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PMID: 21771342 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Detection of copy number variations in rice using array-based comparative genomic hybridization.

BMC genomics ·Vol. 12 ·2011-07-20 ·Pages 372

Yu P, Wang C, Xu Q, Feng Y, Yuan X, Yu H, Wang Y, Tang S, Wei X

Abstract

Copy number variations (CNVs) can create new genes, change gene dosage, reshape gene structures, and modify elements regulating gene expression. As with all types of genetic variation, CNVs may influence phenotypic variation and gene expression. CNVs are thus considered major sources of genetic variation. Little is known, however, about their contribution to genetic variation in rice. To detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 718,256 oligonucleotide probes with a median probe spacing of 500 bp. We compiled a high-resolution map of CNVs in the rice genome, showing 641 CNVs between the genomes of the rice cultivars 'Nipponbare' (from O. sativa ssp. japonica) and 'Guang-lu-ai 4' (from O. sativa ssp. indica). The CNVs identified vary in size from 1.1 kb to 180.7 kb, and encompass approximately 7.6 Mb of the rice genome. The largest regions showing copy gain and loss are of 37.4 kb on chromosome 4, and 180.7 kb on chromosome 8. In addition, 85 DNA segments were identified, including some genic sequences. Contracted genes greatly outnumbered duplicated ones. Many of the contracted genes corresponded to either the same genes or genes involved in the same biological processes; this was also the case for genes involved in disease and defense. We detected CNVs in rice by array-based comparative genomic hybridization. These CNVs contain known genes. Further discussion of CNVs is important, as they are linked to variation among rice varieties, and are likely to contribute to subspecific characteristics.

MeSH Terms
Comparative Genomic Hybridization/methods DNA Copy Number Variations/genetics Genomics INDEL Mutation/genetics Oligonucleotide Array Sequence Analysis/methods Oligonucleotide Probes/genetics Oryza/genetics,growth & development Polymerase Chain Reaction Species Specificity
Chemicals
Oligonucleotide Probes
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Yu Ping
State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
Wang Caihong
Xu Qun
Feng Yue
Yuan Xiaoping
Yu Hanyong
Wang Yiping
Tang Shengxiang
Wei Xinghua
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Article Info
Journal
BMC genomics
Abbr.
BMC Genomics
ISSN
1471-2164
DOI
10.1186/1471-2164-12-372
Published
2011-07-20
Epub
2011-00-20
Pages
372
Language
English
Region
England
NLM ID
100965258
PMCID
PMC3156786
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2164-12-372 PMC Full Text View journal details
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