Statistical analyses of the ocular traits were performed with commercial software (SPSS ver. 14.0; SPSS Inc., Chicago, IL). Outlier detection and removal proceeded as follows. First, using the finding that the bilateral ocular traits correlated highly in fellow eyes (range of Pearson correlation coefficients, 0.82–0.97; all
P < 0.001), data points that fell outside the 99% CI of a fitted regression line in a scatter plot of trait values in right versus left eyes were set as missing values. Second, after taking the average trait value of the bilateral traits, trait values beyond three standard deviations from the mean were also set as missing values. For the WL population, this resulted in the removal of data for 1, 4, 5, 8, and 5 individuals for the traits, radius of corneal curvature, anterior chamber depth, lens thickness, vitreous chamber depth, and axial length, respectively. Similarly, in the AIL population, 7, 5, 6, 11, 8, 6, 7, and 3 individuals were removed for the traits, radius of corneal curvature, anterior chamber depth, lens thickness, vitreous chamber depth, axial length, corneal thickness, eye diameter, and eye weight, respectively. As well as these trait values that were deliberately excluded, a small number of chickens were missing phenotype information for certain traits (e.g., due to equipment failure). The final number of WL and AIL chicks used in the analysis of each trait is shown in
Table 2, broken down by sex. All ocular traits were deemed to be normally distributed (by the Kolmogorov-Smirnov test), and hence no transformations of the traits were made before heritability analysis.