Effect of Selection on Breed Composition

Breed composition is known to affect production-related traits in beef cattle, with the relative proportion of Bos taurus and Bos indicus of particular relevance.

Crossbreeding is a common practice in livestock production to improve productivity. Hybrid vigor confers a performance advantage over straight-bred lines or breeds, which is not as evident after a few generations. The use of crossbreds also provides the opportunity to retain beneficial traits (or alleles) from ancestral breeds in subsequent generations, e.g. the parasite resistance of Zebu breeds, or the shorter post-partum anoestrous interval observed in Angus cattle. Thereafter, breed composition often has a significant effect on production traits, which is even more pronounced when comparing across different populations.

By combining genotype data from a target population with genotype data from a panel of reference breeds, we can replace pedigree-based breed composition with an estimated SNP-based breed composition. We used 50K SNP data and a model-based approach to estimate the breed composition from a stable composite crossbred herd formed by crosses between five breeds around 20 years ago, which has not had additional animals introduced to it since then. There were more than 6,700 animals available for analyses, these were a representative subset of the herd, born between 2001 and 2013.

The estimated SNP-based breed composition resembled the pedigree-based composition from the formation of the breed. On average, the estimated genome-wide breed composition did not change substantially over several generations of selection, and it was not significantly associated with genomically-enhanced breeding values for various production traits. Nevertheless, there is still variation, and we obtained evidence that inbreeding in this herd has been effectively controlled.

We hypothesize that selection pressure on production traits would result in the maintenance of relatively small genomic fragments carrying the favorable alleles from a given ancestral population, rather than shifting the overall breed composition. This would impact on the local ancestry of genomic fragments but would be diluted in a genome-wide analysis. Preliminary analyses supported the hypothesis. The selection of relatively small genomic fragments might have been facilitated in this case by the intensive and diverse crossbreeding during the formation of this composite breed. Further analyses using sequence data to explore the ancestry of genomic segments and their association with production traits should assist the identification of favorable alleles kept in the selected population.

CSIRO Livestock contact

Laercio Porto-Neto