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Ye J, Fan Y, Zhang H, Teng W, Teng K, Wu J, Fan X, Wang S, Yue Y. Octoploids Show Enhanced Salt Tolerance through Chromosome Doubling in Switchgrass ( Panicum virgatum L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1383. [PMID: 38794454 PMCID: PMC11124981 DOI: 10.3390/plants13101383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Polyploid plants often exhibit enhanced stress tolerance. Switchgrass is a perennial rhizomatous bunchgrass that is considered ideal for cultivation in marginal lands, including sites with saline soil. In this study, we investigated the physiological responses and transcriptome changes in the octoploid and tetraploid of switchgrass (Panicum virgatum L. 'Alamo') under salt stress. We found that autoploid 8× switchgrass had enhanced salt tolerance compared with the amphidiploid 4× precursor, as indicated by physiological and phenotypic traits. Octoploids had increased salt tolerance by significant changes to the osmoregulatory and antioxidant systems. The salt-treated 8× Alamo plants showed greater potassium (K+) accumulation and an increase in the K+/Na+ ratio. Root transcriptome analysis for octoploid and tetraploid plants with or without salt stress revealed that 302 upregulated and 546 downregulated differentially expressed genes were enriched in genes involved in plant hormone signal transduction pathways and were specifically associated with the auxin, cytokinin, abscisic acid, and ethylene pathways. Weighted gene co-expression network analysis (WGCNA) detected four significant salt stress-related modules. This study explored the changes in the osmoregulatory system, inorganic ions, antioxidant enzyme system, and the root transcriptome in response to salt stress in 8× and 4× Alamo switchgrass. The results enhance knowledge of the salt tolerance of artificially induced homologous polyploid plants and provide experimental and sequencing data to aid research on the short-term adaptability and breeding of salt-tolerant biofuel plants.
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Affiliation(s)
- Jiali Ye
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yupu Fan
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Xianyang 712100, China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Hui Zhang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
| | - Wenjun Teng
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
| | - Ke Teng
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
| | - Juying Wu
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
| | - Xifeng Fan
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
| | - Shiwen Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Xianyang 712100, China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yuesen Yue
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
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Emerging Function of Ecotype-Specific Splicing in the Recruitment of Commensal Microbiome. Int J Mol Sci 2022; 23:ijms23094860. [PMID: 35563250 PMCID: PMC9100151 DOI: 10.3390/ijms23094860] [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: 03/19/2022] [Revised: 04/15/2022] [Accepted: 04/25/2022] [Indexed: 12/20/2022] Open
Abstract
In recent years, host-microbiome interactions in both animals and plants has emerged as a novel research area for studying the relationship between host organisms and their commensal microbial communities. The fitness advantages of this mutualistic interaction can be found in both plant hosts and their associated microbiome, however, the driving forces mediating this beneficial interaction are poorly understood. Alternative splicing (AS), a pivotal post-transcriptional mechanism, has been demonstrated to play a crucial role in plant development and stress responses among diverse plant ecotypes. This natural variation of plants also has an impact on their commensal microbiome. In this article, we review the current progress of plant natural variation on their microbiome community, and discuss knowledge gaps between AS regulation of plants in response to their intimately related microbiota. Through the impact of this article, an avenue could be established to study the biological mechanism of naturally varied splicing isoforms on plant-associated microbiome assembly.
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Tossi VE, Martínez Tosar LJ, Laino LE, Iannicelli J, Regalado JJ, Escandón AS, Baroli I, Causin HF, Pitta-Álvarez SI. Impact of polyploidy on plant tolerance to abiotic and biotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:869423. [PMID: 36072313 PMCID: PMC9441891 DOI: 10.3389/fpls.2022.869423] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/25/2022] [Indexed: 05/04/2023]
Abstract
Polyploidy, defined as the coexistence of three or more complete sets of chromosomes in an organism's cells, is considered as a pivotal moving force in the evolutionary history of vascular plants and has played a major role in the domestication of several crops. In the last decades, improved cultivars of economically important species have been developed artificially by inducing autopolyploidy with chemical agents. Studies on diverse species have shown that the anatomical and physiological changes generated by either natural or artificial polyploidization can increase tolerance to abiotic and biotic stresses as well as disease resistance, which may positively impact on plant growth and net production. The aim of this work is to review the current literature regarding the link between plant ploidy level and tolerance to abiotic and biotic stressors, with an emphasis on the physiological and molecular mechanisms responsible for these effects, as well as their impact on the growth and development of both natural and artificially generated polyploids, during exposure to adverse environmental conditions. We focused on the analysis of those types of stressors in which more progress has been made in the knowledge of the putative morpho-physiological and/or molecular mechanisms involved, revealing both the factors in common, as well as those that need to be addressed in future research.
