Detecting parent of origin and dominant QTL in a two-generation commercial poultry pedigree using variance component methodology

Abstract

Introduction: Variance component QTL methodology was used to analyse three candidate regions on chicken chromosomes 1, 4 and 5 for dominant and parent-of-origin QTL effects. Data were available for bodyweight and conformation score measured at 40 days from a two-generation commercial broiler dam line. One hundred dams were nested in 46 sires with phenotypes and genotypes on 2708 offspring. Linear models were constructed to simultaneously estimate fixed, polygenic and QTL effects. Different genetic models were compared using likelihood ratio test statistics derived from the comparison of full with reduced or null models. Empirical thresholds were derived by permutation analysis.

Results: Dominant QTL were found for bodyweight on chicken chromosome 4 and for bodyweight and conformation score on chicken chromosome 5. Suggestive evidence for a maternally expressed QTL for bodyweight and conformation score was found on chromosome 1 in a region corresponding to orthologous imprinted regions in the human and mouse.

Conclusion: Initial results suggest that variance component analysis can be applied within commercial populations for the direct detection of segregating dominant and parent of origin effects.

Figure 1

Interval mapping of additive and dominant QTL effects on chicken chromosomes 1, 4 and 5 for weight (top) and conformation-score (bottom). The Y-axis shows the scaled rank of the test statistic obtained when compared to 1000 permutations of genotype within dam for 18 positions on chromosome 4 for weight and conformation-score. Test add is rank of test statistic obtained for model testing for additive QTL, addom is test statistic obtained from testing for both additive and dominant QTL effects and dom is test between two models for dominance only. Dam effect was fitted. Solid line at top is 5% empirical linkage group-wise significance

Figure 2

Interval mapping of parent of origin QTL effects for body-weight on chicken chromosomes 1, 4 and 5. The Y-axis shows the scaled rank of the test statistic obtained when compared to 1000 permutations of genotype within dam for 18 positions on chromosome 4 for conformation score. Mat and pat are testing for maternally or paternally expressed QTL respectively. Mat + pat is fitting both maternal and paternal expression and imp is testing difference between add model versus mat + pat model. Dashed line at top is 5% empirical linkage group-wise significance

Figure 3

Interval mapping of parent of origin QTL effects for conformation-score on chicken chromosomes 1, 4 and 5. The Y-axis shows the scaled rank of the test statistic obtained when compared to 1000 permutations of genotype within dam for 18 positions on chromosome 4 for conformation score. Mat and pat are testing for maternally or paternally expressed QTL respectively. Mat + pat is fitting both maternal and paternal expression and imp is testing difference between add model versus mat + pat model. Dashed line at top is 5% empirical linkage group-wise significance