FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / Genome Res / Identification of copy number variants in horses.
Genome research2012; 22(5); 899-907; doi: 10.1101/gr.128991.111

Identification of copy number variants in horses.

Abstract: Copy number variants (CNVs) represent a substantial source of genetic variation in mammals. However, the occurrence of CNVs in horses and their subsequent impact on phenotypic variation is unknown. We performed a study to identify CNVs in 16 horses representing 15 distinct breeds (Equus caballus) and an individual gray donkey (Equus asinus) using a whole-exome tiling array and the array comparative genomic hybridization methodology. We identified 2368 CNVs ranging in size from 197 bp to 3.5 Mb. Merging identical CNVs from each animal yielded 775 CNV regions (CNVRs), involving 1707 protein- and RNA-coding genes. The number of CNVs per animal ranged from 55 to 347, with median and mean sizes of CNVs of 5.3 kb and 99.4 kb, respectively. Approximately 6% of the genes investigated were affected by a CNV. Biological process enrichment analysis indicated CNVs primarily affected genes involved in sensory perception, signal transduction, and metabolism. CNVs also were identified in genes regulating blood group antigens, coat color, fecundity, lactation, keratin formation, neuronal homeostasis, and height in other species. Collectively, these data are the first report of copy number variation in horses and suggest that CNVs are common in the horse genome and may modulate biological processes underlying different traits observed among horses and horse breeds.
Get Full Text
Publication Date: 2012-03-01 PubMed ID: 22383489PubMed Central: PMC3337435DOI: 10.1101/gr.128991.111Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research identifies the presence and impact of genetic variability, specifically copy number variants (CNVs), in horses across 15 different breeds and a gray donkey. The study suggests that these CNVs could influence traits seen across various horse breeds.

Research Methodology

  • The researchers used a whole-exome tiling array and the array comparative genomics hybridization methodology to conduct this study. The whole-exome tiling array is a method that targets protein-coding regions in a genome, while array comparative genomic hybridization is a method that detects and maps DNA copy number variations.
  • The study was conducted on 16 horses and 1 gray donkey to identify possible CNVs. The selection represented 15 different horse breeds.

Findings

  • The researchers identified 2368 CNVs in the horses and the donkey. CNVs are differences in the number of copies of a specific gene in a genome. These variations ranged in size from 197 base pairs (bp) to 3.5 Megabases (Mb).
  • The study found that the number of CNVs per animal ranged from 55 to 347. The study also calculated that the median and mean sizes of CNVs were 5.3 kb and 99.4 kb, respectively.
  • When the researchers merged identical CNVs across all the animals, they identified 775 CNV regions (CNVRs), involving 1707 protein- and RNA-coding genes.

Implications

  • About 6% of the investigated genes were affected by a CNV.
  • Based on the biological process enrichment analysis, CNVs primarily affected genes involved in sensory perception, signal transduction, and metabolism.
  • Significant observations were made of CNVs in genes that regulate various functions in other species. These include blood group antigens (blood typing), coat color, fecundity (reproductive rate), lactation, keratin formation (component of hair), neuronal homeostasis (brain cell stability), and height.
  • This study is the first of its kind to report copy number variation in horses. It also indicates that CNVs may modulate biological processes underlying different traits observed among horses and horse breeds. It’s therefore an essential addition to understanding horse genetics and potential breeding consequences.