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Affiliation(s)
- Vanesa E. Tossi
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Leandro J. Martínez Tosar
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Departamento de Biotecnología, Alimentos, Agro y Ambiental (DEBAL), Facultad de Ingeniería y Ciencias Exactas, Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina
| | - Leandro E. Laino
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Jesica Iannicelli
- Instituto Nacional de Tecnología, Agropecuaria (INTA), Instituto de Genética “Ewald A. Favret”, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Biodiversidad y Biología Experimental (IBBEA), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - José Javier Regalado
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Alejandro Salvio Escandón
- Instituto Nacional de Tecnología, Agropecuaria (INTA), Instituto de Genética “Ewald A. Favret”, Buenos Aires, Argentina
| | - Irene Baroli
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Biodiversidad y Biología Experimental (IBBEA), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Irene Baroli,
| | - Humberto Fabio Causin
- Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Humberto Fabio Causin,
| | - Sandra Irene Pitta-Álvarez
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- *Correspondence: Sandra Irene Pitta-Álvarez, ;
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Garcia-Lozano M, Natarajan P, Levi A, Katam R, Lopez-Ortiz C, Nimmakayala P, Reddy UK. Altered chromatin conformation and transcriptional regulation in watermelon following genome doubling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:588-600. [PMID: 33788333 DOI: 10.1111/tpj.15256] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Polyploidy has played a crucial role in plant evolution, development and function. Synthetic autopolyploid represents an ideal system to investigate the effects of polyploidization on transcriptional regulation. In this study, we deciphered the impact of genome duplication at phenotypic and molecular levels in watermelon. Overall, 88% of the genes in tetraploid watermelon followed a >1:1 dosage effect, and accordingly, differentially expressed genes were largely upregulated. In addition, a great number of hypomethylated regions (1688) were identified in an isogenic tetraploid watermelon. These differentially methylated regions were localized in promoters and intergenic regions and near transcriptional start sites of the identified upregulated genes, which enhances the importance of methylation in gene regulation. These changes were reflected in sophisticated higher-order chromatin structures. The genome doubling caused switching of 108 A and 626 B compartments that harbored genes associated with growth, development and stress responses.
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Affiliation(s)
- Marleny Garcia-Lozano
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Amnon Levi
- USDA, ARS, U.S. Vegetable Lab, Charleston, SC, USA
| | - Ramesh Katam
- Department of Biological Sciences, Florida A&M University, Tallahassee, FL, USA
| | - Carlos Lopez-Ortiz
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
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5
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Li H, Chen FJ, Yang WL, Qiao HZ, Zhang SJ. Quercetin improves cognitive disorder in aging mice by inhibiting NLRP3 inflammasome activation. Food Funct 2020; 12:717-725. [PMID: 33338087 DOI: 10.1039/d0fo01900c] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Quercetin is one of the most abundant dietary flavonoid compounds, and its mechanism for combating age-related neurodegenerative diseases is unclear. In this study, quercetin (35 and 70 mg kg-1, orally administered for 4 weeks) was administered to 7-month-old aging mice (senescence-accelerated mouse prone 8 mice). As a result, it was found that quercetin could improve spatial learning and memory impairment displayed by aging mice in the Morris water maze. The results of immunoblotting reflected the protein expressions of the longevity factor (sirtuin1), inflammasomes (NLRP3 and ASC), synaptic marker (PSD95) and neurotrophic factors (BDNF and NGF) in the hippocampus of the brain. It indicated that the intervention of quercetin could increase the expression of sirtuin1 and prevent neuroinflammation, which was evident from the decrease in the protein levels of the astrocyte marker (GFAP) and inflammatory factors (cleaved-caspase 1, IL-1β and IL-18). In addition, quercetin could reduce the levels of malondialdehyde (MDA) and reactive oxygen species (ROS) in the hippocampus of aging mice. Current data indicated that quercetin might improve neuroinflammation in aging mice by regulating the Sirtuin1/NLRP3 pathway.
