Detection of copy number variation and selection signatures on the X chromosome in Chinese indigenous sheep with different types of tail |
Zhu, Caiye
(College of Animal Science and Technology, Gansu Agricultural University)
Li, Mingna (College of Animal Science and Technology, Gansu Agricultural University) Qin, Shizhen (College of Animal Science and Technology, Gansu Agricultural University) Zhao, Fuping (National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences) Fang, Suli (College of Animal Science and Technology, Gansu Agricultural University) |
1 | Safdarian M, Zamiri MJ, Hashemi M, Noorolahi H. Relationships of fat-tail dimensions with fat-tail weight and carcass characteristics at different slaughter weights of Torki-Ghashghaii sheep. Meat Sci 2008;80:686-9. https://doi.org/10.1016/j.meatsci.2008.03.007 DOI |
2 | Ma Y, Zhang H, Zhang Q, Ding X. Identification of selection footprints on the X chromosome in pig. PloS one 2014;9: e94911. https://doi.org/10.1371/journal.pone.0094911 DOI |
3 | Zhu C, Fan H, Yuan Z, et al. Detection of selection signatures on the X chromosome in three sheep breeds. Int J Mol Sci 2015;16:20360-74. https://doi.org/10.3390/ijms160920360 DOI |
4 | Rubin CJ, Megens HJ, Martinez Barrio A, et al. Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci USA 2012;109;19529-36. https://doi.org/10.1073/pnas.1217149109 DOI |
5 | Browning BL, Browning SR. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 2009;84: 210-23. https://doi.org/10.1016/j.ajhg.2009.01.005 DOI |
6 | 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;17:1665-74. https://doi.org/10.1101/gr.6861907 DOI |
7 | Jakobsson M, Scholz SW, Scheet P, et al. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 2008;451:998-1003. https://doi.org/10.1038/nature06742 DOI |
8 | Glessner JT, Reilly MP, Kim CE, et al. Strong synaptic transmission impact by copy number variations in schizophrenia. Proc Natl Acad Sci USA 2010;107:10584-9. https://doi.org/10.1073/pnas.1000274107 DOI |
9 | Redon R, Ishikawa S, Fitch KR, et al. Global variation in copy number in the human genome. Nature 2006;444:444-54. https://doi.org/10.1038/nature05329 DOI |
10 | Maceachern S, Hayes B, Mcewan J, Goddard M. An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle. BMC Genomics 2009;10:181. https://doi.org/10.1186/1471-2164-10-181 |
11 | Xu Y, Yu W, Xiong Y, et al. Molecular characterization and expression patterns of serine/arginine-rich specific kinase 3 (SPRK3) in porcine skeletal muscle. Mol Biol Rep 2011;38:2903-9. https://doi.org/10.1007/s11033-010-9952-1 DOI |
12 | Wilkinson S, Lu ZH, Megens HJ, et al. Signatures of diversifying selection in European pig breeds. Plos Genet 2013;9: e1003453. https://doi.org/10.1371/journal.pgen.1003453 DOI |
13 | Xiong X, Tao R, DePinho RA, Dong XC. Deletion of hepatic FoxO1/3/4 genes in mice significantly impacts on glucose metabolism through downregulation of gluconeogenesis and upregulation of glycolysis. PLoS One 2013;8:e74340. https://doi.org/10.1371/journal.pone.0074340 DOI |
14 | Hossein MM, Ardeshir NJ, Mohammad MS, Dodds KG, Mcewan JC. Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genet 2012;13:10. https://doi.org/10.1186/1471-2156-13-10 DOI |
15 | Mills RE, Walter K, Stewart C, et al. Mapping copy number variation by population-scale genome sequencing. Nature 2011;470:59-65. https://doi.org/10.1038/nature09708 DOI |
16 | Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med 2010;61:437-55. https://doi.org/10.1146/annurev-med-100708-204735 DOI |
17 | Giuffra E, Törnsten 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;13:569-77. https://doi.org/10.1007/s00335-002-2184-5 DOI |
18 | Zhu C, Fan H, Yuan Z, et al. Detection of selection signatures on the X chromosome in three sheep breeds. Int J Mol Sci 2015;16:20360-74. https://doi.org/10.3390/ijms160920360 DOI |
19 | Stainton JJ, Haley CS, Charlesworth B, Kranis A, Watson K, Wiener P. Detecting signatures of selection in nine distinct lines of broiler chickens. Anim Genet 2015;46:37-49. https://doi.org/10.1111/age.12252 DOI |
20 | Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution 1984;38:1358-70. https://doi.org/10.2307/2408641 DOI |
21 | Heyer E, Segurel L. Looking for signatures of sex-specific demography and local adaptation on the X chromosome. Genome Biol 2010;11:203. https://doi.org/10.1186/gb-2010-11-1-203 |
22 | Jiang L, Jiang J, Yang J, et al. Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins. BMC Genomics 2013;14:131. https://doi.org/10.1186/1471-2164-14-131 |
23 | Ashburner M, Ball CA, Blake JA, B et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 2000;25:25-9. https://doi.org/10.1038/75556 DOI |
24 | Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010;38 (Database issue):D355-60. https://doi.org/10.1093/nar/gkp896 DOI |
25 | Zeng Tao ZF, Wang Guangkai, WU Mingming, et al. Genomewide detection of signatures in sheep populations with use of population differentiation index Fst. Acta Vet Zootec Sin 2013;44:1891-9. DOI |
26 | Clop A, Vidal O, Amills M. Copy number variation in the genomes of domestic animals. Anim Genet 2012;43:503-17. https://doi.org/10.1111/j.1365-2052.2012.02317.x DOI |
27 | Marenne G, Rodriguez-Santiago B, Closas MG, et al. Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study. Hum Mutat 2011;32:240-8. https://doi.org/10.1002/humu.21398 DOI |
28 | Moradi MH, Nejati-Javaremi A, Moradi-Shahrbabak M, Dodds KG, McEwan JC. Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genet 2012;13:10. https://doi.org/10.1186/1471-2156-13-10 |
29 | Zhu C, Fan H, Yuan Z, et al. Detection of selection signatures on the X chromosome in three sheep breeds. Int J Mol Sci 2015;16:20360-74. https://doi.org/10.3390/ijms160920360 DOI |
30 | Qiu J, Cheng R, Zhou X, et al. Gene expression profiles of adipose tissue of high-fat diet-induced obese rats by cDNA microarrays. Mol Biol Rep 2010;37:3691-5. https://doi.org/10.1007/s11033-010-0021-6 DOI |