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Liberal Â, Fernandes Â, Ferreira ICFR, Vivar-Quintana AM, Barros L. Effect of different physical pre-treatments on physicochemical and techno-functional properties, and on the antinutritional factors of lentils (Lens culinaris spp). Food Chem 2024; 450:139293. [PMID: 38631207 DOI: 10.1016/j.foodchem.2024.139293] [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: 02/12/2024] [Revised: 04/05/2024] [Accepted: 04/07/2024] [Indexed: 04/19/2024]
Abstract
Lentils have a valuable physicochemical profile, which can be affected by the presence of antinutrients that may impair the benefits arising from their consumption. Different treatments can be used to reduce these undesirable compounds, although they can also affect the general composition and behaviour of the lentils. Thus, the effect of different processing methods on the physicochemical and techno-functional properties, as well as on the antinutritional factors of different lentil varieties was studied. Phytic acid was eliminated during germination, while tannins and trypsin inhibitors are mostly affected by cooking. Functional properties were also altered by processing, these being dependent on the concentration of different nutrients in lentils. All the studied treatments affected the physicochemical profile of lentils and their functional properties. Cooking and germination appear to be the most effective in reducing antinutritional factors and improving the physicochemical profile of the lentils, meeting the current nutritional demands of today's society.
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Affiliation(s)
- Ângela Liberal
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Ângela Fernandes
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal.
| | - Isabel C F R Ferreira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | | | - Lillian Barros
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
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Kc S, Nguyen KH, Nicholson V, Walgren A, Trent T, Gollub E, Ramero S, Holehouse AS, Sukenik S, Boothby TC. Disordered proteins interact with the chemical environment to tune their protective function during drying. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582506. [PMID: 38464187 PMCID: PMC10925285 DOI: 10.1101/2024.02.28.582506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The conformational ensemble and function of intrinsically disordered proteins (IDPs) are sensitive to their solution environment. The inherent malleability of disordered proteins combined with the exposure of their residues accounts for this sensitivity. One context in which IDPs play important roles that is concomitant with massive changes to the intracellular environment is during desiccation (extreme drying). The ability of organisms to survive desiccation has long been linked to the accumulation of high levels of cosolutes such as trehalose or sucrose as well as the enrichment of IDPs, such as late embryogenesis abundant (LEA) proteins or cytoplasmic abundant heat soluble (CAHS) proteins. Despite knowing that IDPs play important roles and are co-enriched alongside endogenous, species-specific cosolutes during desiccation, little is known mechanistically about how IDP-cosolute interactions influence desiccation tolerance. Here, we test the notion that the protective function of desiccation-related IDPs is enhanced through conformational changes induced by endogenous cosolutes. We find that desiccation-related IDPs derived from four different organisms spanning two LEA protein families and the CAHS protein family, synergize best with endogenous cosolutes during drying to promote desiccation protection. Yet the structural parameters of protective IDPs do not correlate with synergy for either CAHS or LEA proteins. We further demonstrate that for CAHS, but not LEA proteins, synergy is related to self-assembly and the formation of a gel. Our results suggest that functional synergy between IDPs and endogenous cosolutes is a convergent desiccation protection strategy seen among different IDP families and organisms, yet, the mechanisms underlying this synergy differ between IDP families.
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Khan A, Tian R, Bean SR, Yerka M, Jiao Y. Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in sorghum seeds. Commun Biol 2024; 7:841. [PMID: 38987396 PMCID: PMC11237005 DOI: 10.1038/s42003-024-06525-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Cereal seeds are vital for food, feed, and agricultural sustainability because they store and provide essential nutrients to human and animal food and feed systems. Unraveling molecular processes in seed development is crucial for enhancing cereal grain yield and quality. We analyze spatiotemporal transcriptome and metabolome profiles during sorghum seed development in the inbred line 'BTx623'. Morphological and molecular analyses identify the key stages of seed maturation, specifying starch biosynthesis onset at 5 days post-anthesis (dpa) and protein at 10 dpa. Transcriptome profiling from 1 to 25 dpa reveal dynamic gene expression pathways, shifting from cellular growth and embryo development (1-5 dpa) to cell division, fatty acid biosynthesis (5-25 dpa), and seed storage compounds synthesis in the endosperm (5-25 dpa). Network analysis identifies 361 and 207 hub genes linked to starch and protein synthesis in the endosperm, respectively, which will help breeders enhance sorghum grain quality. The availability of this data in the sorghum reference genome line establishes a baseline for future studies as new pangenomes emerge, which will consider copy number and presence-absence variation in functional food traits.
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Affiliation(s)
- Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Ran Tian
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Scott R Bean
- Grain Quality and Structure Research Unit, Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Melinda Yerka
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada-Reno, Reno, NV, 89557, USA
| | - Yinping Jiao
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
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Jiang H, Xie L, Gu Z, Mei H, Wang H, Zhang J, Wang M, Xu Y, Zhou C, Han L. MtPIN4 plays critical roles in amino acid biosynthesis and metabolism of seed in Medicago truncatula. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:689-704. [PMID: 38701004 DOI: 10.1111/tpj.16787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024]
Abstract
The regulation of seed development is critical for determining crop yield. Auxins are vital phytohormones that play roles in various aspects of plant growth and development. However, its role in amino acid biosynthesis and metabolism in seeds is not fully understood. In this study, we identified a mutant with small seeds through forward genetic screening in Medicago truncatula. The mutated gene encodes MtPIN4, an ortholog of PIN1. Using molecular approaches and integrative omics analyses, we discovered that auxin and amino acid content significantly decreased in mtpin4 seeds, highlighting the role of MtPIN4-mediated auxin distribution in amino acid biosynthesis and metabolism. Furthermore, genetic analysis revealed that the three orthologs of PIN1 have specific and overlapping functions in various developmental processes in M. truncatula. Our findings emphasize the significance of MtPIN4 in seed development and offer insights into the molecular mechanisms governing the regulation of seed size in crops. This knowledge could be applied to enhance crop quality by targeted manipulation of seed protein regulatory pathways.
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Affiliation(s)
- Hongjiao Jiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Lijun Xie
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Zhiqun Gu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Hongyao Mei
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Haohao Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Jing Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Minmin Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Yiteng Xu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
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Ashraf U, Anjum SA, Naseer S, Abbas A, Abrar M, Nawaz M, Luo K. Gamma amino butyric acid (GABA) application modulated the morpho-physiological and yield traits of fragrant rice under well-watered and drought conditions. BMC PLANT BIOLOGY 2024; 24:569. [PMID: 38886652 PMCID: PMC11184787 DOI: 10.1186/s12870-024-05272-5] [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: 03/12/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Changing climate is causing erratic rainfall and prolonged drought periods, thus posing serious threats to crop productivity. Owing to severity of drought events, it is imperative to take proactive measures to enhance the resilience of drought sensitive crops like rice. Therefore, the present study was carried out to improve the drought stress tolerance in rice through gamma amino butyric acid (GABA) application. METHODS The experiment was included four GABA concentrations i.e., 0 mM as control, 1 mM, 1.5 mM, and 2 mM, two water levels i.e., 100% and 50% field capacity (referred as FC100 for well-watered and FC50 for drought conditions, respectively), and two fragrant rice cultivars i.e., Super Basmati and Basmati-515. RESULTS The findings unveiled a comprehensive improvement in various parameters with GABA application in fragrant rice under both well-watered (FC100) and water-limited (FC50) conditions, compared to the control. Specifically, GABA induced enhancements were observed in plant height, root length, fresh weight, dry weight, total soluble protein content, and total free amino acid content across both cultivars. Moreover, GABA application significantly improved peroxidase (POD) and catalase (CAT) enzyme activities, alongside elevating anthocyanin levels, while concurrently reducing H2O2 contents in both FC100 and FC50 treatments. Furthermore, the positive impact of GABA extended to morphological traits, with notable increases in panicle length, total tillers and productive tillers per hill, branch and grain numbers per panicle, and 1000-grain weight for Super Basmati and Basmati 515 cultivars under both water regimes, compared to Ck. Similarly, the grain yield increased by 31.01% and 27.32% under FC100 and 36.85% and 27.71% under FC50 in Super Basmati and Basmati-515, respectively, in response to GABA application, compared to Ck. Additionally, principal component analysis (PCA) revealed significant variances attributed to Dim1 and Dim2, with 86.1% and 4.0% of the variance, respectively, across three bi-plots encompassing rice cultivars, water levels, and GABA treatments. Notably, all tested indices, except for H2O2 and non-productive tillers per hill, exhibited positive correlations amongst themselves and with rice yield, further emphasizing the beneficial effects of GABA application on fragrant rice under well-watered and drought conditions. CONCLUSIONS GABA significantly improved fragrant rice performance under both well-watered (FC100) and water-limited (FC50) conditions. Moreover, integrating GABA application into rice cultivation practices could not only improve the crop resilience to drought stress but also potentially benefiting the future food and nutritional security globally. However, however; further research is needed to understand the cellular and molecular mechanisms of the functionality of GABA in fragrant rice, particularly under drought conditions.
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Affiliation(s)
- Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Punjab, 54770, Pakistan.
| | - Shakeel Ahmad Anjum
- Department of Agronomy, University of Agriculture, Faisalabad, Punjab, 38040, Pakistan
| | - Sidra Naseer
- Department of Botany, Faculty of Sciences, University of Agriculture, Faisalabad, Punjab, 38040, Pakistan
| | - Anees Abbas
- Department of Agronomy, University of Agriculture, Faisalabad, Punjab, 38040, Pakistan
| | - Muhammad Abrar
- State Key Laboratory of Grassland Agroecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mohsin Nawaz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Kebo Luo
- Jieyang Research Institute of Agricultural Sciences, Jieyang, China.
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Punia A, Kumari M, Chouhan M, Saini V, Joshi R, Kumar A, Kumar R. Proteomic and metabolomic insights into seed germination of Ferula assa-foetida. J Proteomics 2024; 300:105176. [PMID: 38604334 DOI: 10.1016/j.jprot.2024.105176] [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: 12/14/2023] [Revised: 03/01/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Cold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in Ferula assa-foetida remains ambiguous. Here, we used cold stratification (4 °C in the dark) to induce germination in F. assa-foetida and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated F. assa-foetida seed. Results highlight the common and unique regulatory mechanisms like signaling cascade, reactivation of energy metabolism, activation of ROS scavenging system, DNA repair, gene expression cascade, cytoskeleton, and cell wall modulation in F. assa-foetida germination. A protein-protein interaction network identifies 18 hub protein species central to the interactome and could be a key player in F. assa-foetida germination. Further, the predominant metabolic pathways like glucosinolate biosynthesis, arginine and proline metabolism, cysteine and methionine metabolism, aminoacyl-tRNA biosynthesis, and carotenoid biosynthesis in germinating seed may indicate the regulation of carbon and nitrogen metabolism is prime essential to maintain the physiology of germinating seedlings. The findings of this study provide a better understanding of cold stratification-induced seed germination, which might be utilized for genetic modification and traditional breeding of Ferula assa-foetida. SIGNIFICANCE: Seed germination is the fundamental checkpoint for plant growth and development, which has ecological significance. Ferula assa-foetida L., commonly known as "asafoetida," is a medicinal and food crop with huge therapeutic potential. To date, our understanding of F. assa-foetida seed germination is rudimentary. Therefore, studying the molecular mechanism that governs dormancy decay and the onset of germination in F. assa-foetida is essential for understanding the basic principle of seed germination, which could offer to improve genetic modification and traditional breeding.
