Genome-wide association study for somatic cell score in Valdostana Red Pied cattle breed using pooled DNA

BMC Genetics

Alessandro Bagnato²  Ehud Lipkin³  Morris Soller³  Maria C Cozzi⁴  Mario Vevey¹  Fabiola Canavesi⁴  Antonia B Samoré²  Fausta Schiavini⁴  Erika Frigo⁴  Maria G Strillacci⁴ 

[1] Associazione Nazionale Allevatori Bovini di Razza Valdostana (A.N.A.Bo.Ra.Va.), Fraz. Favret, 5, Gressan, 11020, AO, Italy;Dipartimento di Scienze e Tecnologie Agro - Alimentari, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy;Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel;Department of Health, Animal Science and Food Safety (VESPA), University of Milan, Via Celoria 10, Milan, 20133, Italy

关键词: SCS;    Valdostana Red Pied breed;    GWAS;    Mastitis;   

Others  :  1085474
DOI  :  10.1186/s12863-014-0106-7

 received in 2014-07-01, accepted in 2014-09-25,  发布年份 2014

【 摘 要 】

Background

Mastitis is a major disease of dairy cattle occurring in response to environmental exposure to infective agents with a great economic impact on dairy industry. Somatic cell count (SCC) and its log transformation in somatic cell score (SCS) are traits that have been used as indirect measures of resistance to mastitis for decades in selective breeding. A selective DNA pooling (SDP) approach was applied to identify Quantitative Trait Loci (QTL) for SCS in Valdostana Red Pied cattle using the Illumina Bovine HD BeadChip.

Results

A total of 171 SNPs reached the genome-wide significance for association with SCS. Fifty-two SNPs were annotated within genes, some of those involved in the immune response to mastitis. On BTAs 1, 2, 3, 4, 9, 13, 15, 17, 21 and 22 the largest number of markers in association to the trait was found. These regions identified novel genomic regions related to mastitis (1-Mb SNP windows) and confirmed those already mapped. The largest number of significant SNPs exceeding the threshold for genome-wide significant signal was found on BTA 15, located at 50.43-51.63 Mb.

Conclusions

The genomic regions identified in this study contribute to a better understanding of the genetic control of the mastitis immune response in cattle and may allow the inclusion of more detailed QTL information in selection programs.

