With less than a week until the December 03 index release day I am thinking what more do I want or need to learn about genomics in the world of dairy cattle breeding. I have friends that entirely use genomic information to breed and market while others are riding along and using higher indexing young sires but otherwise remain in the prove it to me “I am from Missouri camp”.  Here at The Bullvine we have provided thoughts in the past on genomics (Read more: Genomics at Work – August 2013). Today we decided to further document some areas that we feel are important to watch for and questions we are searching for answers to so that you don’t miss this opportunity.


“Does it really work?” is the question most often asked. The verdict is still out for many breeders. (Read more: Is the Genomic System Really Working?, The Truth About Genomic Indexes – “show me” that they work! And What Happens If Genomics Doesn’t Work?)

Except for a few preliminary reports by a couple genetic evaluation centers little has been published verifying that using genomics actually works. Breeders need the truth and nothing but the truth based on scientific analysis. We can likely expect the report to say that it assists with increasing the rate of genetic advancement but that: i) on an individual animal basis it is not as accurate as a 99% reliable daughter proven A.I. bull;  ii) for young bulls, heifers and cows it increases the accuracy of indexes ; iii) for traits for which we have limited farm data it is still too early to make  an accurate assessment; and iv) it is in fact the most important step forward in breeding since we got broadly based proven sires.  The message to our scientist and industry leaders is that breeders need to know the facts. The industry depends on breeders being successful. (Read more: CANADIAN BULL PROOFS – You’ve Got to Prove It to Use It!)

With the indexes of young animals today exceeding their older counterparts by a significant amount, breeders need to know the facts so they can decide on the extent to which they should use genomic information in their breeding plan (Read more: What’s the plan?).

Intensity of Use

It is well known that concern exists among all players, from breeders to scientists, on the increased rate of inbreeding.  (Read more: Twenty Things Every Dairy Breeder Should Know About Inbreeding, 6 Steps to Understanding & Managing Inbreeding in Your Herd and INBREEDING: Does Genomics Affect the Balancing Act?)

A study of the sires of top ranking young animals shows the following:

  • Sires of top fifty August 2013 gTPI young bulls – Mogul (21); Uno (8); Supersire (7); McCutchen (3); Facebook (2); Lithium (2),..plus seven others
  • Sires of top fifty August 2013 NM$ young bulls – Mogul (13); Supersire (10); Uno (8); Robust (3); Shamrock (3); Epic (3); Lithium (2); Facebook (2); ..plus six others.
  • Sires of top fifty August 2013 gLPI young bulls – Mogul (17); Supersire (9), McCutchen (5); Bookem (5); Mixer (3); Epic (2); Lexor (2); Iota (2); ..plus five others.
  • Sires of top fifty gLPI heifers (Sept-Nov releases) – Supersire (11); McCutchen (6); Enforcer (5); Mogul (5); Liquid Gold (4); Munition (4); Morgan (3); Cashmoney (2); ..plus ten others

Even though most of these bulls are not themselves closely related it is concerning that only a few bulls come to the top on all these lists. 66% of the above lists are over 6.0% inbred and only one is below 5.0% inbred. Outcross sires (Read more: 12 Sires to Use in Order to Reduce Inbreeding and GOING OFF THE MAP: 14 Outcross Holstein Sires That Don’t Include GPS) has been recommended as a solution yet Oman, Planet, Shottle and Bolton are prominent is the ancestry of the bulls above. It is time that we stop worrying about inbreeding and start finding practical solutions. Do we need to designate breeding lines and then doing line crossing like is done in crops, poultry and swine?  Why are A.I. organizations not using alternate sires of sons? Is it that those alternates do not come up as high on total merit index ranking lists? If that is the case should total merit index be the criteria used when selecting young bulls to be sampled or marketed. Should the inbreeding coefficient of every bull be a required number to be published?  There are solutions but it takes effort and leadership to stop the runaway train.