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Affiliation(s)
- Ashwani Punia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Manglesh Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Monika Chouhan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishal Saini
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Robin Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashok Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India
| | - Rajiv Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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7
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Billah M, Renju L, Wei H, Qanmber G, Da Y, Lan Y, Qing-di Y, Fuguang L, Zhaoen Y. A cotton mitochondrial alternative electron transporter, GhD2HGDH, induces early flowering by modulating GA and photoperiodic pathways. PHYSIOLOGIA PLANTARUM 2024; 176:e14378. [PMID: 38887925 DOI: 10.1111/ppl.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 06/20/2024]
Abstract
D-2-hydroxyglutarate dehydrogenase (D2HGDH) is a mitochondrial enzyme containing flavin adenine dinucleotide FAD, existing as a dimer, and it facilitates the specific oxidation of D-2HG to 2-oxoglutarate (2-OG), which is a key intermediate in the tricarboxylic acid (TCA) cycle. A Genome-wide expression analysis (GWEA) has indicated an association between GhD2HGDH and flowering time. To further explore the role of GhD2HGDH, we performed a comprehensive investigation encompassing phenotyping, physiology, metabolomics, and transcriptomics in Arabidopsis thaliana plants overexpressing GhD2HGDH. Transcriptomic and qRT-PCR data exhibited heightened expression of GhD2HGDH in upland cotton flowers. Additionally, early-maturing cotton exhibited higher expression of GhD2HGDH across all tissues than delayed-maturing cotton. Subcellular localization confirmed its presence in the mitochondria. Overexpression of GhD2HGDH in Arabidopsis resulted in early flowering. Using virus-induced gene silencing (VIGS), we investigated the impact of GhD2HGDH on flowering in both early- and delayed-maturing cotton plants. Manipulation of GhD2HGDH expression levels led to changes in photosynthetic pigment and gas exchange attributes. GhD2HGDH responded to gibberellin (GA3) hormone treatment, influencing the expression of GA biosynthesis genes and repressing DELLA genes. Protein interaction studies, including yeast two-hybrid, luciferase complementation (LUC), and GST pull-down assays, confirmed the interaction between GhD2HGDH and GhSOX (Sulfite oxidase). The metabolomics analysis demonstrated GhD2HGDH's modulation of the TCA cycle through alterations in various metabolite levels. Transcriptome data revealed that GhD2HGDH overexpression triggers early flowering by modulating the GA3 and photoperiodic pathways of the flowering core factor genes. Taken together, GhD2HGDH positively regulates the network of genes associated with early flowering pathways.
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Affiliation(s)
- Masum Billah
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Liu Renju
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Hu Wei
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ghulam Qanmber
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Da
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Lan
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Yan Qing-di
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Li Fuguang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Zhaoen
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
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Gonçalves JDP, Gasparini K, Picoli EADT, Costa MDBL, Araujo WL, Zsögön A, Ribeiro DM. Metabolic control of seed germination in legumes. JOURNAL OF PLANT PHYSIOLOGY 2024; 295:154206. [PMID: 38452650 DOI: 10.1016/j.jplph.2024.154206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Seed development, dormancy, and germination are connected with changes in metabolite levels. Not surprisingly, a complex regulatory network modulates biosynthesis and accumulation of storage products. Seed development has been studied profusely in Arabidopsis thaliana and has provided valuable insights into the genetic control of embryo development. However, not every inference applies to crop legumes, as these have been domesticated and selected for high seed yield and specific metabolic profiles and fluxes. Given its enormous economic relevance, considerable work has contributed to shed light on the mechanisms that control legume seed growth and germination. Here, we summarize recent progress in the understanding of regulatory networks that coordinate seed metabolism and development in legumes.
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Affiliation(s)
- Júlia de Paiva Gonçalves
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil; National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| | - Karla Gasparini
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil; National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| | | | | | - Wagner Luiz Araujo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil; National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil; National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| | - Dimas Mendes Ribeiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil; National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
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9
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Tremblay BJM, Santini CP, Cheng Y, Zhang X, Rosa S, Qüesta JI. Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition. Nat Commun 2024; 15:1724. [PMID: 38409232 PMCID: PMC10897432 DOI: 10.1038/s41467-024-46082-5] [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: 07/21/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.
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Affiliation(s)
- Benjamin J M Tremblay
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Cristina P Santini
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Yajiao Cheng
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Xue Zhang
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Julia I Qüesta
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain.
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10
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Cao D, Ma Y, Cao Z, Hu S, Li Z, Li Y, Wang K, Wang X, Wang J, Zhao K, Zhao K, Qiu D, Li Z, Ren R, Ma X, Zhang X, Gong F, Jung MY, Yin D. Coordinated Lipid Mobilization during Seed Development and Germination in Peanut ( Arachis hypogaea L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3218-3230. [PMID: 38157443 PMCID: PMC10870768 DOI: 10.1021/acs.jafc.3c06697] [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: 09/17/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
Peanut (Arachis hypogaea L.) is one of the most important oil crops in the world due to its lipid-rich seeds. Lipid accumulation and degradation play crucial roles in peanut seed maturation and seedling establishment, respectively. Here, we utilized lipidomics and transcriptomics to comprehensively identify lipids and the associated functional genes that are important in the development and germination processes of a large-seed peanut variety. A total of 332 lipids were identified; triacylglycerols (TAGs) and diacylglycerols were the most abundant during seed maturation, constituting 70.43 and 16.11%, respectively, of the total lipids. Significant alterations in lipid profiles were observed throughout seed maturation and germination. Notably, TAG (18:1/18:1/18:2) and (18:1/18:2/18:2) peaked at 23386.63 and 23392.43 nmol/g, respectively, at the final stage of seed development. Levels of hydroxylated TAGs (HO-TAGs) increased significantly during the initial stage of germination. Accumulation patterns revealed an inverse relationship between free fatty acids and TAGs. Lipid degradation was determined to be regulated by diacylglycerol acyltransferase, triacylglycerol lipase, and associated transcription factors, predominantly yielding oleic acid, linoleic acid, and linolenic acid. Collectively, the results of this study provide valuable insights into lipid dynamics during the development and germination of large-seed peanuts, gene resources, and guiding future research into lipid accumulation in an economically important crop.
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Affiliation(s)
- Di Cao
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Yongzhe Ma
- College
of Food Science, Woosuk University, Samrea-Up, Wanju-Kun, Jeonbuk Province 55338, Republic of Korea
| | - Zenghui Cao
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Sasa Hu
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Zhan Li
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Yanzhe Li
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Kuopeng Wang
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Xiaoxuan Wang
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Jinzhi Wang
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Kunkun Zhao
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Kai Zhao
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Ding Qiu
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Zhongfeng Li
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Rui Ren
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Xingli Ma
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Xingguo Zhang
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Fangping Gong
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
| | - Mun Yhung Jung
- College
of Food Science, Woosuk University, Samrea-Up, Wanju-Kun, Jeonbuk Province 55338, Republic of Korea
| | - Dongmei Yin
- College
of Agronomy & Peanut Functional Genome and Molecular Breeding
Engineering, Henan Agricultural University, Zhengzhou 450000, People’s Republic of China
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11
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Fuenzalida M, Gómez MI, Ferrada E, Díaz C, Escudero V, González-Guerrero M, Jordana X, Roschzttardtz H. Using an embryo specific promoter to modify iron distribution pattern in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111931. [PMID: 38030036 DOI: 10.1016/j.plantsci.2023.111931] [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: 09/25/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
Iron is an essential micronutrient for life. During the development of the seed, iron accumulates during embryo maturation. In Arabidopsis thaliana, iron mainly accumulates in the vacuoles of only one cell type, the cell layer that surrounds provasculature in hypocotyl and cotyledons. Iron accumulation pattern in Arabidopsis is an exception in plant phylogeny, most part of the dicot embryos accumulate iron in several cell layers including cortex and, in some cases, even in protodermis. It remains unknown how does iron reach the internal cell layers of the embryo, and in particular, the molecular mechanisms responsible of this process. Here, we use transgenic approaches to modify the iron accumulation pattern in an Arabidopsis model. Using the SDH2-3 embryo-specific promoter, we were able to express VIT1 ectopically in both a wild type background and a mutant vit1 background lacking expression of this vacuolar iron transporter. These manipulations modify the iron distribution pattern in Arabidopsis from one cell layer to several cell layers, including protodermis, cortex cells, and the endodermis. Interestingly, total seed iron content was not modified compared with the wild type, suggesting that iron distribution in embryos is not involved in the control of the total iron amount accumulated in seeds. This experimental model can be used to study the processes involved in iron distribution patterning during embryo maturation and its evolution in dicot plants.
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Affiliation(s)
- Marlene Fuenzalida
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Chile
| | - María Isabel Gómez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Chile
| | - Evandro Ferrada
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Cristóbal Díaz
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Chile
| | - Viviana Escudero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid, Spain
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid, Spain; Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Spain
| | - Xavier Jordana
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Chile
| | - Hannetz Roschzttardtz
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Chile.
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12
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Meitzel T. Good things come to those who wait - a 42-year study challenges 'trade-off' theories. THE NEW PHYTOLOGIST 2024; 241:521-522. [PMID: 37915141 DOI: 10.1111/nph.19350] [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] [Indexed: 11/03/2023]
Abstract
This article is a Commentary on Chen et al. (2024), 241: 623–631.
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Affiliation(s)
- Tobias Meitzel
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Stadt Seeland OT Gatersleben, 06466, Germany
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE, 33883, Villenave d'Ornon, France
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13
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Wang L, Zhu Y, Jiang J, Tan G, Ma Q, Zhang H. Dynamic changes in the levels of metabolites and endogenous hormones during the germination of Zanthoxylum nitidum (Roxb.) DC. Seeds. PLANT SIGNALING & BEHAVIOR 2023; 18:2251750. [PMID: 37639213 PMCID: PMC10464536 DOI: 10.1080/15592324.2023.2251750] [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: 07/14/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023]
Abstract
Accumulating experimental data have shown that endogenous hormones play important roles in regulating seed dormancy and germination. Zanthoxylum nitidum is a medicinal plant that propagates via seeds, which require a long dormancy period for normal germination, and complex changes in metabolites occur during the germination process. However, the regulatory network of endogenous hormones and metabolites during the germination of Z. nitidum seeds remains unclear. This study investigated the dynamic changes in the levels of metabolites and endogenous hormones during the germination of Z. nitidum seeds. The results revealed an increase in the levels of gibberellin 3 (GA3), 12-oxophytodienoic acid (OPDA), 1-aminocyclopropane-1-carboxylic acid (ACC) and trans-zeatin (TZ) and decrease in the levels of abscisic acid (ABA), jasmonic acid (JA), N-[(-)-jasmonoyl]-(S)-isoleucine (JA-Ile) and trans-zeatin riboside (TZR). Overall, 112 differential metabolites (DAMs) were screened from 3 seed samples (Sa, Sb and Sc), most of which are related to primary metabolism. A total of 16 DAMs (including 3 monosaccharides, 3 phosphate lipids, 3 carboxylic acids, 1 amino acid, 2 pyrimidines, and 4 nucleotides) were identified in the three sample comparison pairs (Sa vs Sb, Sa vs Sc, and Sb vs Sc); these DAMs were significantly enriched in purine metabolism; glycerophospholipid metabolism, citrate cycle (TCA cycle), alanine, aspartate and glutamate metabolism and pyruvate metabolism. OPDA, ACC and GAs were significantly positively correlated with upregulated metabolites, whereas ABA and JA were significantly positively correlated with downregulated metabolites. Finally, a hypothetical metabolic network of endogenous hormones that regulate seed germination was constructed. This study deepens our understanding of the importance of endogenous hormonal profiles that mediate seed germination.
