ORIGINAL ARTICLE Genetic evaluation of somatic cell score in dairy cattle considering first and later lactations as two different but correlated traits E. Negussie, M. Koivula, E.A. Ma ¨ ntysaari & M. Lidauer MTT Agrifood Research Finland, Biotechnology and Food Research, Biometrical Genetics, Jokioinen, Finland Introduction Increased genetic susceptibility to mastitis has accompanied the rapid genetic increase in milk yield, and genetic selection for mastitis resistance should be considered in the breeding programmes. How- ever, direct selection for mastitis resistance has been considered inefficient because of the low heritability, the cost, and problems associated with its routine recording (Lund et al. 1994; Po ¨ so ¨ & Ma ¨ ntysaari 1996). The link between somatic cell score (SCS) and infection in the udder offers a possibility to use SCS as indicator of mastitis (Emanuelson et al. 1988; Mrode and Swanson 1996; Po ¨ so ¨ & Ma ¨ ntysaari 1996; Kadarmideen and Pryce 2001; Carle ´n et al. 2004). As a result, many countries rely on SCS as means of identifying and controlling mastitis. SCS as an indic- tor trait for selection against mastitis has the advant- age of being less expensive and highly heritable. Currently several countries have included SCS in their breeding objectives. However, the methods used for the analyses of SCS records differ largely Correspondence E. Negussie, MTT Agrifood Research Finland, Biotechnology and Food Research, Biometrical Genetics, 31600 Jokioinen, Finland. Tel: +358 3 4188 3627; Fax: +358 3 4188 3627; E-mail: enyew.negussie@mtt.fi Received: 1 September 2005; accepted: 9 March 2006 Summary A test-day (TD) random regression model (RRM) was described for the genetic evaluation of somatic cell score (SCS) where first and later lacta- tions were considered as two different but correlated traits. A two-step covariance function procedure was used to estimate variance–covari- ances and associated genetic parameters. Analysis of estimated breeding values (EBV), ranking of top bulls and cows and some computational aspects were used to compare RRM with TD repeatability model (RPM) and lactation average model (LAM). Residuals were analysed to assess the relative fit of TD models. Comparison between RRM and RPM showed that RRM has lower mean squared error and gave better fit to the data. For young bulls and cows, the standard deviation (SD) of EBVs was highest for RRM and lowest for LAM implying efficient utilization of information on SCS, in terms of revealing more genetic variation. A much lower correlation of EBVs ranging from 0.80 to 0.92 and signifi- cant re-ranking of top bulls and cows were observed between RRM and LAM. The lower across-lactation correlation between RRM and LAM indicated that LAM is directed to give more weight to first lactation breeding values. The RRM, where SCS in the first and later lactations was considered as two different but correlated traits was able to make effective use of available information on young bulls and cows, and could offer an opportunity to breeders to utilize EBVs for first and later lactations. J. Anim. Breed. Genet. ISSN 0931-2668 ª 2006 The Authors 224 Journal compilation ª 2006 Blackwell Verlag, Berlin • J. Anim. Breed. Genet. 123 (2006) 224–238