African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12488

Review

Applications of genomic copy number variations on livestock: A review

Habtamu Abera Goshu
  • Habtamu Abera Goshu
  • Department Animal Science, Chinese Academy of Agricultural Science, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, 730050, Gansu, China.
  • Google Scholar
Min Chu
  • Min Chu
  • Department Animal Science, Chinese Academy of Agricultural Science, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, 730050, Gansu, China.
  • Google Scholar
Ping Yan
  • Ping Yan
  • Department Animal Science, Chinese Academy of Agricultural Science, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, 730050, Gansu, China.
  • Google Scholar


  •  Received: 27 March 2018
  •  Accepted: 25 October 2018
  •  Published: 26 October 2018

References

Ajmone-Marsan P (2010). On the origin of cattle: how aurochs became cattle and colonized the world. Evolutionary Anthropology Issues News and Reviews 19:148-157.
Crossref

 

Alvarez CE, Akey JM (2012).Copy number variation in the domestic dog. Mammalian Genome, 23: 144-163.
Crossref

 
 

Beckmann JS, Estivill X, Antonarakis SE (2007).Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nature Reviews Genetics 8:639-646.
Crossref

 
 

Bekele D, Abera H, Bodena F (2015). Characterization of Indigenous Chicken Production and Utilization in western Oromia, Ethiopia. British Journal of Poultry Science 4:53-59.

 
 

Ben Sassi N, González-Recio Ó, de Paz-del RR, Rodríguez-Ramilo ST, Fernández AI (2016). Associated effects of copy number variants on economically important traits in Spanish Holstein dairy cattle. Journal of Dairy Science 99:6371-6380.
Crossref

 
 

Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF, Garcia JF (2012). Copy number variation of individual cattle genomes using next-generation sequencing. Genome Research 22:778-790.
Crossref

 
 

Bickhart DM, Liu GE (2014). The challenges and importance of structural variation detection in livestock. Frontiers in Genetics 5:37.
Crossref

 
 

Bouwman AC, Daetwyler HD, Chamberlain AJ, Ponce CH, Sargolzaei M, Schenkel FS, Sahana G, Govignon-Gion A, Boitard S, Dolezal M, Pausch H, Brøndum RF, Bowman PJ, Thomsen B, Guldbrandtsen B, Lund MS, Servin B, Garrick DJ, Reecy J, Vilkki J, Bagnato A, Wang M, Hoff JL, Schnabel RD, Taylor JF, Vinkhuyzen AAE, Panitz F, Bendixen C, Holm LE, Gredler B, Hozé C, Boussaha M, Sanchez MP, Rocha D, Capitan A, Tribout T, Barbat A, Croiseau P, Drögemüller C, Jagannathan V, Vander Jagt C, Crowley JJ, Bieber A, Purfield DC, Berry DP, Emmerling R, Götz KU, Frischknecht M, Russ I, Sölkner J, Van Tassell CP, Fries R, Stothard P, Veerkamp RF, Boichard D, Goddard ME, Hayes BJ (2018). Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals. Nature Genetics 50(3):362-367.
Crossref

 
 

Brenig B, Beck J, Floren C, Bornemann-Kolatzki K, Wiedemann I, Hennecke S, Swalve H, Sch€utz E (2013).Molecular genetics of coat colour variations in White Galloway and White Park cattle. Animal Genetics 44:450-453.
Crossref

 
 

Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alfoldi J, Barrio AM, Pielberg G, Rafati N, Sayyab S, Turner-Maier J,Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L (2014). Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 345:1074-1079.
Crossref

 
 

Chen C, Qiao R, Wei R, Guo Y, Ai H, Ma J, Ren J, Huang L (2012). A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits. BMC Genomics 13:733.
Crossref

 
 

Clop A, Vidal O, Amills M (2012).Copy number variation in the genomes of domestic animals. Animal Genetics 43:503-17.
Crossref

 
 

Conrad DF, Pinto D, Redon R, Feuk L, Gokcume, O, Zhang Y, Aerts J, Andrews TD, Barnes C,Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J; Wellcome Trust Case Control Consortium, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME (2010). Origins and functional impact of copy number variation in the human genome. Nature 464:704-12.
Crossref

 
 

Curi R, Oliveira H, Silveira A, Lopes C (2005). Effects of polymorphic microsatellites in the regulatory region of IGF1 and GHR on growth and carcass traits in beef cattle. Animal Genetics 36:58-62.
Crossref