Cite This Article

APA
Doan R, Cohen N, Harrington J, Veazey K, Juras R, Cothran G, McCue ME, Skow L, Dindot SV. (2012). Identification of copy number variants in horses. Genome Res, 22(5), 899-907. https://doi.org/10.1101/gr.128991.111

Publication

Genome research
ISSN: 1549-5469
NlmUniqueID: 9518021
Country: United States
Language: English
Volume: 22
Issue: 5
Pages: 899-907

Researcher Affiliations

Doan, Ryan
  • Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
Cohen, Noah
    Harrington, Jessica
      Veazey, Kylee
        Juras, Rytis
          Cothran, Gus
            McCue, Molly E
              Skow, Loren
                Dindot, Scott V

                  MeSH Terms

                  • Animals
                  • Base Sequence
                  • Bone Morphogenetic Protein Receptors, Type I / genetics
                  • Cluster Analysis
                  • Comparative Genomic Hybridization
                  • DNA Copy Number Variations
                  • Exome
                  • Genome
                  • Horses / genetics
                  • Molecular Sequence Annotation
                  • Molecular Sequence Data
                  • Phenotype
                  • gp100 Melanoma Antigen / genetics

                  References

                  This article includes 38 references
                  1. Boone PM, Bacino CA, Shaw CA, Eng PA, Hixson PM, Pursley AN, Kang SH, Yang Y, Wiszniewska J, Nowakowska BA, del Gaudio D, Xia Z, Simpson-Patel G, Immken LL, Gibson JB, Tsai AC, Bowers JA, Reimschisel TE, Schaaf CP, Potocki L, Scaglia F, Gambin T, Sykulski M, Bartnik M, Derwinska K, Wisniowiecka-Kowalnik B, Lalani SR, Probst FJ, Bi W, Beaudet AL, Patel A, Lupski JR, Cheung SW, Stankiewicz P. Detection of clinically relevant exonic copy-number changes by array CGH.. Hum Mutat 2010 Dec;31(12):1326-42.
                    pmc: PMC3158569pubmed: 20848651doi: 10.1002/humu.21360google scholar: lookup
                  2. Brunberg E, Andersson L, Cothran G, Sandberg K, Mikko S, Lindgren G. A missense mutation in PMEL17 is associated with the Silver coat color in the horse.. BMC Genet 2006 Oct 9;7:46.
                    pmc: PMC1617113pubmed: 17029645doi: 10.1186/1471-2156-7-46google scholar: lookup
                  3. Cañon J, Checa ML, Carleos C, Vega-Pla JL, Vallejo M, Dunner S. The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data.. Anim Genet 2000 Feb;31(1):39-48.
                    pubmed: 10690360doi: 10.1046/j.1365-2052.2000.00591.xgoogle scholar: lookup
                  4. Chen WK, Swartz JD, Rush LJ, Alvarez CE. Mapping DNA structural variation in dogs.. Genome Res 2009 Mar;19(3):500-9.
                    pmc: PMC2661804pubmed: 19015322doi: 10.1101/gr.083741.108google scholar: lookup
                  5. Chu MX, Liu ZH, Jiao CL, He YQ, Fang L, Ye SC, Chen GH, Wang JY. Mutations in BMPR-IB and BMP-15 genes are associated with litter size in Small Tailed Han sheep (Ovis aries).. J Anim Sci 2007 Mar;85(3):598-603.
                    pubmed: 17040942doi: 10.2527/jas.2006-324google scholar: lookup
                  6. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen 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, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME. Origins and functional impact of copy number variation in the human genome.. Nature 2010 Apr 1;464(7289):704-12.
                    pmc: PMC3330748pubmed: 19812545doi: 10.1038/nature08516google scholar: lookup
                  7. DeBolt S. Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales.. Genome Biol Evol 2010 Jul 12;2:441-53.
                    pmc: PMC2997553pubmed: 20624746doi: 10.1093/gbe/evq033google scholar: lookup
                  8. Fadista J, Thomsen B, Holm LE, Bendixen C. Copy number variation in the bovine genome.. BMC Genomics 2010 May 6;11:284.
                    pmc: PMC2902221pubmed: 20459598doi: 10.1186/1471-2164-11-284google scholar: lookup
                  9. 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. Copy number variation: new insights in genome diversity.. Genome Res 2006 Aug;16(8):949-61.
