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Background  In pig and poultry breeding programs, the breeding goal is to improve crossbred (CB) performance, whereas selection in the purebred (PB) lines is often based on PB performance. Thus, response to selection may be suboptimal, because the genetic correlation between PB and CB performance (   \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$r_{pc}$$\end{document}    r   pc) is generally lower than 1. Accurate estimates of the    \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$r_{pc}$$\end{document}    r   pcare needed, so that breeders can decide if they should collect data from CB animals.    \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$r_{pc}$$\end{document}    r   pccan be estimated either from pedigree or genomic relationships, which may produce different results. With genomic relationships, the    \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$r_{pc}$$\end{document}    r   pcestimate could be improved when relationships between purebred and crossbred animals are based only on the alleles that originate from the PB line of interest. This work presents the first comparison of estimated    \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$r_{pc}$$\end{document}    r   pcand variance components of body weight in broilers, using pedigree-based or genotype-based models, where the breed-of-origin of alleles was either ignored or considered. We used genotypes and body weight measurements of PB and CB animals that have a common sire line.    Results  Our results showed that the    \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$r_{pc}$$\end{document}    r   pcestimates depended on the relationship matrix used. Estimates were 5 to 25% larger with genotype-based models than with pedigree-based models. Moreover,    \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$r_{pc}$$\end{document}    r   pcestimates were similar (max. 7% difference) regardless of whether the model considered breed-of-origin of alleles or not. Standard errors of    \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$r_{pc}$$\end{document}    r   pcestimates were smaller with genotype-based than with pedigree-based methods, and smaller with models that ignored breed-of-origin than with models that considered breed-of-origin.    Conclusions  We conclude that genotype-based models can be useful for estimating    \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$r_{pc}$$\end{document}    r   pc, even when the PB and CB animals that have phenotypes are closely related. Considering breed-of-origin of alleles did not yield different estimates of    \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$r_{pc}$$\end{document}    r   pc, probably because the parental breeds of the CB animals were distantly related.    Electronic supplementary material  The online version of this article (10.1186/s12711-019-0447-9) contains supplementary material, which is available to authorized users.

Estimating the purebred-crossbred genetic correlation of body weight in broiler chickens with pedigree or genomic relationships