1
|
Wei Y, Wang M, Wang M, Yu D, Wei X. Elevated CO 2 concentration enhance carbon and nitrogen metabolism and biomass accumulation of Ormosiahosiei. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108725. [PMID: 38772164 DOI: 10.1016/j.plaphy.2024.108725] [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: 10/05/2023] [Revised: 04/28/2024] [Accepted: 05/10/2024] [Indexed: 05/23/2024]
Abstract
Elevated CO2 concentrations may inhibit photosynthesis due to nitrogen deficiency, but legumes may be able to overcome this limitation and continue to grow. Our study confirms this conjecture well. First, we placed the two-year-old potted saplings of Ormosia hosiei (O. hosiei) (a leguminous tree species) in the open-top chamber (OTC) with three CO2 concentrations of 400 (CK), 600 (E1), and 800 μmol·mol-1 (E2) to simulate the elevated CO2 concentration environment. After 146 days, the light saturation point (LSP), light compensation point (LCP), apparent quantum efficiency (AQE), and dark respiration rate (Rd) of O. hosiei were increased under increasing CO2 concentration and obtain the maximum ribulose diphosphate (RuBP) carboxylation rate (Vc max) and RuBP regenerated photosynthetic electron transfer rate (Jmax) were also significantly increased under E2 treatment (P < 0.05). This results in a significant increase of the maximum assimilation rate (Amax) under elevated CO2 concentrations. Sucrose phosphate synthase (SPS) activity in sucrose metabolism increased in the leaves, more soluble sugars, starches, and sucrose was produced, but sucrose content only in leaves increased at E2, and more carbon flows to the roots. The activity of the NH4+ assimilating enzymes glutamine synthetase (GS), glutamate synthetase (GOGAT), and glutamate dehydrogenase (GDH) in the leaves of O. hosiei increases under elevated CO2 concentrations to promote nitrogen synthesis that reduces the content of ammonium nitrogen and increases the content of nitrate nitrogen. In addition, under E1 conditions, sucrose synthase (SS), direction of synthesis activity was highest and sucrose invertase (INV) activity was lowest, this means that the balance of C and N metabolism is maintained. While under E2 conditions SS activity decreased and INV activity increased, this increased C/N and nitrogen use efficiency. So, the elevated CO2 concentration promotes the accumulation of O. hosiei biomass, especially in the aboveground part, but did not have a significant effect on the accumulation of root biomass. This means that O. hosiei is able to cope under the elevated CO2 concentration without showing photosynthetic adaptation during the experimental period.
Collapse
Affiliation(s)
- Yi Wei
- College of Forestry, Guizhou University, Guiyang, China
| | - Mingbin Wang
- College of Forestry, Guizhou University, Guiyang, China
| | - Man Wang
- College of Forestry, Guizhou University, Guiyang, China
| | - Dalong Yu
- College of Forestry, Guizhou University, Guiyang, China
| | - Xiaoli Wei
- College of Forestry, Guizhou University, Guiyang, China; Institute for Forest Resources and the Environment of Guizhou, Guizhou University, Guiyang, China.
| |
Collapse
|
2
|
Banuelos J, Martínez-Romero E, Montaño NM, Camargo-Ricalde SL. Folates in legume root nodules. PHYSIOLOGIA PLANTARUM 2021; 171:447-452. [PMID: 32984974 DOI: 10.1111/ppl.13218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/04/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
Folates are multifunctional metabolites in plants that are essential for cell division, nucleic acids and amino acid synthesis. During symbiotic nitrogen fixation in legumes, these cofactors are needed for de novo purine biosynthesis, meaning that changes in the folate pools could directly affect the flow of fixed nitrogen to the plant. Its role related to symbiotic nitrogen fixation has not been yet explored, but recent data suggest a relevant role during the first steps. Transcriptomic, metabolomic and proteomic analyses indicate that folates are accumulated in symbiotic plant tissue, as they are involved, not only in de novo purines biosynthesis, but in nitrogen translocation, endoreduplication and phytohormones biosynthesis. Understanding the possible implication of folate pools during the nitrogen fixation and assimilation, might aid for new engineering targets, in relation to the two transformylations or the production of glycine by serine hydroxymethyltransferase during the de novo purine biosynthetic pathway. In this review, we intend to deliver and discuss the available evidence that support a relevant role of folates during the symbiotic nitrogen fixation.
