Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis

Persistent Link:
http://hdl.handle.net/10150/610017
Title:
Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis
Author:
Tian, Zhixi; Yu, Yanjun; Lin, Feng; Yu, Yeisoo; SanMiguel, Phillip; Wing, Rod; McCouch, Susan; Ma, Jianxin; Jackson, Scott
Affiliation:
Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA; Arizona Genomics Institute, The University of Arizona, Tucson, AZ 85721, USA; Genomics Core Facility, Purdue University, West Lafayette, IN 47907, USA; Department of Plant breeding and Genetics, Cornell University, NY 14853, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
Issue Date:
2011
Publisher:
BioMed Central
Citation:
Tian et al. BMC Genomics 2011, 12:142 http://www.biomedcentral.com/1471-2164/12/142
Journal:
BMC Genomics
Rights:
© 2011 Tian 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:Extensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, the nature, timing, lineages and adaptation of local genomic rearrangement in closely related species (e.g., within a genus) and haplotype variation of genomic rearrangement within populations have not been well documented.RESULTS:We previously identified a hotspot for genic rearrangement and transposon accumulation in the Orp region of Asian rice (Oryza sativa, AA) by comparison with its orthologous region in sorghum. Here, we report the comparative analysis of this region with its orthologous regions in the wild progenitor species (O. nivara, AA) of Asian rice and African rice (O. glaberrima) using the BB genome Oryza species (O. punctata) as an outgroup, and investigation of transposon insertion sites and a segmental inversion event in the AA genomes at the population level. We found that Orp region was primarily and recently expanded in the Asian rice species O. sativa and O. nivara. LTR-retrotransposons shared by the three AA-genomic regions have been fixed in all the 94 varieties that represent different populations of the AA-genome species/subspecies, indicating their adaptive role in genome differentiation. However, LTR-retrotransposons unique to either O. nivara or O. sativa regions exhibited dramatic haplotype variation regarding their presence or absence between or within populations/subpopulations.CONCLUSIONS:The LTR-retrotransposon insertion hotspot in the Orp region was formed recently, independently and concurrently in different AA-genome species, and that the genic rearrangements detected in different species appear to be differentially triggered by transposable elements. This region is located near the end of the short arm of chromosome 8 and contains a high proportion of LTR-retrotransposons similar to observed in the centromeric region of this same chromosome, and thus may represent a genomic region that has recently switched from euchromatic to heterochromatic states. The haplotype variation of LTR-retrotransposon insertions within this region reveals substantial admixture among various subpopulations as established by molecular markers at the whole genome level, and can be used to develop retrotransposon junction markers for simple and rapid classification of O. sativa germplasm.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-12-142
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/12/142

Full metadata record

DC FieldValue Language
dc.contributor.authorTian, Zhixien
dc.contributor.authorYu, Yanjunen
dc.contributor.authorLin, Fengen
dc.contributor.authorYu, Yeisooen
dc.contributor.authorSanMiguel, Phillipen
dc.contributor.authorWing, Roden
dc.contributor.authorMcCouch, Susanen
dc.contributor.authorMa, Jianxinen
dc.contributor.authorJackson, Scotten
dc.date.accessioned2016-05-20T08:56:34Z-
dc.date.available2016-05-20T08:56:34Z-
dc.date.issued2011en
dc.identifier.citationTian et al. BMC Genomics 2011, 12:142 http://www.biomedcentral.com/1471-2164/12/142en
dc.identifier.doi10.1186/1471-2164-12-142en
dc.identifier.urihttp://hdl.handle.net/10150/610017-
dc.description.abstractBACKGROUND:Extensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, the nature, timing, lineages and adaptation of local genomic rearrangement in closely related species (e.g., within a genus) and haplotype variation of genomic rearrangement within populations have not been well documented.RESULTS:We previously identified a hotspot for genic rearrangement and transposon accumulation in the Orp region of Asian rice (Oryza sativa, AA) by comparison with its orthologous region in sorghum. Here, we report the comparative analysis of this region with its orthologous regions in the wild progenitor species (O. nivara, AA) of Asian rice and African rice (O. glaberrima) using the BB genome Oryza species (O. punctata) as an outgroup, and investigation of transposon insertion sites and a segmental inversion event in the AA genomes at the population level. We found that Orp region was primarily and recently expanded in the Asian rice species O. sativa and O. nivara. LTR-retrotransposons shared by the three AA-genomic regions have been fixed in all the 94 varieties that represent different populations of the AA-genome species/subspecies, indicating their adaptive role in genome differentiation. However, LTR-retrotransposons unique to either O. nivara or O. sativa regions exhibited dramatic haplotype variation regarding their presence or absence between or within populations/subpopulations.CONCLUSIONS:The LTR-retrotransposon insertion hotspot in the Orp region was formed recently, independently and concurrently in different AA-genome species, and that the genic rearrangements detected in different species appear to be differentially triggered by transposable elements. This region is located near the end of the short arm of chromosome 8 and contains a high proportion of LTR-retrotransposons similar to observed in the centromeric region of this same chromosome, and thus may represent a genomic region that has recently switched from euchromatic to heterochromatic states. The haplotype variation of LTR-retrotransposon insertions within this region reveals substantial admixture among various subpopulations as established by molecular markers at the whole genome level, and can be used to develop retrotransposon junction markers for simple and rapid classification of O. sativa germplasm.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/12/142en
dc.rights© 2011 Tian 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.titleExceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysisen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentDepartment of Agronomy, Purdue University, West Lafayette, IN 47907, USAen
dc.contributor.departmentArizona Genomics Institute, The University of Arizona, Tucson, AZ 85721, USAen
dc.contributor.departmentGenomics Core Facility, Purdue University, West Lafayette, IN 47907, USAen
dc.contributor.departmentDepartment of Plant breeding and Genetics, Cornell University, NY 14853, USAen
dc.contributor.departmentDepartment of Biological Sciences, Purdue University, West Lafayette, IN 47907, 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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