Genome-wide copy number variations in Oryza sativa L.Report as inadecuate

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BMC Genomics

, 14:649

Plant genomics


BackgroundCopy number variation CNV can lead to intra-specific genome variations. It is not only part of normal genetic variation, but also is the source of phenotypic differences. Rice Oryza sativa L. is a model organism with a well-annotated genome, but investigation of CNVs in rice lags behind its mammalian counterparts.

ResultsWe comprehensively assayed CNVs using high-density array comparative genomic hybridization in a panel of 20 Asian cultivated rice comprising six indica, three aus, two rayada, two aromatic, three tropical japonica, and four temperate japonica varieties. We used a stringent criterion to identify a total of 2886 high-confidence copy number variable regions CNVRs, which span 10.28 Mb or 2.69% of the rice genome, overlapping 1321 genes. These genes were significantly enriched for specific biological functions involved in cell death, protein phosphorylation, and defense response. Transposable elements TEs and other repetitive sequences were identified in the majority of CNVRs. Chromosome 11 showed the greatest enrichment for CNVs. Of subspecies-specific CNVRs, 55.75% and 61.96% were observed in only one cultivar of ssp. indica and ssp. japonica, respectively. Some CNVs with high frequency differences among groups resided in genes underlying rice adaptation.

ConclusionsHigher recombination rates and the presence of homologous gene clusters are probably predispositions for generation of the higher number of CNVs on chromosome 11 by non-allelic homologous recombination events. The subspecies-specific variants are enriched for rare alleles, which suggests that CNVs are relatively recent events that have arisen within breeding populations. A number of the CNVs identified in this study are candidates for generation of group-specific phenotypes.

AbbreviationsCNVCopy number variant

CNVRCopy number variable region

TETransposable element

SNPSingle-nucleotide polymorphism

LDLinkage disequilibrium

GWASGenome-wide association studies

aCGHarray comparative genomic hybridization

SDSegmental duplication

LINELong interspersed nuclear element

SINEShort interspersed nuclear element

LTRLong terminal repeat

GOGene ontology

NAHRNon-allelic homologous recombination.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-649 contains supplementary material, which is available to authorized users.

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Author: Ping Yu - Cai-Hong Wang - Qun Xu - Yue Feng - Xiao-Ping Yuan - Han-Yong Yu - Yi-Ping Wang - Sheng-Xiang Tang - Xing-Hua W


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