Collapse
Affiliation(s)
- Jacob Banuelos
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autonoma Metropolitana, Mexico City, Mexico
| | | | - Noé Manuel Montaño
- Departamento de Biología, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Sara Lucía Camargo-Ricalde
- Departamento de Biología, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Mexico City, Mexico
| |
Collapse
|
3
|
Janská A, Svoboda P, Spiwok V, Kučera L, Ovesná J. The dehydration stress of couch grass is associated with its lipid metabolism, the induction of transporters and the re-programming of development coordinated by ABA. BMC Genomics 2018; 19:317. [PMID: 29720087 PMCID: PMC5930771 DOI: 10.1186/s12864-018-4700-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
Background The wild relatives of crop species represent a potentially valuable source of novel genetic variation, particularly in the context of improving the crop’s level of tolerance to abiotic stress. The mechanistic basis of these tolerances remains largely unexplored. Here, the focus was to characterize the transcriptomic response of the nodes (meristematic tissue) of couch grass (a relative of barley) to dehydration stress, and to compare it to that of the barley crown formed by both a drought tolerant and a drought sensitive barley cultivar. Results Many of the genes up-regulated in the nodes by the stress were homologs of genes known to be mediated by abscisic acid during the response to drought, or were linked to either development or lipid metabolism. Transporters also featured prominently, as did genes acting on root architecture. The resilience of the couch grass node arise from both their capacity to develop an altered, more effective root architecture, but also from their formation of a lipid barrier on their outer surface and their ability to modify both their lipid metabolism and transporter activity when challenged by dehydration stress. Conclusions Our analysis revealed the nature of dehydration stress response in couch grass. We suggested the tolerance is associated with lipid metabolism, the induction of transporters and the re-programming of development coordinated by ABA. We also proved the applicability of barley microarray for couch grass stress-response analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4700-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Anna Janská
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Svoboda
- Division of Crop Genetics and Breeding, Crop Research Institute, Prague, Czech Republic. .,Factulty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic.
| | - Vojtěch Spiwok
- Factulty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Ladislav Kučera
- Division of Crop Genetics and Breeding, Crop Research Institute, Prague, Czech Republic
| | - Jaroslava Ovesná
- Division of Crop Genetics and Breeding, Crop Research Institute, Prague, Czech Republic
| |
Collapse
|
4
|
Kudo T, Sasaki Y, Terashima S, Matsuda-Imai N, Takano T, Saito M, Kanno M, Ozaki S, Suwabe K, Suzuki G, Watanabe M, Matsuoka M, Takayama S, Yano K. Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants. Genes Genet Syst 2016; 91:111-125. [PMID: 27040147 DOI: 10.1266/ggs.15-00065] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In quantitative gene expression analysis, normalization using a reference gene as an internal control is frequently performed for appropriate interpretation of the results. Efforts have been devoted to exploring superior novel reference genes using microarray transcriptomic data and to evaluating commonly used reference genes by targeting analysis. However, because the number of specifically detectable genes is totally dependent on probe design in the microarray analysis, exploration using microarray data may miss some of the best choices for the reference genes. Recently emerging RNA sequencing (RNA-seq) provides an ideal resource for comprehensive exploration of reference genes since this method is capable of detecting all expressed genes, in principle including even unknown genes. We report the results of a comprehensive exploration of reference genes using public RNA-seq data from plants such as Arabidopsis thaliana (Arabidopsis), Glycine max (soybean), Solanum lycopersicum (tomato) and Oryza sativa (rice). To select reference genes suitable for the broadest experimental conditions possible, candidates were surveyed by the following four steps: (1) evaluation of the basal expression level of each gene in each experiment; (2) evaluation of the expression stability of each gene in each experiment; (3) evaluation of the expression stability of each gene across the experiments; and (4) selection of top-ranked genes, after ranking according to the number of experiments in which the gene was expressed stably. Employing this procedure, 13, 10, 12 and 21 top candidates for reference genes were proposed in Arabidopsis, soybean, tomato and rice, respectively. Microarray expression data confirmed that the expression of the proposed reference genes under broad experimental conditions was more stable than that of commonly used reference genes. These novel reference genes will be useful for analyzing gene expression profiles across experiments carried out under various experimental conditions.
