A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement

Persistent Link:
http://hdl.handle.net/10150/610086
Title:
A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement
Author:
He, Ruifeng; Salvato, Fernanda; Park, Jeong-Jin; Kim, Min-Jeong; Nelson, William; Balbuena, Tiago; Willer, Mark; Crow, John; May, Greg; Soderlund, Carol; Thelen, Jay; Gang, David
Affiliation:
Institute of Biological Chemistry, Washington State University, PO Box 646340, Pullman, WA 99164, USA; Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA; BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA; National Center for Genome Resources, Santa Fe, NM 87505, USA; Current Address: Departamento de Tecnologia, Universidade Estadual Paulista, Jaboticabal, SP 14884-900, Brazil
Issue Date:
2014
Publisher:
BioMed Central
Citation:
He et al. BMC Plant Biology 2014, 14:46 http://www.biomedcentral.com/1471-2229/14/46
Journal:
BMC Plant Biology
Rights:
© 2014 He et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant.RESULTS:We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease.CONCLUSIONS:A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease.
EISSN:
1471-2229
DOI:
10.1186/1471-2229-14-46
Keywords:
Transcriptomics; Proteomics; Metabolomics; Rhizome; Invasive species; Disease resistance; Rice blast; Rice
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2229/14/46

Full metadata record

DC FieldValue Language
dc.contributor.authorHe, Ruifengen
dc.contributor.authorSalvato, Fernandaen
dc.contributor.authorPark, Jeong-Jinen
dc.contributor.authorKim, Min-Jeongen
dc.contributor.authorNelson, Williamen
dc.contributor.authorBalbuena, Tiagoen
dc.contributor.authorWiller, Marken
dc.contributor.authorCrow, Johnen
dc.contributor.authorMay, Gregen
dc.contributor.authorSoderlund, Carolen
dc.contributor.authorThelen, Jayen
dc.contributor.authorGang, Daviden
dc.date.accessioned2016-05-20T08:58:15Z-
dc.date.available2016-05-20T08:58:15Z-
dc.date.issued2014en
dc.identifier.citationHe et al. BMC Plant Biology 2014, 14:46 http://www.biomedcentral.com/1471-2229/14/46en
dc.identifier.doi10.1186/1471-2229-14-46en
dc.identifier.urihttp://hdl.handle.net/10150/610086-
dc.description.abstractBACKGROUND:The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant.RESULTS:We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease.CONCLUSIONS:A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2229/14/46en
dc.rights© 2014 He et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.subjectTranscriptomicsen
dc.subjectProteomicsen
dc.subjectMetabolomicsen
dc.subjectRhizomeen
dc.subjectInvasive speciesen
dc.subjectDisease resistanceen
dc.subjectRice blasten
dc.subjectRiceen
dc.titleA systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvementen
dc.typeArticleen
dc.identifier.eissn1471-2229en
dc.contributor.departmentInstitute of Biological Chemistry, Washington State University, PO Box 646340, Pullman, WA 99164, USAen
dc.contributor.departmentDepartment of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USAen
dc.contributor.departmentBIO5 Institute, The University of Arizona, Tucson, AZ 85721, USAen
dc.contributor.departmentNational Center for Genome Resources, Santa Fe, NM 87505, USAen
dc.contributor.departmentCurrent Address: Departamento de Tecnologia, Universidade Estadual Paulista, Jaboticabal, SP 14884-900, Brazilen
dc.identifier.journalBMC Plant Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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