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

作     者：Yu, Ping Wang, Caihong Xu, Qun Feng, Yue Yuan, Xiaoping Yu, Hanyong Wang, Yiping Tang, Shengxiang Wei, Xinghua 

作者机构：China Natl Rice Res Inst State Key Lab Rice Biol Hangzhou Zhejiang Peoples R China 

出 版 物：《BMC GENOMICS》 (BMC基因)

年 卷 期：2011年第12卷第1期

页      面：372-372页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 09[农学] 0836[工学-生物工程] 

基　　金：MOA, China China National Rice Research Institute [2009RG001-3] 

主　　题：Rice Genome Circular Binary Segmentation aCGH Data Bacterial Blight Resistance Gene China National Rice Research Institute 

摘      要：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. Conclusion: 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.