Collapse
Affiliation(s)
- Toru Kudo
- School of Agriculture, Meiji University
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Baloglu MC, Inal B, Kavas M, Unver T. Diverse expression pattern of wheat transcription factors against abiotic stresses in wheat species. Gene 2014; 550:117-22. [DOI: 10.1016/j.gene.2014.08.025] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/12/2014] [Accepted: 08/13/2014] [Indexed: 12/14/2022]
|
6
|
Zhang T, Zhao X, Huang L, Liu X, Zong Y, Zhu L, Yang D, Fu B. Tissue-specific transcriptomic profiling of Sorghum propinquum using a rice genome array. PLoS One 2013; 8:e60202. [PMID: 23536906 PMCID: PMC3607598 DOI: 10.1371/journal.pone.0060202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 02/22/2013] [Indexed: 11/18/2022] Open
Abstract
Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were expressed predominantly in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in Oryza longistaminata and S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development.
Collapse
Affiliation(s)
- Ting Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liyu Huang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyue Liu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Zong
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linghua Zhu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Daichang Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (BF); (DY)
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (BF); (DY)
| |
Collapse
|
7
|
Liao D, Pajak A, Karcz SR, Chapman BP, Sharpe AG, Austin RS, Datla R, Dhaubhadel S, Marsolais F. Transcripts of sulphur metabolic genes are co-ordinately regulated in developing seeds of common bean lacking phaseolin and major lectins. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:6283-95. [PMID: 23066144 PMCID: PMC3481216 DOI: 10.1093/jxb/ers280] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The lack of phaseolin and phytohaemagglutinin in common bean (dry bean, Phaseolus vulgaris) is associated with an increase in total cysteine and methionine concentrations by 70% and 10%, respectively, mainly at the expense of an abundant non-protein amino acid, S-methyl-cysteine. Transcripts were profiled between two genetically related lines differing for this trait at four stages of seed development using a high density microarray designed for common bean. Transcripts of multiple sulphur-rich proteins were elevated, several previously identified by proteomics, including legumin, basic 7S globulin, albumin-2, defensin, albumin-1, the Bowman-Birk type proteinase inhibitor, the double-headed trypsin inhibitor, and the Kunitz trypsin inhibitor. A co-ordinated regulation of transcripts coding for sulphate transporters, sulphate assimilatory enzymes, serine acetyltransferases, cystathionine β-lyase, homocysteine S-methyltransferase and methionine gamma-lyase was associated with changes in cysteine and methionine concentrations. Differential gene expression of sulphur-rich proteins preceded that of sulphur metabolic enzymes, suggesting a regulation by demand from the protein sink. Up-regulation of SERAT1;1 and -1;2 expression revealed an activation of cytosolic O-acetylserine biosynthesis. Down-regulation of SERAT2;1 suggested that cysteine and S-methyl-cysteine biosynthesis may be spatially separated in different subcellular compartments. Analysis of free amino acid profiles indicated that enhanced cysteine biosynthesis was correlated with a depletion of O-acetylserine. These results contribute to our understanding of the regulation of sulphur metabolism in developing seed in response to a change in the composition of endogenous proteins.
