With nearly all chairs filled, people stood along the back wall and even sat on the floor to hear discussions on genomics.
Holstein Association’s Tom Lawlor continues with his genomic presentation….
5 of top 25 GTPI cows scored 83 or higher were imputed. Can have more confidence in them – reliabilities have gone up with additional genomic information added.
Errors made -
farmers didn’t know changes were coming
farmers didn’t know why the change was recommended
farmers didn’t see any evidence that the change was right
farmers didn’t know what the avg. change in TPI on their cows would be
April lessons
Yes, it’s a cow business, but a people business too
Need to explain when & why a change is going to be made, what it will do, who it will impact and how the change will lead to more accurate genetic evaluations
What’s ahead
advances in technology
new testing tools – DNA chips; greater use of haplotypes & imputation
new traits – fertility
implementation of new research findings
imputation process will go from 3K (markers) to 50K (markers)
USDA changes
May 2010 start of monthly genomic evaluations
If a SNP-marker could not be determined, the marker with the higher allele frequency from the base population was used – this will be changed to the current population.
July 2010, USDA along with 8 other countries will submit its genomic evaluations to Interbull for a validation test. Countries passing the test will be eligble to market genomic test bulls in Europe.
August 2010 Two new traits introduced – cow and heifer conception rates – only calculated on herds participating in AI testing program
December 2010 Two new traits introduced – sire conception rate on conventional semen and sire conception rate on sexed semen
December 2010 genotypes from the 3K SNP chip may receive official GTPAs AND a code indicating whether a 3k, 50K or HD SNP chip will be included in the genetic evaluation files
April 2011 – USDA’s target date for having a resolution for the cow adjustments so genotyped and imputed cows are on the same base as the cows that are not genotyped.
Making genotyped and non-genotyped cows more comparable -
reduce heritability
differential adjustment by herd
….Keep hitting refreshed as we’ll update the entire time the meeting goes on!
March 2013 Genomic testing of all males & females will be available to all
QUESTIONS
David Winkels – MN
Winkels presented independent research he had done on questions regarding bull proofs – all which he documented on paper (but not enough copies to blanket the capacity crowd) including discrepancies he had found in both type and production based on genomic proofs and conventional proofs. Winkels questioned the reliability of the current system as well as the ability for an average dairyman to get all information available.
Why has this been allowed to happen?
Lawlor: Different sources of information get combined together to give us the final evaluation. We add in genomic and foreign information to come up with an official evaluation to release to the industry. Availability of that information is there and put out in between full updates. Don’t continue to put numbers side by side.
But why have we thrown all conventional things out the window?
Lawlor: Again, we do use traditional information – and we are using genomic information as well. These genomics are more accurate. We have made the decision to use genomic as official because its the most complete and enhanced evaluation.
Willard Peck (NY) – limit time at microphone to two minutes
and seconded…
Paul Buhr (WI) – I’m a breeder first, dairyman second and farmer third. We are breeders here – and should be addresses as such. This system does an excellent job for commercial breeders. A high percentage of our genetics is in commercial dairies. If we adopt this – we will only recognize one set of perfect genes. When we achieve that – and it will be done – we will have bred ourselves in a corner. And that won’t bode well for our Holstein breed. We must promote different breeding goals so that we don’t have the paradox of breeding for health traits while decreasing vitality and fertility. The only solution is crossbreeding and then we will have smaller market share for the registered breeders.
Lawlor: You have made some good points but you’ve hit on one that’s quite important – our main focus was to talk about the April evaluations. We want to regain people’s confidence in genomic predictions. But you’re right. Genomics – we are learning as we go. We still need to find the outlyers and address that challenge. The good thing is that genomics are available on all traits – so we can look at individual traits – so we can find outlyers for production, etc… Let’s not focus on one single description of what makes a good cow. We need to have accurate information on a variety of traits. Narrowing down to a few bloodlines and having high genomic animals in those fews – that’s not what we’re looking for. Unfortunately we haven’t figured out how to find those outlyers.
Glen Brown (UT): The last minute decision on these adjustments seems to be based on being validated by Interbull in July. If that’s the case, when did we know that these adjustments needed to be made? Who is Interbull? Who validates us? Who evaluates USDA and Holstein’s judgments on evaluations?