 
 

da Silva JM, Poliana FG, da Silva LO, Carrijo Cintra L, Rezende PS, Michel EBY, Rodrigues Caetano A (2016). Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harbouring QTLs affecting production traits. BMC Genomics 17:454.
Crossref

 
 

Da Silva VH, Regitano LCdeA, Geistlinger L, Pértille F, Giachetto PF, Brassaloti RA, Morosini NS, Zimmer R, Coutinho LL (2016b). Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. PLoS ONE 11(6): e0157711.
Crossref

 
 

Darwin C (1859).On the Origin of Species by Means of Natural Selection, or, the Preservation of Favoured Races in the Struggle for Life. 6th Edn.London: John Murray.

 
 

de Almeida Santana MH, Oliveira Junior GA, Mello Cesar AS,Freua MC, Gomes RC, Silva SL,Leme PR, Fukumasu H,Carvalho ME (2016). Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle. Journal of Applied Genetics 57:495-504.
Crossref

 
 

Decker JE, Pires JC, Gavin CC, Stephanie DM, Michael PH, Kefei C, Alan C, Johanna V, Christopher MS, Alexandre RC, Gary SJ, Rick AB, Olivier H, Lori SE, Pamela W, Jong-Joo K, Kwan SK, Tad SS, Curt PT, Holly LN, John CM, Rudiger B, Luiz LC, Masroor EB, Gregory AW, Matthew CM, Megan MR, JaeWoo K, Robert DS, Jeremy FT (2009). Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proceedings of the National Academy of Sciences of the United States of America 106:18644–18649.
Crossref

 
 

Dekkers JCM (2004). Commercial application of marker-and gene-assisted selection in livestock: Strategies and lessons. Animal Science 82:313-328.

 
 

Durán Aguilar MD, Rom Ponce SI, Ruiz Lopez,FJ, Gonzalez Padilla E, Vasquez Pelaez, CG, Bagnato A, Strillacci MG (2016). Genome-wide association study for milk somatic cell score in Holstein cattle using copy number variation as markers. Journal of Animal Breeding and Genetics 134:49-59.
Crossref

 
 

Durkin K, Coppieters W, Dro¨gemu¨ller C, Ahariz N, Cambisano N, Druet T, Fasquelle C, Hile A, Horin P, Huang L, Kamatani Y, Karim L, Lathrop M, Moser S, Oldenbroek K, Rieder S, Sartelet A, Sölkner J, Stålhammar H, Zelenika D, Zhang Z, Leeb T, Georges M, Charlier C (2012). Serial translocation by means of circular intermediates underlies colour sidedness in cattle. Nature 482:81-84.
Crossref

 
 

Feuk L, Carson AR, Scherer SW (2006). Structural variation in the human genome. Nature Reviews Genetics 7:85-97.
Crossref

 
 

Fontanesi L, Russo V (2013). Molecular genetics of coat colour in pigs. Acta argiculturae Slovenica 4:15-20.

 
 

Fontanesi L, Beretti F, Riggio V, Dall'Olio S, Davoli R, Russo V, Portolano B (2009). Copy number variation and missense mutations of the agouti signalling protein (ASIP) gene in goat breeds with different coat colors. Cytogenetic Genome Research 126:333-347.
Crossref

 
 

Fontanesi L, Dall'Olio S, Beretti F, Portolano B, Russo V (2011). Coat colours in the Massese sheep breed are associated with mutations in the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes. Animal 5: 8-17.
Crossref

 
 

Fontanesi L, Martelli PL, Beretti F, Riggio V, Dall'Olio S, Colombo M, CasadioR, Russo V, Portolano B (2010). An initial comparative map of copy number variations in the goat (Capra hircus) genome. BMC Genomics 11:639.
Crossref

 
 

Fontanesi L, Scotti E, Russo V (2012). Haplotype variability in the bovine MITF gene and association with piebaldism in Holstein and Simmental cattle breeds. Animal Genetics 43:250-256.
Crossref

 
 

Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, Carter NP, Scherer SW, Lee C (2006). Copy number variation: new insights in genome diversity. Genome Research 16(8):949-961.
Crossref

 
 

Gao Y, Jiang J, Yang S, Hou Y, Liu GE, Zhang S, Zhang Q, Sun D (2017). CNV discovery for milk composition traits in dairy cattle using whole genome resequencing. BMC Genomics 18:265.
Crossref