Collapse
Affiliation(s)
- Dengqun Liao
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Agnieszka Pajak
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Steven R. Karcz
- Agriculture and Agri-Food Canada, Bioproducts and Bioprocesses, Saskatoon Research Centre, 107 Science Place, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - B. Patrick Chapman
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Andrew G. Sharpe
- National Research Council Canada, Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Ryan S. Austin
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Raju Datla
- National Research Council Canada, Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sangeeta Dhaubhadel
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Frédéric Marsolais
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
8
|
Díaz-Leal JL, Gálvez-Valdivieso G, Fernández J, Pineda M, Alamillo JM. Developmental effects on ureide levels are mediated by tissue-specific regulation of allantoinase in Phaseolus vulgaris L. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4095-106. [PMID: 22442417 DOI: 10.1093/jxb/ers090] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The ureides allantoin and allantoate are key molecules in the transport and storage of nitrogen in ureide legumes. In shoots and leaves from Phaseolus vulgaris plants using symbiotically fixed nitrogen as the sole nitrogen source, ureide levels were roughly equivalent to those of nitrate-supported plants during the whole vegetative stage, but they exhibited a sudden increase at the onset of flowering. This rise in the level of ureides, mainly in the form of allantoate, was accompanied by increases in allantoinase gene expression and enzyme activity, consistent with developmental regulation of ureide levels mainly through the tissue-specific induction of allantoate synthesis catalysed by allantoinase. Moreover, surprisingly high levels of ureides were also found in non-nodulated plants fertilized with nitrate, at both early and late developmental stages. The results suggest that remobilized N from lower leaves is probably involved in the sharp rise in ureides in shoots and leaves during early pod filling in N(2)-fixing plants and in the significant amounts of ureides observed in non-nodulated plants.
Collapse
Affiliation(s)
- Juan Luis Díaz-Leal
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, 1 planta, Universidad de Córdoba, 14071, Córdoba, Spain
| | | | | | | | | |
Collapse
|
9
|
Valdés-López O, Thibivilliers S, Qiu J, Xu WW, Nguyen TH, Libault M, Le BH, Goldberg RB, Hill CB, Hartman GL, Diers B, Stacey G. Identification of quantitative trait loci controlling gene expression during the innate immunity response of soybean. PLANT PHYSIOLOGY 2011; 157:1975-86. [PMID: 21963820 PMCID: PMC3327182 DOI: 10.1104/pp.111.183327] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 09/29/2011] [Indexed: 05/21/2023]
Abstract
Microbe-associated molecular pattern-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. However, most of our knowledge of MTI comes from studies of model systems with relatively little work done with crop plants. In this work, we report on variation in both the microbe-associated molecular pattern-triggered oxidative burst and gene expression across four soybean (Glycine max) genotypes. Variation in MTI correlated with the level of pathogen resistance for each genotype. A quantitative trait locus analysis on these traits identified four loci that appeared to regulate gene expression during MTI in soybean. Likewise, we observed that both MTI variation and pathogen resistance were quantitatively inherited. The approach utilized in this study may have utility for identifying key resistance loci useful for developing improved soybean cultivars.
Collapse
Affiliation(s)
- Oswaldo Valdés-López
- Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
| | - Sandra Thibivilliers
- Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
| | - Jing Qiu
- Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
| | - Wayne Wenzhong Xu
- Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
| | - Tran H.N. Nguyen
- Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
| | | | - Brandon H. Le
- Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
| | - Robert B. Goldberg
- Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
| | - Curtis B. Hill
- Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
| | - Glen L. Hartman
- Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
| | - Brian Diers
- Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
| | - Gary Stacey
- Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
| |
Collapse
|
10
|
