Genome-wide association analysis to identify genotype × environment interaction for milk protein yield and level of somatic cell score as environmental descriptors in German Holsteins

Journal of Dairy Science

Volumn 96, Issue 11, 2013, Pages 7318-7324

  Streit, M ^a   Reinhardt, F ^b   Thaller, G ^c   Bennewitz, J ^a  

^a UNIVERSITY OF HOHENHEIM   (Germany)

^b Vereinigte Informationssysteme Tierhaltung wV VIT   (Germany)

^c UNIVERSITY OF KIEL   (Germany)

Author keywords

Association analysis; Genotype environment interaction; Reaction norm; Somatic cell score

Indexed keywords

BOS;

MILK PROTEIN;

ANIMAL; BOVINAE; CELL COUNT; CHEMISTRY; GENETIC ASSOCIATION; GENOTYPE; GENOTYPE ENVIRONMENT INTERACTION; MILK; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

ANIMALS; CATTLE; CELL COUNT; GENE-ENVIRONMENT INTERACTION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; MILK; MILK PROTEINS; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84886240572     PISSN: 00220302     EISSN: 15253198     Source Type: Journal    
DOI: 10.3168/jds.2013-7133     Document Type: Article

References (28)

1. Barkema H.W., Schukken Y.H., Lam T.J.G.M., Beiboer M.L., Wilmink H., Benedictus G., Brand A. Incidence of clinical mastitis in dairy herds grouped in three categories by bulk milk somatic cell counts. J. Dairy Sci. 1998, 81:411-419.
2. Barkema H.W., van der Ploeg J.D., Schukken Y.H., Lam T.J.G.M., Benedictus G., Brand A. Management style and its associations with bulk milk somatic cell count and incidence rate of clinical mastitis. J. Dairy Sci. 1999, 82:1655-1663.
3. Bennewitz J., Reinsch N., Guiard V., Fritz S., Thomsen H., Looft C., Kühn C., Schwerin M., Weimann C., Erhardt G., Reinhardt F., Reents R., Boichard D., Kalm E. Multiple quantitative trait loci mapping with cofactors and application of alternative variants of the false discovery rate in an enlarged granddaughter design. Genetics 2004, 168:1019-1027. a.
4. Bennewitz J., Reinsch N., Paul S., Looft C., Kaupe B., Weimann C., Erhardt G., Thaller G., Kühn C., Schwerin M., Thomsen H., Reinhardt F., Reents R., Kalm E. The DGAT1 K232A mutation is not solely responsible for the milk production quantitative trait locus on the bovine chromosome 14. J. Dairy Sci. 2004, 87:431-442. b.
5. Dufour S., Fréchette A., Barkema H.W., Mussell A., Scholl D.T. Invited review: Effect of udder health management practices on herd somatic cell count. J. Dairy Sci. 2011, 94:563-579. 10.3168/jds.2010-3715.
6. Fikse W.F., Rekaya R., Weigel K.A. Assessment of environmental descriptors for studying genotype by environment interaction. Livest. Prod. Sci. 2003, 82:223-231. 10.1016/S0301-6226(03)00009-5.
7. Gilmour A.R., Gogel B.J., Cullis B.R., Thompson R. Genetics and Analysis of Quantitative Traits. ASReml User Guide 3.0 2009, VSN International Ltd, Hemel Hempstead, UK.
8. Hayes B.J., Bowman P.J., Chamberlain A.J., Savin K., van Tassell C.P., Sonstegard T.S., Goddard M.E. A validated genome wide association study to breed cattle adapted to an environment altered by climate change. PLoS ONE 2009, 4:e6676.
9. Hayes B.J., Carrick M., Bowman P., Goddard M.E. Genotype × environment interaction for milk production of daughters of Australian dairy sires from test-day records. J. Dairy Sci. 2003, 86:3736-3744.
10. Kolmodin R., Bijma P. Response to mass selection when the genotype by environment interaction is modelled as a linear reaction norm. Genet. Sel. Evol. 2004, 36:435-454.