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Affiliation(s)
- Liang Wang
- Research and Development Center, China Resources Sanjiu Medical & Pharmaceutical CO., LTD., Shenzhen, China
| | - Yanxia Zhu
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Key Laboratory for High-quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Jianping Jiang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Key Laboratory for High-quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guiyu Tan
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Key Laboratory for High-quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Qing Ma
- Research and Development Center, China Resources Sanjiu Medical & Pharmaceutical CO., LTD., Shenzhen, China
| | - Hongsheng Zhang
- Research and Development Center, China Resources Sanjiu Medical & Pharmaceutical CO., LTD., Shenzhen, China
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14
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Sun Y, Zhang F, Wei J, Song K, Sun L, Yang Y, Qin Q, Yang S, Li Z, Xu G, Sun S, Xue Y. Phosphate Transporter OsPT4, Ubiquitinated by E3 Ligase OsAIRP2, Plays a Crucial Role in Phosphorus and Nitrogen Translocation and Consumption in Germinating Seed. RICE (NEW YORK, N.Y.) 2023; 16:54. [PMID: 38052756 PMCID: PMC10697913 DOI: 10.1186/s12284-023-00666-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023]
Abstract
Phosphorus (P) and nitrogen (N) are essential macronutrients necessary for plant growth and development. OsPT4 is a high-affinity phosphate (Pi) transporter that has a positive impact on nutrient uptake and seed development. In this study, the expression patterns of different Pi transporter genes in germinating seeds were determined, and the relative expression of OsPT4 was induced in Pi-deficient seeds and gradually increased with the passage of germination time. The analysis of P, N, Pi, and amino acid concentrations in germinating seeds of OsPT4 mutants showed that the OsPT4 mutation caused P and N retention and a continuous reduction in multiple amino acid concentrations in germinating seeds. Transcriptome analysis and qRT-PCR results also indicated that the OsPT4 mutation inhibits the expression of genes related to P and N transportation and amino acid synthesis in germinating seeds. In addition, the paraffin section and TUNEL assay of OsPT4 mutant germinating seeds suggests that OsPT4 mutation causes programmed cell death (PCD) delayed in the aleurone layer and inhibition of leaf outgrowth. Moreover, we also found that OsPT4 was ubiquitinated by OsAIRP2, which is a C3HC4-type RING E3 Ub ligase. Our studies illustrate that OsPT4 plays a crucial role in P and N collaborative translocation and consumption in germinating seeds. It also provides a theoretical basis for the molecules and physiological mechanisms of P and N cross-talk under suppressed Pi uptake conditions.
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Affiliation(s)
- Yafei Sun
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Fang Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jia Wei
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Ke Song
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Lijuan Sun
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Yang Yang
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Qin Qin
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Shiyan Yang
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Zhouwen Li
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yong Xue
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.
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15
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Caldana C, Carrari F, Fernie AR, Sampathkumar A. How metabolism and development are intertwined in space and time. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:347-359. [PMID: 37433681 DOI: 10.1111/tpj.16391] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
Developmental transitions, occurring throughout the life cycle of plants, require precise regulation of metabolic processes to generate the energy and resources necessary for the committed growth processes. In parallel, the establishment of new cells, tissues, and even organs, alongside their differentiation provoke profound changes in metabolism. It is increasingly being recognized that there is a certain degree of feedback regulation between the components and products of metabolic pathways and developmental regulators. The generation of large-scale metabolomics datasets during developmental transitions, in combination with molecular genetic approaches has helped to further our knowledge on the functional importance of metabolic regulation of development. In this perspective article, we provide insights into studies that elucidate interactions between metabolism and development at the temporal and spatial scales. We additionally discuss how this influences cell growth-related processes. We also highlight how metabolic intermediates function as signaling molecules to direct plant development in response to changing internal and external conditions.
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Affiliation(s)
- Camila Caldana
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Fernando Carrari
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arun Sampathkumar
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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16
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Dace HJ, Adetunji AE, Moore JP, Farrant JM, Hilhorst HW. A review of the role of metabolites in vegetative desiccation tolerance of angiosperms. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102410. [PMID: 37413962 DOI: 10.1016/j.pbi.2023.102410] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/25/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023]
Abstract
The survival of extreme water deficit stress by tolerant organisms requires a coordinated series of responses, including those at cellular, transcriptional, translational and metabolic levels. Small molecules play a pivotal role in creating the proper chemical environment for the preservation of cellular integrity and homeostasis during dehydration. This review surveys recent insights in the importance of primary and specialised metabolites in the response to drying of angiosperms with vegetative desiccation tolerance, i.e. the ability to survive near total loss of water. Important metabolites include sugars such as sucrose, trehalose and raffinose family of oligosaccharides, amino acids and organic acids, as well as antioxidants, representing a common core mechanism of desiccation tolerance. Additional metabolites are discussed in the context of species specificity and adaptation.
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Affiliation(s)
- Halford Jw Dace
- Laboratory of Plant Physiology, Wageningen University and Research, The Netherlands
| | - Ademola E Adetunji
- Department of Molecular and Cell Biology, University of Cape Town, South Africa
| | - John P Moore
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, South Africa
| | - Jill M Farrant
- Department of Molecular and Cell Biology, University of Cape Town, South Africa.
| | - Henk Wm Hilhorst
- Laboratory of Plant Physiology, Wageningen University and Research, The Netherlands; Department of Molecular and Cell Biology, University of Cape Town, South Africa.
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17
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Niu M, Chen X, Zhou W, Guo Y, Yuan X, Cui J, Shen Z, Su N. Multi-omics analysis provides insights intro lysine accumulation in quinoa (Chenopodium quinoa Willd.) sprouts. Food Res Int 2023; 171:113026. [PMID: 37330848 DOI: 10.1016/j.foodres.2023.113026] [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: 03/21/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/19/2023]
Abstract
Lysine, the first limiting essential amino acid, the deficiency of which seriously affects the health of human and animals. In this study, quinoa germination significantly increased the nutrients, especially lysine content. To better understanding the underlying molecular mechanism of lysine biosynthesis, isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics, RNA-sequencing (RNA-Seq) technology and liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) platform-based phytohormones analyses were conducted. Through proteome analyses, a total of 11,406 differentially expressed proteins were identified, which were mainly related to secondary metabolites. The lysine-rich storage globulins and endogenous phytohormones probably contributed the increased lysine content in quinoa during germination. Furthermore, aspartic acid semialdehyde dehydrogenase is essential for lysine synthesis in addition to aspartate kinase and dihydropyridine dicarboxylic acid synthase. Protein-protein interaction analysis indicated lysine biosynthesis is associated with "amino metabolism" and "starch and sucrose metabolism". Above all, our study screens the candidate genes participated in lysine accumulation and explores the factors affected lysine biosynthesis by multi-omics analysis. These information not only paves a foundation for breeding lysine-rich quinoa sprouts but also provides valuable multi-omics resource to explore the characteristic of nutrients during quinoa germination.
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Affiliation(s)
- Mengyang Niu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xuan Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wen Zhou
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Youyou Guo
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Jin Cui
- College of Life Sciences, Zhejiang University, Hangzhou, China.
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Nana Su
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
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18
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Huang Y, Song J, Hao Q, Mou C, Wu H, Zhang F, Zhu Z, Wang P, Ma T, Fu K, Chen Y, Nguyen T, Liu S, Jiang L, Wan J. WEAK SEED DORMANCY 1, an aminotransferase protein, regulates seed dormancy in rice through the GA and ABA pathways. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107923. [PMID: 37549571 DOI: 10.1016/j.plaphy.2023.107923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/03/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023]
Abstract
Seed dormancy is a critical trait that enhances plant survival by preventing seed germination at the wrong time or under unsuitable conditions. Lack of seed dormancy in rice can lead to pre-harvest sprouting on mother plants leading to reduced yield and seed quality. Although some genes have been identified, knowledge of regulation of seed dormancy is limited. Here, we characterized a weak seed dormancy mutant named weak seed dormancy 1 (wsd1) that showed a higher seed germination percentage than the wild-type following the harvest ripeness. We cloned the WSD1 encoding an aminotransferase protein using a MutMap approach. WSD1 was stably expressed after imbibition and its protein was localized in the endoplasm reticulum. A widely targeted metabolomics assay and amino acid analysis showed that WSD1 had a role in regulating homeostasis of amino acids. PAC treatment and RNA-seq analysis showed that WSD1 regulates seed dormancy by involvement in the GA biosynthesis pathway. GA1 content and expression of GA biosynthesis-related genes were increased in the wsd1 mutant compared with the wild-type. The wsd1 mutant had reduced sensitivity to ABA. Our overall results indicated that WSD1 regulates seed dormancy by balancing the ABA and GA pathways.
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Affiliation(s)
- Yunshuai Huang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiawei Song
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qixian Hao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changling Mou
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongming Wu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fulin Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ziyan Zhu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ping Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tengfei Ma
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kai Fu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaping Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Thanhliem Nguyen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China; Faculty of Natural Sciences, Quynhon University, Quynhon, 590000, Binhdinh, Viet Nam
| | - Shijia Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianmin Wan
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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19
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Girija A, Hacham Y, Dvir S, Panda S, Lieberman-Lazarovich M, Amir R. Cystathionine γ-synthase expression in seeds alters metabolic and DNA methylation profiles in Arabidopsis. PLANT PHYSIOLOGY 2023; 193:595-610. [PMID: 37300538 DOI: 10.1093/plphys/kiad330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 06/12/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) seeds expressing the feedback-insensitive form of cystathionine γ-synthase (AtD-CGS), the key gene of methionine (Met) synthesis, under the control of a seed-specific phaseolin promoter (SSE plants) show a significant increase in Met content. This elevation is accompanied by increased levels of other amino acids (AAs), sugars, total protein, and starch, which are important from a nutritional aspect. Here, we investigated the mechanism behind this phenomenon. Gas chromatography-mass spectrometry (GC-MS) analysis of SSE leaves, siliques, and seeds collected at 3 different developmental stages showed high levels of Met, AAs, and sugars compared to the control plants. A feeding experiment with isotope-labeled AAs showed an increased flux of AAs from nonseed tissues toward the developing seeds of SSE. Transcriptome analysis of leaves and seeds displayed changes in the status of methylation-related genes in SSE plants that were further validated by methylation-sensitive enzymes and colorimetric assay. These results suggest that SSE leaves have higher DNA methylation rates than control plants. This occurrence apparently led to accelerated senescence, together with enhanced monomer synthesis, which further resulted in increased transport of monomers from the leaves toward the seeds. The developing seeds of SSE plants, however, show reduced Met levels and methylation rates. The results provide insights into the role of Met in DNA methylation and gene expression and how Met affects the metabolic profile of the plant.
