Abstract
Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus–Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA) and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus–Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage—indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals. This was most likely due to inaccuracies in the pedigree-based estimation of breed composition, which supported the case for using genomic information to complement and/or replace pedigree information when estimating breed composition. Comparison with a supervised analysis where purebreds are used as the training set suggest that accurate predictions can be achieved even in the absence of purebred population information.
Highlights
Around 40% of all beef cattle in the United States are located in the subtropical southern and southeastern parts of the country (Cundiff et al, 2012)
Angus–Brahman crosses are typically better suited for beef production than other Zebu–Taurine combinations in subtropical parts of the United States (Chase et al, 2004)
Since Brangus is a composite breed derived from Angus and Brahman, the Brangus cattle and their progeny were considered as crossbreds between the two parental breeds as recommended by Kuehn et al (2011)
Summary
Around 40% of all beef cattle in the United States are located in the subtropical southern and southeastern parts of the country (Cundiff et al, 2012). Crossbreeding between European Taurine and Zebu (Bos indicus) breeds is a common strategy used to enhance beef production in tropical and subtropical areas (Lamy et al, 2012) These crossbreds combine the production performance of Taurine cattle with the tropical adaptation of Zebu cattle, and usually outperform purebred cattle from the parental breeds in subtropical conditions due to heterosis (Burrow, 2015). Whether a particular Taurine–Zebu combination is optimal depends on the specific production environment under consideration It has been suggested (Cundiff et al, 2012) that, in subtropical regions of the United States such as the Gulf Cost, cattle with a 1:1 Taurine to Zebu ratio would be preferred whereas a 3:4 Taurine to Zebu ratio would be better suited to the more northern but still subtropical parts of the United States such as Southeastern Oklahoma and most of Texas
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