Yin F, Pajak A, Chapman R, Sharpe A, Huang S, Marsolais F. Analysis of common bean expressed sequence tags identifies sulfur metabolic pathways active in seed and sulfur-rich proteins highly expressed in the absence of phaseolin and major lectins. BMC Genomics 2011; 12:268. [PMID: 21615926 PMCID: PMC3115882 DOI: 10.1186/1471-2164-12-268] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 05/26/2011] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND A deficiency in phaseolin and phytohemagglutinin is associated with a near doubling of sulfur amino acid content in genetically related lines of common bean (Phaseolus vulgaris), particularly cysteine, elevated by 70%, and methionine, elevated by 10%. This mostly takes place at the expense of an abundant non-protein amino acid, S-methyl-cysteine. The deficiency in phaseolin and phytohemagglutinin is mainly compensated by increased levels of the 11S globulin legumin and residual lectins. Legumin, albumin-2, defensin and albumin-1 were previously identified as contributing to the increased sulfur amino acid content in the mutant line, on the basis of similarity to proteins from other legumes. RESULTS Profiling of free amino acid in developing seeds of the BAT93 reference genotype revealed a biphasic accumulation of gamma-glutamyl-S-methyl-cysteine, the main soluble form of S-methyl-cysteine, with a lag phase occurring during storage protein accumulation. A collection of 30,147 expressed sequence tags (ESTs) was generated from four developmental stages, corresponding to distinct phases of gamma-glutamyl-S-methyl-cysteine accumulation, and covering the transitions to reserve accumulation and dessication. Analysis of gene ontology categories indicated the occurrence of multiple sulfur metabolic pathways, including all enzymatic activities responsible for sulfate assimilation, de novo cysteine and methionine biosynthesis. Integration of genomic and proteomic data enabled the identification and isolation of cDNAs coding for legumin, albumin-2, defensin D1 and albumin-1A and -B induced in the absence of phaseolin and phytohemagglutinin. Their deduced amino acid sequences have a higher content of cysteine than methionine, providing an explanation for the preferential increase of cysteine in the mutant line. CONCLUSION The EST collection provides a foundation to further investigate sulfur metabolism and the differential accumulation of sulfur amino acids in seed of common bean. Identification of sulfur-rich proteins whose levels are elevated in seed lacking phaseolin and phytohemagglutinin and sulfur metabolic genes may assist the improvement of protein quality.
Collapse
Affiliation(s)
- Fuqiang Yin
- Department of Bioscience and Biotechnology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | | | | | | | | | | |
Collapse
|
11
|
Yang SS, Tu ZJ, Cheung F, Xu WW, Lamb JFS, Jung HJG, Vance CP, Gronwald JW. Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 2011; 12:199. [PMID: 21504589 DOI: 10.1186/1471-2164-12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 04/19/2011] [Indexed: 05/23/2023] Open
Abstract
BACKGROUND Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. RESULTS Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. In addition, 341,984 ESTs were generated from ES and PES internodes of genotype 773 using the GS FLX Titanium platform. The first alfalfa (Medicago sativa) gene index (MSGI 1.0) was assembled using the Sanger ESTs available from GenBank, the GS FLX Titanium EST sequences, and the de novo assembled Illumina sequences. MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1,294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Out of 55 SNPs randomly selected for experimental validation, 47 (85%) were polymorphic between the two genotypes. We also identified numerous allelic variations within each genotype. Digital gene expression analysis identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. CONCLUSIONS Our results demonstrate that RNA-Seq can be successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a forage crop and cellulosic feedstock.
Collapse
Affiliation(s)
- S Samuel Yang
- USDA-Agricultural Research Service, Plant Science Research Unit, St, Paul, MN 55108, USA.
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Yang SS, Tu ZJ, Cheung F, Xu WW, Lamb JFS, Jung HJG, Vance CP, Gronwald JW. Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 2011; 12:199. [PMID: 21504589 PMCID: PMC3112146 DOI: 10.1186/1471-2164-12-199] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 04/19/2011] [Indexed: 02/08/2023] Open
Abstract
Background Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. Results Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. In addition, 341,984 ESTs were generated from ES and PES internodes of genotype 773 using the GS FLX Titanium platform. The first alfalfa (Medicago sativa) gene index (MSGI 1.0) was assembled using the Sanger ESTs available from GenBank, the GS FLX Titanium EST sequences, and the de novo assembled Illumina sequences. MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1,294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Out of 55 SNPs randomly selected for experimental validation, 47 (85%) were polymorphic between the two genotypes. We also identified numerous allelic variations within each genotype. Digital gene expression analysis identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. Conclusions Our results demonstrate that RNA-Seq can be successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a forage crop and cellulosic feedstock.
Collapse
Affiliation(s)
- S Samuel Yang
- USDA-Agricultural Research Service, Plant Science Research Unit, St, Paul, MN 55108, USA.