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Affiliation(s)
- Aiswarya Girija
- MIGAL-Galilee Research Institute, Plant Metabolism Lab, Kiryat Shmona 11016, Israel
| | - Yael Hacham
- MIGAL-Galilee Research Institute, Plant Metabolism Lab, Kiryat Shmona 11016, Israel
- Department of Biotechnology, Tel Hai College, Upper Galilee 1220800, Israel
| | - Shachar Dvir
- MIGAL-Galilee Research Institute, Plant Metabolism Lab, Kiryat Shmona 11016, Israel
- Department of Biotechnology, Tel Hai College, Upper Galilee 1220800, Israel
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| | - Rachel Amir
- MIGAL-Galilee Research Institute, Plant Metabolism Lab, Kiryat Shmona 11016, Israel
- Department of Biotechnology, Tel Hai College, Upper Galilee 1220800, Israel
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20
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Amir R, Martínez-Force E, Shi J, Alonso AP. Editorial: Metabolic architecture of developing seeds and grains. FRONTIERS IN PLANT SCIENCE 2023; 14:1258353. [PMID: 37615018 PMCID: PMC10443588 DOI: 10.3389/fpls.2023.1258353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 07/27/2023] [Indexed: 08/25/2023]
Affiliation(s)
- Rachel Amir
- Department of Plant Sciences, Galilee Research Institute (MIGAL), Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Upper Galilee, Israel
| | - Enrique Martínez-Force
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la GRASA-CSIC, Seville, Spain
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Ana Paula Alonso
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
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21
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Zhang Y, Fernie AR. The Role of TCA Cycle Enzymes in Plants. Adv Biol (Weinh) 2023; 7:e2200238. [PMID: 37341441 DOI: 10.1002/adbi.202200238] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 04/29/2023] [Indexed: 06/22/2023]
Abstract
As one of the iconic pathways in plant metabolism, the tricarboxylic acid (TCA) cycle is commonly thought to not only be responsible for the oxidization of respiratory substrate to drive ATP synthesis but also provide carbon skeletons to anabolic processes and contribute to carbon-nitrogen interaction and biotic stress responses. The functions of the TCA cycle enzymes are characterized by a saturation transgenesis approach, whereby the constituent expression of proteins is knocked out or reduced in order to investigate their function in vivo. The alteration of TCA cycle enzyme expression results in changed plant growth and photosynthesis under controlled conditions. Moreover, improvements in plant performance and postharvest properties are reported by overexpression of either endogenous forms or heterologous genes of a number of the enzymes. Given the importance of the TCA cycle in plant metabolism regulation, here, the function of each enzyme and its roles in different tissues are discussed. This article additionally highlights the recent finding that the plant TCA cycle, like that of mammals and microbes, dynamically assembles functional substrate channels or metabolons and discusses the implications of this finding to the current understanding of the metabolic regulation of the plant TCA cycle.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
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22
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Peng C, Wu Y, Cai H, Hu Y, Huang W, Shen Y, Yang H. Methodological and physiological study of seed dormancy release in Tilia henryana. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154046. [PMID: 37390779 DOI: 10.1016/j.jplph.2023.154046] [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: 05/21/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023]
Abstract
Tilia henryana is a rare tree of the Tilia family, found exclusively in China. Its seeds have severe dormancy features that limit its normal conditions of reproduction and renewal. Its seeds have severe dormant characteristics that limit its normal conditions of reproduction and renewal. The Dormancy in T. henryana seeds is a comprehensive dormancy (PY + PD) caused by mechanical and permeability barriers of seed coat and the presence of germination inhibitor in endosperm. L9 (34) orthogonal test was used to determine the best procedure for releasing the dormancy of T. henryana seeds, that is, first treating the seeds with H2SO4 for 15 min, followed by the application of 1 g L-1 GA3, stratification at 5 °C for 45 days, and finally germination at 20 °C, which can achieve a 98% seed germination rate. Large amounts of fat are consumed throughout the dormancy release process. As quantities of protein and starch marginally increase, soluble sugars are continuously decreased. Acid phosphatase and amylase activities increased rapidly, and the combined enzyme activities of G-6-PDH and 6-PGDH related to the PPP were also significantly increased. The levels of GA and ZR continued to increase, while the levels of ABA and IAA gradually decreased, among which GA and ABA changed most rapidly. The total amino acids content continued to decrease. Asp, Cys, Leu, Phe, His, Lys and Arg decreased with dormancy release, while Ser, Glu, Ala, Ile, Pro and Gaba showed an upward trend. The physical dormancy of T. henryana seeds is broken with H2SO4 in order to make the seed coat more permeable, which is a prerequisite for germination. As a result, the seeds can absorb water and engage in physiological metabolic activities, particularly the hydrolysis and metabolism of fat, which supply a significant amount of energy for dormancy release. In addition, rapid variations in the levels of different endogenous hormones and free amino acids, induced by cold stratification and GA3 application, are another important factor promoting the quick physiological activation of seeds and breaking the endosperm barrier.
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Affiliation(s)
- ChenYin Peng
- College of Forestry, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing, Jiangsu, 210037, PR China; Co-innovation Center for Sustainable Forestry in Southern China, Southern Tree Inspection Center National Forestry Administration, 159 Longpan Road, Xuanwu District, Nanjing, Jiangsu, 210037, PR China
| | - Yu Wu
- College of Forestry, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing, Jiangsu, 210037, PR China; Co-innovation Center for Sustainable Forestry in Southern China, Southern Tree Inspection Center National Forestry Administration, 159 Longpan Road, Xuanwu District, Nanjing, Jiangsu, 210037, PR China
| | - Hao Cai
- College of Forestry, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing, Jiangsu, 210037, PR China
| | - YaMei Hu
- College of Forestry, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing, Jiangsu, 210037, PR China
| | - WenHui Huang
- College of Forestry, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing, Jiangsu, 210037, PR China
| | - YongBao Shen
- College of Forestry, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing, Jiangsu, 210037, PR China; Co-innovation Center for Sustainable Forestry in Southern China, Southern Tree Inspection Center National Forestry Administration, 159 Longpan Road, Xuanwu District, Nanjing, Jiangsu, 210037, PR China.
| | - Hui Yang
- Myddelton College, Denbigh, LL16 3EN, United Kingdom
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23
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Née G, Krüger T. Dry side of the core: a meta-analysis addressing the original nature of the ABA signalosome at the onset of seed imbibition. FRONTIERS IN PLANT SCIENCE 2023; 14:1192652. [PMID: 37476171 PMCID: PMC10354442 DOI: 10.3389/fpls.2023.1192652] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/08/2023] [Indexed: 07/22/2023]
Abstract
The timing of seedling emergence is a major agricultural and ecological fitness trait, and seed germination is controlled by a complex molecular network including phytohormone signalling. One such phytohormone, abscisic acid (ABA), controls a large array of stress and developmental processes, and researchers have long known it plays a crucial role in repressing germination. Although the main molecular components of the ABA signalling pathway have now been identified, the molecular mechanisms through which ABA elicits specific responses in distinct organs is still enigmatic. To address the fundamental characteristics of ABA signalling during germination, we performed a meta-analysis focusing on the Arabidopsis dry seed proteome as a reflexion basis. We combined cutting-edge proteome studies, comparative functional analyses, and protein interaction information with genetic and physiological data to redefine the singular composition and operation of the ABA core signalosome from the onset of seed imbibition. In addition, we performed a literature survey to integrate peripheral regulators present in seeds that directly regulate core component function. Although this may only be the tip of the iceberg, this extended model of ABA signalling in seeds already depicts a highly flexible system able to integrate a multitude of information to fine-tune the progression of germination.
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24
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Chen H, Visscher AM, Ai Q, Yang L, Pritchard HW, Li W. Intra-Specific Variation in Desiccation Tolerance of Citrus sinensis 'bingtangcheng' (L.) Seeds under Different Environmental Conditions in China. Int J Mol Sci 2023; 24:ijms24087393. [PMID: 37108552 PMCID: PMC10139128 DOI: 10.3390/ijms24087393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Intra-specific variation in seed storage behaviour observed in several species has been related to different maternal environments. However, the particular environmental conditions and molecular processes involved in intra-specific variation of desiccation tolerance remain unclear. We chose Citrus sinensis 'bingtangcheng' for the present study due to its known variability in desiccation tolerance amongst seed lots. Six seed lots of mature fruits were harvested across China and systematically compared for drying sensitivity. Annual sunshine hours and average temperature from December to May showed positive correlations with the level of seed survival of dehydration. Transcriptional analysis indicated significant variation in gene expression between relatively desiccation-tolerant (DT) and -sensitive (DS) seed lots after harvest. The major genes involved in late seed maturation, such as heat shock proteins, showed higher expression in the DT seed lot. Following the imposition of drying, 80% of stress-responsive genes in the DS seed lot changed to the stable levels seen in the DT seed lot prior to and post-desiccation. However, the changes in expression of stress-responsive genes in DS seeds did not improve their tolerance to desiccation. Thus, higher desiccation tolerance of Citrus sinensis 'bingtangcheng' seeds is modulated by the maternal environment (e.g., higher annual sunshine hours and seasonal temperature) during seed development and involves stable expression levels of stress-responsive genes.
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Affiliation(s)
- Hongying Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Anne M Visscher
- Trait Diversity and Function Department, Royal Botanic Gardens, Kew, Wakehurst, Ardingly, West Sussex RH17 6TN, UK
| | - Qin Ai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Lan Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hugh W Pritchard
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Trait Diversity and Function Department, Royal Botanic Gardens, Kew, Wakehurst, Ardingly, West Sussex RH17 6TN, UK
| | - Weiqi Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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25
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Le XH, Millar AH. The diversity of substrates for plant respiration and how to optimize their use. PLANT PHYSIOLOGY 2023; 191:2133-2149. [PMID: 36573332 PMCID: PMC10069909 DOI: 10.1093/plphys/kiac599] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/09/2022] [Indexed: 06/18/2023]
Abstract
Plant respiration is a foundational biological process with the potential to be optimized to improve crop yield. To understand and manipulate the outputs of respiration, the inputs of respiration-respiratory substrates-need to be probed in detail. Mitochondria house substrate catabolic pathways and respiratory machinery, so transport into and out of these organelles plays an important role in committing substrates to respiration. The large number of mitochondrial carriers and catabolic pathways that remain unidentified hinder this process and lead to confusion about the identity of direct and indirect respiratory substrates in plants. The sources and usage of respiratory substrates vary and are increasing found to be highly regulated based on cellular processes and environmental factors. This review covers the use of direct respiratory substrates following transport through mitochondrial carriers and catabolism under normal and stressed conditions. We suggest the introduction of enzymes not currently found in plant mitochondria to enable serine and acetate to be direct respiratory substrates in plants. We also compare respiratory substrates by assessing energetic yields, availability in cells, and their full or partial oxidation during cell catabolism. This information can assist in decisions to use synthetic biology approaches to alter the range of respiratory substrates in plants. As a result, respiration could be optimized by introducing, improving, or controlling specific mitochondrial transporters and mitochondrial catabolic pathways.
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Affiliation(s)
- Xuyen H Le
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
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26
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Pang X, Liu S, Suo J, Yang T, Hasan S, Hassan A, Xu J, Lu S, Mi S, Liu H, Yao J. Proteome Dynamics Analysis Reveals the Potential Mechanisms of Salinity and Drought Response during Seed Germination and Seedling Growth in Tamarix hispida. Genes (Basel) 2023; 14:genes14030656. [PMID: 36980928 PMCID: PMC10048391 DOI: 10.3390/genes14030656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Understanding the molecular mechanisms of seed germination and seedling growth is vital for mining functional genes for the improvement of plant drought in a desert. Tamarix hispida is extremely resistant to drought and soil salinity perennial shrubs or trees. This study was the first to investigate the protein abundance profile of the transition process during the processes of T. hispida seed germination and seedling growth using label-free proteomics approaches. Our data suggested that asynchronous regulation of transcriptomics and proteomics occurs upon short-term seed germination and seedling growth of T. hispida. Enrichment analysis revealed that the main differentially abundant proteins had significant enrichment in stimulus response, biosynthesis, and metabolism. Two delta-1-pyrroline-5-carboxylate synthetases (P5CS), one Ycf3-interacting protein (Y3IP), one low-temperature-induced 65 kDa protein-like molecule, and four peroxidases (PRX) were involved in both water deprivation and hyperosmotic salinity responses. Through a comparative analysis of transcriptomics and proteomics, we found that proteomics may be better at studying short-term developmental processes. Our results support the existence of several mechanisms that enhance tolerance to salinity and drought stress during seedling growth in T. hispida.
