Lars-Erik Holm

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

Research output: Contribution to conferenceConference abstract for conferenceResearch

  • 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, Austria
  • Alessandro Bagnato, Dept. VESPA, Università degli Studi di Milano, Italy
  • 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
Original languageEnglish
Publication year14 Jan 2013
Number of pages1
Publication statusPublished - 14 Jan 2013
EventInternational Plant & Animal Genome XXI - Town and Country Hotel, San Diego, United States
Duration: 12 Jan 201316 Jan 2013
Conference number: XXI


ConferenceInternational Plant & Animal Genome XXI
LocationTown and Country Hotel
CountryUnited States
CitySan Diego

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