 
 

Ghosh S, Qu Z, Das PJ, Fang E, Juras R, Cothran EG, McDonell S, Kenney DG, Lear TL, Adelson DL, Chowdhary BP, Raudsepp T (2014). Copy number variation in the horse genome. Plos Genetics 10: e1004712.
Crossref

 
 

Gou X, Wang Z, Li N, Qiu F, Xu Z, Yan D,Yang S, Jia J, Kong X, Wei Z, Lu S, Lian L, Wu C, Wang X, Li G, Ma T, Jiang Q, Zhao X, Yang J, Liu B, Wei D, Li H, Yang J, Yan Y, Zhao G, Dong X, Li M, Deng W, Leng J, Wei C, Wang C, Mao H, Zhang H, Ding G, Li Y (2014). Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia. Genome Research 24:1308-1315.
Crossref

 
 

Gu L, Sun C, Gong Y, Yu M, Li S (2017). Novel copy number variation of the TGFβ3 gene is associated with TGFβ3 gene expression and duration of fertility traits in hens. PLoS ONE 12(3):e0173696.
Crossref

 
 

Guo S, Savolainen P, Su J, Zhang Q, Qi D, Zhou J, Zhong Y, Zhao X, Liu J (2006). Origin of mitochondrial DNA diversity of domestic yaks. BMC Evolutionary Biology 6:73.
Crossref

 
 

Han JL, Yang M, Yue YJ, Guo TT, Liu JB, Niu CE, Yang BH (2015). Analysis of agouti signaling protein (ASIP) gene polymorphisms and association with coat color in Tibetan sheep (Ovis aries). Genetics and Molecular Research 14: 1200-1209.
Crossref

 
 

Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME (2009). Invited review: Genomic selection in dairy cattle: progress and challenges. Journal of Dairy Science 92:433-443.
Crossref

 
 

Hayes BJ, Lewin HA, Goddard ME (2013). The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation. Trends in Genetics 29:206-213.
Crossref

 
 

Henrichsen CN, Chaignat E, Reymond A (2009a). Copy number variants, diseases and gene expression. Journal of Human Molecular Genetics 18:(R1):R1–8.
Crossref

 
 

Henrichsen CN, Vinckenbosch N, Zöllner S, Chaignat E, Pradervand S, Schütz F, Ruedi M, Kaessmann H, Reymond A (2009b). Segmental copy number variation shapes tissue transcriptomes. Nature Genetics 41:424-429.
Crossref

 
 

Hiendleder S, Lewalski H, Janke A (2008). Complete mitochondrial genomes of Bos Taurus and Bos indicus provide new insights into intra-species variation, taxonomy and domestication. Cytogenetic and Genome Research 120(1-2):150-6.
Crossref

 
 

Hou Y, Liu GE, Bickhart DM, Cardone MF, Wang K, Kim ES, Matukumalli LK, Ventura M, Song J, VanRaden PM, Sonstegard TS, Van Tassell CP (2011). Genomic characteristics of cattle copy number variations. BMC Genomics 12:127.
Crossref

 
 

Hou Y, Liu GE, Bickhart DM, Matukumalli LK, Li C, Song J, Gasbarre LC, Van Tassell CP, Sonstegard TS (2012). Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle. Functional and Integrative Genomics 12:81-92.
Crossref

 
 

Huang XD, Tan HY, Long R, Liang JB, Wright A-DG (2012). Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos Taurus) from the Qinghai-Tibetan plateau, China. BMC Microbiology 12:237.
Crossref

 
 

Jiang J, Gao Y, Hou Y, Li W, Zhang S, Zhang Q,Sun D (2016). Whole-Genome Resequencing of Holstein Bulls for Indel Discovery and Identification of Genes Associated with Milk Composition Traits in Dairy Cattle. PLoS ONE 11(12): e0168946.
Crossref

 
 

Keel BN, Lindholm-Perry AK, Snelling WM (2016). Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome. Frontiers in Genetics 7:207.
Crossref

 
 

Lai SJ, Chen SY, Liu YP, Yao YG (2007). Mitochondrial DNA sequence diversity and origin of Chinese domestic yak. Animal Genetics 38:77-80.
Crossref

 
 

Lan D, Xiong X, Mipam T-D, Fu C, Li Q, Ai Y, Hou D, Chai Z, Zhong J, Li J (2018). Genetic Diversity, Molecular Phylogeny, and Selection Evidence of Jinchuan Yak Revealed by Whole-Genome Resequencing. G3: Genes Genomes Genetics 8(3):945-952.

