Novel copy number variations of the CHRM3 gene associated with gene expression and growth traits in Chinese Datong yak (Bos grunniens)

References

• Bae JS, Cheong HS, Kim LH, NamGung S, et al. 2010. Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genomics. 11:232. doi: 10.1186/1471-2164-11-232
   PubMed Web of Science ®Google Scholar
• Beckmann JS, Estivill X, Antonarakis SE. 2007. Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet. 8:639–646. doi: 10.1038/nrg2149
   PubMed Web of Science ®Google Scholar
• Bickhart DM, Hou Y, Schroeder SG, Alkan C, et al. 2012. Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res. 22:778–790. doi: 10.1101/gr.133967.111
   PubMed Web of Science ®Google Scholar
• Bickhart DM, Liu GE. 2014. The challenges and importance of structural variation detection in livestock. Front Genet. 5:37. doi: 10.3389/fgene.2014.00037
   PubMed Web of Science ®Google Scholar
• Butte AJ, Dzau VJ, Glueck SB. 2001. Further defining housekeeping, or “maintenance,” genes Focus on “A compendium of gene expression in normal human tissues”. Physiol Genomics. 7:95–96. doi: 10.1152/physiolgenomics.2001.7.2.95
   PubMed Web of Science ®Google Scholar
• Conrad DF, Pinto D, Redon R, Feuk L, et al. 2010. Origins and functional impact of copy number variation in the human genome. Nature. 464:704–712. doi: 10.1038/nature08516
   PubMed Web of Science ®Google Scholar
• Da Silva VH, Regitano LdA, Geistlinger L, Pértille F, Giachetto PF, et al. 2016. Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle. PLoS ONE. 11(6):e0157711. doi: 10.1371/journal.pone.0157711
   PubMed Web of Science ®Google Scholar
• Dekkers JCM. 2004. Commercial application of marker- and gene-assisted selection in livestock: Strategies and lessons. Anim Sci. 82:313–328.
   Google Scholar
• Feuk L, Carson AR, Scherer SW. 2006. Structural variation in the human genome. Nat Rev Genet. 7:85–97. doi:10.1038/nrg1767.
   PubMed Web of Science ®Google Scholar
• Gautam D, Jeon J, Starost MF, Han S-J, Hamdan FF, Cui Y, et al. 2009. Neuronal M3 muscarinic acetylcholine receptors are essential for somatotroph proliferation and normal somatic growth. Proc Natl Acad Sci USA. 106:6398–6403. doi: 10.1073/pnas.0900977106
   PubMed Web of Science ®Google Scholar
• Gilbert RP, Bailey DRC, Shannon NH. 1993. Linear body measurements of cattle before and after 20 years of selection for postweaning gain when fed two different diets. Anim Sci. 71:1712–1720. doi: 10.2527/1993.7171712x
   Web of Science ®Google Scholar
• Hulse AM, Cai JJ. 2013. Genetic variants contribute to gene expression variability in humans. Genet. 193:95–108. doi: 10.1534/genetics.112.146779
   PubMed Web of Science ®Google Scholar
• Knezevic SZ, Streibig JC, Ritz C. 2007. Utilizing R software package for dose-response studies: the concept and data analysis. Weed Technol. 21:840–848. doi: 10.1614/WT-06-161.1
   Web of Science ®Google Scholar
• Lee YS, Lee JH, Lee JY, Kim JJ, et al. 2008. Identification of candidate SNP (single nucleotide polymorphism) for growth and carcass traits Related to QTL on Chromosome 6 in Hanwoo (Korean cattle). Asian-Aust. J Anim Sci. 21:1703–1709.