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Dittami SM, Proux C, Rousvoal S, Peters AF, Cock JM, Coppée JY, Boyen C, Tonon T. Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae). BMC Mol Biol 2011; 12:2. [PMID: 21226968 PMCID: PMC3027116 DOI: 10.1186/1471-2199-12-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 01/13/2011] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Brown algae of the genus Ectocarpus exhibit high levels of genetic diversity and variability in morphological and physiological characteristics. With the establishment of E. siliculosus as a model and the availability of a complete genome sequence, it is now of interest to analyze variability among different species, ecotypes, and strains of the genus Ectocarpus both at the genome and the transcriptome level. RESULTS We used an E. siliculosus gene expression microarray based on EST sequences from the genome-sequenced strain (reference strain) to carry out comparative genome hybridizations for five Ectocarpus strains: four E. siliculosus isolates (the male genome strain, a female strain used for outcrosses with the genome strain, a strain isolated from freshwater, and a highly copper-tolerant strain), as well as one strain of the sister species E. fasciculatus. Our results revealed significant genomic differences between ecotypes of the same species, and enable the selection of conserved probes for future microarray experiments with these strains. In the two closely related strains (a male and a female strain used for crosses), genomic differences were also detected, but concentrated in two smaller genomic regions, one of which corresponds to a viral insertion site. CONCLUSION The high variability between strains supports the concept of E. siliculosus as a complex of cryptic species. Moreover, our data suggest that several parts of the Ectocarpus genome may have evolved at different rates: high variability was detected particularly in transposable elements and fucoxanthin chlorophyll a/c binding proteins.
Collapse
Affiliation(s)
- Simon M Dittami
- UPMC Univ Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
- Current Address: Department of Biology, University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway
| | - Caroline Proux
- Institut Pasteur, Plate-Forme 2- Puces à ADN, 25 rue du docteur Roux, 75724 Paris Cedex 15, France
| | - Sylvie Rousvoal
- UPMC Univ Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
| | - Akira F Peters
- BEZHIN ROSKO, 40 rue des pêcheurs, 29250 Santec, France
- MBA Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - J Mark Cock
- UPMC Univ Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
| | - Jean-Yves Coppée
- Institut Pasteur, Plate-Forme 2- Puces à ADN, 25 rue du docteur Roux, 75724 Paris Cedex 15, France
| | - Catherine Boyen
- UPMC Univ Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
| | - Thierry Tonon
- UPMC Univ Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
| |
Collapse
|
14
|
Mensack MM, Fitzgerald VK, Ryan EP, Lewis MR, Thompson HJ, Brick MA. Evaluation of diversity among common beans (Phaseolus vulgaris L.) from two centers of domestication using 'omics' technologies. BMC Genomics 2010; 11:686. [PMID: 21126341 PMCID: PMC3014982 DOI: 10.1186/1471-2164-11-686] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 12/02/2010] [Indexed: 11/10/2022] Open
Abstract
Background Genetic diversity among wild accessions and cultivars of common bean (Phaseolus vulgaris L.) has been characterized using plant morphology, seed protein allozymes, random amplified polymorphic DNA, restriction fragment length polymorphisms, DNA sequence analysis, chloroplast DNA, and microsatellite markers. Yet, little is known about whether these traits, which distinguish among genetically distinct types of common bean, can be evaluated using omics technologies. Results Three 'omics' approaches: transcriptomics, proteomics, and metabolomics were used to qualitatively evaluate the diversity of common bean from two Centers of Domestication (COD). All three approaches were able to classify common bean according to their COD using unsupervised analyses; these findings are consistent with the hypothesis that differences exist in gene transcription, protein expression, and synthesis and metabolism of small molecules among common bean cultivars representative of different COD. Metabolomic analyses of multiple cultivars within two common bean gene pools revealed cultivar differences in small molecules that were of sufficient magnitude to allow identification of unique cultivar fingerprints. Conclusions Given the high-throughput and low cost of each of these 'omics' platforms, significant opportunities exist for their use in the rapid identification of traits of agronomic and nutritional importance as well as to characterize genetic diversity.
Collapse
Affiliation(s)
- Meghan M Mensack
- Cancer Prevention Laboratory, Department of Horticulture, Colorado State Univ, Fort Collins, CO 80523-1173, USA.
| | | | | | | | | | | |
Collapse
|