                    pubmed: 16809666doi: 10.1101/gr.3677206google scholar: lookup
                  10. Guryev V, Saar K, Adamovic T, Verheul M, van Heesch SA, Cook S, Pravenec M, Aitman T, Jacob H, Shull JD, Hubner N, Cuppen E. Distribution and functional impact of DNA copy number variation in the rat.. Nat Genet 2008 May;40(5):538-45.
                    pubmed: 18443591doi: 10.1038/ng.141google scholar: lookup
                  11. Hoashi T, Muller J, Vieira WD, Rouzaud F, Kikuchi K, Tamaki K, Hearing VJ. The repeat domain of the melanosomal matrix protein PMEL17/GP100 is required for the formation of organellar fibers.. J Biol Chem 2006 Jul 28;281(30):21198-21208.
                    pubmed: 16682408doi: 10.1074/jbc.M601643200google scholar: lookup
                  12. 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. Genomic characteristics of cattle copy number variations.. BMC Genomics 2011 Feb 23;12:127.
                    pmc: PMC3053260pubmed: 21345189doi: 10.1186/1471-2164-12-127google scholar: lookup
                  13. Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.. Nucleic Acids Res 2009 Jan;37(1):1-13.
                    pmc: PMC2615629pubmed: 19033363doi: 10.1093/nar/gkn923google scholar: lookup
                  14. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.. Nat Protoc 2009;4(1):44-57.
                    pubmed: 19131956doi: 10.1038/nprot.2008.211google scholar: lookup
                  15. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tüzün E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR, Eichler EE. Mapping and sequencing of structural variation from eight human genomes.. Nature 2008 May 1;453(7191):56-64.
                    pmc: PMC2424287pubmed: 18451855doi: 10.1038/nature06862google scholar: lookup
                  16. Kijas JW, Barendse W, Barris W, Harrison B, McCulloch R, McWilliam S, Whan V. Analysis of copy number variants in the cattle genome.. Gene 2011 Aug 15;482(1-2):73-7.
                    pubmed: 21620936doi: 10.1016/j.gene.2011.04.011google scholar: lookup
                  17. Kim D, Ackerman SL. The UNC5C netrin receptor regulates dorsal guidance of mouse hindbrain axons.. J Neurosci 2011 Feb 9;31(6):2167-79.
                    pmc: PMC3073835pubmed: 21307253doi: 10.1523/JNEUROSCI.5254-10.2011google scholar: lookup
                  18. Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS. A highly annotated whole-genome sequence of a Korean individual.. Nature 2009 Aug 20;460(7258):1011-5.
                    pmc: PMC2860965pubmed: 19587683doi: 10.1038/nature08211google scholar: lookup
                  19. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M. Paired-end mapping reveals extensive structural variation in the human genome.. Science 2007 Oct 19;318(5849):420-6.
                    pmc: PMC2674581pubmed: 17901297doi: 10.1126/science.1149504google scholar: lookup
                  20. Leroy G, Callède L, Verrier E, Mériaux JC, Ricard A, Danchin-Burge C, Rognon X. Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism.. Genet Sel Evol 2009 Jan 5;41(1):5.
                    pmc: PMC3225878pubmed: 19284689doi: 10.1186/1297-9686-41-5google scholar: lookup
                  21. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, Venter JC. The diploid genome sequence of an individual human.. PLoS Biol 2007 Sep 4;5(10):e254.
                    pmc: PMC1964779pubmed: 17803354doi: 10.1371/journal.pbio.0050254google scholar: lookup
                  22. Liu GE, Hou Y, 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. Analysis of copy number variations among diverse cattle breeds.. Genome Res 2010 May;20(5):693-703.
                    pmc: PMC2860171pubmed: 20212021doi: 10.1101/gr.105403.110google scholar: lookup
                  23. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.. Methods 2001 Dec;25(4):402-8.
                    pubmed: 11846609doi: 10.1006/meth.2001.1262google scholar: lookup
                  24. McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, Leeb T, Lindgren G, Penedo MC, Røed KH, Ryder OA, Swinburne JE, Tozaki T, Valberg SJ, Vaudin M, Lindblad-Toh K, Wade CM, Mickelson JR. A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies.. PLoS Genet 2012 Jan;8(1):e1002451.
