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Genome Wide Association Analysis on Imputed High Density SNP Genotypes in the Italian and Swiss Brown Swiss Dairy Cattle Population for Milk Somatic Cell Count
Abstract
Mastitis is one of the most costly diseases in dairy cattle and a huge concern to animal welfare. Milk Somatic Cell Count (MSCC) is an indirect measure widely used for years to select individuals to reduce mastitis susceptibility in dairy cattle. The purpose of this study was to identify regions underlying phenotypic variation for mastitis resistance in the Brown Swiss dairy cattle population. We report on a whole genome association study on a total of 2,979 mainly Italian-, Swiss- and US-Brown Swiss bulls imputed from Illumina’s Bovine 50k v1 and v2 SNP chip with FImpute to Illumina’s 777k chip for 628,415 SNPs with MAF > 0.5% anchored on the UMD3.1 autosome. Association testing with MSCC-EBVs for 2,834 bulls with EBV reliability greater than 0.3 provided by Interbull, was performed for 604,568 SNPs with MAF > 2% employing EMMAX as implemented in SVS7.7.8. Stratification was controlled by fitting a genomic relationship matrix, calculated as suggested by VanRaden based on all genome wide SNPs in the model. Success of stratification correction was empirically assessed via quantile-quantile plots. Significance was declared employing a false discovery rate approach. Several QTL regions were found across the genome. The most interesting regions were located on BTA6, BTA10, BTA13 and BTA19.
We thank Braunvieh Schweiz and ANARB for providing genotypes and Genotype pool Germany-Austria, Beltsville Agricultural Research Centre and LowInputBreeds, FP7 – project KBBE 222 632 for providing genotypes used for imputation. This study was supported by the FP7 project QUANTOMICS contract n. 222664-2.
... As a result, the selection of cows using novel bovine genome sequencing technologies to control for mastitis-causing pathogens has important implications for reducing production risk and enhancing dairy herd productivity. The recent advance in dairy genomics to identify the gene regions, which affect the resistance to mastitis (Vilkki et al 2013;Bowen 2014;Dolezal et al 2014;Wang et al 2014), will enable dairy farmers to test and identify young animals for mastitis resistance, and avoid costs associated with mastitis. In this paper, we examine the determinants of willingness to pay (WTP) for genotyping animals for susceptibility to a chronic mastitis trait using a survey data. ...
Bovine Mastitis is one of the most prevalent and costly production diseases in the dairy industry in Canada and worldwide causing major animal welfare problems, environmental problems, and productivity losses. In this paper, we examine the effects of risk attitudes and social interactions on the willingness to pay (WTP) for genotyping animals for susceptibility to a chronic mastitis trait. We use contingent valuation with double bounded dichotomous choice questions to elicit producers' WTP. The estimated mean WTP for genotyping is approximately $50 per animal. Compared to the current market prices of commercially available comprehensive genotyping services, this estimate suggests a significant market potential for genotyping to be bundled with economically important disease traits. We also find evidence that both risk attitudes and social interactions have strong effects on the WTP for genotyping. Farmers with higher risk tolerance are willing to pay more for genotyping service. For dairy farmers with more concern about mastitis, risk tolerance has no significant effect on the WTP, while social interactions have a significant effect on the WTP.We also find a strong interaction effect between risk tolerance and social interactions. The findings encourage interest in questions about how risk attitudes, social networks, and their interactions shape the adoption of and the WTP for a novel agricultural technology.
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