Cattle genomics gain credibility in breeding programs

Progeny test still desired | More genomic breeding values needed to improve reliability

TORONTO — The dairy industry is turning upside down how breeders and farmers evaluate their cattle.

In the past, breeders preferred to use animals with a proven track record.

But genetic analysis now allows producers to use younger sires that score high on the tests.

Forty percent of younger bulls were used to produce sons this year, said Marjorie Faust, senior research dir-ector of the genetics company ABS Global.

As well, breeders would have previously used females older than two years because those animals had more offspring and milk records.

However, breeding companies now own more heifers, including pre-puberty heifers.

Their eggs are removed and fertilized with semen from high testing sires and are then used in embryo transfer programs.

“We are seeing many more breeding contracts being made on maiden heifers,” Faust said. “Today in the U.S., genomic estimates are really driving the value of animals in breeding programs and currently the race is on for the big numbers.”

These heifers may also be mated with young bulls, even though neither have performance records.

An emerging trend is analyzing females as well as bulls.

More than 230,000 Holsteins of both sexes have been genotyped in the United States, said Faust.

The bovine genome has three billion base pairs. DNA building blocks are studied using single nucleotide polymorphisms, known as SNPs, to find desirable traits by looking for differences along the sequence.

However, SNPs look only at small pieces of the sequence, so it is possible to miss valuable traits, such as milk production, rate of gain or fertility, said Ben Hayes of the Dairy Futures Co-operative Research Centre in Australia.

Extensive information from large numbers of animals is needed to explain genetic variations and develop more reliable predictions of what to expect from animal performance.

But Hayes said fewer progeny tests are being carried out as genomic information gains credibility, and this could cause the accuracy of predicted cattle performance to drop off.

Supplementing the genomic information beyond SNPs began by building databases on the large numbers of proven animals called reference populations.

The Holstein breed has thousands of bulls with DNA and accurate phenotype records in North America and Europe. Genomic breeding values for traits such as milk production and fertility were created from this store of information.

“The rate of genetic gain you are going to make in your breeding programs when you are using genomic breeding values is partly the result of how reliable those breeding values are,” Hayes said.

“The more reliable breeding values there are, the better the predictor of the true genetic merit.”

Using DNA information to improve cattle more quickly was a major theme for the World Holstein Federation meeting held in Toronto Nov. 6-7.

Faust said even though the genetic estimates are becoming popular, farmers may still want to see progeny records regardless of what the DNA says because the merit of young animals are sometimes overestimated.

Faust said genomic information on individuals is also driving up bull prices by 50 to 200 percent.

Geneticist Sander de Roos of the Cattle Improvement Co-operative in the Netherlands said everyone wants reliable breeding values and the ability to use young bulls with confidence, but a bull that is progeny tested and has produced 100 daughters is still considered more reliable.

Four European countries are collaborating and have tested 23,000 proven animals.

EuroGenomics has added 2,000 animals per year to its database.

The reliability of the database is increasing, but the change is not as great as more animals are added.

The project wants both males and females in the system, but at least 100,000 cows with proven traits are needed for an accurate database if information is collected on 24,000 reference sires.

“If we start genotyping cows, there are plenty of other things we can do with that information,” de Roos said.

However, for the average farmer, using such information on a cow comes down to affordability.

In Europe, genotyping costs $50 per cow, which is considered too high for the average commercial farmer. However, they might pay $10 to $40 if they knew there was a return on their investment.

Farmers could select better heifers and make better mating decisions or decide whether to flush the best cows and breed them with sexed semen.

EuroGenomics offered farmers a deal: free testing for cows and $20 per heifer.

Thirty herds have joined and 6,000 females have been genotyped. The project ultimately wants data on 600 herds and 120,000 females to build a good sized reference population.

It is also trying to build information on crossbreds, but the sequencing takes longer and no reliable data is likely for several years.

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