                    pmc: PMC3257288pubmed: 22253606doi: 10.1371/journal.pgen.1002451google scholar: lookup
                  25. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO. Mapping copy number variation by population-scale genome sequencing.. Nature 2011 Feb 3;470(7332):59-65.
                    pmc: PMC3077050pubmed: 21293372doi: 10.1038/nature09708google scholar: lookup
                  26. Nicholas TJ, Cheng Z, Ventura M, Mealey K, Eichler EE, Akey JM. The genomic architecture of segmental duplications and associated copy number variants in dogs.. Genome Res 2009 Mar;19(3):491-9.
                    pmc: PMC2661811pubmed: 19129542doi: 10.1101/gr.084715.108google scholar: lookup
                  27. Nicholas TJ, Baker C, Eichler EE, Akey JM. A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog.. BMC Genomics 2011 Aug 16;12:414.
                    pmc: PMC3166287pubmed: 21846351doi: 10.1186/1471-2164-12-414google scholar: lookup
                  28. Nielsen HB, Wernersson R, Knudsen S. Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.. Nucleic Acids Res 2003 Jul 1;31(13):3491-6.
                    pmc: PMC169028pubmed: 12824351doi: 10.1093/nar/gkg622google scholar: lookup
                  29. Redon R, 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. Global variation in copy number in the human genome.. Nature 2006 Nov 23;444(7118):444-54.
                    pmc: PMC2669898pubmed: 17122850doi: 10.1038/nature05329google scholar: lookup
                  30. Sharp AJ, Cheng Z, Eichler EE. Structural variation of the human genome.. Annu Rev Genomics Hum Genet 2006;7:407-42.
                    pubmed: 16780417doi: 10.1146/annurev.genom.7.080505.115618google scholar: lookup
                  31. Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease.. Annu Rev Med 2010;61:437-55.
                    pubmed: 20059347doi: 10.1146/annurev-med-100708-204735google scholar: lookup
                  32. Sturn A, Quackenbush J, Trajanoski Z. Genesis: cluster analysis of microarray data.. Bioinformatics 2002 Jan;18(1):207-8.
                    pubmed: 11836235doi: 10.1093/bioinformatics/18.1.207google scholar: lookup
                  33. Vilà C, Leonard JA, Gotherstrom A, Marklund S, Sandberg K, Liden K, Wayne RK, Ellegren H. Widespread origins of domestic horse lineages.. Science 2001 Jan 19;291(5503):474-7.
                    pubmed: 11161199doi: 10.1126/science.291.5503.474google scholar: lookup
                  34. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Lander ES, Lindblad-Toh K. Genome sequence, comparative analysis, and population genetics of the domestic horse.. Science 2009 Nov 6;326(5954):865-7.
                    pmc: PMC3785132pubmed: 19892987doi: 10.1126/science.1178158google scholar: lookup
                  35. Wernersson R, Nielsen HB. OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes.. Nucleic Acids Res 2005 Jul 1;33(Web Server issue):W611-5.
                    pmc: PMC1160160pubmed: 15980547doi: 10.1093/nar/gki399google scholar: lookup
                  36. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. The complete genome of an individual by massively parallel DNA sequencing.. Nature 2008 Apr 17;452(7189):872-6.
                    pubmed: 18421352doi: 10.1038/nature06884google scholar: lookup
                  37. Yang F, Fu B, O'Brien PC, Nie W, Ryder OA, Ferguson-Smith MA. Refined genome-wide comparative map of the domestic horse, donkey and human based on cross-species chromosome painting: insight into the occasional fertility of mules.. Chromosome Res 2004;12(1):65-76.
                    pubmed: 14984103doi: 10.1023/b:chro.0000009298.02689.8agoogle scholar: lookup
                  38. Zhang F, Gu W, Hurles ME, Lupski JR. Copy number variation in human health, disease, and evolution.. Annu Rev Genomics Hum Genet 2009;10:451-81.
                    pmc: PMC4472309pubmed: 19715442doi: 10.1146/annurev.genom.9.081307.164217google scholar: lookup