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Affiliation(s)
- Xin’an Pang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Corps, College of Life Sciences, Tarim University, Alar 843300, China
| | - Shuo Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Jiangtao Suo
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Samira Hasan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Ali Hassan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Jindong Xu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Sushuangqing Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Sisi Mi
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
- Correspondence: (H.L.); (J.Y.)
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (H.L.); (J.Y.)
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27
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Wang C, Lyu Y, Zhang Q, Guo H, Chen D, Chen X. Disruption of BG14 results in enhanced callose deposition in developing seeds and decreases seed longevity and seed dormancy in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1080-1094. [PMID: 36625794 DOI: 10.1111/tpj.16102] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/19/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
Seed longevity is an important trait for agriculture and the conservation of genetic resources. β-1,3-Glucanases were first recognized as pathogenesis-related proteins involved in plant defense, but their roles in seeds are largely unknown. Here, we report a glycosylphosphatidylinositol-anchored β-1,3-glucanase, BG14, that degrades callose in seed embryos and functions in seed longevity and dormancy in Arabidopsis. The loss of function of BG14 significantly decreased seed longevity, whereas functional reversion (RE) and overexpression (OE) lines reversed and increased the impaired phenotype, respectively. The loss of function of BG14 enhanced callose deposition in the embryos of mature seeds, confirmed by quantitative determination and the decreased callose degrading ability in bg14. The drop-and-see (DANS) assay revealed that the fluorescence signal in bg14 was significantly lower than that observed in the other three genotypes. BG14 is located on the periphery of the cell wall and can completely merge with callose at the plasmodesmata of epidermal cells. BG14 was highly expressed in developing seeds and was induced by aging and abscisic acid (ABA). The loss of function of BG14 led to a variety of phenotypes related to ABA, including reduced seed dormancy and reduced responses to treatment with ABA or pacolblltrazol, whereas OE lines showed the opposite phenotype. The reduced ABA response is because of the decreased level of ABA and the lowered expression of ABA synthesis genes in bg14. Taken together, this study demonstrated that BG14 is a bona fide BG that mediates callose degradation in the plasmodesmata of embryo cells, transcriptionally influences ABA synthesis genes in developing seeds, and positively affects seed longevity and dormancy in Arabidopsis.
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Affiliation(s)
- Chengliang Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yuanyuan Lyu
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hongye Guo
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Defu Chen
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xiwen Chen
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
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28
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Magno Massuia de Almeida L, Coquemont-Guyot M, Elie N, Morvan-Bertrand A, Avice JC, Mollier A, Brunel-Muguet S. Repeated heat stress events during the reproductive phase impact the dynamic development of seeds in Brassica napus L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 327:111559. [PMID: 36496054 DOI: 10.1016/j.plantsci.2022.111559] [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: 09/05/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Many studies pointed out the deleterious effects of high temperatures events during the crop reproductive phase on seed yield and quality. However, plant responses to repeated stressing events remain poorly understood, while the increased frequency of extreme abiotic constraints, such as spring and summer heat waves, has been proven as one feature of the on-going and future climate change. The responses of oilseed rape plants subjected to three heat stress sequences that differed in the intensity, the timing of application, the duration and the frequency of the high temperature events were investigated throughout the seed development and maturation phases under controlled conditions. Seed yield and components were measured in three different harvest dates. Biochemical and histological analyses of seeds were carried out in order to monitor the evolution of the main storage compounds (fatty acids, proteins, sugars) involved in seed nutritional quality. Although the effects of heat stress were not significant on total yield, differences in seed number and weight highlighted the strong compensation capacity in indeterminate growth species. Heat stress induced significant decreases and increases in seed oil and protein content respectively, to different extent according to the age of the pods. Soluble sugars concentrations were impacted by heat during seed development, but not when the seeds reached physiological maturity, thus indicating compensatory mechanisms that set up after the stress exposure. Our results led to conclude that the effects of repeated heat stresses on seed yield and quality were tightly related to (i) the optimal temperature of a given compound biosynthesis process, and (ii) the synchrony between the temperature event and the period of biosynthesis of the targeted storage compound. These results highlight the complexity to design thermo-sensitizing protocols to maintain or even improve the various seed quality related criteria, especially in species with indeterminate growth.
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Affiliation(s)
- Lethicia Magno Massuia de Almeida
- Normandie Univ, UNICAEN, INRAE, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, SFR Normandie Végétal (FED 4277), Esplanade de la Paix, 14032 Caen, France
| | - Maëlle Coquemont-Guyot
- Normandie Univ, UNICAEN, Federative Structure 4207 "Normandie Oncologie", Service Unit PLATON, Virtual'His platform, Caen, France
| | - Nicolas Elie
- Normandie Univ, UNICAEN, Federative Structure 4207 "Normandie Oncologie", Service Unit PLATON, Virtual'His platform, Caen, France; Normandie Univ, UNICAEN, Service Unit EMERODE, Centre de Microscopie Appliquée à la Biologie, CMABio³, Caen, France
| | - Annette Morvan-Bertrand
- Normandie Univ, UNICAEN, INRAE, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, SFR Normandie Végétal (FED 4277), Esplanade de la Paix, 14032 Caen, France
| | - Jean-Christophe Avice
- Normandie Univ, UNICAEN, INRAE, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, SFR Normandie Végétal (FED 4277), Esplanade de la Paix, 14032 Caen, France
| | - Alain Mollier
- ISPA, Bordeaux Sciences Agro, INRAE, F-33140 Villenave d'Ornon, France
| | - Sophie Brunel-Muguet
- Normandie Univ, UNICAEN, INRAE, UMR 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, SFR Normandie Végétal (FED 4277), Esplanade de la Paix, 14032 Caen, France.
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29
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Colombo F, Pagano A, Sangiorgio S, Macovei A, Balestrazzi A, Araniti F, Pilu R. Study of Seed Ageing in lpa1-1 Maize Mutant and Two Possible Approaches to Restore Seed Germination. Int J Mol Sci 2023; 24:ijms24010732. [PMID: 36614175 PMCID: PMC9820859 DOI: 10.3390/ijms24010732] [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: 11/10/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 01/03/2023] Open
Abstract
Phytic acid (PA) is a strong anti-nutritional factor with a key antioxidant role in countering reactive oxygen species. Despite the potential benefits of low phytic acid (lpa) mutants, the reduction of PA causes pleiotropic effects, e.g., reduced seed germination and viability loss related to seed ageing. The current study evaluated a historical series of naturally aged seeds and showed that lpa1-1 seeds aged faster as compared to wildtype. To mimic natural ageing, the present study set up accelerated ageing treatments at different temperatures. It was found that incubating the seeds at 57 °C for 24 h, the wildtype germinated at 82.4% and lpa1-1 at 40%. The current study also hypothesized two possible solutions to overcome these problems: (1) Classical breeding was used to constitute synthetic populations carrying the lpa1-1 mutation, with genes pushing anthocyanin accumulation in the embryo (R-navajo allele). The outcome showed that the presence of R-navajo in the lpa1-1 genotype was not able to improve the germinability (-20%), but this approach could be useful to improve the germinability in non-mutant genotypes (+17%). (2) In addition, hydropriming was tested on lpa1-1 and wildtype seeds, and germination was improved by 20% in lpa1-1, suggesting a positive role of seed priming in restoring germination. Moreover, the data highlighted metabolic differences in the metabolome before and after hydropriming treatment, suggesting that the differences in germination could also be mediated by differences in the metabolic composition induced by the mutation.
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Affiliation(s)
- Federico Colombo
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, Università degli Studi di Milano, Via G. Celoria 2, 20133 Milan, Italy
| | - Andrea Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Stefano Sangiorgio
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, Università degli Studi di Milano, Via G. Celoria 2, 20133 Milan, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Fabrizio Araniti
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, Università degli Studi di Milano, Via G. Celoria 2, 20133 Milan, Italy
| | - Roberto Pilu
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, Università degli Studi di Milano, Via G. Celoria 2, 20133 Milan, Italy
- Correspondence:
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Abstract
The seed acts as the primary inoculum source for the plant microbiota. Understanding the processes involved in its assembly and dynamics during germination and seedling emergence has the potential to allow for the improvement of crop establishment. Changes in the bacterial community structure were tracked in 1,000 individual seeds that were collected throughout seed developments of beans and radishes. Seeds were associated with a dominant bacterial taxon that represented more than 75% of all reads. The identity of this taxon was highly variable between the plants and within the seeds of the same plant. We identified selection as the main ecological process governing the succession of dominant taxa during seed filling and maturation. In a second step, we evaluated the seedling transmission of seed-borne taxa in 160 individual plants. While the initial bacterial abundance on seeds was not a good predictor of seedling transmission, the identities of the seed-borne taxa modified the phenotypes of seedlings. Overall, this work revealed that individual seeds are colonized by a few bacterial taxa of highly variable identity, which appears to be important for the early stages of plant development. IMPORTANCE Seeds are key components of plant fitness and are central to the sustainability of the agri-food system. Both the seed quality for food consumption and the seed vigor in agricultural settings can be influenced by the seed microbiota. Understanding the ecological processes involved in seed microbiota assembly will inform future practices for promoting the presence of important seed microorganisms for plant health and productivity. Our results highlighted that seeds were associated with one dominant bacterial taxon of variable taxonomic identity. This variety of dominant taxa was due to (i) spatial heterogeneity between and within plants and (ii) primary succession during seed development. According to neutral models, selection was the main driver of microbial community assembly for both plant species.
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Salvi P, Varshney V, Majee M. Raffinose family oligosaccharides (RFOs): role in seed vigor and longevity. Biosci Rep 2022; 42:BSR20220198. [PMID: 36149314 PMCID: PMC9547172 DOI: 10.1042/bsr20220198] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Seed vigor and longevity are important agronomic attributes, as they are essentially associated with crop yield and thus the global economy. Seed longevity is a measure of seed viability and the most essential property in gene bank management since it affects regeneration of seed recycling. Reduced seed life or storability is a serious issue in seed storage since germplasm conservation and agricultural enhancement initiatives rely on it. The irreversible and ongoing process of seed deterioration comprises a complex gene regulatory network and altered metabolism that results in membrane damage, DNA integrity loss, mitochondrial dysregulation, protein damage, and disrupted antioxidative machinery. Carbohydrates and/or sugars, primarily raffinose family oligosaccharides (RFOs), have emerged as feasible components for boosting or increasing seed vigor and longevity in recent years. RFOs are known to perform diverse functions in plants, including abiotic and biotic stress tolerance, besides being involved in regulating seed germination, desiccation tolerance, vigor, and longevity. We emphasized and analyzed the potential impact of RFOs on seed vigor and longevity in this review. Here, we comprehensively reviewed the molecular mechanisms involved in seed longevity, RFO metabolism, and how RFO content is critical and linked with seed vigor and longevity. Further molecular basis, biotechnological approaches, and CRISPR/Cas applications have been discussed briefly for the improvement of seed attributes and ultimately crop production. Likewise, we suggest advancements, challenges, and future possibilities in this area.