 
 

Larson G, Piperno DR, Allaby RG, Purugganan MD, Andersson L, Arroyo-Kalin M, Barton L, Climer Vigueira C, Denham T, Dobney K, Doust AN, Gepts P, Gilbert MT, Gremillion KJ, Lucas L, Lukens L, Marshall FB, Olsen KM, Pires JC, Richerson PJ, Rubio de Casas R, Sanjur OI, Thomas MG, Fuller DQ (2014). Current perspectives and the future of domestication studies. Proceedings of the National Academy of Sciences of the United States of America 111:6139-6146.
Crossref

 
 

Lee K, Nguyen DT, Choi M, Cha S-Y, Kim J-H, Dadi H, Seo HG, Seo K, Chun T, Park C (2013). Analysis of cattle olfactory subgenome: the first detail study on the characteristics of the complete olfactory receptor repertoire of a ruminant. BMC Genomics 14:596.
Crossref

 
 

Li Y, Wu DD, Boyko AR, Wang GD, Wu SF, Irwin DM, Zhang YP (2014). Population Variation Revealed High-Altitude Adaptation of Tibetan Mastiffs. Molecular biology and evolution 31:1200-1205.
Crossref

 
 

Liang C, Wang L, Wu X, Wang K, Ding X, Wang M, Chu M, Xie X, Qiu Q, Yan P (2016). Genome-wide Association Study Identifies Loci for the Polled Phenotype in Yak. PLoS ONE 11(7):e0158642.
Crossref

 
 

Liang C, Yan P, Yao Y, Pei J, Guo X, Zheng Y, Bao PJ, Chu M (2010). A novel single nucleotide polymorphism (SNP) of the IGF1R gene and the association with growth traits in yak (Brief Report). Archiv Tierzucht 5:626-628.

 
 

Lin S, Lin X, Zhang Z, Jiang M, Rao Y, Nie Q, Zhang X (2018). Copy Number Variation in SOX6 Contributes to Chicken Muscle Development. Genes 9(1):42.
Crossref

 
 

Liu GE, Hou YL, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell'Aquila ME,Gasbarre LC, Lacalandra G, Li RW, Matukumalli LK, Nonneman D, Regitano LC, Smith TP, Song J, Sonstegard TS, Van Tassell CP, Ventura M, Eichler EE, McDaneld TG, Keele JW (2010). Analysis of copy number variations among diverse cattle breeds. Genome Research 20:693-70.
Crossref

 
 

Liu GE, Ventura M, Cellamare A, Chen L, Cheng Z, Zhu B,Li C, Song J, Eichler EE (2009). Analysis of recent segmental duplications in the bovine genome. BMC Genomics 10:571.
Crossref

 
 

Liu J, Zhang L, Xu L, Ren H, Lu J, Zhang X, Zhang S, Zhou X, Wei C, Zhao F, Du L (2013). Analysis of copy number variations in the sheep genome using 50 K SNP Bead Chip array. BMC Genomics 14:229.
Crossref

 
 

Liu M, Lia B, Huanga Y, Yang M, Lana X, Lei C, Qub W, Bai Y, Chena H (2016). Copy number variation of bovine MAPK10 modulates the transcriptional activity and affects growth traits. Livestock Science 194:44-50.
Crossref

 
 

Liu WB, Liu J, Liang CN, Guo X, Bao PJ, Chu M, Ding XZ, Wang HB, Zhu XS, Yan P (2014). Associations of single nucleotide polymorphisms in candidate genes with the polled trait in Datong domestic yaks. Animal Genetics 45:138-141.
Crossref

 
 

Loftus RT, MacHugh DE, Bradley DG, Sharp PM, Cunningham P (1994). Evidence for two independent domestications of cattle. Proceedings of the National Academy of Sciences of the United States of America 91(7):2757-2761.
Crossref

 
 

Lupsk JR, Stankiewicz P (2005). Genomic Disorders: Molecular Mechanisms for Rearrangements and Conveyed Phenotypes. PLoS Genetics 1(6):e49.
Crossref

