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Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

Swanson-Wagner, Ruth; Eichten, Steven; Kumari, Sunita; Tiffin, Peter; Stein, Joshua C; Ware, Doreen; Springer, Nathan M

Description

Individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. Array comparative genomic hybridization (CGH) was used to compare gene content and copy number variation among 19 diverse maize inbreds and 14 genotypes of the wild ancestor of maize, teosinte. We...[Show more]

dc.contributor.authorSwanson-Wagner, Ruth
dc.contributor.authorEichten, Steven
dc.contributor.authorKumari, Sunita
dc.contributor.authorTiffin, Peter
dc.contributor.authorStein, Joshua C
dc.contributor.authorWare, Doreen
dc.contributor.authorSpringer, Nathan M
dc.date.accessioned2015-12-10T23:23:14Z
dc.identifier.issn1088-9051
dc.identifier.urihttp://hdl.handle.net/1885/66866
dc.description.abstractIndividuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. Array comparative genomic hybridization (CGH) was used to compare gene content and copy number variation among 19 diverse maize inbreds and 14 genotypes of the wild ancestor of maize, teosinte. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3410 genes that have either fewer copies or are missing in the genome of at least one genotype relative to B73 (DownCNV/PAV). Many of these DownCNV/PAV are examples of genes present in B73, but missing from other genotypes. Over 70% of the CNV/PAV examples are identified in multiple genotypes, and the majority of events are observed in both maize and teosinte, suggesting that these variants predate domestication and that there is not strong selection acting against them. Many of the genes affected by CNV/PAV are either maize specific (thus possible annotation artifacts) or members of large gene families, suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation.
dc.publisherCold Spring Harbor Laboratory Press
dc.sourceGenome Research
dc.subjectKeywords: article; comparative genomic hybridization; copy number variation; gene content variation; gene dosage; genetic variability; genotype; maize; nonhuman; nucleotide sequence; priority journal; Chromosome Mapping; Comparative Genomic Hybridization; Gene Dosa
dc.titlePervasive gene content variation and copy number variation in maize and its undomesticated progenitor
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume20
dc.date.issued2010
local.identifier.absfor060705 - Plant Physiology
local.identifier.absfor060411 - Population, Ecological and Evolutionary Genetics
local.identifier.ariespublicationU3488905xPUB1358
local.type.statusPublished Version
local.contributor.affiliationSwanson-Wagner, Ruth, University of Minnesota
local.contributor.affiliationEichten, Steven, College of Medicine, Biology and Environment, ANU
local.contributor.affiliationKumari, Sunita, Cold Spring Harbor Laboratory
local.contributor.affiliationTiffin, Peter, University of Minnesota
local.contributor.affiliationStein, Joshua C , Cold Spring Harbor Laboratory
local.contributor.affiliationWare, Doreen, Cold Spring Harbor Laboratory
local.contributor.affiliationSpringer, Nathan M, University of Minnesota
local.description.embargo2037-12-31
local.bibliographicCitation.issue12
local.bibliographicCitation.startpage1689
local.bibliographicCitation.lastpage1699
local.identifier.doi10.1101/gr.109165.110
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
local.identifier.absseo820401 - Maize
dc.date.updated2016-02-24T09:59:24Z
local.identifier.scopusID2-s2.0-78549273825
local.identifier.thomsonID000284835000008
CollectionsANU Research Publications

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