January 11, 2016

Genomic selection: A paradigm shift in animal breeding


By Samantha Kneeskern

January 11, 2016 – Genomic selection can greatly improve breeding programs. Genomic selection has been made possible by sequencing large numbers of single nucleotide polymorphisms (SNP; variations at a single nucleotide marking a specific position in the genome). Then, these markers covering the whole genome can be used to predict (with high accuracy) many breeding values and traits.

Traditionally, breeding was based solely off of phenotype. At the turn of the 21st century, Ben Hayes, Theo Meuwissen, and Mike Goddard published a paper (Meuwissen et al., 2001) that would spark a genomic revolution. Now, 15 years later, they have written a review in the January issue of Animal Frontiers, discussing the current methods of genomic selection, how it deals with practical data, and the future of genomic selection.

A genomic selection success story is dairy cattle. Dairy cattle were one of the first livestock species to use genomic selection, and it is now used in almost all dairy breeding programs. Because of large reference populations for each breed, accuracies of genomic prediction are extremely high for all traits, including productivity, longevity, and somatic cell count. Worldwide, 2 million dairy cattle have now been genotyped. Genotyping has led to increased profitability by selecting productive and efficient heifers to retain in the herd and by knowing the exact bull to breed her to.

However, because the use of these technologies are still in the early stages, many animals are still ungenotyped. But, phenotypic information can still be used to build a breeding value estimation. As an example, the authors explained that by averaging daughters’ production a pseudo-record of the bull can be produced. Therefore, the daughters are phenotyped and the father is genotyped.

In beef cattle, the Angus breed has been more extensively genotyped than any other breed, approximately 52,000 animals. However, because of smaller reference populations and fewer progeny tests, the accuracy is much lower compared to dairy cattle. Furthermore, the economic benefit is not as great as in dairy cattle. Traits such as feed efficiency and beef quality are expensive to record and companies have difficulty justifying the expense. But, if companies implement DNA testing, they can generate genomic prediction equations and models.

Click to read “Development and implementation of genomic predictions in beef cattle” by D.P. Berry, J.F. Garcia, and D.J. Garrick in the January issue of Animal Frontiers.

The swine industry has not used genomic selection near as much as cattle. But the authors state, “By genotyping crossbred pigs and recording their performance in the commercial environment, genomic selection can be used to improve purebred animals for crossbred performance under commercial circumstances. This requires across breed and crossbred genomic selection, which has not yet been demonstrated.”

Click to read “Genomic selection in commercial pig breeding” by Egbert F. Knol, Bjarne Nielsen, and Pieter W. Knap in the January issue of Animal Frontiers.

In poultry production, genomic selection is starting to be used in layers, but for broilers, traits for both sexes are recorded at a young age and the need for genomic selection is not there. However, companies are investigating genomic selection use for disease challenge tests.

Click to read “Implementation of genomic selection in the poultry industry” by A. Wolc and coauthors in the January issue of Animal Frontiers.

“Genomic selection offers two opportunities, which have so far not been fully utilized,” the authors write. First, by combining reproductive technologies with genomic selection, the best embryos can be chosen, improving generation length and quality. Second, using prediction equations on commercial (often crossbred) animals instead of purebred animals, allows the gathering of additional information like meat quality and disease resistance.

In the future, the authors anticipate that across-breed genomic selection will be used and is more accurate to estimate breeding values.

In this month’s issue of Animal Frontiers, you also can find articles explaining genomic selection for use in sheep and goat breeding and horse breeding.


Works Cited

Meuwissen, T.H.E., B.J. Hayes, and M.E. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829.

Meuwissen, T., B. Hayes, and M. Goddard. 2016. Genomic selection: A paradigm shift in animal breeding. Anim. Front. 6(1):6–14 (this issue).