Persistent Link:
http://hdl.handle.net/10150/195887
Title:
Structural Comparative Genomics of Four African Species of Oryza
Author:
Goicoechea, Jose Luis
Issue Date:
2009
Publisher:
The University of Arizona.
Rights:
Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Abstract:
Rice is one of the most important crops in the world and is the first whose genome was completely sequenced. This landmark accomplishment placed O. sativa as a leading model in plant biology, especially for cereals. The genus Oryza includes 23 species, two of them independently domesticated in Asia and Africa. Wild species of Oryza contain a reservoir of useful agronomical traits which could be exploited for the benefit of rice agriculture, which is facing global problems as other crops, mainly due to a rampant increase in the human population and progressive deterioration of soils and water supplies. The Oryza Mapping Alignment Project has opened great opportunities to tap the genetic potential encapsulated in these species. Four BAC libraries generated from the African species of Oryza: O. barthii, O. glaberrima (AA genome), O. punctata (BB genome) and O. brachyantha (FF genome) were fully characterized and shown to provide enough coverage to represent their respective genomes. BAC clones from these libraries were fingerprinted and end-sequenced to assemble physical maps that were heavily manually edited using the sequence of O. sativa as a reference genome. The physical maps showed high coverage for all the species across all chromosomes. Both, BAC libraries and physical maps were used to investigate synteny and structural variation. The four species show high colinearity to the reference genome, although synteny perturbations were detected, including contractions, expansions, and putative inversions and translocations, which potential have an important impact in the evolution of these species.
Type:
text; Electronic Dissertation
Keywords:
Africa; Comparative Genomics; Oryza; Physical Maps; Structural Variation
Degree Name:
Ph.D.
Degree Level:
doctoral
Degree Program:
Plant Science; Graduate College
Degree Grantor:
University of Arizona
Advisor:
Wing, Rod A
Committee Chair:
Wing, Rod A

Full metadata record

DC FieldValue Language
dc.language.isoENen_US
dc.titleStructural Comparative Genomics of Four African Species of Oryzaen_US
dc.creatorGoicoechea, Jose Luisen_US
dc.contributor.authorGoicoechea, Jose Luisen_US
dc.date.issued2009en_US
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.en_US
dc.description.abstractRice is one of the most important crops in the world and is the first whose genome was completely sequenced. This landmark accomplishment placed O. sativa as a leading model in plant biology, especially for cereals. The genus Oryza includes 23 species, two of them independently domesticated in Asia and Africa. Wild species of Oryza contain a reservoir of useful agronomical traits which could be exploited for the benefit of rice agriculture, which is facing global problems as other crops, mainly due to a rampant increase in the human population and progressive deterioration of soils and water supplies. The Oryza Mapping Alignment Project has opened great opportunities to tap the genetic potential encapsulated in these species. Four BAC libraries generated from the African species of Oryza: O. barthii, O. glaberrima (AA genome), O. punctata (BB genome) and O. brachyantha (FF genome) were fully characterized and shown to provide enough coverage to represent their respective genomes. BAC clones from these libraries were fingerprinted and end-sequenced to assemble physical maps that were heavily manually edited using the sequence of O. sativa as a reference genome. The physical maps showed high coverage for all the species across all chromosomes. Both, BAC libraries and physical maps were used to investigate synteny and structural variation. The four species show high colinearity to the reference genome, although synteny perturbations were detected, including contractions, expansions, and putative inversions and translocations, which potential have an important impact in the evolution of these species.en_US
dc.typetexten_US
dc.typeElectronic Dissertationen_US
dc.subjectAfricaen_US
dc.subjectComparative Genomicsen_US
dc.subjectOryzaen_US
dc.subjectPhysical Mapsen_US
dc.subjectStructural Variationen_US
thesis.degree.namePh.D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplinePlant Scienceen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorWing, Rod Aen_US
dc.contributor.chairWing, Rod Aen_US
dc.contributor.committeememberWing, Rod A.en_US
dc.contributor.committeememberYadegari, Raminen_US
dc.contributor.committeememberMachado, Carlosen_US
dc.contributor.committeememberSchumaker, Karenen_US
dc.identifier.proquest10728en_US
dc.identifier.oclc659753533en_US
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