Lawlor: You are right on the rush for the July deadline. The belief is that the USDA genomic evaluations would NOT have passed if these adjustments had not been made. It had to be done – maybe not as quickly, but it had to be done. We all know about the inflation of PTAs – we’ve known about that for a while. USDA suggested a lowered heritability. The Council on Dairy Cattle Breeding is who we look to for approval on changes. That wasn’t done this last cycle because of the rush deadline.
Jim Rickert (WI): Calculating of the TPI formula – needs to be reviewed.
John Meyer – Board of Directors met this week and will be reviewing the current TPI formula – and will decide if changes will be made.
Linda Hodorf (WI) – Changes in August 2010 – information available on cow and heifer conception rate – is that only on herds on AI testing programs? What about other herds that submit this info to their testing centers be included?
Lawlor: Information that is being used for this conception rates is limited to those herds participating on AI testing programs. It is open to everyone else. Right now the process is not in place, but we as an Association need to help individual herds have that information submitted. There will probably be a small fee for that.
Paul Buhr (WI) – Define unique genetic sequence and until recently, I could look at information on the AIPL site on males. That’s no longer – and why can’t I see that on females as well.
Lawlor: Regarding chromosomal display – you just told me something I didn’t know. I don’t know the answer to that. In terms of female information, we have been slow in putting that information forward.
Mark Ulness (WI): Lack of ability to find those outlyers. My feeling is that there’s too strong of a sire influence in these genetic calculations. Cows that have proven themselves through classification and DHIA records, they are reputable. Why are the cows with both high type and milk not found themselves on top of these lists? Like Frosty or Elsie who are both Excellent and have made records of 50,000 lbs of milk? Aren’t they the gold standard of what we want to breed?
Lawlor: That is a goal of us to find outstanding individual cows. Unfortunately – heritability doesn’t always work that way. So all these outstanding cows won’t be good transmitters of these genes in some cases. But we keep looking to try and improve the correlation between those good characteristics.
Chuck Will (MN): Interesting point that has been raised – I have a member of one of the best cow families in the world. A cow with 338,000 lifetime. But she is minus on milk and minus on type (she is 94 points). She is 97 in mammary and is minus on mammary. She has a minus productive life. She has a dtr with 53,000 and is Excellent. I don’t understand on why we use what they COULD do instead of what they HAVE done? Something is wrong with the formula.
Lawlor: I understand you feel passion about breeding good cows and we have a variety of people who like a variety of cows. We can’t stand up and say this is the final answer and this is the only way you can judge cattle. The Association has tried to address this issue – we recognize DOM and GMD cows. Progressive Genetics Award. PBR award. They all address different breeders and different goals. We’d just like you to breed the type of cows that you believe in.
Dave Rama (NY): Genomics – first calves born from the bulls – would it make sense to go through first 30 dtrs and genomic test them? Maybe they’re doing that. If we’re putting all our emphasis there – test the offspring immediately and see if this bull is doing what it’s supposed to be doing instead of waiting 4 years for a proof. It may help with the confidence level in this system. Whatever the government gets involved with – it’s calf scours! These guys know how hard it is to develop good cow families. They have confidence in what they’ve been doing. Right now there’s a lack of confidence in USDA. Tread lightly with the federal government.
Lawlor: Doing the genomic testing of first 30 dtrs – it all comes down to costs. Those that are believers in predictions have worked hard to a cheaper genetic tests. You might see your idea come to pass very quickly. Fewer will go into an active lineup because of that screening. Those that actually get in will be the best of the best. In regards to USDA, they do try to make the information available for us to see. I try to study their numbers so that I can be of service to this association. Need to validate the information – is it reliable? Can we trust it? Should we use it? Yes. Use these tools as you see fit and get the benefits of it. We’re trying to look after your success.
Bill Eustice (MN): I’ve witnessed 40 years of changing TPI formulas and you never know where you’ll be with the next set of changes. Will Holstein consider a poll like this before reviewing the TPI formula? 50.7% breeders ranked type as their highest priority – feet and legs was second highest trait. (according to an HI poll)
Tande: Jonathan Lamb will be heading the GAC committee – talk to him about the TPI formula review.
Kevin Jorgensen (WI): Still feel the compelling need to say that breeders are concerned about the direction of the breed. We can be successful in a variety of paths. Is everything moving to one direction/philosophy? The greatest part of this business is the variety. Our success will come when we listen to our members and encourage diversity.
Ron Wood (PA): Could you have literature passed around by David Winkels copied. It was very confusing and we want to know if it warrants further discussion.