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Affiliation(s)
- Prafull Salvi
- National Agri-Food Biotechnology Institute, Punjab 140308, India
| | - Vishal Varshney
- Govt. Shaheed Gend Singh College, Charama, Chhattisgarh 494337, India
| | - Manoj Majee
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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32
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Methods to promote seed germination in the lacquer tree, Toxicodendron vernicifluum (Stokes) F.A. Barkley. PLoS One 2022; 17:e0272665. [PMID: 35951616 PMCID: PMC9371279 DOI: 10.1371/journal.pone.0272665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/24/2022] [Indexed: 11/19/2022] Open
Abstract
The lacquer tree, Toxicodendron vernicifluum, is a common industrial crop in East Asia. However, T. vernicifluum seeds are extremely difficult to germinate, which poses a major obstacle to establishing seedlings for sap production. In this study, we examined the germination properties of T. vernicifluum seeds in order to establish an inexpensive and effective method to promote seed germination. The seeds are covered with a hard endocarp, which we degrade using conventional sulfuric acid-based methods. Although sulfuric acid was effective in promoting seed germination, the germination rate was less than 5%. In addition to treatment with sulfuric acid, co-treatment with cold temperatures or the phytohormone gibberellic acid increased the germination rate to 22–35%. Seed viability analysis combined with specific gravity-based seed selection revealed that more than half of the seeds housed embryos that were incapable of germination. In additions, specific gravity-based seed selection aided in the selection of seeds capable of germination and improved the germination rate to approximately 47%. Taken together, our results suggest that the low germination rate of T. vernicifluum seeds is due to deep seed dormancy—which is controlled by physical and physiological mechanisms—and low embryo viability. To improve the germination rate of T. vernicifluum seeds, we propose an effective method whereby seeds with good germination capacity are selected based on specific gravity, following which their physiological dormancy is inactivated through cold pretreatment.
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Shi L, Chen Y, Hong J, Shen G, Schreiber L, Cohen H, Zhang D, Aharoni A, Shi J. AtMYB31 is a wax regulator associated with reproductive development in Arabidopsis. PLANTA 2022; 256:28. [PMID: 35781548 DOI: 10.1007/s00425-022-03945-9] [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: 03/25/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
AtMYB31, a R2R3-MYB transcription factor that modulates wax biosynthesis in reproductive tissues, is involved in seed development in Arabidopsis. R2R3-MYB transcription factors play important roles in plant development; yet, the exact role of each of them remains to be resolved. Here we report that the Arabidopsis AtMYB31 is required for wax biosynthesis in epidermis of reproductive tissues, and is involved in seed development. AtMYB31 was ubiquitously expressed in both vegetative and reproductive tissues with higher expression levels in siliques and seeds, while AtMYB31 was localized to the nucleus and cytoplasm. Loss of function of AtMYB31 reduced wax accumulation in the epidermis of silique and flower tissues, disrupted seed coat epidermal wall development and mucilage production, altered seed proanthocyanidin and polyester content. AtMYB31 could direct activate expressions of several wax biosynthetic target genes. Altogether, AtMYB31, a R2R3-MYB transcription factor, regulates seed development in Arabidopsis.
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Affiliation(s)
- Lei Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuqin Chen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Hong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Gaodian Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lukas Schreiber
- Institute of Cellular and Molecular Botany, University of Bonn, 53115, Bonn, Germany
| | - Hagai Cohen
- Institute of Plant Sciences, Agricultural Research Organization, 7505101, Rishon LeZion, Israel
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel.
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Sano N, Lounifi I, Cueff G, Collet B, Clément G, Balzergue S, Huguet S, Valot B, Galland M, Rajjou L. Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination. FRONTIERS IN PLANT SCIENCE 2022; 13:867263. [PMID: 35755645 PMCID: PMC9225960 DOI: 10.3389/fpls.2022.867263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.
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Affiliation(s)
- Naoto Sano
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Imen Lounifi
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- MBCC Group, Master Builders Construction Chemical, Singapore, Singapore
| | - Gwendal Cueff
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Boris Collet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Gilles Clément
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Sandrine Balzergue
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Benoît Valot
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, PAPPSO, Plateforme d'Analyse de Proteomique Paris-Sud-Ouest, Gif-sur-Yvette, France
- Chrono-Environnement Research Team UMR/CNRS-6249, Bourgogne-Franche-Comté University, Besançon, France
| | - Marc Galland
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Loïc Rajjou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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35
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Ralevski A, Apelt F, Olas JJ, Mueller-Roeber B, Rugarli EI, Kragler F, Horvath TL. Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice. Cell Mol Life Sci 2022; 79:334. [PMID: 35652974 PMCID: PMC11071973 DOI: 10.1007/s00018-022-04382-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 11/26/2022]
Abstract
Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh± heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals.
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Affiliation(s)
- Alexandra Ralevski
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Federico Apelt
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, 14476, Potsdam, Germany
| | - Justyna J Olas
- Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Bernd Mueller-Roeber
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, 14476, Potsdam, Germany
- Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Elena I Rugarli
- Department of Biology, Institute for Genetics, University of Cologne, Cologne, Germany
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, 14476, Potsdam, Germany
| | - Tamas L Horvath
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA.
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36
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Skirycz A, Fernie AR. Past accomplishments and future challenges of the multi-omics characterization of leaf growth. PLANT PHYSIOLOGY 2022; 189:473-489. [PMID: 35325227 PMCID: PMC9157134 DOI: 10.1093/plphys/kiac136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The advent of omics technologies has revolutionized biology and advanced our understanding of all biological processes, including major developmental transitions in plants and animals. Here, we review the vast knowledge accumulated concerning leaf growth in terms of transcriptional regulation before turning our attention to the historically less well-characterized alterations at the protein and metabolite level. We will then discuss how the advent of biochemical methods coupled with metabolomics and proteomics can provide insight into the protein-protein and protein-metabolite interactome of the growing leaves. We finally highlight the substantial challenges in detection, spatial resolution, integration, and functional validation of the omics results, focusing on metabolomics as a prerequisite for a comprehensive understanding of small-molecule regulation of plant growth.
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Affiliation(s)
- Aleksandra Skirycz
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Cornell University, Ithaca, New York 14853, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
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37
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Brzozowski LJ, Campbell MT, Hu H, Caffe M, Gutiérrez LA, Smith KP, Sorrells ME, Gore MA, Jannink JL. Generalizable approaches for genomic prediction of metabolites in plants. THE PLANT GENOME 2022; 15:e20205. [PMID: 35470586 DOI: 10.1002/tpg2.20205] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Plant metabolites are important traits for plant breeders seeking to improve nutrition and agronomic performance yet integrating selection for metabolomic traits can be limited by phenotyping expense and degree of genetic characterization, especially of uncommon metabolites. As such, developing generalizable genomic selection methods based on biochemical pathway biology for metabolites that are transferable across plant populations would benefit plant breeding programs. We tested genomic prediction accuracy for >600 metabolites measured by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) in oat (Avena sativa L.) seed. Using a discovery germplasm panel, we conducted metabolite genome-wide association study (mGWAS) and selected loci to use in multikernel models that encompassed metabolome-wide mGWAS results or mGWAS from specific metabolite structures or biosynthetic pathways. Metabolite kernels developed from LC-MS metabolites in the discovery panel improved prediction accuracy of LC-MS metabolite traits in the validation panel consisting of more advanced breeding lines. No approach, however, improved prediction accuracy for GC-MS metabolites. We ranked model performance by metabolite and found that metabolites with similar polarity had consistent rankings of models. Overall, testing biological rationales for developing kernels for genomic prediction across populations contributes to developing frameworks for plant breeding for metabolite traits.
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Affiliation(s)
- Lauren J Brzozowski
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Malachy T Campbell
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Haixiao Hu
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Melanie Caffe
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57006, USA
| | - Lucı A Gutiérrez
- Dep. of Agronomy, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kevin P Smith
- Dep. of Agronomy & Plant Genetics, Univ. of Minnesota, St. Paul, MN, 55108, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Jean-Luc Jannink
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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38
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Araniti F, Prinsi B, Espen L. The Delay of Raphanus raphanistrum subsp. sativus (L.) Domin Seed Germination Induced by Coumarin Is Mediated by a Lower Ability to Sustain the Energetic Metabolism. PLANTS 2022; 11:plants11070843. [PMID: 35406823 PMCID: PMC9002777 DOI: 10.3390/plants11070843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 01/11/2023]
Abstract
In the present study, the mode of action of coumarin using the germination process as a target was investigated. A dose–response curve, built using a range of concentrations from 0 to 800 µM, allowed us to identify a key concentration (400 µM) inhibiting the germination process, reducing its speed without compromising seed development. Successively, short time-course (0–48 h) experiments were carried out to evaluate the biochemical and metabolic processes involved in coumarin-induced germination delay. The results pointed out that coumarin delayed K+, Ca2+, and Mg2+ reabsorption, suggesting a late membrane reorganisation. Similarly, seed respiration was inhibited during the first 24 h but recovered after 48 h. Those results agreed with ATP levels, which followed the same trend. In addition, the untargeted metabolomic analysis allowed to identify, among the pathways significantly impacted by the treatment, amino acids metabolism, the TCA cycle, and the glyoxylate pathway. The results highlighted that coumarin was able to interact with membranes reorganisation, delaying them and reducing the production of ATP, as also supported by pathway analysis and cell respiration. The in vivo 31P-NMR analysis supported the hypothesis that the concentration chosen was able to affect plant metabolism, maintaining, on the other hand, its viability, which is extremely important for studying natural compounds’ mode of action.
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Zhang J, Qian JY, Bian YH, Liu X, Wang CL. Transcriptome and Metabolite Conjoint Analysis Reveals the Seed Dormancy Release Process in Callery Pear. Int J Mol Sci 2022; 23:ijms23042186. [PMID: 35216299 PMCID: PMC8878392 DOI: 10.3390/ijms23042186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 01/09/2023] Open
Abstract
Seed dormancy transition is a vital developmental process for seedling propagation and agricultural production. The process is precisely regulated by diverse endogenous genetic factors and environmental cues. Callery pear (Pyrus calleryana Decne) is an important rootstock species that requires cold stratification to break seed dormancy, but the mechanisms underlying pear seed dormancy release are not yet fully understood. Here, we analyzed the transcriptome profiles at three different stages of cold stratification in callery pear seeds using RNA sequencing combined with phytohormone and sugar content measurements. Significant alterations in hormone contents and carbohydrate metabolism were observed and reflected the dormancy status of the seeds. The expressions of genes related to plant hormone metabolism and signaling transduction, including indole-3-acetic acid (IAA) biosynthesis (ASAs, TSA, NITs, YUC, and AAO) genes as well as several abscisic acid (ABA) and gibberellic acid (GA) catabolism and signaling transduction genes (CYP707As, GA2ox, and DELLAs), were consistent with endogenous hormone changes. We further found that several genes involved in cytokinin (CTK), ethylene (ETH), brassionolide (BR), and jasmonic acid (JA) metabolism and signaling transduction were differentially expressed and integrated in pear seed dormancy release. In accordance with changes in starch and soluble sugar contents, the genes associated with starch and sucrose metabolism were significantly up-regulated during seed dormancy release progression. Furthermore, the expression levels of genes involved in lipid metabolism pathways were also up-regulated. Finally, 447 transcription factor (TF) genes (including ERF, bHLH, bZIP, NAC, WRKY, and MYB genes) were observed to be differentially expressed during seed cold stratification and might relate to pear seed dormancy release. Our results suggest that the mechanism underlying pear seed dormancy release is a complex, transcriptionally regulated process involving hormones, sugars, lipids, and TFs.