                  Citations

                  This article has been cited 44 times.
                  1. Kim YM, Ha SJ, Seong HS, Choi JY, Baek HJ, Yang BC, Choi JW, Kim NY. Identification of Copy Number Variations in Four Horse Breed Populations in South Korea. Animals (Basel) 2022 Dec 12;12(24).
                    doi: 10.3390/ani12243501pubmed: 36552421google scholar: lookup
                  2. Laseca N, Molina A, Valera M, Antonini A, Demyda-Peyrás S. Copy Number Variation (CNV): A New Genomic Insight in Horses. Animals (Basel) 2022 Jun 2;12(11).
                    doi: 10.3390/ani12111435pubmed: 35681904google scholar: lookup
                  3. Polani S, Dean M, Lichter-Peled A, Hendrickson S, Tsang S, Fang X, Feng Y, Qiao W, Avni G, Kahila Bar-Gal G. Sequence Variant in the TRIM39-RPP21 Gene Readthrough is Shared Across a Cohort of Arabian Foals Diagnosed with Juvenile Idiopathic Epilepsy. J Genet Mutat Disord 2022 Jan;1(1).
                    pubmed: 35465405
                  4. Wang M, Liu Y, Bi X, Ma H, Zeng G, Guo J, Guo M, Ling Y, Zhao C. Genome-Wide Detection of Copy Number Variants in Chinese Indigenous Horse Breeds and Verification of CNV-Overlapped Genes Related to Heat Adaptation of the Jinjiang Horse. Genes (Basel) 2022 Mar 28;13(4).
                    doi: 10.3390/genes13040603pubmed: 35456409google scholar: lookup
                  5. Laseca N, Anaya G, Peña Z, Pirosanto Y, Molina A, Demyda Peyrás S. Impaired Reproductive Function in Equines: From Genetics to Genomics. Animals (Basel) 2021 Feb 3;11(2).
                    doi: 10.3390/ani11020393pubmed: 33546520google scholar: lookup
                  6. Li J, Fan Z, Shen F, Pendleton AL, Song Y, Xing J, Yue B, Kidd JM, Li J. Genomic Copy Number Variation Study of Nine Macaca Species Provides New Insights into Their Genetic Divergence, Adaptation, and Biomedical Application. Genome Biol Evol 2020 Dec 6;12(12):2211-2230.
                    doi: 10.1093/gbe/evaa200pubmed: 32970804google scholar: lookup
                  7. Ghosh S, Davis BW, Rosengren M, Jevit MJ, Castaneda C, Arnold C, Jaxheimer J, Love CC, Varner DD, Lindgren G, Wade CM, Raudsepp T. Characterization of A Homozygous Deletion of Steroid Hormone Biosynthesis Genes in Horse Chromosome 29 as A Risk Factor for Disorders of Sex Development and Reproduction. Genes (Basel) 2020 Feb 27;11(3).
                    doi: 10.3390/genes11030251pubmed: 32120906google scholar: lookup
                  8. Ablondi M, Eriksson S, Tetu S, Sabbioni A, Viklund Å, Mikko S. Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines. Genes (Basel) 2019 Nov 27;10(12).
                    doi: 10.3390/genes10120976pubmed: 31783652google scholar: lookup
                  9. Solé M, Ablondi M, Binzer-Panchal A, Velie BD, Hollfelder N, Buys N, Ducro BJ, François L, Janssens S, Schurink A, Viklund Å, Eriksson S, Isaksson A, Kultima H, Mikko S, Lindgren G. Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds. BMC Genomics 2019 Oct 22;20(1):759.
                    doi: 10.1186/s12864-019-6141-zpubmed: 31640551google scholar: lookup
                  10. Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019 Dec;50(6):569-597.
                    doi: 10.1111/age.12857pubmed: 31568563google scholar: lookup
                  11. Beeson SK, Mickelson JR, McCue ME. Exploration of fine-scale recombination rate variation in the domestic horse. Genome Res 2019 Oct;29(10):1744-1752.