McCarthy SD, Roche JF, Forde N (2012). Temporal changes in endometrial gene expression and protein localization of members of the IGF family in cattle: effects of progesterone and pregnancy. Physiological Genomics 44:130-140.
Crossref

 

McTavish EJ, Decker JE, Schnabel RD, Taylor JF, Hillis DM (2013). New World cattle show ancestry from multiple independent domestication events. Proceedings of the National Academy of Sciences of the United States of America 110:E1398-E1406.
Crossref

 
 

Medugorac I, Graf A, Grohs C, Rothammer S, Zagdsuren Y, Gladyr E, Zinovieva N, Barbieri J, Seichter D, Russ I, Eggen A, Hellenthal G, Brem G, Blum H, Krebs S, Capitan A (2017). Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks. Nature Genetics 49(3):470-475
Crossref

 
 

Mesbah-Uddin M, Guldbrandtsen B, Iso-Touru T, Vilkki J, De Koning D-J, Boichard D, Lund MS, Sahana G (2018). Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes 25(1): 49-59.

 
 

Mi J, Zhou J, Huang X, Long R (2017). Lower Methane Emissions from Yak Compared with Cattle in Rusitec Fermenters. PLoS ONE 12(1):e0170044.
Crossref

 
 

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan, C, Abyzov A, Yoon SC, Ye K, Cheetham RK (2011). Mapping copy number variation by population-scale genome sequencing. Nature 470:59-65.
Crossref

 
 

Norris BJ, Whan VA (2008). A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep. Genome Research 18(8):1282-1293.
Crossref

 
 

Noyes H, Brass A, Obara I, Anderson s, Archibald AL, Bradley DG, Fisher P, Freeman A, Gicheru m, Hall L, Hanotte O, Hulme H, McKeever D, Murray C, Oh SJ, Tate C, Smith K, Tapio m, Wamburgu J, Williams DJ, Agaba M, kemp SJ (2011). Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection. Proceedings of the National Academy of Sciences of the United States of America 108:9304-9.

 
 

Park RW, Kim TM, Kasi S, Park PJ (2015).Identification of rare germline copy number variations over-represented in five human cancer types. Molecular Cancer 14:25.
Crossref

 
 

Paudel Y, Madsen O, Megens HJ, Laurent AF, Mirte F, John B, Bastiaansen WM, Richard PM, Crooijmans A, Groenen MAM (2013). Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication. BMC Genomics 14(1):449.
Crossref

 
 

Paudel Y, Madsen O, Megens HJ, Frantz LAF, Bosse M, Crooijmans RPMA, Groenen MAM (2015). Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors. BMC Genomics 16:330.
Crossref

 
 

Pielberg G, Olsson C, Syva¨nen AC, Andersson L (2002). Unexpectedly high allelic diversity at the KIT locus causing dominant white color in the domestic pig. Genetics 160:305-311.

 
 

Porto-Neto LR, Sonstegard TS, Liu GE, Bickhart DM, Da Silva MV, Machado MA, Utsunomiya YT, Garcia JF, Gondro C, Van Tassell CP (2013). Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. BMC Genomics 14:876.
Crossref

 
 

Prinsen RTMM, Strillacci MG, Schiavini F, Santus E, Rossoni A, Maurer V, Bieber A, Gredler B, Dolezal M, Bagnato A (2016). A genome-wide scan of copy number variants using high-density SNPs in Brown Swiss dairy cattle. Livestock Science 191:153-160.
Crossref

 
 

Prinsen RTMM, Rossoni A, Gredler B, Bieber A, Bagnato A, Strillacci MG (2017). A genome-wide association study between CNVs and quantitative traits in Brown Swiss cattle. Livestock Science 202:7-12.
Crossref

 
 

Pryce JE, Daetwyler HD (2011). Designing dairy cattle breeding schemes under genomic selection: a review of international research. Animal Production Science 52:107-114.
Crossref

 
 

Qiu Q, Wang L, Wang K, Yang Y, Ma T, Wang Z, Zhang X, Ni Z, Hou F, Long Abbott R, Lenstra J, Liu J (2015). Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions. Nature Communication 6:10283.
Crossref

 
 