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40
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Eliášová K, Konrádová H, Dobrev PI, Motyka V, Lomenech AM, Fischerová L, Lelu-Walter MA, Vondráková Z, Teyssier C. Desiccation as a Post-maturation Treatment Helps Complete Maturation of Norway Spruce Somatic Embryos: Carbohydrates, Phytohormones and Proteomic Status. FRONTIERS IN PLANT SCIENCE 2022; 13:823617. [PMID: 35237290 PMCID: PMC8882965 DOI: 10.3389/fpls.2022.823617] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/04/2022] [Indexed: 06/12/2023]
Abstract
Exposure of Norway spruce (Picea abies) somatic embryos and those of many other conifers to post-maturation desiccation treatment significantly improves their germination. An integration analysis was conducted to understand the underlying processes induced during the desiccation phase at the molecular level. Carbohydrate, protein and phytohormone assays associated with histological and proteomic studies were performed for the evaluation of markers and actors in this phase. Multivariate comparison of mature somatic embryos with mature desiccated somatic embryos and/or zygotic embryos provided new insights into the processes involved during the desiccation step of somatic embryogenesis. Desiccated embryos were characterized by reduced levels of starch and soluble carbohydrates but elevated levels of raffinose family oligosaccharides. Desiccation treatment decreased the content of abscisic acid and its derivatives but increased total auxins and cytokinins. The content of phytohormones in dry zygotic embryos was lower than in somatic embryos, but their profile was mostly analogous, apart from differences in cytokinin profiles. The biological processes "Acquisition of desiccation tolerance", "Response to stimulus", "Response to stress" and "Stored energy" were activated in both the desiccated somatic embryos and zygotic embryos when compared to the proteome of mature somatic embryos before desiccation. Based on the specific biochemical changes of important constituents (abscisic acid, raffinose, stachyose, LEA proteins and cruciferins) induced by the desiccation treatment and observed similarities between somatic and zygotic P. abies embryos, we concluded that the somatic embryos approximated to a state of desiccation tolerance. This physiological change could be responsible for the reorientation of Norway spruce somatic embryos toward a stage suitable for germination.
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Affiliation(s)
- Kateřina Eliášová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Hana Konrádová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Petre I. Dobrev
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Václav Motyka
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | | | - Lucie Fischerová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | | | - Zuzana Vondráková
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
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Pang X, Suo J, Liu S, Xu J, Yang T, Xiang N, Wu Y, Lu B, Qin R, Liu H, Yao J. Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida. BMC Genomics 2022; 23:109. [PMID: 35135479 PMCID: PMC8826658 DOI: 10.1186/s12864-022-08341-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/28/2022] [Indexed: 11/23/2022] Open
Abstract
Background Seed germination is a series of ordered physiological and morphogenetic processes and a critical stage in plant life cycle. Tamarix hispida is one of the most salt-tolerant plant species; however, its seed germination has not been analysed using combined transcriptomics and metabolomics. Results Transcriptomic sequencing and widely targeted metabolomics were used to detect the transcriptional metabolic profiles of T. hispida at different stages of seed germination and young seedling growth. Transcriptomics showed that 46,538 genes were significantly altered throughout the studied development period. Enrichment study revealed that plant hormones, such as auxin, ABA, JA and SA played differential roles at varying stages of seed germination and post-germination. Metabolomics detected 1022 metabolites, with flavonoids accounting for the highest proportion of differential metabolites. Combined analysis indicated that flavonoid biosynthesis in young seedling growth, such as rhoifolin and quercetin, may improve the plant’s adaptative ability to extreme desert environments. Conclusions The differential regulation of plant hormones and the accumulation of flavonoids may be important for the seed germination survival of T. hispida in response to salt or arid deserts. This study enhanced the understanding of the overall mechanism in seed germination and post-germination. The results provide guidance for the ecological value and young seedling growth of T. hispida. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08341-x.
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Affiliation(s)
- Xin'an Pang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Corps, College of Life Sciences, Tarim University, Alar, 843300, China
| | - Jiangtao Suo
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Shuo Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Jindong Xu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Tian'ge Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Niyan Xiang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Yue Wu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Bojie Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China.
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China.
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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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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da Fonseca-Pereira P, Pham PA, Cavalcanti JHF, Omena-Garcia RP, Barros JAS, Rosado-Souza L, Vallarino JG, Mutwil M, Avin-Wittenberg T, Nunes-Nesi A, Fernie AR, Araújo WL. The Arabidopsis electron-transfer flavoprotein:ubiquinone oxidoreductase is required during normal seed development and germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:196-214. [PMID: 34741366 DOI: 10.1111/tpj.15566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
The importance of the alternative donation of electrons to the ubiquinol pool via the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO) complex has been demonstrated. However, the functional significance of this pathway during seed development and germination remains to be elucidated. To assess the function of this pathway, we performed a detailed metabolic and transcriptomic analysis of Arabidopsis mutants to test the molecular consequences of a dysfunctional ETF/ETFQO pathway. We demonstrate that the disruption of this pathway compromises seed germination in the absence of an external carbon source and also impacts seed size and yield. Total protein and storage protein content is reduced in dry seeds, whilst sucrose levels remain invariant. Seeds of ETFQO and related mutants were also characterized by an altered fatty acid composition. During seed development, lower levels of fatty acids and proteins accumulated in the etfqo-1 mutant as well as in mutants in the alternative electron donors isovaleryl-CoA dehydrogenase (ivdh-1) and d-2-hydroxyglutarate dehydrogenase (d2hgdh1-2). Furthermore, the content of several amino acids was increased in etfqo-1 mutants during seed development, indicating that these mutants are not using such amino acids as alternative energy source for respiration. Transcriptome analysis revealed alterations in the expression levels of several genes involved in energy and hormonal metabolism. Our findings demonstrated that the alternative pathway of respiration mediated by the ETF/ETFQO complex affects seed germination and development by directly adjusting carbon storage during seed filling. These results indicate a role for the pathway in the normal plant life cycle to complement its previously defined roles in the response to abiotic stress.
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Affiliation(s)
- Paula da Fonseca-Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - Phuong Anh Pham
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - João Henrique F Cavalcanti
- Instituto de Educação, Agricultura e Ambiente, Universidade Federal do Amazonas, Humaitá, Amazonas, Brazil
| | - Rebeca P Omena-Garcia
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Jessica A S Barros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Laise Rosado-Souza
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - José G Vallarino
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Tamar Avin-Wittenberg
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, 9190401, Israel
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
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Peng L, Huang X, Qi M, Pritchard HW, Xue H. Mechanistic insights derived from re-establishment of desiccation tolerance in germinating xerophytic seeds: Caragana korshinskii as an example. FRONTIERS IN PLANT SCIENCE 2022; 13:1029997. [PMID: 36420023 PMCID: PMC9677110 DOI: 10.3389/fpls.2022.1029997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 09/27/2022] [Indexed: 05/13/2023]
Abstract
Germplasm conservation strongly depends on the desiccation tolerance (DT) of seeds. Xerophytic seeds have strong desiccation resistance, which makes them excellent models to study DT. Although some experimental strategies have been applied previously, most methods are difficult to apply to xerophytic seeds. In this review, we attempted to synthesize current strategies for the study of seed DT and provide an in-depth look at Caragana korshinskii as an example. First, we analyze congenital advantages of xerophytes in the study of seed DT. Second, we summarize several strategies used to study DT and illustrate a suitable strategy for xerophytic species. Then, based on our previous studies work with C. korshinskii, a feasible technical strategy for DT re-establishment is provided and we provide illustrate some special molecular mechanisms seen in xerophytic seeds. Finally, several steps to unveil the DT mechanism of xerophytic seeds are suggested, and three scientific questions that the field should consider are listed. We hope to optimize and utilize this strategy for more xerophytic species to more systematically decipher the physiological and molecular processes of seed DT and provide more candidate genes for molecular breeding.
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Affiliation(s)
- Long Peng
- The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xu Huang
- National Engineering Research Center of Tree breeding and Ecological remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Manyao Qi
- National Engineering Research Center of Tree breeding and Ecological remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hugh W. Pritchard
- Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
- Royal Botanic Gardens, Kew, Wakehurst, West Sussex, United Kingdom
| | - Hua Xue
- National Engineering Research Center of Tree breeding and Ecological remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- *Correspondence: Hua Xue,
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Guo H, Lyv Y, Zheng W, Yang C, Li Y, Wang X, Chen R, Wang C, Luo J, Qu L. Comparative Metabolomics Reveals Two Metabolic Modules Affecting Seed Germination in Rice ( Oryza sativa). Metabolites 2021; 11:metabo11120880. [PMID: 34940638 PMCID: PMC8707830 DOI: 10.3390/metabo11120880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/05/2021] [Accepted: 12/13/2021] [Indexed: 12/18/2022] Open
Abstract
The process of seed germination is crucial not only for the completion of the plant life cycle but also for agricultural production and food chemistry; however, the underlying metabolic regulation mechanism involved in this process is still far from being clearly revealed. In this study, one indica variety (Zhenshan 97, with rapid germination) and one japonica variety (Nipponbare, with slow germination) in rice were used for in-depth analysis of the metabolome at different germination stages (0, 3, 6, 9, 12, 24, 36, and 48 h after imbibition, HAI) and exploration of key metabolites/metabolic pathways. In total, 380 annotated metabolites were analyzed by using a high-performance liquid chromatography (HPLC)-based targeted method combined with a nontargeted metabolic profiling method. By using bioinformatics and statistical methods, the dynamic changes in metabolites during germination in the two varieties were compared. Through correlation analysis, coefficient of variation analysis and differential accumulation analysis, 74 candidate metabolites that may be closely related to seed germination were finally screened. Among these candidates, 29 members belong to the ornithine–asparagine–polyamine module and the shikimic acid–tyrosine–tryptamine–phenylalanine–flavonoid module. As the core member of the second module, shikimic acid’s function in the promotion of seed germination was confirmed by exogenous treatment. These results told that nitrogen flow and antioxidation/defense responses are potentially crucial for germinating seeds and seedlings. It deepens our understanding of the metabolic regulation mechanism of seed germination and points out the direction for our future research.
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Affiliation(s)
- Hao Guo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (H.G.); (Y.L.); (W.Z.); (C.Y.); (Y.L.); (X.W.); (J.L.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- College of Tropical Crops, Hainan University, Haikou 570228, China; (R.C.); (C.W.)
| | - Yuanyuan Lyv
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (H.G.); (Y.L.); (W.Z.); (C.Y.); (Y.L.); (X.W.); (J.L.)
- College of Tropical Crops, Hainan University, Haikou 570228, China; (R.C.); (C.W.)
| | - Weikang Zheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (H.G.); (Y.L.); (W.Z.); (C.Y.); (Y.L.); (X.W.); (J.L.)
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (H.G.); (Y.L.); (W.Z.); (C.Y.); (Y.L.); (X.W.); (J.L.)
| | - Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (H.G.); (Y.L.); (W.Z.); (C.Y.); (Y.L.); (X.W.); (J.L.)
| | - Xuyang Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (H.G.); (Y.L.); (W.Z.); (C.Y.); (Y.L.); (X.W.); (J.L.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ridong Chen
- College of Tropical Crops, Hainan University, Haikou 570228, China; (R.C.); (C.W.)
| | - Chao Wang
- College of Tropical Crops, Hainan University, Haikou 570228, China; (R.C.); (C.W.)
