Genomic prediction offers glimpse of tomorrow…today


Source: Genome Alberta

Seeing the future can have its pros and cons. For researchers on the Genome Alberta project to promote adoption of genomic prediction tools in beef cattle, however, catching a glimpse of the future should go a long way to improving beef production efficiency and quality through genomic selection.

“Genomic prediction for beef performance starts with predicting breed composition for any cattle in the field, especially crossbred animals,” said Dr. Changxi Li, a research scientist with Agriculture and Agri-Food Canada (AAFC) who serves as an AAFC Professor and Chair in Bovine Genomics at the University of Alberta.

Backtrack or look ahead?

“After a number of years of breeding, producers may not have all the information they need on their herd’s breed composition. They then have to go back and track the parents of each generation and calculate the percentage that each parent contributed to the offspring. This can be hard to do one by one, especially with crossbreeds where one bull serves 20 or 25 cows.”

Using DNA profiles, producers can take a hair sample from each animal and spend $40 to genotype them. Scientists can then predict the precise fraction of various breeds in each cow in the herd based solely on DNA markers. There is no need for producers to provide a history of the herd, as the hair, ear tissue, blood or semen can be genotyped and matched with the standard genome profiles of pure breeds in the database.

“As part of our project, we have refined the genotypes for 14 major beef breeds in Canada, including Red and Black Angus,” said Dr. Li. “The DNA profile allows us to do this, as each purebred has a genome signature. By comparing the signature of those purebreds to any cattle in your herd, we can determine the exact percentage of the genome that each cow inherited from those 14 breeds, so we cover a lot of ground.”

Knowing precise breed composition of breeds in a cow herd will offer producers an opportunity to “fine-tune” their herd via science-based mating to achieve optimal retained hybrid vigor and improved performance due to crossbreeding.

The other piece of the prediction puzzle is genetic merit. Where hybrid vigor refers to the gene combination of both parents, which lasts for the life cycle of the animal, genetic merit relates to genes inherited from both parents that can be passed down to the next generation.

This beef genomic prediction trial aims to predict the genetic merit of  breeding candidates based on 50,000-100,000 DNA markers or single nucleotide polymorphisms (SNPs), using a reference population of approximately 11,000 Canadian beef cattle.

Currently, the project can predict the genetic merit or genomic expected progeny difference (gEPD, also called molecular EPD or mEPD) for feed efficiency. This includes dry matter intake and residual feed intake, which relate to growth in terms of average daily gain, and carcass traits including carcass weight, lean meat yield, rib-eye area, back fat thickness and marbling.

The project is also developing genomic prediction tools for fertility traits to select replacement heifers that are more fertile. As well, in crossbred cattle, the project will predict genomic breed composition (gBC) and then genomic retained heterozygosity (gRHET), a key determinant of retained hybrid vigor. Detailed project  information can be found at

The above sample report provides information on EPDs of various traits and their relative ranking in the herd for a candidate bull.  The bull has an above average genetic merit on carcass weight and  carcass marbling, whereas genetic merits for other traits are below average.

DNA is the way

“We are trying to expand this project to demonstrate the potential to as many beef producers as possible. If we can make these tools available to all producers, they can monitor their herds’ genetics scientifically rather than by memory. Some producers take a liking to a particular bull or cow, but in the end, your best results come from the DNA profile.”

Ultimately, it is those results that will sell producers on this brave new technology. One study found that a 10% improvement in heterozygosity means a cow stays in your herd longer and produces more offspring, leading to a savings of about $161 per cow per year.

“Nobody wants to select a cow and by next year it is dry and needs to be culled. Even though improvement for one generation may not be that obvious via gEPD selection, when you do it over and over again the best genes will accumulate in the cow herd, and that is your ultimate goal.”


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