified the sequence of some biological events. Conclusions Our study revealed molecular events occurring at the transcriptional level during seed germination and determined their order. These events were further verified by patterns of changes of metabolites and physiological indexes. Our findings lay a foundation for the elucidation of the molecular mechanisms responsible for poplar seed germination.
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Affiliation(s)
- Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Hancheng Zhao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jinyuan Chen
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhuang Zuo
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xue Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jiahuan Huang
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Chengjun Yang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xiuli Zhang
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Peng Zhang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xiankui Quan
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China. .,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
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49
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Chen W, Chen R, Wang H, Li Y, Zhang Y, Li S. Tuning chromosomal gene expression in Escherichia coli by combining single-stranded oligonucleotides mediated recombination and kil counter selection system. J Biotechnol 2019; 307:63-68. [PMID: 31678458 DOI: 10.1016/j.jbiotec.2019.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/03/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
Abstract
Extensively modulating gene expression to achieve optimal flux is a critical step in metabolic engineering. Gene expression is usually modulated at the transcriptional level by controlling the strength of a promoter. However, this type of modulation is often hampered by its inability to fully sample the complete continuum of transcriptional control. In Escherichia coli, this limitation can be solved by constructing promoters with a wide range of strengths. In this study, a highly efficient method was developed to modulate a particular chromosomal gene of E. coli at a wide range of expression levels. This was achieved by combining highly efficient single-stranded oligonucleotide-mediated recombination and a stringent counter selection system kil. Using this strategy, a chromosomal library, with a range from 0.3% to 388% relative to the wild lac promoter, was easily obtained. The strength of our chromosomal promoter library was approximately 5-60 times wider in range than those of libraries reported before.
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Affiliation(s)
- Wei Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Ruyi Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Hui Wang
- School of Biological Medicine, Beijing City University, Beijing, 10084, China
| | - Yujuan Li
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yunyi Zhang
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Shanhu Li
- Beijing Institute of Biotechnology, Beijing 100850, China.
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50
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Kim DY, Hong MJ, Seo YW. Genome-wide transcript analysis of inflorescence development in wheat. Genome 2019; 62:623-633. [PMID: 31269405 DOI: 10.1139/gen-2018-0200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The process of inflorescence development is directly related to yield components that determine the final grain yield in most cereal crops. Here, microarray analysis was conducted for four different developmental stages of inflorescence to identify genes expressed specifically during inflorescence development. To select inflorescence-specific expressed genes, we conducted meta-analysis using 1245 Affymetrix GeneChip array sets obtained from various development stages, organs, and tissues of members of Poaceae. The early stage of inflorescence development was accompanied by a significant upregulation of a large number of cell differentiation genes, such as those associated with the cell cycle, cell division, DNA repair, and DNA synthesis. Moreover, key regulatory genes, including the MADS-box gene, KNOTTED-1-like homeobox genes, GROWTH-REGULATING FACTOR 1 gene, and the histone methyltransferase gene, were highly expressed in the early inflorescence development stage. In contrast, fewer genes were expressed in the later stage of inflorescence development, and played roles in hormone biosynthesis and meiosis-associated genes. Our work provides novel information regarding the gene regulatory network of cell division, key genes involved in the differentiation of inflorescence in wheat, and regulation mechanism of inflorescence development that are crucial stages for determining final grain number per spike and the yield potential of wheat.
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Affiliation(s)
- Dae Yeon Kim
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
| | - Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Yong Weon Seo
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
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