                    doi: 10.1101/gr.243311.118pubmed: 31434677google scholar: lookup
                  12. Rinker DC, Specian NK, Zhao S, Gibbons JG. Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift. Proc Natl Acad Sci U S A 2019 Jul 2;116(27):13446-13451.
                    doi: 10.1073/pnas.1901093116pubmed: 31209046google scholar: lookup
                  13. Wang C, Chen H, Wang X, Wu Z, Liu W, Guo Y, Ren J, Ding N. Identification of copy number variations using high density whole-genome SNP markers in Chinese Dongxiang spotted pigs. Asian-Australas J Anim Sci 2019 Dec 1;32(12):1809-1815.
                    doi: 10.5713/ajas.18.0696pubmed: 30744341google scholar: lookup
                  14. Liu S, Kang X, Catacchio CR, Liu M, Fang L, Schroeder SG, Li W, Rosen BD, Iamartino D, Iannuzzi L, Sonstegard TS, Van Tassell CP, Ventura M, Low WY, Williams JL, Bickhart DM, Liu GE. Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo ( Bubalus bubalis ). Funct Integr Genomics 2019 May;19(3):409-419.
                    doi: 10.1007/s10142-019-00657-4pubmed: 30734132google scholar: lookup
                  15. Genova F, Longeri M, Lyons LA, Bagnato A, Strillacci MG. First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data. BMC Genomics 2018 Dec 10;19(1):895.
                    doi: 10.1186/s12864-018-5297-2pubmed: 30526495google scholar: lookup
                  16. Schurink A, da Silva VH, Velie BD, Dibbits BW, Crooijmans RPMA, Franҫois L, Janssens S, Stinckens A, Blott S, Buys N, Lindgren G, Ducro BJ. Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity. BMC Genet 2018 Jul 30;19(1):49.
                    doi: 10.1186/s12863-018-0657-0pubmed: 30060732google scholar: lookup
                  17. Bhanuprakash V, Chhotaray S, Pruthviraj DR, Rawat C, Karthikeyan A, Panigrahi M. Copy number variation in livestock: A mini review. Vet World 2018 Apr;11(4):535-541.
                    doi: 10.14202/vetworld.2018.535-541pubmed: 29805222google scholar: lookup
                  18. Yang M, Lv J, Zhang L, Li M, Zhou Y, Lan X, Lei C, Chen H. Association study and expression analysis of CYP4A11 gene copy number variation in Chinese cattle. Sci Rep 2017 May 11;7:46599.
                    doi: 10.1038/srep46599pubmed: 28492277google scholar: lookup
                  19. Gim JA, Kim HS. Identification and Expression of Equine MER-Derived miRNAs. Mol Cells 2017 Apr;40(4):262-270.
                    doi: 10.14348/molcells.2017.2295pubmed: 28320202google scholar: lookup
                  20. Xu L, Haasl RJ, Sun J, Zhou Y, Bickhart DM, Li J, Song J, Sonstegard TS, Van Tassell CP, Lewin HA, Liu GE. Systematic Profiling of Short Tandem Repeats in the Cattle Genome. Genome Biol Evol 2017 Jan 1;9(1):20-31.
                    doi: 10.1093/gbe/evw256pubmed: 28172841google scholar: lookup
                  21. McQueen CM, Dindot SV, Foster MJ, Cohen ND. Genetic Susceptibility to Rhodococcus equi. J Vet Intern Med 2015 Nov-Dec;29(6):1648-59.
                    doi: 10.1111/jvim.13616pubmed: 26340305google scholar: lookup
                  22. Bertolini F, Scimone C, Geraci C, Schiavo G, Utzeri VJ, Chiofalo V, Fontanesi L. Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms. PLoS One 2015;10(7):e0131925.
                    doi: 10.1371/journal.pone.0131925pubmed: 26151450google scholar: lookup
