苏尼特羊拷贝数变异的基因组分布特征研究

›› 2013, Vol. 40 ›› Issue (10): 173-178.

苏尼特羊拷贝数变异的基因组分布特征研究

刘佳森^1,2, 张莉¹, 李蕴华², 赵福平¹, 魏彩虹¹, 杜立新¹

1. 中国农业科学院北京畜牧兽医研究所, 北京 100193;
2. 内蒙古农牧业科学院畜牧研究所, 内蒙古呼和浩特 010031

收稿日期:2013-03-18 出版日期:2013-10-20 发布日期:2013-12-19
通讯作者: 杜立新 E-mail:lxdu@263.net;Tel:010-62819997
作者简介:刘佳森(1980-),男,内蒙古人,博士,副研究员,研究方向:基因组学与生物信息学。张莉(1975-),女,新疆人,副研究员,研究方向:动物分子遗传育种。刘佳森和张莉对本文具有同等贡献,并列为第一作者。
基金资助:
国家自然科学基金(30972094);十二五863项目(2011AA100307-02);国家现代农业产业－肉羊体系(CARS-39-04B);内蒙古农牧业科学院青年创新基金(2011QNJJM07)。

Genomic Characteristics of Copy Number Variations in Sunite Sheep

LIU Jia-sen^1,2, ZHANG Li¹, LI Yun-hua², ZHAO Fu-ping¹, WEI Cai-hong¹, DU Li-xin¹

1. Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
2. Institute of Animal Science, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, Inner Mongolia Autonomous Region, Hohhot 010031, China

Received:2013-03-18 Online:2013-10-20 Published:2013-12-19

摘要/Abstract

摘要： 本试验利用Illumina OvineSNP50 BeadChip芯片对71只苏尼特羊进行了分型,共检测到134个拷贝数变异区域(copy number variation regions,CNVR),大小范围为29.48 kb~1.30 Mb之间,总长度达到25.95 Mb。基因注释及功能分析结果显示,这些基因与嗅觉感官知觉、化学刺激的感官知觉、感官知觉、识别等环境应答有关。选取5个CNVR进行qPCR验证,其中3个CNVR得到验证。通过对苏尼特羊基因组拷贝数变异的分析可以进一步了解绵羊基因组结构的特点,为今后开展绵羊基因组结构变异与重要经济性状的关联研究提供参考。

关键词: 苏尼特羊; 基因组; 拷贝数变异; 单核苷酸多态

Abstract: In this study, 71 Sunite sheep were genotyped using Illumina OvineSNP50 BeadChip array, a total of 134 CNV regions (CNVR) across the genome were identified, which covered 25.95 Mb of the sheep genome.CNVR size on autosomes range from 29.48 kb to 1.30 Mb. Functional indicated that the most genes overrepresented in environmental responses, which involved in sensory perception of smell, sensory perception of chemical stimulus, sensory perception, cognition. To confirm these findings, quantitative PCR (qPCR) was performed for 5 CNVR and 3 of them were successfully validated. Our findings would be of help to understand the sheep genome and provide preliminary foundation for investigating the association between important economic traits and CNV.

Key words: Sunite sheep; genome; copy number variation; single nucleotide polymorphism

中图分类号:

刘佳森, 张莉, 李蕴华, 赵福平, 魏彩虹, 杜立新. 苏尼特羊拷贝数变异的基因组分布特征研究[J]. , 2013, 40(10): 173-178.

LIU Jia-sen, ZHANG Li, LI Yun-hua, ZHAO Fu-ping, WEI Cai-hong, DU Li-xin. Genomic Characteristics of Copy Number Variations in Sunite Sheep[J]. , 2013, 40(10): 173-178.

参考文献

1 Archibald A L, Cockett N E, Dalrymple B P,et al. The sheep genome reference sequence: A work in progress. Anim Genet,2010, 41(5):449~453.
2 Beckmann J S, Estivill X, Antonarakis S E. Copy number variants and genetic traits: Closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet,2007, 8(8):639~646.
3 Chen W K, Swartz J D, Rush L J,et al. Mapping DNA structural variation in dogs. Genome Res,2009, 19(3):500~509.
4 Fadista J, Nygaard M, Holm L E,et al. A snapshot of CNVs in the pig genome. PLoS One,2008, 3(12):e3916.
5 Fadista J, Thomsen B, Holm L E,et al. Copy number variation in the bovine genome. BMC Genomics,2010, 11:284.
6 Feuk L, Carson A R, Scherer S W. Structural variation in the human genome. Nat Rev Genet,2006, 7(2):85~97.
7 Fontanesi L, Beretti F, Martelli P L,et al. A first comparative map of copy number variations in the sheep genome. Genomics,2011, 97(3):158~165.
8 Freeman J L, Perry G H, Feuk L,et al. Copy number variation: New insights in genome diversity. Genome Res,2006, 16(8):949~961.
9 Giuffra E, Tornsten A, Marklund S,et al. A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT. Mamm Genome,2002, 13(10):569~577.
10 Hollox E J, Armour J A, Barber J C. Extensive normal copy number variation of a beta-defensin antimicrobial-gene cluster. Am J Hum Genet,2003, 73(3):591~600.
11 Huang D W, Sherman B T, Tan Q,et al. The DAVID gene functional classification tool: A novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol,2007, 8(9):R183.
12 Komura D, Shen F, Ishikawa S,et al. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Research,2006, 16(12):1575~1584.
13 Lee A S, Gutierrez-Arcelus M, Perry G H,et al. Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. Hum Mol Genet,2008, 17(8):1127~1136.
14 Liu G E, Hou Y, Zhu B,et al. Analysis of copy number variations among diverse cattle breeds. Genome Res,2010, 20(5):693~703.
15 Moon S, Kim Y J, Hong C B,et al. Data-driven approach to detect common copy-number variations and frequency profiles in a population-based Korean cohort. Eur J Hum Genet,2011, 19(11):1167~1172.
16 Purcell S, Neale B, Todd-Brown K,et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet,2007, 81(3):559~575.
17 Redon R, Ishikawa S, Fitch K R,et al. Global variation in copy number in the human genome. Nature,2006, 444(7118):444~454.
18 Schoumans J, Ruivenkamp C, Holmberg E,et al. Detection of chromosomal imbalances in children with idiopathic mental retardation by array based comparative genomic hybridisation (array-CGH). J Med Genet,2005, 42(9):699~705.
19 Seroussi E, Glick G, Shirak A,et al. Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs. BMC Genomics,2010, 11:673.
20 Stankiewicz P, Lupski J R. Genome architecture, rearrangements and genomic disorders. Trends Genet,2002, 18(2):74~82.
21 Sudmant P H, Kitzman J O, Antonacci F,et al. Diversity of human copy number variation and multicopy genes. Science,2010, 330(6004):641~646.
22 Wain L V, Armour J A, Tobin M D. Genomic copy number variation, human health, and disease. Lancet,2009, 374(9686):340~350.
23 Wang K, Li M, Hadley D,et al. PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res,2007, 17(11):1665~1674.
24 Wang X, Nahashon S, Feaster T K,et al. An initial map of chromosomal segmental copy number variations in the chicken. BMC Genomics,2010, 11:351.
25 Wright D, Boije H, Meadows J R,et al. Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens. PLoS Genet,2009, 5(6):e1000512.

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