Finding the Best

Breeders of very elite indexing animals want to know which bulls will ring the bell for them when they flush their top virgin heifers. Some of those breeders feel that there are certain sires more capable than others at leaving top of the list progeny? Put another way can two bulls be ranked the same for total merit but one leaves progeny that are very consistent for their genomic values while the other bull produces progeny that range more in value. Breeders are willing to gamble and use the bull that appears to be able to produce list toppers. Breeders are asking the question – have our scientists studied this and is their an answer to the question of why some families consistently throw the high outliers?

Which are the Future Parents

As well with more and more emphasis being given to management, health and fertility traits in dairy cattle selection the question becomes which are the young bulls or elite heifers for the future. Could it be that they should be 90%RK for Production and 99%RK for Durability and 99%Rk for Health & Fertility? Attention needs to be given to matter with a view to the needs for the next ten plus years. (Read more: Total Merit Indexes: Are they helping or hurting?, Does Your Breeding Program Save You Labor? and  Are Your Genetics Wasting Feed and Labor?)

Health / Disease Resistance

No doubt we have only scratched the surface on what the DNA profile of an animal can tell use about an animal’s ability to remain healthy and disease free.  Even though breeders would like to have the answers today, the absence of farm data to match to the DNA will likely mean that this area of breeding will be relatively inaccurate for some time into the future. That does not mean that we should not continue to study this area, it is just that we can not expect answers quickly.

Female Fertility

Here again we are dealing with an area where there is limited farm data, or the farm data is not in connected data bases that can be used to correlate female fertility with DNA profiles. Is there farm data out there that tells us when heifers reach puberty? No. Are there genetic differences in when heifers can be first bred? Likely but we do not know. To go even further what about female conception rates? Biologically up to 90% of the time a sperm fertilizes an egg, yet only 65% of heifers and 40% of cows in Holsteins actually become pregnant. The inability of a fertilized egg to implant is significant but knowing the genetics of that is still a long ways off. Maybe there is research in other species that might be useful for linking female fertility with DNA profiles.

Breeders who flush females know that to be financially successful a cow or heifer must give many viable embryos. And that there are differences amongst cow families in how many embryos produced. (Read more: What Comes First The Chicken Or The Egg? And Investing in Dairy Cattle Genetics – Think Outside the Box) One question yet to be answered is by using IVF on poor flushing families are we, in fact, hindering reproduction from a genetic perspective. Yes more questions than answers but remember that the most common reason for cows being culled is infertility. So we do not need bull dams being genetically inferior for reproduction.


With lameness in dairy cattle being targeted as a big time problem in animal care circles, is it time that a mobility index be produced? Can we take our current DNA profiles and calculate such an index? It matters little that we know a host of traits about feet and legs when breeders are most concerned about a cow or heifer’s ability to move freely and comfortably in the environment is which she lives. (Read more: Cow Mobility: One Step Forward or Two Steps Back?)

Getting with the Program

Perhaps some of our ‘thought list’ will be possible in the next year or two. One thing we know is that for traits to be able to be evaluated we need more animals both recorded for performance and DNA profiled.  Of immediate concern is that without broad based field data for calf and heifer performance we are limited in what we can accurately know about this important cost center.  Any breeders not currently DNA profiling all their heifer calves are denying themselves future opportunities to advance their herds. Cost is frequently given as the reason for not DNA profiling, yet the cost is only about equal to officially milk recording a cow for a year. The information obtained can be used early in life including which heifers to keep, how to manage them and which sires to breed them to.

The Bullvine Bottom Line

Like almost everything else in genetic advancement, genomics does not have all the answers. It does not have 100% accuracy but it sure does shorten the generation interval in dairy cattle breeding.  Opportunity knocks for the breeders that do profile their animals. And every month with new facts coming out on genomics, the opportunity for greater return on investment increases for participating breeders.

The Dairy Breeders No BS Guide to Genomics


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