Hostname: page-component-586b7cd67f-rdxmf Total loading time: 0 Render date: 2024-11-22T09:42:37.320Z Has data issue: false hasContentIssue false
  • English
  • Français

An alternative experimental case–control design for genetic association studies on bovine mastitis

Published online by Cambridge University Press:  18 August 2016

S. Biffani ,
M. Del Corvo ,
R. Capoferri ,
A. Pedretti ,
M. Luini ,
J. L. Williams ,
G. Pagnacco ,
F. Minvielle  and
G. Minozzi
S. Biffani
Affiliation:
Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via Einstein, 26900, Lodi, Italy
M. Del Corvo
Affiliation:
Parco Tecnologico Padano Srl, Via Einstein, 26900, Lodi, Italy
R. Capoferri
Affiliation:
Istituto Sperimentale Italiano ‘Lazzaro Spallanzani’, 26027, Cremona, Italy
A. Pedretti
Affiliation:
Parco Tecnologico Padano Srl, Via Einstein, 26900, Lodi, Italy
M. Luini
Affiliation:
Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Einstein, 26900, Lodi, Italy
J. L. Williams
Affiliation:
School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy SA 5371, Australia
G. Pagnacco
Affiliation:
Department of Veterinary Sciences, University of Milan, Via Celoria 10, 20133, Milan, Italy
F. Minvielle
Affiliation:
Institut National de la Recherche Agronomique (INRA), UMR 1313 Génétique Animale et Biologie Intégrative, F-78352 Jouy-en-Josas, France
G. Minozzi*
Affiliation:
Parco Tecnologico Padano Srl, Via Einstein, 26900, Lodi, Italy Department of Veterinary Sciences, University of Milan, Via Celoria 10, 20133, Milan, Italy
*
†E-mail: giulietta.minozzi@unimi.it
Get access

Abstract

The possibility of using genetic control strategies to increase disease resistance to infectious diseases relies on the identification of markers to include in the breeding plans. Possible incomplete exposure of mastitis-free (control) animals, however, is a major issue to find relevant markers in genetic association studies for infectious diseases. Usually, designs based on elite dairy sires are used in association studies, but an epidemiological case–control strategy, based on cows repeatedly field-tested could be an alternative for disease traits. To test this hypothesis, genetic association results obtained in the present work from a cohort of Italian Holstein cows tested for mastitis over time were compared with those from a previous genome-wide scan on Italian Holstein sires genotyped with 50k single nucleotide polymorphisms for de-regressed estimated breeding values for somatic cell counts (SCCs) on Bos taurus autosome (BTA6) and BTA14. A total of 1121 cows were selected for the case–control approach (cases=550, controls=571), on a combination of herd level of SCC incidence and of within herd individual level of SCC. The association study was conducted on nine previously identified markers, six on BTA6 and four on BTA14, using the R statistical environment with the ‘qtscore’ function of the GenABEL package, on high/low adjusted linear score as a binomial trait. The results obtained in the cow cohort selected on epidemiological information were in agreement with those obtained from the previous sire genome-wide association study (GWAS). Six out of the nine markers showed significant association, four on BTA14 (rs109146371, rs109234250, rs109421300, rs109162116) and two on BTA6 (rs110527224 and rs42766480). Most importantly, using mastitis as a case study, the current work further validated the alternative use of historical field disease data in case–control designs for genetic analysis of infectious diseases in livestock.

