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Báo cáo sinh học: " Prediction of haplotypes for ungenotyped animals and its effect on marker-assisted breeding value estimation"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí sinh học quốc tế đề tài: Prediction of haplotypes for ungenotyped animals and its effect on marker-assisted breeding value estimation | Mulder et al. Genetics Selection Evolution 2010 42 10 http www.gsejournal.Org content 42 1 10 GSE Ge n et i cs Selection Evolution RESEARCH Open Access 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 accuracy of predicted haplotype copies for ungenotyped animals ranged between 0.59 and 0.64 depending on haplotype length. Because powerful BLUP-software was used the method was computationally very efficient. The accuracy of total EBV increased for genotyped animals when marker-assisted breeding value estimation was compared with conventional breeding value estimation but for ungenotyped animals the increase was marginal unless the heritability was smaller than 0.1. .