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

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Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle. / Vilkki, Johanna; Iso-Touru, Terhi; Schulman, Nina F; Dolezal, Malies A; Bagnato, Alessandro; Soller, Morris; Panitz, Frank; Holm, Lars-Erik.

2013. Abstract from International Plant & Animal Genome XXI , San Diego, United States.

Research output: Contribution to conferenceConference abstract for conferenceResearch

Harvard

Vilkki, J, Iso-Touru, T, Schulman, NF, Dolezal, MA, Bagnato, A, Soller, M, Panitz, F & Holm, L-E 2013, 'Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle', International Plant & Animal Genome XXI , San Diego, United States, 12/01/2013 - 16/01/2013.

APA

Vilkki, J., Iso-Touru, T., Schulman, N. F., Dolezal, M. A., Bagnato, A., Soller, M., ... Holm, L-E. (2013). Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle. Abstract from International Plant & Animal Genome XXI , San Diego, United States.

CBE

Vilkki J, Iso-Touru T, Schulman NF, Dolezal MA, Bagnato A, Soller M, Panitz F, Holm L-E. 2013. Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle. Abstract from International Plant & Animal Genome XXI , San Diego, United States.

MLA

Vilkki, Johanna et al. Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle. International Plant & Animal Genome XXI , 12 Jan 2013, San Diego, United States, Conference abstract for conference, 2013. 1 p.

Vancouver

Vilkki J, Iso-Touru T, Schulman NF, Dolezal MA, Bagnato A, Soller M et al. Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle. 2013. Abstract from International Plant & Animal Genome XXI , San Diego, United States.

Author

Vilkki, Johanna ; Iso-Touru, Terhi ; Schulman, Nina F ; Dolezal, Malies A ; Bagnato, Alessandro ; Soller, Morris ; Panitz, Frank ; Holm, Lars-Erik. / Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle. Abstract from International Plant & Animal Genome XXI , San Diego, United States.1 p.

Bibtex

@conference{72536722533b48859da0a6f3c02e86d4,
title = "Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle",
abstract = "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",
author = "Johanna Vilkki and Terhi Iso-Touru and Schulman, {Nina F} and Dolezal, {Malies A} and Alessandro Bagnato and Morris Soller and Frank Panitz and Lars-Erik Holm",
note = "P0556; International Plant & Animal Genome XXI , PAG ; Conference date: 12-01-2013 Through 16-01-2013",
year = "2013",
month = "1",
day = "14",
language = "English",

}

RIS

TY - ABST

T1 - Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle

AU - Vilkki, Johanna

AU - Iso-Touru, Terhi

AU - Schulman, Nina F

AU - Dolezal, Malies A

AU - Bagnato, Alessandro

AU - Soller, Morris

AU - Panitz, Frank

AU - Holm, Lars-Erik

N1 - P0556

PY - 2013/1/14

Y1 - 2013/1/14

N2 - 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

AB - 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

M3 - Conference abstract for conference

ER -