Keywords

experimental designassociation studymastitiscattlegenetic marker
Type
Research Article
Information
animal , Volume 11 , Issue 4 , April 2017 , pp. 574 - 579
Copyright
© The Animal Consortium 2016 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abdel-Shafy, H, Bortfeldt, RH, Reissmann, M and Brockmann, GA 2014. Short communication: validation of somatic cell score-associated loci identified in a genome-wide association study in German Holstein cattle. Journal of Dairy Science 97, 2481–2486.Google Scholar
Ali, AKA and Shook, GE 1980. An optimum transformation for somatic cell concentration in milk. Journal of Dairy Science 63, 487–490.Google Scholar
Anacleto, O, Garcia-Cortés, LA, Lipschutz-Powell, D, Woolliams, JA and Doeschl-Wilson, AB 2015. A novel statistical model to estimate host genetic effects affecting disease transmission. Genetics 201, 871–884.CrossRefGoogle ScholarPubMed
Aulchenko, YS, Ripke, S, Isaacs, A and van Duijn, CM 2007. GenABEL: an R package for genome-wide association analysis. Bioinformatics 23, 1294–1296.Google Scholar
Bates, D, Maechler, M, Bolker, B and Walker, S 2015. Fitting linear mixed-effects models using lme4. Journal of Statistical Software 67, 1–48.CrossRefGoogle Scholar
Bermingham, ML, Bishop, SC, Woolliams, JA, Pong-Wong, R, Allen, AR, McBride, SH, Ryder, JJ, Wright, DM, Skuce, RA, McDowell, SW and Glass, EJ 2014. Genome-wide association study identifies novel loci associated with resistance to bovine tuberculosis. Heredity 112, 543–551.Google Scholar
Bishop, SC 2010. Disease resistance: genetics. In Encyclopedia of animal science (ed. WG Pond and AW Bell), pp. 288–290. Marcel Dekker Inc., New York, New York, USA.Google Scholar
Bishop, SC, Doeschl-Wilson, AB and Woolliams, JA 2012. Uses and implications of field disease data for livestock genomic and genetics studies. Frontiers in Genetics 3, 114.CrossRefGoogle ScholarPubMed
Bishop, SC and Stear, MJ 2003. Modelling of host genetics and resistance to infectious diseases: understanding and controlling nematode infections. Veterinary Parasitology 115, 147–166.Google Scholar
Bishop, SC and Woolliams, JA 2010. On the genetic interpretation of disease data. PLoS One 28, e8940.Google Scholar
Bishop, SC and Woolliams, JA 2014. Genomics and disease resistance studies in livestock. Livestock Science 166, 190–198.Google Scholar
Bradley, AJ and Green, MJ 2005. Use and interpretation of somatic cell count data in dairy cows. In Practice 27, 310–315.Google Scholar
Cole, JB, Wiggans, GR, Ma, L, Sonstegard, TS, Lawlor, TJ Jr, Crooker, BA, Van Tassell, CP, Yang, J, Wang, S, Matukumalli, LK and Da, Y 2011. Genome-wide association analysis of thirtyone production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows. BMC Genomics 12, 408.Google Scholar
Davies G, Genini S, Bishop SC and Giuffra E 2009. An assessment of the opportunities to dissect host genetic variation in resistance to infectious diseases in livestock. Animal 3, 415–436.Google Scholar
Doeschl-Wilson, AB, Bishop, SC, Kyriazakis, I and Villanueva, B 2012. Novel methods for quantifying individual host response to infectious pathogens for genetic analyses. Frontiers in Genetics 3, 266.Google Scholar
Gonda, MG, Kirkpatrick, BW, Shook, GE and Collins, MT 2007. Identification of a QTL on BTA20 affecting susceptibility to Mycobacterium avium ssp. paratuberculosis infection in US Holsteins. Animal Genetics 38, 389–396.Google Scholar
Lillehammer, M, Meuwissen, TH and Sonesson, AK 2011. A comparison of dairy cattle breeding designs that use genomic selection. Journal of Dairy Science 94, 493–500.Google Scholar
Liu, B, Rayment, SA, Gyurko, C, Oppenheim, FG, Offner, GD and Troxler, RF 2000. The recombinant N-terminal region of human salivary mucin MG2 (MUC7) contains a binding domain for oral Streptococci and exhibits candidacidal activity. Biochemical Journal 3, 557–564.Google Scholar
Lively, CM 2010. The effect of host genetic diversity on disease spread. The American Naturalist 175, 149–152.Google Scholar
Lund, MS, Guldbrandtsen, B, Buitenhuis, AJ, Thomsen, B and Bendixen, C 2008. Detection of quantitative trait loci in Danish Holstein cattle affecting clinical mastitis, somatic cell score, udder conformation traits, and assessment of associated effects on milk yield. Journal of Dairy Science 91, 4028–4036.Google Scholar
Lund, MS, Sahana, G, Andersson-Eklund, L, Hastings, N, Fernandez, A, Schulman, N, Thomsen, B, Viitala, S, Williams, JL, Sabry, A, Viinalass, H and Vilkki, J 2007. Joint analysis of quantitative trait loci for clinical mastitis and somatic cell score on five chromosomes in three Nordic dairy cattle breeds. Journal of Dairy Science 90, 5282–5290.CrossRefGoogle ScholarPubMed