11. Kolmodin R., Strandberg E., Madsen P., Jensen J., Jorjani H. Genotype by environment interaction in Nordic dairy cattle studied using reaction norms. Acta Agric. Scand. A Anim. Sci. 2002, 52:11-24.
12. König S., Dietl G., Raeder I., Swalve H.H. Genetic relationships for dairy performance between large-scale and small-scale farm conditions. J. Dairy Sci. 2005, 88:4087-4096.
13. Kühn C., Freyer G., Weikard R., Goldammer T., Schwerin M. Detection of QTL for milk production traits in cattle by application of a specifically developed marker map of BTA6. Anim. Genet. 1999, 30:333-340.
14. Lillehammer M., Hayes B.J., Meuwissen T.H.E., Goddard M.E. Gene by environment interactions for production traits in Australian dairy cattle. J. Dairy Sci. 2009, 92:4008-4017. a.
15. Lillehammer M., Ødegård J., Meuwissen T.H.E. Reducing the bias of estimates of genotype by environment interactions in random regression sire models. Genet. Sel. Evol. 2009, 41:30. b.
16. Lynch M., Walsh B. Genetics and Analysis of Quantitative Traits. Sinauer Associates Inc 1998, Publishers, Sunderland, MA.
17. Matukumalli L.K., Lawley C.T., Schnabel R.D., Taylor J.F., Allan M.F., Heaton M.P., O'Connell J., Moore S.S., Smith T.P.L., Sonstegard T.S., van Tassell C.P. Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 2009, 4:e5350.
18. Pryce J.E., Bolormaa S., Chamberlain A.J., Bowman P.J., Savin K., Goddard M.E., Hayes B.J. A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes. J. Dairy Sci. 2010, 93:3331-3345. 10.3168/jds.2009-2893.
19. Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A.R., Bender D., Maller J., Sklar P., de Bakker P.I.W., Daly M.J., Sham P.C. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 2007, 81:559-575.
20. Qanbari S., Pimentel E.C.G., Tetens J., Thaller G., Lichtner P., Sharifi A.R., Simianer H. The pattern of linkage disequilibrium in German Holstein cattle. Anim. Genet. 2010, 41:346-356.
21. Scheet P., Stephens M. A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. 2006, 78:629-644.
22. Storey J.D., Tibshirani R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 2003, 100:9440-9445.
23. Strandberg E., Brotherstone S., Wall E., Coffey M.P. Genotype by environment interaction for first-lactation female fertility traits in UK dairy cattle. J. Dairy Sci. 2009, 92:3437-3446. 10.3168/jds.2008-1844.
24. Streit M., Reinhardt F., Thaller G., Bennewitz J. Reaction norms and genotype-by-environment interaction in the German Holstein dairy cattle. J. Anim. Breed. Genet. 2012, 129:380-389. 10.1111/j.1439-0388.2012.00999.x.
25. Streit M., Wellmann R., Reindardt F., Thaller G., Piepho H.P., Bennewitz J. Using genome-wide association analysis to characterize environmental sensitivity of milk traits in dairy cattle. G3 (Bethesda) 2013, 3:1085-1093. 10.1534/g3.113.006536.
26. Thaller G., Krämer W., Winter A., Kaupe B., Erhardt G., Fries R. Effects of DGAT1 variants on milk production traits in German cattle breeds. J. Anim. Sci. 2003, 81:1911-1918.
27. Veerkamp R.F., Mulder H.A., Calus M.P.L., Windig J.J., ten Napel J. Statistical genetics to improve robustness of dairy cows. Proc. Assoc. Adv. Anim. Breed. Genet. 2009, 18:406-413.
28. Wang X., Wurmser C., Pausch H., Jung S., Reindardt F., Tetens J., Thaller G., Fries R. Identification and dissection of four major QTL affecting milk fat content in the German Holstein-Friesian population. PLoS ONE 2012, 7:e40711.