Volckaert et al. Genetics Selection Evolution 2012, 44:15 http://www.gsejournal.org/content/44/1/15 correlations. Parentage assignment was implemented using three software packages [i.e., CERVUS v.3.0; [8], PAPA v.2.0; [9], VITASSIGN v.1.0; [10]] in order to con- stitute families with the highest possible certainty. The genotyping error rate was set to 1%. The assignment was tested for power and performance and locus-specific polymorphism information content (PIC) values were calculated. Heritabilities and phenotypic correlations were calcu- lated using phenotypic data collected on 930 animals. Eight animals were removed because of missing pheno- types. Thus, the dataset used to estimate heritability values comprised 922 animals, with missing values in some variables (see Table 1). Heritabilities were esti- mated using ASReml fitting an animal model. Several fixed effects were tested (sample set, day, tube number and assay number in cortisol assays) to check if they influenced the trait in question. With the exception of cortisol, the model was TRAIT ¼ μ þ A þ E: TRAIT represents the phenotypic trait, μ the trait mean, A the additive genetic effect and E the environ- mental effect. Only sample set was found to have an ef- fect on cortisol and therefore sample set was added as fixed effect to the model. Phenotypic correlations were calculated with the soft- ware GENSTAT v.10. Parentage assignment and contributions The 1151 progeny and 56 parents were genotyped at 29 microsatellite loci. The number of alleles per locus varied between two and 10 and PIC values varied between 0.124 and 0.767 [see Additional file 2]. A power analysis was conducted with the rarefaction method and showed that 10 loci were sufficient for a reliable assignment (details not shown). A core group of five families contributed 71.5% to the progeny, six families made a measurable contribution and 80 families only a very small contribution. This is a highly skewed family representation of at least 748 dam x sire combinations with a low effective breeding size, which might affect the estimates through the unwanted genetic drift (or limited Mendelian sampling) caused by the Page 2 of 5 skewed representation. For the heritability and correlation analyses, 922 offspring were used from which two females (5.9%) and 10 males (45.5%) contributed the most [see Additional file 3]. Our study shows that within a single breeding day, the majority of the progeny can be produced with the contribution of just two females and 10 males, which amounts to an effective population size (Ne) of 6.7 while there were 43 participating breeders and a total number of initial individuals of 57 (Ne/N = 0.12). Thus, artificial insemination provides the best guarantee to set up experimental crosses since during natural spawning the number of families with significant contribution can be small. Phenotypes Basic descriptive statistics for the phenotypes are shown in Table 1. Mean cortisol levels were constant over the time of blood collection as indicated by the horizontal regression lines in Figure 1 (range of coefficients of lin- ear regression per tank −0.153 to 0.109; r2 = 2.10-3). Heritabilities and correlations Heritability values for growth traits ranged from 0.54 ± 0.21 for BW to 0.65 ± 0.22 for SL (Table 2). Such heritability estimates support the large proportion of phenotypic vari- ation explained by the QTL detected in Massault et al. [7] and the reasons are discussed therein. For response to stress, the heritability of CORT was 0.08 ± 0.06. However, as noted above, the family structure is clearly suboptimal to estimate heritabilities as evidenced by the high standard errors of the estimates [11]. As expected, the phenotypic correlation between BW and SL was high (0.94), whereas CORT was not phenotypically correlated to either growth trait. The genetic correlation between SL and BW was high (0.94) and that between CORT and SL or BW was negative (−0.55 and −0.60, respectively). These estimates confirm data from previous studies in European seabass [12], rain- bow trout [13] and Nile tilapia [14]. The value for body weight heritability obtained in our study also agrees with estimates previously reported in European sea bass, which range from medium heritabilities (0.2 in [12], 0.38-0.44 in [15] and 0.39 in [16,17]) to high heritabilities when taking into account different environments (0.31-0.60 in [18]). Generally, body length and body weight have moderate to high heritability values in teleost fishes: 0.6 in Coho salmon, Table 1 Phenotypic traits for which genetic parameters were estimated in European sea bass Trait (unit) Body weight (g) Standard length (cm) Cortisol (ng.ml-1) Abbreviation BW SL CORT Mean 41.6 13.4 318.5 Standard deviation 14.31 1.60 141.36 Number of individuals 914 876 713 Coefficient of variation (%) 34.4 11.9 44.4 Traits, abbreviation and measurements of mean, standard deviation and coefficient of variation.