prediction of haplotypes for ungenotyped animals and its effect on marker-assisted breeding value estimation预测的单体型ungenotyped动物及其对分子标记辅助育种值估计的影响.pdfVIP

Mulder et al. Genetics Selection Evolution 2010, 42:10 Ge n e t i c s /content/42/1/10 Se l e c t i o n Evolution R E S E A R C H Open Access Research Prediction of haplotypes for ungenotyped animals and its effect on marker-assisted breeding value estimation Han A Mulder*, Mario PL Calus and Roel F Veerkamp Abstract Background: In livestock populations, missing genotypes on a large proportion of animals are a major problem to implement the estimation of marker-assisted breeding values using haplotypes. The objective of this article is to develop a method to predict haplotypes of animals that are not genotyped using mixed model equations and to investigate the effect of using these predicted haplotypes on the accuracy of marker-assisted breeding value estimation. Methods: For genotyped animals, haplotypes were determined and for each animal the number of haplotype copies (nhc) was counted, i.e. 0, 1 or 2 copies. In a mixed model framework, nhc for each haplotype were predicted for ungenotyped animals as well as for genotyped animals using the additive genetic relationship matrix. The heritability of nhc was assumed to be 0.99, allowing for minor genotyping and haplotyping errors. The predicted nhc were subsequently used in marker-assisted breeding value estimation by applying random regression on these covariables. To evaluate the method, a population was simulated with one additive QTL and an additive polygenic genetic effect. The QTL was located in the middle of a haplotype based on SNP-markers. Results: The