   Google Scholar
• Lehnert SA, Reverter A, Byrne KA, Wang Y, et al. 2007. Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds. BMC Dev Biol. 7:95. doi: 10.1186/1471-213X-7-95
   PubMed Web of Science ®Google Scholar
• Liu M, Lia B, Huanga Y, Yang M, Lana X, et al. 2016. Copy number variation of bovine MAPK10 modulates the transcriptional activity and affects growth traits. Liv Sci. 194:44–50. doi: 10.1016/j.livsci.2016.09.014
   Web of Science ®Google Scholar
• Liu GE, Xu L, Huang K. 2014. Recent Advances in studying of copy number variation and gene expression. Gene Exp Genet Genomics. 7:1–5. doi: 10.4137/GGG.S14286
   Google Scholar
• Lupski JR, Stankiewicz P. 2005. Genomic disorders: Molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet. 6:e49. doi: 10.1371/journal.pgen.0010049
   Google Scholar
• Merla G, Howald C, Henrichsen CN, Lyle R, et al. 2006. Submicroscopic deletion in patients with Williams-Beuren syndrome influences expression levels of the nonhemizygous flanking genes. A J Hum Genet. 79:332–341. doi: 10.1086/506371
   PubMed Web of Science ®Google Scholar
• Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. 2006. Global variation in copy number in the human genome. Nature. 444:444–454. doi: 10.1038/nature05329
   PubMed Web of Science ®Google Scholar
• Schmittgen TD, Livak KJ. 2008. Analyzing real-time PCR data by the comparative CT method. Nat Protoc. 3:1101–1111. doi: 10.1038/nprot.2008.73
   PubMed Web of Science ®Google Scholar
• Shi T, Yao X, Mingjuan Y, Yongzhen H, Xianyong L, Chuzhao L, et al. 2016. Copy number variations at LEPR gene locus associated with gene expression and phenotypic traits in Chinese cattle. Anim Sci. 87:336–343. doi: 10.1111/asj.12531
   PubMed Web of Science ®Google Scholar
• Stothard P, Choi J-W, Basu U, Sumner-Thomson JM, Meng Y, et al. 2011. Whole-genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics. 12:559. doi: 10.1186/1471-2164-12-559
   PubMed Web of Science ®Google Scholar
• Stranger BE, Forrest MS, Dunning M, Ingle CE, et al. 2007. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Sci. 315:848–853. doi: 10.1126/science.1136678
   PubMed Web of Science ®Google Scholar
• Weston-Green K, Huang XF, Lian J, Deng C. 2012. Effects of olanzapine on muscarinic M3 receptor binding density in the brain relates to weight gain, plasma insulin, and metabolic hormone levels. Eur Neuropsychopharmacol. 22:364–373. doi: 10.1016/j.euroneuro.2011.09.003
   PubMed Web of Science ®Google Scholar
• Wong KK, de Leeuw RJ, Dosanjh NS, Kimm LR, et al. 2007. A comprehensive analysis of common copy-number variations in the human genome. A J Hum Genet. 80:91–104. doi: 10.1086/510560
   PubMed Web of Science ®Google Scholar
• Xu Y, Shi T, Cai H, Zhou Y, Lan X, Zhang C, et al. 2014. Associations of MYH3 gene copy number variations with transcriptional expression and growth traits in Chinese cattle. Gene. 535:106–111. doi: 10.1016/j.gene.2013.11.057
   PubMed Web of Science ®Google Scholar
• Xu Y, Zhang LZ, Shi T, Zhou Y, Cai HF, et al. 2013. Copy number variations of MICAL-L2 shaping gene expression contribute to different phenotypes of cattle. Mamm Genome. 24:508–516. doi: 10.1007/s00335-013-9483-x
   PubMed Web of Science ®Google Scholar
• Xu JW, Zheng L, Li L-J, Yao Y-F, Hua H, et al. 2018. Novel copy number variation of the KLF3 gene is associated with growth traits in beef cattle. Gene. 680:99–104. https://doi.org/10.1016/j.gene.2018.08.040.
   PubMed Web of Science ®Google Scholar
• Yang M, Jingqiao LV, Liangzhi Z, Mingxun L, et al. 2017. Association study and expression analysis of CYP4A11 gene copy number variation in Chinese cattle. Sci Rep. 7:46599. doi: 10.1038/srep46599
   PubMed Web of Science ®Google Scholar
• Yim SH, Chung YJ, Jin EH, Shim SC, Kim JY, Kim YS, et al. 2011. The potential role of VPREB1 gene copy number variation in susceptibility to rheumatoid arthritis. Mol Immunol. 48:1338–1343. doi: 10.1016/j.molimm.2010.11.009
   PubMed Web of Science ®Google Scholar
• Yoo CK, Park HB, Lee JB, Jung EJ, et al. 2014. QTL analysis of body weight and carcass body length traits in an F2 intercross between Landrace and Korean native pigs. Anim Gene. 45(t):589–592. doi: 10.1111/age.12166
   PubMedGoogle Scholar
• Zhang F, Gu W, Hurles ME, Lupski JR. 2009. Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet. 10:451–481. doi: 10.1146/annurev.genom.9.081307.164217
   PubMed Web of Science ®Google Scholar
• Zhang L, Jia S, YangM XY, Li C, Sun J, et al. 2014. Detection of copy number variations and their effects in Chinese bulls. BMC Genomics. 15:480. doi: 10.1186/1471-2164-15-480
   PubMed Web of Science ®Google Scholar
• Zhang X, Wang K, Wang L, Yang Y, Ni Z, et al. 2016. Genome-wide patterns of copy number variation in the Chinese yak genome. BMC Genomics. 17:379. doi: 10.1186/s12864-016-2702-6
   PubMed Web of Science ®Google Scholar
• Zhang GM, Zheng L, He H, Song CC, et al. 2018. Associations of GBP2 gene copy number variations with growth traits and transcriptional expression in Chinese cattle. Gene. 647:101–106. doi: 10.1016/j.gene.2018.01.004
   PubMed Web of Science ®Google Scholar
• Zhou Y, Utsunomiya T, Xu L, El Hamidi Abdel H, et al. 2016. Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus. BMC Genomics. 17:1–9. doi: 10.1186/s12864-015-2294-6
   PubMed Web of Science ®Google Scholar