Qiu Q, Zhang G, Ma T, Qian W, Wang J, Ye Z, Cao C, Hu Q, Kim J, Larkin DM, Auvil L, Capitanu B, Ma J, Lewin HA, Qian X, Lang Y, Zhou R, Wang L, Wang K, Xia J, Liao S, Pan S, Lu X, Hou H, Wang Y, Zang X, Yin Y, Ma H, Zhang J, Wang Z, Zhang Y, Zhang D, Yonezawa T, Hasegawa M, Zhong Y, Liu W, Zhang Y, Huang Z, Zhang S, Long R, Yang H, Wang J, Lenstra JA, Cooper DN, Wu Y, Wang J, Shi P, Wang J, Liu J (2012). The yak genome and adaptation to life at high altitude. Nature Genetics 44:946-949.
Crossref

 
 

Rao YS, Li J, Zhang R, Lin XR, Xu JG, Xie L, He J, Zhang XQ (2016). Copy number variation identification and analysis of the chicken genome using a 60K SNP Bead Chip. Poultry Science 95:1750-1756.
Crossref

 
 

Redon R1, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME (2006). Global variation in copy number in the human genome. Nature 444(7118):444-454.
Crossref

 
 

Reymond A, Henrichsen CN, Harewood L, Merla G (2007). Side effects of genome structural changes. Current Opinion in Genetics and Development 17:381-386.
Crossref

 
 

Rothschild MF, Plastow GS (2014). Applications of genomics to improve livestock in the developing world. Livestock Science 166:76-83.
Crossref

 
 

Rubin CJ, Megens HJ, Martinez BA, Maqbool K, Sayyab S, Schwochow D, Wang C, Carlborg O, Jern P, Jorgensen CB,Archibald AL, Fredholm M, Groenen MA, Andersson L (2012). Strong signatures of selection in the domestic pig genome. Proceedings of the National Academy of Sciences of the United States of America 9:19529- 19536.
Crossref

 
 

Sasaki S, Ibi T, Akiyama T, Fukushima M, Sugimoto Y (2016). Loss of maternal ANNEXIN A10 via a 34-kb deleted-type copy number variation is associated with embryonic mortality in Japanese Black cattle. BMC Genomics 17:968.
Crossref

 
 

Sermyagin AA, Gladyr EA, Kharitonov, SN, Ermilov AN, Strekozov, NI, Strekozov NI, Brem G, Zinovieva NA (2016). Genome-wide association study for milk production and reproduction traits in Russian Holstein cattle population. Agricultural Biology 51:182-193
Crossref

 
 

Shao B, Long R, Ding Y, Wang J, Ding L, Wang H (2010). Morphological adaptations of yak (Bos grunniens) tongue to the foraging environment of the Qinghai-Tibetan Plateau. Journal of Animal Science 88:2594-2603.
Crossref

 
 

Shi T, Yao X, Mingjuan Y, Yongzhen H, Xianyong L, Chuzhao L, Xinglei Q, Xiaoming Y, Hong C (2016). Copy number variations at LEPR gene locus associated with gene expression and phenotypic traits in Chinese cattle. Journal of Animal Science 87:336-343.
Crossref

 
 

Shin DH, Lee HJ, Cho S, Kim HJ, Hwang JY, Lee CK,Jeong JY, Yoon D, Kim H (2014). Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level. BMC Genomics 15:240.
Crossref

 
 

Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS (2011). Whole genome resequencing of Black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12:559.
Crossref

 
 

Tian R, Yin D, Liu Y, Seim I, Xu S, Yang G (2017). Adaptive Evolution of Energy Metabolism-Related Genes in Hypoxia-Tolerant Mammals. Frontiers in Genetics 8:205.
Crossref

 
 

Upadhyay M, da Silva VH, Megens H-J, Visker MHPW, Ajmone-Marsan P, Bâlteanu VA, Dunner S, Garcia JF, Ginja C, Kantanen J, Groenen MAM, Crooijmans RPMA (2017). Distribution and Functionality of Copy Number Variation across European Cattle Populations. Frontiers in Genetics 8:108.
Crossref

 
 

Utsunomiya YT, Do Carmo AS, Carvalheiro R, Neves HH, Matos MC, Zavarez LB, O'Brien AMP, Sölkner J, McEwan JC, Cole JB (2013). Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height. BMC Genetics 14:52.
Crossref

 
 

VanRaden PM, Van Tassell CP, Wiggans GR, Sonstegard TS, Schnabel RD, Taylor JF, Schenkel FS (2009). Invited review: reliability of genomic predictions for North American Holstein bulls. Journal of Dairy Science 92(1):16-24.
Crossref