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Affiliation(s)
- Han Li
- Department of Neurology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
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Chen MX, Zhang KL, Zhang M, Das D, Fang YM, Dai L, Zhang J, Zhu FY. Alternative splicing and its regulatory role in woody plants. TREE PHYSIOLOGY 2020; 40:1475-1486. [PMID: 32589747 DOI: 10.1093/treephys/tpaa076] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 05/22/2023]
Abstract
Alternative splicing (AS) is an important post-transcriptional process to enhance proteome diversity in eukaryotic organisms. In plants, numerous reports have primarily focused on AS analysis in model plant species or herbaceous plants, leading to a notable lack of research on AS in woody plants. More importantly, emerging evidence indicates that many important traits, including wood formation and stress resistance, in woody plants are controlled by AS. In this review article, we summarize the current progress of all kinds of AS studies in different tree species at various stages of development and in response to various stresses, revealing the significant role played by AS in woody plants, as well as the similar properties and differential regulation within their herbaceous counterparts. Furthermore, we propose several potential strategies to facilitate the functional characterization of splicing factors in woody plants and evaluate a general pipeline for the systematic characterization of splicing isoforms in a complex AS regulatory network. The utilization of genetic studies and high-throughput omics integration approaches to analyze AS genes and splicing factors is likely to further advance our understanding of AS modulation in woody plants.
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Affiliation(s)
- Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, 410128, China
| | - Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Debatosh Das
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Yan-Ming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Lei Dai
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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Ambastha V, Leshem Y. Differential cell persistence is observed in the Arabidopsis female gametophyte during heat stress. PLANT REPRODUCTION 2020; 33:111-116. [PMID: 32405809 DOI: 10.1007/s00497-020-00390-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/05/2020] [Indexed: 05/22/2023]
Abstract
The central cell withstands heat stress better than the egg and antipodal cells. Insilco analysis of transcriptomic data identified several heat responsive genes which are central cell specific. Crop damage due to heat stress (HS) is a major cause of yield lost. Plants are particularly susceptible to negative effects of HS during gametophyte development and fertilization. Extensive studies have been performed on the male gametophyte under HS, but how the female gametophyte copes with HS is largely unknown. To learn how the different cell types of the female gametophyte reacts to HS, we studied unfertilized CDC123::H2B:YFP ovules. We found that the YFP-specific florescent signal persisted in the central cell during HS significantly more than the egg cell. We also found that the fluorescent signal persistence was the lowest in the antipodal cells. This finding suggests that the reaction of the female gametophyte to HS is rather unique and differentially mediated according to the cell's identity. In addition, mining through published transcriptomic datasets we found that several important heat stress responsive genes which are extremely upregulated during HS (more than 64-fold) are specifically expressed in the CC but not in the EC. Further research such as comparative transcriptomics and cell biology will likely shed more light on the phenomena reported here and increase our basic understandings about the ways sexual reproduction processes are affected by heat stress.
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Affiliation(s)
- Vivek Ambastha
- Department of Plant Sciences, MIGAL - Galilee Research Institute, 2 Tarshish St., P.O.B. 831, 11016, Kiryat-Shmona, Israel
| | - Yehoram Leshem
- Department of Plant Sciences, MIGAL - Galilee Research Institute, 2 Tarshish St., P.O.B. 831, 11016, Kiryat-Shmona, Israel.
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Song XM, Wang JP, Sun PC, Ma X, Yang QH, Hu JJ, Sun SR, Li YX, Yu JG, Feng SY, Pei QY, Yu T, Yang NS, Liu YZ, Li XQ, Paterson AH, Wang XY. Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization. HORTICULTURE RESEARCH 2020; 7:20. [PMID: 32133148 PMCID: PMC7035258 DOI: 10.1038/s41438-020-0253-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/12/2019] [Accepted: 01/15/2020] [Indexed: 05/04/2023]
Abstract
Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants. Plants have evolved adaptive mechanisms to cope with cold stress. Here, through the genomic analysis of Arabidopsis, three Brassica species and 17 other representative species, we found that both cold-related genes (CRGs) and their collinearity were preferentially retained after polyploidization followed by genome instability, while genome-wide gene sets exhibited a variety of other expansion mechanisms. The cold-related regulatory network was increased in Brassicaceae genomes, which were recursively affected by polyploidization. By combining our findings regarding the selective retention of CRGs from this ecological genomics study with the available knowledge of cold-induced chromosome doubling, we hypothesize that cold stress may have contributed to the success of polyploid plants through both increasing polyploidization and selectively maintaining CRGs during evolution. This hypothesis requires further biological and ecological exploration to obtain solid supporting evidence, which will potentially contribute to understanding the generation of polyploids and to the field of ecological genomics.