Madouasse, A, Browne, WJ, Huxley, JN, Toni, F, Bradley, AJ and Green, MJ 2012. Risk factors for a high somatic cell count at the first milk recording in a large sample of UK dairy herds. Journal of Dairy Science 95, 1873–1884.Google Scholar
Meredith, BK, Berry, DP, Kearney, F, Finlay, EK, Fahey, AG, Bradley, DG and Lynn, DJ 2013. A genome-wide association study for somatic cell score using the Illumina high-density bovine beadchip identifies several novel QTL potentially related to mastitis susceptibility. Frontiers in Genetics 6, 229.Google Scholar
Minozzi, G, Buggiotti, L, Stella, A, Strozzi, F, Luini, M and Williams, JL 2010. Genetic loci involved in antibody response to Mycobacterium avium ssp. paratuberculosis in cattle. PloS One 5, e11117.Google Scholar
Minozzi, G, Nicolazzi, EL, Strozzi, F, Stella, A, Negrini, R, Ajmone-Marsan, P and Williams, JL 2011. Genome wide scan for somatic cell counts in Holstein bulls. BMC Proceedings 5, S17.Google Scholar
Neibergs, HL, Seabury, CM, Wojtowicz, AJ, Wang, Z, Scraggs, E, Kiser, JN, Neupane, M, Womack, JE, Van Eenennaam, A, Hagevoort, GR, Lehenbauer, TW, Aly, S, Davis, J and Taylor, JF, Bovine Respiratory Disease Complex Coordinated Agricultural Project Research Team 2014. Susceptibility loci revealed for bovine respiratory disease complex in pre-weaned Holstein calves. BMC Genomics 15, 1164.CrossRefGoogle ScholarPubMed
Nilsen, H, Olsen, HG, Hayes, B, Nome, T, Sehested, E, Svendsen, M, Meuwissen, TH and Lien, S 2009. Characterization of a QTL region affecting clinical mastitis and protein yield on BTA6. Animal Genetics 40, 701–712.Google Scholar
Reents, R, Jamrozik, J, Schaeffer, LR and Dekkers, JC 1995. Estimation of genetic parameters for test day records of somatic cell score. Journal of Dairy Science 78, 2847–2857.CrossRefGoogle ScholarPubMed
Rupp, R and Boichard, D 2003. Genetics of resistance to mastitis in dairy cattle. Veterinary Research 34, 671–688.CrossRefGoogle ScholarPubMed
Sahana, G, Guldbrandtsen, B, Thomsen, B and Lund, MS 2013. Confirmation and fine-mapping of clinical mastitis and somatic cell score QTL in Nordic Holstein cattle. Animal Genetics 44, 620–626.Google Scholar
Schaid, DJ, Rowland, CM, Tines, DE, Jacobson, RM and Poland, GA 2002. Score tests for association between traits and haplotypes when linkage phase is ambiguous. American Journal of Human Genetics 70, 425–434.Google Scholar
Schulman, NF, Viitala, SM, De Koning, DJ, Virta, J, Maki-Tanila, A and Vilkki, JH 2004. Quantitative trait loci for health traits in Finnish Ayrshire cattle. Journal of Dairy Science 87, 443–449.CrossRefGoogle ScholarPubMed
Settles, M, Zanella, R, McKay, SD, Schnabel, RD, Taylor, JF, Whitlock, R, Schukken, Y, Van Kessel, JS, Smith, JM and Neibergs, H 2009. A whole genome association analysis identifies loci associated with Mycobacterium avium subsp. paratuberculosis infection status in US Holstein cattle. Animal genetics 40, 655–662.Google Scholar
Sodeland, M, Kent, MP, Olsen, HG, Opsal, MA, Svendsen, M, Sehested, E, Hayes, BJ and Lien, S 2011. Quantitative trait loci for clinical mastitis on chromosomes 2, 6, 14 and 20 in Norwegian Red cattle. Animal Genetics 42, 457–465.Google Scholar
Springbett, AJ, MacKenzie, K, Woolliams, JA and Bishop, SC 2003. The contribution of genetic diversity to the spread of infectious diseases in livestock populations. Genetics 165, 1465–1474.Google Scholar
Thompson-Crispi, K, Atalla, H, Miglior, F and Mallard, BA 2014. Bovine mastitis: frontiers in immunogenetics. Frontiers in Immunology 7, 493.Google Scholar
Tiezzi, F, Parker-Gaddis, KL, Cole, JB, Clay, JS and Maltecca, C 2015. A genome-wide association study for clinical mastitis in first parity US Holstein cows using single-step approach and genomic matrix re-weighting procedure. PLoS One 10, e0114919.Google Scholar
Tomley, FM and Shirley, MW 2009. Livestock infectious diseases and zoonoses. Philosophical Transactions of the Royal Society B 364, 2637–2642.Google Scholar
Winter, A, Krämer, W, Werner, FA, Kollers, S, Kata, S, Durstewitz, G, Buitkamp, J, Womack, JE, Thaller, G and Fries, R 2002. Association of a lysine-232/alanine polymorphism in a bovine gene encoding acyl-CoA: diacylglycerol acyltransferase (DGAT1) with variation at a quantitative trait locus for milk fat content. Proceedings of the National Academy of Sciences of the United States of America 9, 9300–9305.Google Scholar