Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum

Persistent Link:
http://hdl.handle.net/10150/610398
Title:
Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum
Author:
Hass-Jacobus, Barbara; Futrell-Griggs, Montona; Abernathy, Brian; Westerman, Rick; Goicoechea, Jose-Luis; Stein, Joshua; Klein, Patricia; Hurwitz, Bonnie; Zhou, Bin; Rakhshan, Fariborz; Sanyal, Abhijit; Gill, Navdeep; Lin, Jer-Young; Walling, Jason; Luo, Mei; Ammiraju, Jetty; Kudrna, Dave; Kim, Hye; Ware, Doreen; Wing, Rod; Miguel, Phillip; Jackson, Scott
Affiliation:
Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA; Department of Horticulture, Purdue University, West Lafayette, Indiana 47907, USA; Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, New York 14853, USA; The Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA; Present address: Microarray Shared Resource-AGTC, Mayo Clinic, Rochester, MN 55905, USA
Issue Date:
2006
Publisher:
BioMed Central
Citation:
BMC Genomics 2006, 7:199 doi:10.1186/1471-2164-7-199
Journal:
BMC Genomics
Rights:
© 2006 Hass-Jacobus 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:With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. The genus Oryza includes 23 species that shared a common ancestor 8-10 million years ago making this an ideal model for investigations into the processes underlying domestication, as many of the Oryza species are still undergoing domestication. This study integrates high-throughput, hybridization-based markers with BAC end sequence and fingerprint data to construct physical maps of rice chromosome 1 orthologues in two wild Oryza species. Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40-50 million years ago.RESULTS:Overgo markers, in conjunction with fingerprint and BAC end sequence data, were used to build sequence-ready BAC contigs for two wild Oryza species. The markers drove contig merges to construct physical maps syntenic to rice chromosome 1 in the wild species and provided evidence for at least one rearrangement on chromosome 1 of the O. sativa versus Oryza officinalis comparative map. When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatches; of these, 41% gave positive hybridization signals. Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa.CONCLUSION:The results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species. As interspecific markers, overgos can be used successfully to construct physical maps in species which diverged less than 8 million years ago, and can be used in a more limited fashion to examine colinearity among species which diverged as much as 40 million years ago. Additionally, overgos are able to provide evidence of genomic rearrangements in comparative physical mapping studies.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-7-199
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/7/199

Full metadata record

DC FieldValue Language
dc.contributor.authorHass-Jacobus, Barbaraen
dc.contributor.authorFutrell-Griggs, Montonaen
dc.contributor.authorAbernathy, Brianen
dc.contributor.authorWesterman, Ricken
dc.contributor.authorGoicoechea, Jose-Luisen
dc.contributor.authorStein, Joshuaen
dc.contributor.authorKlein, Patriciaen
dc.contributor.authorHurwitz, Bonnieen
dc.contributor.authorZhou, Binen
dc.contributor.authorRakhshan, Fariborzen
dc.contributor.authorSanyal, Abhijiten
dc.contributor.authorGill, Navdeepen
dc.contributor.authorLin, Jer-Youngen
dc.contributor.authorWalling, Jasonen
dc.contributor.authorLuo, Meien
dc.contributor.authorAmmiraju, Jettyen
dc.contributor.authorKudrna, Daveen
dc.contributor.authorKim, Hyeen
dc.contributor.authorWare, Doreenen
dc.contributor.authorWing, Roden
dc.contributor.authorMiguel, Phillipen
dc.contributor.authorJackson, Scotten
dc.date.accessioned2016-05-20T09:05:56Z-
dc.date.available2016-05-20T09:05:56Z-
dc.date.issued2006en
dc.identifier.citationBMC Genomics 2006, 7:199 doi:10.1186/1471-2164-7-199en
dc.identifier.doi10.1186/1471-2164-7-199en
dc.identifier.urihttp://hdl.handle.net/10150/610398-
dc.description.abstractBACKGROUND:With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. The genus Oryza includes 23 species that shared a common ancestor 8-10 million years ago making this an ideal model for investigations into the processes underlying domestication, as many of the Oryza species are still undergoing domestication. This study integrates high-throughput, hybridization-based markers with BAC end sequence and fingerprint data to construct physical maps of rice chromosome 1 orthologues in two wild Oryza species. Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40-50 million years ago.RESULTS:Overgo markers, in conjunction with fingerprint and BAC end sequence data, were used to build sequence-ready BAC contigs for two wild Oryza species. The markers drove contig merges to construct physical maps syntenic to rice chromosome 1 in the wild species and provided evidence for at least one rearrangement on chromosome 1 of the O. sativa versus Oryza officinalis comparative map. When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatchesen
dc.description.abstractof these, 41% gave positive hybridization signals. Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa.CONCLUSION:The results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species. As interspecific markers, overgos can be used successfully to construct physical maps in species which diverged less than 8 million years ago, and can be used in a more limited fashion to examine colinearity among species which diverged as much as 40 million years ago. Additionally, overgos are able to provide evidence of genomic rearrangements in comparative physical mapping studies.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/7/199en
dc.rights© 2006 Hass-Jacobus 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.titleIntegration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghumen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentDepartment of Agronomy, Purdue University, West Lafayette, Indiana 47907, USAen
dc.contributor.departmentDepartment of Horticulture, Purdue University, West Lafayette, Indiana 47907, USAen
dc.contributor.departmentArizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USAen
dc.contributor.departmentCold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USAen
dc.contributor.departmentUSDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, New York 14853, USAen
dc.contributor.departmentThe Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USAen
dc.contributor.departmentPresent address: Microarray Shared Resource-AGTC, Mayo Clinic, Rochester, MN 55905, USAen
dc.identifier.journalBMC Genomicsen
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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