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Affiliation(s)
- Xiao-Ming Song
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210 China
| | - Jin-Peng Wang
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210 China
| | - Peng-Chuan Sun
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210 China
| | - Xiao Ma
- Library, North China University of Science and Technology, Tangshan, 063210 China
| | - Qi-Hang Yang
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Jing-Jing Hu
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Sang-Rong Sun
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Yu-Xian Li
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210 China
| | - Ji-Gao Yu
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Shu-Yan Feng
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Qiao-Ying Pei
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Tong Yu
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Nan-Shan Yang
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Yin-Zhe Liu
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Xiu-Qing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick E3B 4Z7 Canada
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605 USA
| | - Xi-Yin Wang
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210 China
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Ruiz M, Oustric J, Santini J, Morillon R. Synthetic Polyploidy in Grafted Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:540894. [PMID: 33224156 PMCID: PMC7674608 DOI: 10.3389/fpls.2020.540894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/28/2020] [Indexed: 05/05/2023]
Abstract
Synthetic polyploids have been extensively studied for breeding in the last decade. However, the use of such genotypes at the agronomical level is still limited. Polyploidization is known to modify certain plant phenotypes, while leaving most of the fundamental characteristics apparently untouched. For this reason, polyploid breeding can be very useful for improving specific traits of crop varieties, such as quality, yield, or environmental adaptation. Nevertheless, the mechanisms that underlie polyploidy-induced novelty remain poorly understood. Ploidy-induced phenotypes might also include some undesired effects that need to be considered. In the case of grafted or composite crops, benefits can be provided both by the rootstock's adaptation to the soil conditions and by the scion's excellent yield and quality. Thus, grafted crops provide an extraordinary opportunity to exploit artificial polyploidy, as the effects can be independently applied and explored at the root and/or scion level, increasing the chances of finding successful combinations. The use of synthetic tetraploid (4x) rootstocks may enhance adaptation to biotic and abiotic stresses in perennial crops such as apple or citrus. However, their use in commercial production is still very limited. Here, we will review the current and prospective use of artificial polyploidy for rootstock and scion improvement and the implications of their combination. The aim is to provide insight into the methods used to generate and select artificial polyploids and their limitations, the effects of polyploidy on crop phenotype (anatomy, function, quality, yield, and adaptation to stresses) and their potential agronomic relevance as scions or rootstocks in the context of climate change.
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Affiliation(s)
- Marta Ruiz
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Julie Oustric
- Laboratoire Biochimie et Biologie Moléculaire du Végétal, CNRS, UMR 6134 SPE, Université de Corse, Corte, France
| | - Jérémie Santini
- Laboratoire Biochimie et Biologie Moléculaire du Végétal, CNRS, UMR 6134 SPE, Université de Corse, Corte, France
| | - Raphaël Morillon
- CIRAD, UMR AGAP, Equipe SEAPAG, F-97170 Petit-Bourg, Guadeloupe, France - AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- *Correspondence: Raphaël Morillon,
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Ye J, Zhang Y, Cui H, Liu J, Wu Y, Cheng Y, Xu H, Huang X, Li S, Zhou A, Zhang X, Bolund L, Chen Q, Wang J, Yang H, Fang L, Shi C. WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. Nucleic Acids Res 2019; 46:W71-W75. [PMID: 29788377 PMCID: PMC6030983 DOI: 10.1093/nar/gky400] [Citation(s) in RCA: 327] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/10/2018] [Indexed: 12/20/2022] Open
Abstract
WEGO (Web Gene Ontology Annotation Plot), created in 2006, is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. Owing largely to the rapid development of high-throughput sequencing and the increasing acceptance of GO, WEGO has benefitted from outstanding performance regarding the number of users and citations in recent years, which motivated us to update to version 2.0. WEGO uses the GO annotation results as input. Based on GO's standardized DAG (Directed Acyclic Graph) structured vocabulary system, the number of genes corresponding to each GO ID is calculated and shown in a graphical format. WEGO 2.0 updates have targeted four aspects, aiming to provide a more efficient and up-to-date approach for comparative genomic analyses. First, the number of input files, previously limited to three, is now unlimited, allowing WEGO to analyze multiple datasets. Also added in this version are the reference datasets of nine model species that can be adopted as baselines in genomic comparative analyses. Furthermore, in the analyzing processes each Chi-square test is carried out for multiple datasets instead of every two samples. At last, WEGO 2.0 provides an additional output graph along with the traditional WEGO histogram, displaying the sorted P-values of GO terms and indicating their significant differences. At the same time, WEGO 2.0 features an entirely new user interface. WEGO is available for free at http://wego.genomics.org.cn.
