Genome-wide Association Study of Resistance to Mastitis in Czech Holstein Cattle
Keywords:association study, GWAS, SNP, cattle, Bos taurus
Clinical mastitis is an inflammatory disease of the mammary gland that largely impacts dairy farming profitability and welfare. Globally, a massive scientific effort is being made to elucidate the possible link of certain genotypes to the susceptibility to this disease. After data pruning controlling for genotype missingness, minor allele frequency, and population stratification, 51 557 SNPs from 1 042 animals have been analysed using the general linear model (GLM). Two SNPs, BTA-121769-no-rs and BTB-00265951, have demonstrated statistically significant associations (–log10(p) > 6.0134), both located on the chromosome BTA6. The detected SNPs have been annotated within a reference genome. They have been found to lie outside of transcribed regions but within the vicinity of genes essential for the immune response. This finding further supports the case for their significance in the resistance to mastitis. In addition, 14 relatively weaker associations (–log10(p) > 4) have been observed across chromosomes BTA1, 2, 9, 14, 19, 24 and 25.
Abdel-Shafy, H.,et al. (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(4): 2481-2486. https://doi.org/10.3168/jds.2013-7149
Atashi, H. et al. (2020). Genome-wide association for milk production and lactation curve parameters in Holstein dairy cows. Journal of Animal Breeding and Genetics, 137(3): 292-304. https://doi.org/10.1111/jbg.12442
Bourens, M. & Barrientos, A. (2017). Human mitochondrial cytochrome c oxidase assembly factor COX18 acts transiently as a membrane insertase within the subunit 2 maturation module. Journal of Biological Chemistry, 292(19): 7774-7783. https://doi.org/10.1074/jbc.M117.778514
Bradbury, P.J., et al. (2007). TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 23: 2633-2635. https://doi.org/10.1093/bioinformatics/btm308
Fang, L. et al. (2017). Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle. Scientific Reports, 7: 45560. DOI: 10.1038/srep45560
Gebreyesus, G. et al. (2019). Reliability of genomic prediction for milk fatty acid composition by using a multi-population reference and incorporating GWAS results. Genetics Selection Evolution, 51: 16. https://doi.org/10.1186/s12711-019-0460-z
Gilbert, F.B. et al. (2013). Differential response of bovine mammary epithelial cells to Staphylococcus aureus or Escherichia coli agonists of the innate immune system. Veterinary Research, 44(1):40. https://doi.org/10.1186/1297-9716-44-40
Hellwege, J.N., et al. (2017). Population Stratification in Genetic Association Studies. Current Protocols in Human Genetics, 95: 1.22.1-1.22.23. https://doi.org/10.1002/cphg.48
Hofírek, B. & Haas, D. (2003). Kategorizace zdraví mléčné žlázy, klinické formy mastitid a jejich terapie. Sborník referátů odborného semináře mastitidy skotu ČBS a VFU 1:10-22.
Jiang, J. et al. (2019). A Large-Scale Genome-Wide Association Study in U.S. Holstein Cattle. Frontiers in Genetics, 10: 412. https://doi.org/10.3389/fgene.2019.00412
Jiang, L. et al. (2010). Genome wide association studies for milk production traits in Chinese Holstein population. PLoS One, 5(10): e13661. https://doi.org/10.1371/journal.pone.0013661
Kašná, E. et al. (2018). First national recording of health traits in dairy cows in the Czech Republic. ICAR Technical Series 23:173-177.
Kvapilík, J. (2014). Mastitidy dojených krav a ekonomické ztráty. Veterinářství 64(12): 946-955.
Olsen, H.G. et al. 2016. Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production. Genetics Selection Evolution, 48(1):79. https://doi.org/10.1186/s12711-016-0257-2
Pearson, T.A. & Manolio, T.A. (2008). How to interpret a genome-wide association study. JAMA, 299(11):1335-44. https://doi.org/10.1001/jama.299.11.1335
Purcell, S. et al. (2007). PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81. https://doi.org/10.1086/519795
R Core Team. 2020. R: A language and environment for statistical computing. R Foundation for Statistical Computing. Available from: https://www.R-project.org/ (accessed February 2021).
Rollin, E. et al. (2015). The cost of clinical mastitis in the first 30 days of lactation: An economic modeling tool. Preventive Veterinary Medicine, 122(3): 257-264. . https://doi.org/10.1016/j.prevetmed.2015.11.006.
Sahana, G. et al. (2014). Genome-wide association study using high-density single nucleotide polymorphism arrays and whole-genome sequences for clinical mastitis traits in dairy cattle. Journal of Dairy Science, 97(11): 7258-7275. https://doi.org/10.3168/jds.2014-8141
Snelling, W.M. (2019). A survey of polymorphisms detected from sequences of popular beef breeds. Journal of Animal Science, 93(11): 5128-5143. https://doi.org/10.2527/jas.2015-9356
Sodeland, M. et al. (2011). Quantitative trait loci for clinical mastitis on chromosomes 2, 6, 14 and 20 in Norwegian Red cattle. Animal Genetics, 42(5): 457-65. https://doi.org/10.1111/j.1365-2052.2010.02165.x
Strillacci, M.G. et al. (2014). Genome-wide association study for somatic cell score in Valdostana Red Pied cattle breed using pooled DNA. BMC Genetics, 15:106. https://doi.org/10.1186/s12863-014-0106-7
Szyda, J. et al. (2019. The genetic background of clinical mastitis in Holstein-Friesian cattle. Animal 13(10): 2156-2163. https://doi.org/10.1017/S1751731119000338
Tiezzi, F. et al. (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, (e0114919) DOI: 10.1371/journal.pone.0114919. https://doi.org/10.1371/journal.pone.0114919
Turner, S. (2018). qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. Journal of Open Source Software, 3(25):731. https://doi.org/10.1101/005165
Waller, K.P. (2000). Mammary gland immunology around parturition. Influence of stress, nutrition and genetics. Advances in Experimental Medicine and Biology 480: 231–245. https://doi.org/10.1007/0-306-46832-8_29.
Welderufael, B.G. et al. (2018). Genome-Wide Association Study for Susceptibility to and Recoverability From Mastitis in Danish Holstein Cows. Frontiers in Genetics, 9:141. https://doi.org/10.3389/fgene.2018.00141
Wolfová, M. et al. (2006). Incidence and economics of clinical mastitis in five Holstein herds in the Czech Republic. Preventive veterinary medicine 77(1-2): 48–64. https://doi.org/10.1016/j.prevetmed.2006.06.002
Yates, A.D. et al. (2020). Ensembl 2020, Nucleic Acids Research, 48(D1): D682–D688.
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