title: Detection of copy number variations in rice using array-based comparative genomic hybridization.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Yu
authors.forename: Caihong
authors.initials: C
authors.lastname: Wang
authors.forename: Qun
authors.initials: Q
authors.lastname: Xu
authors.forename: Yue
authors.initials: Y
authors.lastname: Feng
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Yuan
authors.forename: Hanyong
authors.initials: H
authors.lastname: Yu
authors.forename: Yiping
authors.initials: Y
authors.lastname: Wang
authors.forename: Shengxiang
authors.initials: S
authors.lastname: Tang
authors.forename: Xinghua
authors.initials: X
authors.lastname: Wei
mesh_terms: D055028:Comparative Genomic Hybridization / Q000379:methods*; D056915:DNA Copy Number Variations / Q000235:genetics*; D023281:Genomics; D054643:INDEL Mutation / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D016133:Polymerase Chain Reaction; D013045:Species Specificity
chemical_list: D015345:Oligonucleotide Probes