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dc.contributor.authorBRADLEY, DANIELen
dc.date.accessioned2015-03-18T15:59:22Z
dc.date.available2015-03-18T15:59:22Z
dc.date.issued2013en
dc.date.submitted2013en
dc.identifier.citationMeredith, B.K. Berry, D.P. Kearney, F. Finlay, E.K. Fahey, A.G. Bradley, D.G. Lynn, D.J., 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, 4, NOV, 2013, 229-en
dc.identifier.otherYen
dc.identifier.urihttp://hdl.handle.net/2262/73603
dc.descriptionPUBLISHEDen
dc.description.abstractMastitis is an inflammation-driven disease of the bovine mammary gland that occurs in response to physical damage or infection and is one of the most costly production-related diseases in the dairy industry worldwide. We performed a genome-wide association study (GWAS) to identify genetic loci associated with somatic cell score (SCS), an indicator trait of mammary gland inflammation. A total of 702 Holstein-Friesian bulls were genotyped for 777,962 single nucleotide polymorphisms (SNPs) and associated with SCS phenotypes. The SCS phenotypes were expressed as daughter yield deviations (DYD) based on a large number of progeny performance records. A total of 138 SNPs on 15 different chromosomes reached genome-wide significance (corrected p-value ≤ 0.05) for association with SCS (after correction for multiple testing). We defined 28 distinct QTL regions and a number of candidate genes located in these QTL regions were identified. The most significant association (p-value = 1.70 × 10−7) was observed on chromosome 6. This QTL had no known genes annotated within it, however, the Ensembl Genome Browser predicted the presence of a small non-coding RNA (a Y RNA gene) in this genomic region. This Y RNA gene was 99% identical to human RNY4. Y RNAs are a rare type of non-coding RNA that were originally discovered due to their association with the autoimmune disease, systemic lupus erythematosus. Examining small-RNA sequencing (RNAseq) data being generated by us in multiple different mastitis-pathogen challenged cell-types has revealed that this Y RNA is expressed (but not differentially expressed) in these cells. Other QTL regions identified in this study also encoded strong candidate genes for mastitis susceptibility. A QTL region on chromosome 13, for example, was found to contain a cluster of β-defensin genes, a gene family with known roles in innate immunity. Due to the increased SNP density, this study also refined the boundaries for several known QTL for SCS and mastitis.en
dc.description.sponsorshipThis material is based upon works supported by the Science Foundation Ireland under Grant No. [09/IN.1/B2642]. We also acknowledge funding provided for this project through the Teagasc Walsh Fellowship scheme and Teagasc RMIS 6018 as well as The Irish Department of Agriculture, Food and Marine Research Stimulus Fund (11/S/112). Further acknowledgments must go to the SFI\ HEA Irish Centre for High-End Computing (ICHEC) for the provision of computational facilities and support and to Per Madsen for his generous help with the DMU softwareen
dc.format.extent229en
dc.language.isoenen
dc.relation.ispartofseriesFrontiers in Geneticsen
dc.relation.ispartofseries4en
dc.relation.ispartofseriesNOVen
dc.rightsYen
dc.subjectQTL for SCS and mastitisen
dc.subject.lcshQTL for SCS and mastitisen
dc.titleA genome-wide association study for somatic cell score using the Illumina high-density bovine beadchip identifies several novel QTL potentially related to mastitis susceptibilityen
dc.typeJournal Articleen
dc.contributor.sponsorScience Foundation Ireland (SFI)en
dc.type.supercollectionscholarly_publicationsen
dc.type.supercollectionrefereed_publicationsen
dc.identifier.peoplefinderurlhttp://people.tcd.ie/dbradleyen
dc.identifier.rssinternalid102072en
dc.identifier.doihttp://dx.doi.org/10.3389/fgene.2013.00229en
dc.rights.ecaccessrightsopenAccess
dc.contributor.sponsorGrantNumber09/IN.1/B2642en
dc.identifier.rssurihttp://www.scopus.com/inward/record.url?eid=2-s2.0-84890292620&partnerID=40&md5=c8eeb51fa817b181054630777578623ben


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