 
 

Wang MD, Dzama K, Hefer CA, Muchadeyi FC (2015). Genomic population structure and prevalence of copy number variations in South African Nguni cattle. BMC Genomics 16:894 .
Crossref

 
 

Wang X, Nahashon S, Feaster TK, Bohannon-Stewart A, Adefope N (2010). An initial map of chromosomal segmental copy number variations in the chicken. BMC Genomics 11:351.
Crossref

 
 

Wang ZF, Shen X, Liu B, Su JP, Yonezawa T, Yu Y, Guo SC, Ho SYW, Vila C, Hasegawa M, Liu J (2010). Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal. Journal Biogeography 37: 2332-2344.
Crossref

 
 

Wei C, Wang H, Liu G, Zhao F, Kijas J W, Ma Y, Lu J, Zhang L, Cao J, Wu M, Wang G, Liu R, Liu Z, Zhang S, Liu C, Du L (2016).Genome-wide analysis reveals adaptation to high altitudes in Tibetan sheep. Scientific Reports 6:26770.
Crossref

 
 

Weischenfeldt J, Symmons O, Spitz F, Korbel JO (2013). Phenotypic impact of genomic structural variation: insights from and for human disease. Nature Reviews of Genetics 14:125-138.
Crossref

 
 

Wiggans GR, Sonstegard TS, VanRaden PM, Matukumalli LK, Schnabel RD, Taylor JF, Schenkel FS, Van Tassell CP (2009). Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada. Journal of Dairy Science 92:3431-3436.
Crossref

 
 

Whittow GC (2000). Sturkie's Avian Physiology. 5th Edn. Manoa, Honolulu, Hawaii Tian R, Yin D, Liu Y, Seim I, Xu S, Yang G (2017). Adaptive Evolution of Energy Metabolism-Related Genes in Hypoxia-Tolerant Mammals. Frontiers in Genetics 8:205.

 
 

Wright D, Boije H, Meadows JRS, Bed'hom B, Gourichon D, Vieaud A, Tixier-Boichard M, Rubin CJ, Imsland F, Hallböök F, Andersson L (2009). Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens. PLoS Genetics 5:e1000512.
Crossref

 
 

WU Xiao Y, Ding X, Chu M, Guo X, Bao PJ, Liang CN, Yan P (2015). Novel SNP of EPAS1 gene associated with higher haemoglobin concentration revealed the hypoxia adaptation of yak (Bos grunniens). Journal of Integrative Agriculture 14(4):741-748.
Crossref

 
 

Wu Y, Fan H, Jing S, Xia J, Chen Y, Zhang L, Gao X, Li J, Gao H, Ren H (2015). A genome-wide scan for copy number variations using high-density single nucleotide polymorphism array in Simmental cattle. Animal Genetics 46:289-298.
Crossref

 
 

Xiong X, Fu M, Lan D, Li J, Zi X, Zhong J (2015). Yak response to high-altitude hypoxic stress by altering mRNA expression and DNA methylation of hypoxia-inducible factors. Animal Biotechnology 26(3):222-229.
Crossref

 
 

Xu L, Bickhart DM, Cole JB, Schroeder SG, Song J, Tassell CP, Sonstegard TS, Liu GE (2015). Genomic Signatures Reveal New Evidences for Selection of Important Traits in Domestic Cattle. Molecular Biology and Evolution 32(3):711-725.
Crossref

 
 

Xu L, Hou Y, Bickhart DM, ZhouY, Hay EH, Song J, Sonstegard TS, Van Tassell CP, Liu GE (2016). Population-genetic properties of differentiated copy number variations in cattle. Scientific Reports 6:23161.
Crossref

 
 

Xu L, Cole JB, Bickhart DM, Hou Y, Song J, VanRaden PM, Sonstegard TS, Van Tassell CP, Liu GE (2014). Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BMC Genomics 15: 683.
Crossref

 
 

Xu Y, Jiang Y, Shi T, Cai H, Lan X, Zhao X, Plath M, Chen H (2017). Whole-genome sequencing reveals mutational landscape underlying phenotypic differences between two widespread Chinese cattle breeds. PLoS ONE 12(8):e0183921.
Crossref

 
 

Xu Y, Shi T, Cai H, Zhou Y, Lan X, Zhang C, Lei C, Qi X, Chen H (2014). Associations of MYH3 gene copy number variations with transcriptional expression and growth traits in Chinese cattle. Genetics 535:106-111.

