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a b s t r a c tThe aim of this paper is to identify differences in genetic variation of fatty acid (FA) composition in milk in different breeds. Data used included Meuse-Rhine-Yssel (MRY) and Holstein Friesian (HF) cattle breeds which were raised in the Netherlands. Both populations participated in the same milk recording system, but differed in selection history, where in the MRY there has been relatively very little emphasis on selection for high-input high-output production systems compared to HF. Differences in genetic variation were investigated by estimating breed specific additive genetic variances and heritabilities for FA contents in milk of MRY and HF. Mid Infrared Spectrometry spectra were used to predict total fat percentage and detailed FA contents in milk (14 individual FA and 14 groups of FA in g of fat/dL of milk). The dataset for MRY contained 2916 records from 2049 registered cows having at least 50% genes of MRY origin and the dataset used for HF contained 155,319 records from 96,315 registered cows having at least 50% genes of HF origin. Variance components of individual FA content in milk for the different breeds were estimated using a single trait animal model. Additive genetic variances for FA produced through de novo synthesis (short chain FA, C12:0, C14:0, and partly C16:0), C14:1 c-9 and C16:1 c-9 were significantly higher (P o0.001) for HF compared to MRY. Heritabilities of the individual FA, C4:0 to C18:0, for HF ranged from 0.28 to 0.52 and for MRY from 0.17 to 0.34. Heritabilities of the individual C18 unsaturated FA for HF ranged from 0.11 to 0.34 and for MRY from 0.10 to 0.26. Although the mean content in milk for the FA C18:2 c-9, t-11 was low in both breeds, the additive genetic variance in our dataset was significantly higher for MRY (Po 0.05) compared to HF. Heritabilities of the groups of FA for HF ranged from 0.19 to 0.53 and for MRY from 0.11 to 0.28. For the majority of the FA, the additive genetic variances for HF were significantly higher compared to MRY, except for most of the poly-unsaturated FA. The results for the poly-unsaturated FA, however, may be affected by the lower accuracy of the predictions for these FA. In conclusion, our results show that the HF breed has substantially larger genetic variance for most FA compared to MRY.