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (H.G.); (Y.L.); (W.Z.); (C.Y.); (Y.L.); (X.W.); (J.L.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- College of Tropical Crops, Hainan University, Haikou 570228, China; (R.C.); (C.W.)
| | - Lianghuan Qu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (H.G.); (Y.L.); (W.Z.); (C.Y.); (Y.L.); (X.W.); (J.L.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
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Liu B, Sun G, Liu C, Liu S. LEAFY COTYLEDON 2: A Regulatory Factor of Plant Growth and Seed Development. Genes (Basel) 2021; 12:genes12121896. [PMID: 34946844 PMCID: PMC8701892 DOI: 10.3390/genes12121896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription factors are key molecules in the regulation of gene expression in all organisms. The transcription factor LEAFY COTYLEDON 2 (LEC2), which belongs to the DNA-binding protein family, contains a B3 domain. The transcription factor is involved in the regulation of important plant biological processes such as embryogenesis, somatic embryo formation, seed storage protein synthesis, fatty acid metabolism, and other important biological processes. Recent studies have shown that LEC2 regulates the formation of lateral roots and influences the embryonic resetting of the parental vernalization state. The orthologs of LEC2 and their regulatory effects have also been identified in some crops; however, their regulatory mechanism requires further investigation. Here, we summarize the most recent findings concerning the effects of LEC2 on plant growth and seed development. In addition, we discuss the potential molecular mechanisms of the action of the LEC2 gene during plant development.
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Song Y, Gao X, Wu Y. Key Metabolite Differences Between Korean Pine ( Pinus koraiensis) Seeds With Primary Physiological Dormancy and No-Dormancy. FRONTIERS IN PLANT SCIENCE 2021; 12:767108. [PMID: 34880891 PMCID: PMC8647843 DOI: 10.3389/fpls.2021.767108] [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: 08/30/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Pinus Koraiensis seeds have physiological dormancy. Cold stratification releases seed dormancy. The changes in metabolite profiles of dormant seeds and cold stratified seeds during shorter incubation time in a favorable condition for seed germination have been studied. However, a more-long-term detection of the changes in metabolites in dormant seeds can identify the real metabolic pathways responsible for dormancy. Metabolite composition was investigated in embryo and megagametophyte of primary physiological dormant seeds (DS) of P. Koraiensis collected at 0, 1, 2, 4, and 6 weeks of incubation and of non-primary physiological dormant seeds (NDS) sampled at 0 and 1 week of incubation, seed coat rupture stage, and radicle protrusion stage. Embryos contained higher levels of most metabolites than megagametophyte. Strong accumulation of most metabolites in DS occurred at 1 and 4 weeks of incubation. A larger reduction in the relative levels of most phosphorylated sugars and amino acids in NDS was found between 1-week-incubation and seed coat rupture stage. The relative levels of metabolites involved in carbohydrate metabolism, especially the pentose phosphate pathway (PPP) and tricarboxylic acid (TCA) cycle, were higher in the embryos of 4-week-incubated DS, but the relative contents of intermediate metabolites of most amino acid metabolism were lower compared to 1-week-incubated NDS. We suggested that the disturbed carbohydrate metabolism and amino acid metabolism in the embryos of DS after 4 weeks of incubation maybe related to primary dormancy. Our study provides information for a better understanding of the mechanism of seed dormancy.
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Affiliation(s)
- Yuan Song
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang, China
- Karst Environmental Geological Hazard Prevention Laboratory of Guizhou Minzu University, Guiyang, China
| | - Xiaoye Gao
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang, China
| | - Yunjie Wu
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang, China
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Wang Y, Zhang J, Sun M, He C, Yu K, Zhao B, Li R, Li J, Yang Z, Wang X, Duan H, Fu J, Liu S, Zhang X, Zheng J. Multi-Omics Analyses Reveal Systemic Insights into Maize Vivipary. PLANTS (BASEL, SWITZERLAND) 2021; 10:2437. [PMID: 34834800 PMCID: PMC8618366 DOI: 10.3390/plants10112437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Maize vivipary, precocious seed germination on the ear, affects yield and seed quality. The application of multi-omics approaches, such as transcriptomics or metabolomics, to classic vivipary mutants can potentially reveal the underlying mechanism. Seven maize vivipary mutants were selected for transcriptomic and metabolomic analyses. A suite of transporters and transcription factors were found to be upregulated in all mutants, indicating that their functions are required during seed germination. Moreover, vivipary mutants exhibited a uniform expression pattern of genes related to abscisic acid (ABA) biosynthesis, gibberellin (GA) biosynthesis, and ABA core signaling. NCED4 (Zm00001d007876), which is involved in ABA biosynthesis, was markedly downregulated and GA3ox (Zm00001d039634) was upregulated in all vivipary mutants, indicating antagonism between these two phytohormones. The ABA core signaling components (PYL-ABI1-SnRK2-ABI3) were affected in most of the mutants, but the expression of these genes was not significantly different between the vp8 mutant and wild-type seeds. Metabolomics analysis integrated with co-expression network analysis identified unique metabolites, their corresponding pathways, and the gene networks affected by each individual mutation. Collectively, our multi-omics analyses characterized the transcriptional and metabolic landscape during vivipary, providing a valuable resource for improving seed quality.
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Affiliation(s)
- Yiru Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (M.S.); (R.L.); (J.L.); (Z.Y.); (J.F.)
| | - Junli Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng 475000, China; (J.Z.); (K.Y.); (B.Z.); (X.W.); (H.D.)
| | - Minghao Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (M.S.); (R.L.); (J.L.); (Z.Y.); (J.F.)
| | - Cheng He
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA; (C.H.); (S.L.)
| | - Ke Yu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng 475000, China; (J.Z.); (K.Y.); (B.Z.); (X.W.); (H.D.)
| | - Bing Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng 475000, China; (J.Z.); (K.Y.); (B.Z.); (X.W.); (H.D.)
| | - Rui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (M.S.); (R.L.); (J.L.); (Z.Y.); (J.F.)
| | - Jian Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (M.S.); (R.L.); (J.L.); (Z.Y.); (J.F.)
| | - Zongying Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (M.S.); (R.L.); (J.L.); (Z.Y.); (J.F.)
| | - Xiao Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng 475000, China; (J.Z.); (K.Y.); (B.Z.); (X.W.); (H.D.)
| | - Haiyang Duan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng 475000, China; (J.Z.); (K.Y.); (B.Z.); (X.W.); (H.D.)
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (M.S.); (R.L.); (J.L.); (Z.Y.); (J.F.)
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA; (C.H.); (S.L.)
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng 475000, China; (J.Z.); (K.Y.); (B.Z.); (X.W.); (H.D.)
| | - Jun Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (M.S.); (R.L.); (J.L.); (Z.Y.); (J.F.)
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DeMers LC, Raboy V, Li S, Saghai Maroof MA. Network Inference of Transcriptional Regulation in Germinating Low Phytic Acid Soybean Seeds. FRONTIERS IN PLANT SCIENCE 2021; 12:708286. [PMID: 34531883 PMCID: PMC8438133 DOI: 10.3389/fpls.2021.708286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/23/2021] [Indexed: 05/14/2023]
Abstract
The low phytic acid (lpa) trait in soybeans can be conferred by loss-of-function mutations in genes encoding myo-inositol phosphate synthase and two epistatically interacting genes encoding multidrug-resistance protein ATP-binding cassette (ABC) transporters. However, perturbations in phytic acid biosynthesis are associated with poor seed vigor. Since the benefits of the lpa trait, in terms of end-use quality and sustainability, far outweigh the negatives associated with poor seed performance, a fuller understanding of the molecular basis behind the negatives will assist crop breeders and engineers in producing variates with lpa and better germination rate. The gene regulatory network (GRN) for developing low and normal phytic acid soybean seeds was previously constructed, with genes modulating a variety of processes pertinent to phytic acid metabolism and seed viability being identified. In this study, a comparative time series analysis of low and normal phytic acid soybeans was carried out to investigate the transcriptional regulatory elements governing the transitional dynamics from dry seed to germinated seed. GRNs were reverse engineered from time series transcriptomic data of three distinct genotypic subsets composed of lpa soybean lines and their normal phytic acid sibling lines. Using a robust unsupervised network inference scheme, putative regulatory interactions were inferred for each subset of genotypes. These interactions were further validated by published regulatory interactions found in Arabidopsis thaliana and motif sequence analysis. Results indicate that lpa seeds have increased sensitivity to stress, which could be due to changes in phytic acid levels, disrupted inositol phosphate signaling, disrupted phosphate ion (Pi) homeostasis, and altered myo-inositol metabolism. Putative regulatory interactions were identified for the latter two processes. Changes in abscisic acid (ABA) signaling candidate transcription factors (TFs) putatively regulating genes in this process were identified as well. Analysis of the GRNs reveal altered regulation in processes that may be affecting the germination of lpa soybean seeds. Therefore, this work contributes to the ongoing effort to elucidate molecular mechanisms underlying altered seed viability, germination and field emergence of lpa crops, understanding of which is necessary in order to mitigate these problems.
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Affiliation(s)
- Lindsay C. DeMers
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Victor Raboy
- National Small Grains Germplasm Research Center, Agricultural Research Service (USDA), Aberdeen, ID, United States
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - M. A. Saghai Maroof
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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Chen S, Ren C, Zhai J, Yu J, Zhao X, Li Z, Zhang T, Ma W, Han Z, Ma C. CAFU: a Galaxy framework for exploring unmapped RNA-Seq data. Brief Bioinform 2021; 21:676-686. [PMID: 30815667 PMCID: PMC7299299 DOI: 10.1093/bib/bbz018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/23/2019] [Accepted: 01/27/2019] [Indexed: 12/13/2022] Open
Abstract
A widely used approach in transcriptome analysis is the alignment of short reads to a reference genome. However, owing to the deficiencies of specially designed analytical systems, short reads unmapped to the genome sequence are usually ignored, resulting in the loss of significant biological information and insights. To fill this gap, we present Comprehensive Assembly and Functional annotation of Unmapped RNA-Seq data (CAFU), a Galaxy-based framework that can facilitate the large-scale analysis of unmapped RNA sequencing (RNA-Seq) reads from single- and mixed-species samples. By taking advantage of machine learning techniques, CAFU addresses the issue of accurately identifying the species origin of transcripts assembled using unmapped reads from mixed-species samples. CAFU also represents an innovation in that it provides a comprehensive collection of functions required for transcript confidence evaluation, coding potential calculation, sequence and expression characterization and function annotation. These functions and their dependencies have been integrated into a Galaxy framework that provides access to CAFU via a user-friendly interface, dramatically simplifying complex exploration tasks involving unmapped RNA-Seq reads. CAFU has been validated with RNA-Seq data sets from wheat and Zea mays (maize) samples. CAFU is freely available via GitHub: https://github.com/cma2015/CAFU.
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Affiliation(s)
- Siyuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Chengzhi Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Jingjing Zhai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Jiantao Yu
- College of Information Engineering, Northwest Agriculture and Forestry University
| | - Xuyang Zhao
- College of Information Engineering, Northwest Agriculture and Forestry University
| | - Zelong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Ting Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Wenlong Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Zhaoxue Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
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