【 授权许可】

   
2014 Strillacci et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

【 参考文献 】

• [1]Sender G, Korwin-Kossakowska A, Pawlik A, Galal Abdel Hameed K, Oprządek J: Genetic basis of mastitis resistance in dairy cattle – a review. Ann Anim Sci 2013, 13:663-673.
• [2]Knap PW, Bishop SC: Relationships between genetic change and infectious disease in domestic livestock. Br Soc Anim Sci 2000, 27:65-80.
• [3]Schukken YH, Günther J, Fitzpatrick J, Fontaine MC, Goetze L, Holst O, Leigh J, Petzl W, Schuberth HJ, Sipka A, Smith DG, Quesnell R, Watts J, Yancey R, Zerbe H, Gurjar A, Zadoks RN, Seyfert HM: Host-response patterns of intramammary infections in dairy cows. Vet Immunol Immunopathol 2011, 144(3–4):270-289.
• [4]Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME: Invited review: genomic selection in dairy cattle: progress and challenges. J Dairy Sci 2009, 92(2):433-443.
• [5]Meuwissen TH, Solberg TR, Shepherd R, Woolliams J: A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value. Genet Sel Evol 2009, 5:41-42.
• [6]Pryce JE, Bolormaa S, Chamberlain AJ, Bowman PJ, Savin K, Goddard ME, Hayes BJ: 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(7):3331-3345.
• [7]Meredith B, Lynn D, Berry D, Kearney F, Bradkey D, Finlay E, Fahey A: A genome-wide association study for somatic cell score using the illumine high density bovine beadchip identifies several novel QTL potentially related to mastitis susceptibility. Front Genet 2013, 4:229.
• [8]Darvasi A, Soller M: Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus. Genetics 1994, 138:1365-1373.
• [9]Janicki PK, Vealey R, Liu J, Escajeda J, Postula M, Welker K: Genome-wide association study using pooled DNA to identify candidate markers mediating susceptibility to postoperative nausea and vomiting. Anesthesiology 2011, 115(1):54-64.
• [10]Bagnato A, Soller M, Lipkin E, Samoré AB, Velayutham D, Schiavini F, Rossoni A, Dolezal MA: Genome Wide Association Analysis in Italian Brown Swiss for Somatic Cell Count [abstract]. Program and Book of Abstract 4th International Conference on Quantitative Genetics: Understanding Variation in Complex Trait 2012, 234-235.
• [11]Jensen K, Günther J, Talbot R, Petzl W, Zerbe H, Schuberth HJ, Seyfert HM, Glass EJ: Escherichia coli- and Staphylococcus aureus-induced mastitis differentially modulate transcriptional responses in neighbouring uninfected bovine mammary gland quarters. BMC Genomics 2013, 16:14-36.
• [12]Moyes KM, Drackley JK, Morin DE, Loor JJ: Greater expression of TLR2, TLR4, and IL6 due to negative energy balance is associated with lower expression of HLA-DRA and HLA-A in bovine blood neutrophils after intramammary mastitis challenge with Streptococcus uberis. Funct Integr Genomics 2010, 10(1):53-61.
• [13]Sugimoto M, Sugimoto Y: Variant in the 5′ untranslated region of insulin-like growth factor 1 receptor is associated with susceptibility to mastitis in cattle. G3 (Bethesda) 2012, 2(9):1077-1084.
• [14]Mizushima N: Autophagy: process and function. Genes Dev 2007, 21(22):2861-2873.
• [15]Jiang L, Sørensen P, Thomsen B, Edwards SM, Skarman A, Røntved CM, Lund MS, Workman CT: Gene prioritization for livestock diseases by data integration. Physiol Genomics 2012, 44(5):305-317.
• [16]Heeg K, Dalpke A: TLR-induced negative regulatory circuits: role of suppressor of cytokine signaling (SOCS) proteins in innate immunity. Vaccine 2003, 21(Suppl 2):S61-S67.
• [17]Brenaut P, Lefèvre L, Rau A, Laloë D, Pisoni G, Moroni P, Bevilacqua C, Martin P: Contribution of mammary epithelial cells to the immune response during early stages of a bacterial infection to Staphylococcus aureus. Vet Res 2014, 45:16. BioMed Central Full Text
• [18]Wang C, Wang J, Ju Z, Zhai R, Zhou L, Li Q, Li J, Li R, Huang J, Zhong J: Reconstruction of metabolic network in the bovine mammary gland tissue. Mol Biol Rep 2012, 39(7):7311-7318.
• [19]Gilbert FB, Cunha P, Jensen K, Glass EJ, Foucras G, Robert-Granié C, Rupp R, Rainard P: Differential response of bovine mammary epithelial cells to Staphylococcus aureus or Escherichia coli agonists of the innate immune system. Vet Res 2013, 44:40. BioMed Central Full Text
• [20]Cates EA, Connor EE, Mosser DM, Bannerman DD: Functional characterization of bovine TIRAP and MyD88 in mediating bacterial lipopolysaccharide-induced endothelial NF-kappaB activation and apoptosis. Comp Immunol Microbiol Infect Dis 2009, 32(6):477-490.
• [21]Lund MS, Guldbrandtsen B, Buitenhuis AJ, Thomsen B, Bendixen C: 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. J Dairy Sci 2008, 91:4028-4036.
• [22]Rupp R, Boichard D: Genetics of resistance to mastitis in dairy cattle. Vet Res 2003, 34:671-688.
• [23]Holmberg M, Andersson-Eklund L: Quantitative trait loci affecting health traits in Swedish dairy cattle. J Dairy Sci 2004, 87:2653-2659.
• [24]Sahana G, Guldbrandtsen B, Thomsen B, Lund MS: Confirmation and fine-mapping of clinical mastitis and somatic cell score QTL in Nordic Holstein cattle. Anim Genet 2013, 44(6):620-626.
• [25]Abdel-Shafy H, Bortfeldt RH, Reissmann M, Brockmann GA: Short communication: validation of somatic cell score-associated loci identified in a genome-wide association study in German Holstein cattle. J Dairy Sci 2014, 97(4):2481-2486.
• [26]Wiggans GR, Shook GE: A lactation measure of somatic cell count. J Dairy Sci 1987, 70(12):2666-2672.
• [27]Gilmour AR, Gogel BJ, Cullis BR, Thompson R: ASReml User Guide Release 3.0. Hemel Hempstead. UK: VSN Int. Ltd; 2009.
• [28][http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=28-07.pdf] webcite Mistzal I, Tsuruta S, Strabel T, Auvray B, Druet T, Lee D: BLUPF90 and Related Programs (BGF90). []
• [29]VanRaden PM, Wiggans GR: Derivation, calculation, and use of national animal model information. J Dairy Sci 1991, 74(8):2737-2746.
• [30]Janicki PK, Liu J: Accuracy of allele frequency estimates in pool DNA analyzed by high-density Illumina Human 610-Quad microarray. Intern J Genomics Proteomics 2009, 5:1.
• [31]Strillacci MG, Frigo E, Canavesi F, Ungar Y, Schiavini F, Zaniboni L, Reghenzani L, Cozzi MC, Samoré AB, Kashi Y, Shimoni E, Tal-Stein R, Soller M, Lipkin E, Bagnato A: QTL mapping for conjugated linoleic acid, vaccenic acid and Δ9-desaturase in Italian Brown Swiss dairy cattle using selective DNA pooling. Anim Gen 2014, 45:485-499.
• [32]Bagnato A, Schiavini F, Rossoni A, Maltecca C, Dolezal M, Medugorac I, Sölkner J, Russo V, Fontanesi L, Friedmann A, Soller M, Lipkin E: Quantitative trait loci affecting milk yield and protein percent in a three-country Brown Swiss population. J Dairy Sci 2008, 91:767-783.
• [33]Stephens MA: Tests based on EDF statistics. In Goodness-of-Fit Techniques. Edited by D'Agostino RB, Stephens MA. Marcel D, New York; 1986:97-193.
• [34]Royston P: A remark on Algorithm AS 181: The W test for normality. Applied Statistics 44th edition. 1995, 547-551.
• [35]Marsaglia G, Tsang WW, Jingbo W: Evaluating Kolmogorov’s distribution. J Stat Softw 2003, 8:1-4.
• [36]Jiang J, Jiang L, Zhou B, Fu W, Liu JF, Zhang Q: Snat: a SNP annotation tool for bovine by integrating various sources of genomic information. BMC Genet 2011, 12:85. BioMed Central Full Text
• [37]Pant SD, Schenkel FS, Verschoor CP, You Q, Kelton DF, Moore SS, Karrow NA: A principal component regression based genome wide analysis approach reveals the presence of a novel QTL on BTA7 for MAP resistance in holstein cattle. Genomics 2010, 95(3):176-182.