Genome-wide copy number variations in Oryza sativa L.
BACKGROUND
Copy 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.


RESULTS
We 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.


CONCLUSIONS
Higher 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.
State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China. weixinghua@caas.cn.
Ping
P
Yu
Cai-Hong
CH
Wang
Qun
Q
Xu
Yue
Y
Feng
Xiao-Ping
XP
Yuan
Han-Yong
HY
Yu
Yi-Ping
YP
Wang
Sheng-Xiang
SX
Tang
Xing-Hua
XH
Wei
D001208:Asia; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D017124:Conserved Sequence / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D056916:Segmental Duplications, Genomic; D013045:Species Specificity