Derivation of parentage and breed-of-origin of alleles in a crossbred broiler dataset

Pig and poultry breeding programs rely on crossbreeding. With genomic selection, widespread use of crossbred performance in breeding programs comes within reach. Commercial crossbreds, however, may have unknown pedigrees and their genomes include DNA from two to four different breeds, depending on the crossbreeding scheme. SNP information allows: 1) derivation of parentage, provided that genotypes of parents are available, and 2) derivation of breed-of-origin of alleles in crossbreds, provided that sufficient genotypes of purebred animals are available to determine frequencies of segregating haplotypes for each of the parental breeds. We derived both parentage and breed-of-origin of alleles in a broiler dataset that comprised 5882 purebred and 10,943 three-way crossbred offspring that were generated by natural mating of 164 purebred sires to 660 purebred and 1031 F1 crossbred hens. Numbers of offspring per sire had a very skewed distribution, ranging from 1 to 275 crossbreds and 1 to 155 purebreds. Breed-of-origin could be derived for 99.74% of the alleles of the 1031 F1 crossbred hens and for 98.10% of the alleles of the 10,943 three-way crossbred offspring. Visual inspection of the assigned breed-of-origin, however, suggested that there are some errors in assignment of the maternal alleles. Further tuning of the algorithm, or adding more purebred animals of the dam lines to the analysis, may help to resolve those errors. The achieved percentage of assignment to the sire line appears sufficient to proceed with subsequent analyses requiring only the breed-of-origin of the paternal alleles to be known.