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Affiliation(s)
- Jia Ye
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Yong Zhang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Huihai Cui
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jiawei Liu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Yuqing Wu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,University of Auckland, Auckland, 1010, New Zealand
| | - Yun Cheng
- Zhejiang Hospital, Hangzhou, Zhejiang, 310013, China
| | - Huixing Xu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | | | - Shengting Li
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - An Zhou
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | | | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, Shandong, 266555, China.,Institute of Biomedicine, Aarhus University, Aarhus, DK-8000, Denmark
| | - Qiang Chen
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China.,Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, 350014, China.,Department of Stem Cell Research Institute, Fujian Medical University Stem Cell Research Institute, Fuzhou, Fujian, 350000, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | | | - Lin Fang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Chunmei Shi
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China.,Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, 350014, China.,Department of Stem Cell Research Institute, Fujian Medical University Stem Cell Research Institute, Fuzhou, Fujian, 350000, China
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11
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Wang Z, Zhao Z, Fan G, Dong Y, Deng M, Xu E, Zhai X, Cao H. A comparison of the transcriptomes between diploid and autotetraploid Paulownia fortunei under salt stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:1-11. [PMID: 30804626 PMCID: PMC6352521 DOI: 10.1007/s12298-018-0578-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/08/2018] [Accepted: 06/29/2018] [Indexed: 05/06/2023]
Abstract
Paulownia is a tree species grown in many countries. Our previous study reveals that tetraploid Paulownia fortunei is more tolerant to salt stress than its corresponding diploid tree. To investigate the molecular mechanisms of salt stress tolerance in P. fortunei, the transcriptomes of normal and salt-stressed diploid and tetraploid were investigated. After assembling the clean reads, we obtained 130,842 unigenes. The unigenes were aligned against six public databases (Nr, Nt, Swiss-Prot, COG, KEGG, GO) to discover homologs and assign functional annotations. We retrieved 7983 and 15,503 differentially expressed unigenes (DEUs) between the normal and the salt-stressed diploid and tetraploid P. fortunei, respectively. We identified dozens of important DEUs including 3 related to photosynthesis, 10 related to plant growth and development and 11 related to osmolytes. Some of these DEUs were upregulated in tetraploid compared to diploid and others were upregulated under salt stress. Quantitative reverse transcriptase polymerase chain reaction verified the expression patterns of 15 unigenes. Our results provided insights into the molecular aspects why tetraploid is stronger and more energetic than diploid under saline environment. This study provides useful information for further studies on the molecular mechanisms of salt tolerance in other tree plants.
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Affiliation(s)
- Zhe Wang
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Zhenli Zhao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Yanpeng Dong
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Minjie Deng
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Enkai Xu
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan People’s Republic of China
| | - Xiaoqiao Zhai
- Henan Academy of Forestry, Zhengzhou, Henan People’s Republic of China
| | - Heping Cao
- Southern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, New Orleans, LA 70124 USA
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12
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Robinson DO, Coate JE, Singh A, Hong L, Bush M, Doyle JJ, Roeder AHK. Ploidy and Size at Multiple Scales in the Arabidopsis Sepal. THE PLANT CELL 2018; 30:2308-2329. [PMID: 30143539 PMCID: PMC6241276 DOI: 10.1105/tpc.18.00344] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/10/2018] [Accepted: 08/22/2018] [Indexed: 05/02/2023]
Abstract
Ploidy and size phenomena are observed to be correlated across several biological scales, from subcellular to organismal. Two kinds of ploidy change can affect plants. Whole-genome multiplication increases ploidy in whole plants and is broadly associated with increases in cell and organism size. Endoreduplication increases ploidy in individual cells. Ploidy increase is strongly correlated with increased cell size and nuclear volume. Here, we investigate scaling relationships between ploidy and size by simultaneously quantifying nuclear size, cell size, and organ size in sepals from an isogenic series of diploid, tetraploid, and octoploid Arabidopsis thaliana plants, each of which contains an internal endopolyploidy series. We find that pavement cell size and transcriptome size increase linearly with whole-organism ploidy, but organ area increases more modestly due to a compensatory decrease in cell number. We observe that cell size and nuclear size are maintained at a constant ratio; the value of this constant is similar in diploid and tetraploid plants and slightly lower in octoploid plants. However, cell size is maintained in a mutant with reduced nuclear size, indicating that cell size is scaled to cell ploidy rather than to nuclear size. These results shed light on how size is regulated in plants and how cells and organisms of differing sizes are generated by ploidy change.
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Affiliation(s)
- Dana O Robinson
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Jeremy E Coate
- Department of Biology, Reed College, Portland, Oregon 97202
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, Biomedical Engineering, University of Delaware, Newark, Delaware 19716
| | - Lilan Hong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Max Bush
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jeff J Doyle
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, New York 14853
- School of Integrative Plant Science, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, New York 14853
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