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

Rowe SJ, Pong-Wong R, Haley CS, Knott SA, De Koning DJ - Genet. Sel. Evol. (2009)

Bottom Line: Different genetic models were compared using likelihood ratio test statistics derived from the comparison of full with reduced or models.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, UK. Suzanne.Rowe@Roslin.ed.ac.uk

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 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.

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Related in: MedlinePlus

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
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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

Mentions: Figure 1 shows QTL effects under additive and dominant QTL models for bodyweight and conformation score. There were chromosome-wide significant dominant QTL effects for conformation score on chromosomes 4 and 5. These effects were considerable, explaining 6.2 and 4.5% of the phenotypic variance, respectively. Table 3 shows that the dominant QTL explains all of the QTL variance (i.e. the estimated additive effect of the QTL is zero when a model with both an additive and dominant QTL effect is fitted).


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

Rowe SJ, Pong-Wong R, Haley CS, Knott SA, De Koning DJ - Genet. Sel. Evol. (2009)

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
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2637028&req=5

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
Mentions: Figure 1 shows QTL effects under additive and dominant QTL models for bodyweight and conformation score. There were chromosome-wide significant dominant QTL effects for conformation score on chromosomes 4 and 5. These effects were considerable, explaining 6.2 and 4.5% of the phenotypic variance, respectively. Table 3 shows that the dominant QTL explains all of the QTL variance (i.e. the estimated additive effect of the QTL is zero when a model with both an additive and dominant QTL effect is fitted).

Bottom Line: Different genetic models were compared using likelihood ratio test statistics derived from the comparison of full with reduced or models.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, UK. Suzanne.Rowe@Roslin.ed.ac.uk

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 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.

Show MeSH
Related in: MedlinePlus