Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle

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  • Johanna Vilkki, MTT Agrifood Research Finland, Jokioinen, Finland
  • Terhi Iso-Touru, MTT Agrifood Research Finland, Jokioinen, Finland
  • Nina F Schulman, MTT Agrifood Research Finland, Jokioinen, Finland
  • Malies A Dolezal, Vetmeduni Vienna, Østrig
  • Alessandro Bagnato, Dept. VESPA, Università degli Studi di Milano, Italien
  • Morris Soller, Hebrew University of Jerusalem, Israel
  • Frank Panitz
  • Lars-Erik Holm
Mastitis is the most common disease of dairy cattle, causing high economic losses each year. Studies to locate QTL affecting clinical mastitis and milk somatic cell counts have been carried out to increase our understanding of the disease. As part of the EU FP7 Quantomics project, we have used most recent genomic tools to characterize QTL affecting mastitis incidence in the Finnish Ayrshire cattle. Clinical mastitis diagnoses from -15 to 50 days and 51 to 300 days of first lactation and SCC (geometric mean of SCS observations between 5 to 170 days of first lactation) were included. In total, 1920 progeny tested bulls were genotyped with the Illumina BovineSNP50 chip. After quality control, 38473 SNPs were analyzed using a mixed linear model (software package DMU). Associations (5% Bonferroni threshold) were detected in 9 peaks on 5 chromosomes. A set of 238 of the bulls were re-genotyped with the BovineHD chip, and the remaining bulls imputed to high density genotypes using Beagle software. GWAS was repeated with the imputed HD-data with GRAMMAS (GenABEL in R). Thereby 17 peaks on 12 chromosomes were identified. Eight high priority peaks were defined based on both 50K and imputed HD results, and overlap with previous QTL findings. Eighteen ancestral Finnish Ayrshire bulls were sequenced to over 20X coverage, and this data was used to identify sequence variations in regions flanking 2.5 Mb each side of the high priority peaks. The variations were ranked according to estimated effect by a pipeline developed within the Quantomics project
OriginalsprogEngelsk
Udgivelsesår14 jan. 2013
Antal sider1
StatusUdgivet - 14 jan. 2013
BegivenhedInternational Plant & Animal Genome XXI - Town and Country Hotel, San Diego, USA
Varighed: 12 jan. 201316 jan. 2013
Konferencens nummer: XXI

Konference

KonferenceInternational Plant & Animal Genome XXI
NummerXXI
LokationTown and Country Hotel
LandUSA
BySan Diego
Periode12/01/201316/01/2013

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