Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake

Functional and Integrative Genomics

Volumn 12, Issue 4, 2012, Pages 717-723

  Hou, Yali ^a,b   Bickhart, Derek M ^a   Chung, Hoyoung ^a,c   Hutchison, Jana L ^a   Norman, H Duane ^a   Connor, Erin E ^a   Liu, George E ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b China National Center for Bioinformation   (China)

^c National Institute of Animal Science   (South Korea)

Author keywords

Cattle genome; Copy number variation (CNV); Feed efficiency; Residual feed intake (RFI); Single nucleotide polymorphism (SNP)

Indexed keywords

DNA;

ANIMAL FOOD; ARTICLE; BONE DEVELOPMENT; CATTLE FARMING; CELL CYCLE; COPY NUMBER VARIATION; COW; DNA DETERMINATION; FEEDING BEHAVIOR; FOOD INTAKE; GENE FUNCTION; GENETIC ANALYSIS; GENOTYPE PHENOTYPE CORRELATION; IMMUNE RESPONSE; NONHUMAN; ORGANOGENESIS; PRIORITY JOURNAL; ANIMAL; CATTLE; EATING; GENETICS; IMMUNITY; PHYSIOLOGY; POPULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALIA; BOS;

ANIMAL FEED; ANIMALS; CATTLE; DNA COPY NUMBER VARIATIONS; EATING; IMMUNITY; OSTEOGENESIS; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION;

EID: 84877055598     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-012-0295-y     Document Type: Article

References (28)

1. Bae JS, Cheong HS, Kim LH, NamGung S, Park TJ, Chun JY, Kim JY, Pasaje CF, Lee JS, Shin HD (2010) Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genomics 11:232
2. Baldwin RL, McLeod KR, Capuco AV (2004) Visceral tissue growth and proliferation during the bovine lactation cycle. J Dairy Sci 87:2977-2986
3. Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF, Garcia JF, Van Tassell CP, Sonstegard TS, Eichler EE, Liu GE (2012) Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res 22:778-790
4. Connor EE, Hutchison JL, Olson KM, Norman HD (2012) Triennial Lactation Symposium: opportunities for improving milk production efficiency in dairy cattle. J Anim Sci 90:1687-1694
5. Fadista J, Thomsen B, Holm LE, Bendixen C (2010) Copy number variation in the bovine genome. BMC Genomics 11:284
6. Henrichsen CN, Vinckenbosch N, Zollner S, Chaignat E, Pradervand S, Schutz F, Ruedi M, Kaessmann H, Reymond A (2009) Segmental copy number variation shapes tissue transcriptomes. Nat Genet 41:424-429
7. Hou Y, Liu GE, Bickhart DM, Matukumalli LK, Li C, Song J, Gasberre LC, Van Tassell CP, Sonstegard TS (2011a) Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle. Funct Integr Genomics 12:81-92
8. Hou Y, Liu GE, Bickhart DM, Cardone MF, Wang K, Kim ES, Matukumalli LK, Ventura M, Song J, VanRadan PM, Sonstegard TS, Van Tassell CP (2011b) Genomic characteristics of cattle copy number variations. BMC Genomics 12:127
9. Hou Y, Bickhart DM, Hvinden ML, Li C, Song J, Boichard DA, Fritz S, Eggen A, Denise S, Wiggans GR, Sonstegard TS, Van Tassell CP, Liu GE (2012) Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. BMC Genomics 13:376, Epub ahead of print
10. Huntington GB, Reynolds CK (1987) Oxygen consumption and metabolite flux of bovine portal-drained viscera and liver. J Nutr 117:1167-1173
11. Koch RM, Swiger LA, Chambers D, Gregory KE (1963) Efficiency of food use in beef cattle. J Anim Sci 22:486-494
12. 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 LCD, Smith TPL, 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 Res 20:693-703
13. Lopez-Villalobos N, Berry DP, Horan B, Buckley F, Kennedy E, O'Donovan M, Shalloo L, Dillon P (2008) Genetics of residual energy intake in Irish grazing dairy cows. Proc NZ Soc Anim Prod 78:97-100
14. Machado P, Pereira R, Rocha AM, Manco L, Fernandes N, Miranda J, Ribeiro L, do Rosário VE, Amorim VA, Gusmao L, Arez AP (2010) Malaria: looking for selection signatures in the human PKLR gene region. Br J Haematol 149:775-784
15. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM (2009) Finding the missing heritability of complex diseases. Nature 461:747-753
16. McCarroll SA (2008) Extending genome-wide association studies to copy-number variation. Hum Mol Genet 17:R135-R142
17. National Research Council (2001) Nutrient requirements of dairy cattle, 7th rev edn. National Academy Press, Washington, DC
18. Orth R (1992) Sample day and lactation report. DHIA 200 Fact Sheet A-2. Mid-states DRPC, Ames, IA
19. Prendiville R, Pierce KM, Buckley F (2009) An evaluation of production efficiencies among lactating Holstein-Friesian, Jersey, and Jersey × Holstein-Friesian cows at pasture. J Dairy Sci 92:6176-6185
20. Prendiville R, Pierce KM, Delaby L, Buckley F (2011) Animal performance and production efficiencies of Holstein-Friesian, Jersey and Jersey × Holstein-Friesian cows throughout lactation. Livest Sci 138(1):25-33
21. Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L (2007) Challenges and standards in integrating surveys of structural variation. Nat Genet 39:S7-S15
22. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavare S, Deloukas P, Hurles ME, Dermitzakis ET (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315:848-853
23. Van Arendonk JAM, Nieuwhof GJ, Vos H, Korver S (1991) Genetic aspects of feed intake and efficiency in lactating dairy heifers. Livest Prod Sci 29:263-275
24. van Eerden E, van den Brand H, De Vries RG, Parmentier HK, de Jong MC, Kemp B (2004a) Residual feed intake and its effect on Salmonella enteritidis infection in growing layer hens. Poult Sci 83:1904-1910
25. van Eerden E, van den Brand H, Parmentier HK, de Jong MC, Kemp B (2004b) Phenotypic selection for residual feed intake and its effect on humoral immune responses in growing layer hens. Poult Sci 83:1602-1609
26. Veerkamp RF, Emmans GC, Cromie AR, Simm G (1995) Variance components for residual feed intake in dairy cows. Livest Prod Sci 41(2):111-120
27. Zanella A, Fermo E, Bianchi P, Chiarelli LR, Valentini G (2007) Pyruvate kinase deficiency: the genotype-phenotype association. Blood Rev 21:217-231
28. 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