Genomics

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Genetic VisionsGenetic progress just got faster with the release of Genomic Evaluations. A quick bit of history - prior to 1935 there was no national program for evaluating dairy cattle breeding and no real genetic progress was made. Over the past 74 years various programs and/or traits have been introduced, each increasing the rate of genetic progress in differing amounts and improving the dairy cow. The recent employment of genomic evaluations is projected to have one of the largest impacts on genetic gain for our industry, ultimately assisting dairy producers in selecting the best genetics for their herd.

Genomics...Early Innovations

Genetic VisionsAccelerated Genetics is the true A.I. industry leader and pioneer in DNA research and application of the test results. Over twenty years ago Genetic Visions, Inc., Accelerated Genetics' research subsidiary, began using genetic markers to assist with identifying young animals that had superior genetic potential. Most of the attention centered around choosing among full siblings, when the animals were young, when progeny or performance data was absent or for sex-limited traits. Genetic Visions also developed generic applications used in dairy herds including identifying carriers of recessive defects and finding parentage errors. Again, Accelerated Genetics was the leader in the industry offering these services for customers and A.I. partners around the world.

Accelerated Genetics along with other members of the Cooperative Dairy DNA Repository, provided critical DNA samples for the foundation studies of the USDA's Bovine Genome Selection research. And through Genetic Visions' extensive bovine DNA storage from its years of research, vast amounts of DNA with a wider ancestry was provided, thus further adding to the accuracy of the new genomic evaluations. In fact, Genetic Visions is the only bovine research lab with extensive records and blood samples of bull dams existing prior to 1996.

Genomics...Offers A Genetic Map

Traditionally for young bulls the only information available was their Parent Averages (PA) based on their pedigree. Now with genomics, a genetic map of what traits they inherited from each of their parents is available and summarized into genomic evaluations.

The genomic evaluation of a young sire includes the combination of their PA and genotypic data, providing more reliable results. Having an accurate estimate of young sires as parents in various breeding programs and gives the potential to more rapidly increased genetic progress. For sires that have progeny with type and production data, their genomic estimates are a combination of their genotypic data, PA. and progeny data.

Genomic evaluation results look like Traditional PTAs (for yield, type, and management traits) and STA's (for linear traits), so producers don't need to learn a new evaluation system. The industry will label bulls that have been genomically tested. But some sires won't have their genomic estimates included in their January Sire Summary information instead their Traditional PTA and STA data will be used, here's why:

  1. Some bulls haven't been genomically tested by their A.I. company.
  2. Some bulls have a high reliability from their Traditional genetic evaluations, so the higher reliable estimate is used.
  3. Some bulls have a MACE Interbull proof and currently there is no mechanism in place for them to handle genomic evaluations.

Genomics...Our Approach

All Accelerated Genetics sires in the Holstein and Jersey breeds have been genomically tested, both young and proven sires. This policy was initiated so that our sire's evaluations would be more accurate and to help better manage our bull populations. Accelerated Genetics firmly believes in validating what the genomic research has shown, by continuing our PACE young sire program. Young sires will continue to go through our PACE program, randomly sampled by herds all over the U.S.

We have also incorporated the use of genomic results into how we acquire bulls for our PACE program. Meaning we are selecting sires with the highest quality genomic scores while keeping a diversified pedigree. Overall the PACE herds will have the advantage of much better genetics due to removal of bottom end bulls prior to sampling.

The genomic selection process at Accelerated Genetics can be easiest explained when looking at full siblings as all are assigned same Traditional PAs. Only after getting the genomic estimates for their PTAs and STAs can you really see the differences between full sibling bull calves. And sometimes the difference between full siblings can be significant.

Table 1. Application of Genomic PTAs to Contract Bulls
Animal
Traditional NM$
Genomic NM$
Traditional PL
Genomic PL
Bull A
415.5
411
1.3
1.3
Bull B
415.5
207
1.3
-0.2
Bull C
415.5
472
1.3
1.4

 

For example in Table 1, we compared three full sibling bull calves using Net Merit (NM$) and Productive Life (PL) as traits. In the past a bull stud may have chosen Bull B, based on his physical appearance and conformation. Now, with the help of genomic analysis, it is clear that Bull B is not even close to his siblings on NM$ or PL. So the bull stud would want to avoid Bull B and purchase Bull C, whose Genomic NM$ is clearly higher than his Traditional NM$. The same would be true for females genomically tested.

Clearly with genomic evaluations, PACE herds will benefit by sampling more genetically superior, higher reliable young sires than in the past. And producers will be able to make more rapid genetic progress, with bulls that have been pre-selected according to their genomic profile, particularly for low heritability traits like fertility, longevity and health traits.

Another way for producers to cash in on genetic progress is by using GeneFORCE sires. Accelerated Genetics is making a select few highly-valued, genomically-tested sires available. These sires have a high probability of being highly sought after proven bulls and do have a place in the market, but our PACE program is still greatly valued.

Genomics...Another Way To View It

Traditional PedigreeGenetic selection is not an exact science. However Genomics providing a new, powerful tool to help better predict results. Typically when we think about what traits are inherited from a dam or sire we believe it is all equal. This viewpoint is shown in Figure 1 (picture above). It displays how an offspring is expected to inherit approximately 50% from each parent, 25% from each grandparent and 12.5% from each great-grandparent. This is true when you consider a large group of animals, but is it true for an individual?

Genomic PedigreeNo, its not true for looking at an individual, look at Figure 2 (pictured to the left). It demonstrates that for a given chromosome an individual can inherit more than what is traditionally expected from a given ancestor. The color illustration clearly shows that the sire and dam did not inherit an equal amount from their parents. Here both the sire and dam received more than 50% from their respective dams. The same is true for their offspring. Figure 2 provides the visual for an animal's genetic map and is useful when estimating the genetic potential of individuals.

Genomics...What It Provides

The fact remains genomics are exciting and the industry is diving into the use of this genetic selection tool. Genomic evaluations will bring many changes. This includes the following:

  1. Significant improvement in accuracy over Traditional PA values (355 Traditional PA versus 65% Genomic PTA).
  2. Younger animals can be used as parents, reducing the generation intervals and enhancing genetic gain.
  3. Dairy Sire Summaries will continue to be three times a year, but Genomic PTA's will be made available 6-8 times a year for both cows and bulls.
  4. Reduction of parentage errors because of the ability to better identify heritage.
  5. Another option for a sexed semen source through use of GeneFORCE sires.

Furthermore, research at the USDA and Genetic Visions will increase the reliabilities of future sire evaluations and further uncover the bovine genetic map continuing genetic progress at an increasing rate. Remember..."The Genomics Revolution" was empowered by Accelerated Genetics' Innovations!

Genomic Selection - A Practical Explanation

By: Dr. Kent Weigel - Associate Professor and Extension Specialist in Dairy Genetics, University of Wisconsin-Madison... Read more...

Questions and Answers on Genomics

By: Dr. Ole Meland - Vice President of Genetics, Accelerated Genetics...Read more...