                  23. van den Broek M, Bolat I, Nijkamp JF, Ramos E, Luttik MA, Koopman F, Geertman JM, de Ridder D, Pronk JT, Daran JM. Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains. Appl Environ Microbiol 2015 Sep;81(18):6253-67.
                    doi: 10.1128/AEM.01263-15pubmed: 26150454google scholar: lookup
                  24. Pezer Ž, Harr B, Teschke M, Babiker H, Tautz D. Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions. Genome Res 2015 Aug;25(8):1114-24.
                    doi: 10.1101/gr.187187.114pubmed: 26149421google scholar: lookup
                  25. Radke DW, Lee C. Adaptive potential of genomic structural variation in human and mammalian evolution. Brief Funct Genomics 2015 Sep;14(5):358-68.
                    doi: 10.1093/bfgp/elv019pubmed: 26003631google scholar: lookup
                  26. Ghosh S, Qu Z, Das PJ, Fang E, Juras R, Cothran EG, McDonell S, Kenney DG, Lear TL, Adelson DL, Chowdhary BP, Raudsepp T. Copy number variation in the horse genome. PLoS Genet 2014 Oct;10(10):e1004712.
                    doi: 10.1371/journal.pgen.1004712pubmed: 25340504google scholar: lookup
                  27. Zhang Q, Ma Y, Wang X, Zhang Y, Zhao X. Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array. Mol Genet Genomics 2015 Feb;290(1):319-27.
                    doi: 10.1007/s00438-014-0923-4pubmed: 25248638google scholar: lookup
                  28. Wang Y, Tang Z, Sun Y, Wang H, Wang C, Yu S, Liu J, Zhang Y, Fan B, Li K, Liu B. Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays. PLoS One 2014;9(9):e106780.
                    doi: 10.1371/journal.pone.0106780pubmed: 25198154google scholar: lookup
                  29. Park KD, Kim H, Hwang JY, Lee CK, Do KT, Kim HS, Yang YM, Kwon YJ, Kim J, Kim HJ, Song KD, Oh JD, Kim H, Cho BW, Cho S, Lee HK. Copy number deletion has little impact on gene expression levels in racehorses. Asian-Australas J Anim Sci 2014 Sep;27(9):1345-54.
                    doi: 10.5713/ajas.2013.13857pubmed: 25178379google scholar: lookup
                  30. McQueen CM, Doan R, Dindot SV, Bourquin JR, Zlatev ZZ, Chaffin MK, Blodgett GP, Ivanov I, Cohen ND. Identification of genomic loci associated with Rhodococcus equi susceptibility in foals. PLoS One 2014;9(6):e98710.
                    doi: 10.1371/journal.pone.0098710pubmed: 24892408google scholar: lookup
                  31. Zhao Q, Han MJ, Sun W, Zhang Z. Copy number variations among silkworms. BMC Genomics 2014 Mar 31;15:251.
                    doi: 10.1186/1471-2164-15-251pubmed: 24684762google scholar: lookup
                  32. Molin AM, Berglund J, Webster MT, Lindblad-Toh K. Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array. BMC Genomics 2014 Mar 19;15:210.
                    doi: 10.1186/1471-2164-15-210pubmed: 24640994google scholar: lookup
                  33. Gurgul A, Semik E, Pawlina K, Szmatoła T, Jasielczuk I, Bugno-Poniewierska M. The application of genome-wide SNP genotyping methods in studies on livestock genomes. J Appl Genet 2014 May;55(2):197-208.
                    doi: 10.1007/s13353-014-0202-4pubmed: 24566962google scholar: lookup
                  34. Wang W, Wang S, Hou C, Xing Y, Cao J, Wu K, Liu C, Zhang D, Zhang L, Zhang Y, Zhou H. Genome-wide detection of copy number variations among diverse horse breeds by array CGH. PLoS One 2014;9(1):e86860.
