Validation of the role of a SNP in the VPS35 gene and its effect on non-co-agulating milk in Swedish Red Cattle

Abstract: From earlier studies, it is clear that nearly 20 % of the Swedish red (SR) dairy herd possess milk that doesn’t coagulate within 40 minutes after rennet addition. This is a problem when processing milk into cheese because lower cheese yield is the result of non-coagulating (NC) milk. An estimate of 17.5 M SEK could be gained if cheese yield increased with one percent. The current payment strategies for milk from Swe-dish dairies favours a high total protein content and high yield. However, there is a moderate unfavourable genetic correlation between total protein content and NC milk in SR cows, which could possibly lead to an increase of NC milk within the SR cattle population. Much of the literature in the subject suggests that the largest contribution to differences in milk quality has a genetic background, which allows breeding cows with better milk quality. A polymorphism in the VPS35 gene has previously been suggested to be in strong association with NC milk in SR cows. The aim of this thesis was to validate a SNP in the VPS35 gene that has been found to influence NC milk. This validation included genotyping of the SNP in 1046 SR cows, estimation of the heritability for NC and the effect of this SNP on the proportion of NC milk. If the SNP is proven to be significant for NC milk, it can be relevant to include it in breed-ing programmes for SR cows. Phenotype records were available on the following animals: 382 animals sampled between 2010 and 2011 and 603 animals sampled be-tween 2016 and 2017. We compared the real genotypes obtained from this study and genotypes from previous imputed data that was available for 382 animals. Based on this comparison, we validated and re-estimated the effect of the VPS35 SNP with the 603 genotyped animals, that haven’t yet undergone a genome-wide association study (GWAS). The results showed high correlation between the imputed and the real data and high heritability for NC milk. However, for the 603 animals that haven’t yet un-dergone a GWAS, the effect of the VPS35 SNP was low as well as the heritability.