Boman et al. Genetics Selection Evolution 2010, 42:4 http://www.gsejournal.org/content/42/1/4 Table 2 Number of lambs per genotype group for various traits c.960 c.2360 Weigth gain/d from birth to weaning (g) Weaning weight (kg) Carcass weight gain/d from birth to slaugther (g) Carcass traits GG 78 78 59 59 GG AG 216 219 165 167 AA 114 114 84 84 GG 105 107 92 94 G(delG) AG 106 107 89 89 Page 3 of 7 (delG)(delG) GG 19 19 15 15 Guanine is found at the mutated position in wild types, both in the c.960 and the c.2360 position, while (delG) and adenine (A) respectively, are found when the mutations are present. Carcass traits are carcass weight, carcass conformation class and carcass fat class. national prediction of breeding values for traits recorded in the autumn. An equivalent model, analysing the same data with the same software, was used to estimate the allelic effects rather than the genotype class effects: Yijklmno  a 2360x1  d 2360x 2  a 960x 3  d 960x 4  intx 5  GDj  S k  R l  ADm  fy n  io  e ijklmno where the regression coefficients for the additive and dominant allelic effect of c.2360G>A (a2360, d2360) and c.960delG (a960, d960) are given as well as their interac- tion (int), while the x’es are indicator (dummy) variables; x1 is the number of c.2360G>A alleles (0, 1, 2), x2 is 1 if heterozygous in c.2360 and 0 otherwise, x3 is the num- ber of c.960delG alleles (0, 1, 2), x4 is 1 if heterozygous in c.960 and 0 otherwise, x5 is 1 for compound hetero- zygotes and 0 otherwise, and the other terms are defined as in the model above. To test the impact of the two MSTN-mutations in the first model, the wild type individuals (GG_GG, for cDNA position 960 and 2360, respectively) were used as reference. We also wanted to test the impact of the gen- otypes carrying the c.960delG-mutation, against the group GG_AA. Hypothesis testing was done by the fol- lowing contrasts, using V3.1 of PEST [8], with variance components from the DMUAI run as input: 1. H0: MSTN-genotype - GG_GG (wild type) = 0, where MSTN-genotype is GG_AG, GG_AA, G(delG) _GG, G(delG)_AG or (delG)(delG)_GG against H1: MSTN-genotype - GG_GG (wild type) ≠ 0. 2. H0: MSTN-genotype - GG_AA = 0, where MSTN-genotype is G(delG)_GG, G(delG)_AG or (delG)(delG)_GG, against H1: MSTN-genotype - GG_AA ≠ 0. Hypothesis testing for the allelic effects in the second model was done by the following contrasts, using the same software and variance components: 1. H0: regression coefficient = 0, where regression coefficient is the additive, dominance and interaction terms a2360, d2360, a960 d960 and int, against H1: regression coefficient ≠ 0. 2. H0: a960 - a2360 = 0, against H1: a960 - a2360 ≠ 0. Note that since the two models are equivalent, some of the tests are identical. Estimation of variance components for daily carcass weight gain did not converge due to little information in the data. The heritability was therefore set to 15%. Results The number of homozygous c.960delG ewes was low (Table 1), and thus their progeny were omitted from the analysis. In the autumn, 644 lambs (50.9% females) were recorded with weaning weight (Table 2) and 508 were slaughtered. However, due to recruitment, only 41.2% of the slaughtered lambs were females. The mean age of the dams was 3.1 years, ranging from 1 to 7 years. The average number of lambs weaned was 2.3, ranging from 1 to 4. Eleven lambs were bottle fed. None of the animals homozygous for either mutation carried the other mutation, implying that no crossover had occurred between the two mutations. The lambs could therefore be divided into six genotype groups, depending on which combination of mutations and wild type allele they carried (Table 2). Homozygous c.960delG-lambs were only produced the second year, since the rams used the first year did not carry this mutation. The group of homozygous individuals for c.960delG was significantly different from the reference groups, both the wild type (GG_GG) and GG_AA for three of the observed traits (Table 3). The homozygous c.960delG animals had lower daily weaning weight gain (312 g per day), lower weaning weight (44.6 kg), but higher carcass weight (23.3 kg). Daily gain of slaughter weight was very similar for all groups, ranging from 134 to 143 g per day, with no significant differences. For carcass conformation and carcass fat, both muta- tions increased or decreased, respectively, scores in comparison to those of the reference MSTN groups numerically (Table 3). For both traits, all genotype groups differed significantly (P < 0.05) from the wild type group (GG_GG), except GG_AG for carcass con- formation. For both carcass conformation and carcass fat, the genotype G(delG)_GG was not significantly