                    doi: 10.1371/journal.pone.0086860pubmed: 24497987google scholar: lookup
                  35. Metzger J, Philipp U, Lopes MS, da Camara Machado A, Felicetti M, Silvestrelli M, Distl O. Analysis of copy number variants by three detection algorithms and their association with body size in horses. BMC Genomics 2013 Jul 18;14:487.
                    doi: 10.1186/1471-2164-14-487pubmed: 23865711google scholar: lookup
                  36. Tian M, Wang Y, Gu X, Feng C, Fang S, Hu X, Li N. Copy number variants in locally raised Chinese chicken genomes determined using array comparative genomic hybridization. BMC Genomics 2013 Apr 17;14:262.
                    doi: 10.1186/1471-2164-14-262pubmed: 23594354google scholar: lookup
                  37. Chen C, Qiao R, Wei R, Guo Y, Ai H, Ma J, Ren J, Huang L. 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 2012 Dec 27;13:733.
                    doi: 10.1186/1471-2164-13-733pubmed: 23270433google scholar: lookup
                  38. Côté O, Lillie BN, Hayes MA, Clark ME, van den Bosch L, Katavolos P, Viel L, Bienzle D. Multiple secretoglobin 1A1 genes are differentially expressed in horses. BMC Genomics 2012 Dec 19;13:712.
                    doi: 10.1186/1471-2164-13-712pubmed: 23253434google scholar: lookup
                  39. Togla O, Bhardwaj S, Kadyan S, Wani YM, Mukherjee S, Mukherjee A. Mapping copy number variable regions correlated with reproduction and production traits in Karan Fries cattle mammalian genomics. Mamm Genome 2025 Dec;36(4):1141-1152.
                    doi: 10.1007/s00335-025-10152-wpubmed: 40815312google scholar: lookup
                  40. Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D. Whole-Genome Resequencing Analysis of Copy Number Variations Associated with Athletic Performance in Grassland-Thoroughbred. Animals (Basel) 2025 May 18;15(10).
                    doi: 10.3390/ani15101458pubmed: 40427335google scholar: lookup
                  41. Sharma NK, Singh P, Saha B, Bhardwaj A, Iquebal MA, Pal Y, Nayan V, Jaiswal S, Giri SK, Legha RA, Bhattacharya TK, Kumar D, Rai A. Genome wide landscaping of copy number variations for horse inter-breed variability. Anim Biotechnol 2025 Dec;36(1):2446251.
                    doi: 10.1080/10495398.2024.2446251pubmed: 39791493google scholar: lookup
                  42. Liu X, Chen W, Huang B, Wang X, Peng Y, Zhang X, Chai W, Khan MZ, Wang C. Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits. Front Vet Sci 2023;10:1334434.
                    doi: 10.3389/fvets.2023.1334434pubmed: 38274664google scholar: lookup
                  43. Tang X, Zhu B, Ren R, Chen B, Li S, Gu J. Genome-wide copy number variation detection in a large cohort of diverse horse breeds by whole-genome sequencing. Front Vet Sci 2023;10:1296213.
                    doi: 10.3389/fvets.2023.1296213pubmed: 38076560google scholar: lookup
                  44. Choudhury MP, Wang Z, Zhu M, Teng S, Yan J, Cao S, Yi G, Liu Y, Liao Y, Tang Z. Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses. Genes (Basel) 2023 Oct 13;14(10).
                    doi: 10.3390/genes14101934pubmed: 37895283google scholar: lookup
                  Subscribe to our newsletter
                  Join 99,359 horse owners like you who receive our email updates on horse health and nutrition.