 
 

Xu Y, Zhang LZ, Shi T, Zhou Y, Cai HF, Lan X, Zhang C, Lei C, Chen H (2013). Copy number variations of MICAL-L2 shaping gene expression contribute to different phenotypes of cattle. Mammalian Genome 24:508-516.
Crossref

 
 

Yamada T, Sasaki S, Sukegawa S, Yoshioka S, Takahagi Y, Morita M, Murakami H, Morimatsu F, Fujita T (2009). Association of a single nucleotide polymorphism in titin gene with marbling in Japanese Black beef cattle. BMC Research Notes 2:78.
Crossref

 
 

Yang J, Li WR, Lv FH, He SG, Tian SL, Peng WF, Sun YW, Zhao YX, Tu XL, Zhang M, Xie XL, Wang YT,Li JQ, Liu YG, Shen ZQ,Wang F,Liu GJ, Lu HF, Kantanen J, Han JL, Li MH, Liu MJ (2016). Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments. Molecular Biology and Evolution 33(10):2576-2592.
Crossref

 
 

Yang L, Xu L,Zhu B, Niu H,Zhang W, Miao J, Shi X, Zhang M, Chen Y, Zhang L, Gao X, Gao H, Li L, Liu GE, Li J (2017). Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle. Scientific Reports 7:14299.
Crossref

 
 

Yang M, Lv J, Zhang L, Li M, Zhou Y, Lan X, Lei C, Chen H (2017). Association study and expression analysis of CYP4A11 gene copy number variation in Chinese cattle. Scientific Reports 7:46599.
Crossref

 
 

Yue XP, Chang TC, DeJarnette JM, Marshall CE, Lei CZ, Liu WS (2013). Copy number variation of PRAMEY across breeds and its association with male fertility in Holstein sires. Journal of Dairy Science 96:8024-8034.
Crossref

 
 

Zeder MA (2008). Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact. Proceedings of the National Academy of Sciences of the United States of America 105:11597.
Crossref

 
 

Zhang MQ, Xu X, Luo SJ (2014). The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens). Animal Genetics 45:652-659.
Crossref

 
 

Zhang F, Gu W, Hurles ME, Lupski JR (2009). Copy number variation in human health, disease, and evolution. Annual Review Genomics of Human 10:451-481.
Crossref

 
 

Zhang GM, Zheng L, He H, Song CC, Zhang ZJ, Cao XK, Lei CZ, Lan XY, Qi XL, Chen H, Huang YZ (2018). Associations of GBP2 gene copy number variations with growth traits and transcriptional expression in Chinese cattle. Gene 647:101-106.
Crossref

 
 

Zhang H, Du Z-Q, Dong J-Q, Wang H-X, Shi H-Y, Wang N, Wang SZ, Li H (2014). Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content. BMC Genomics 15:517.
Crossref

 
 

Zhang L, Jia S, Yang M, Xu Y, Li C, Sun J, Huang Y, Lan X, Lei C, Zhou Y (2014). Detection of copy number variations and their effects in Chinese bulls. BMC Genomics 15:480.
Crossref

 
 

Zhang X, Wang K, Wang L, Yang Y, Zhengqiang N, Xiuyue X, Xuemin S, Jin H, Dongshi W, Qiang Q (2016). Genome-wide patterns of copy number variation in the Chinese yak genome. BMC Genomics 17:379.
Crossref

 
 

Zhao J, Yao J, Li F, Yang Z, Sun Z, Qu L, Wang K, Su Y, Zhang A, Montgomery SA, Geng T, Cui H (2016). Identification of candidate genes for chicken early- and late-feathering. Poultry Science 95:1498-1503.
Crossref

 
 

Zhou Y, Connor EE, Wiggans GR, Lu Y, Tempelman RJ, Schroeder SG, Chen H, Liu GE (2018). Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle. BMC Genomics 19:314 .
Crossref

 
 

Zhou Y, Utsunomiya YT, Xu L, Hay el HA, Bickhart DM, Alexandre PA, Rosen BD, Schroeder SG, Carvalheiro R, de Rezende Neves HH, Sonstegard TS, Van Tassell CP, Ferraz JB, Fukumasu H, Garcia JF, Liu GE (2016). Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus. BMC Genomics 17:1-9.