Haplotypes Impacting Fertility
By: Angie Coburn, Associate Vice President-Dairy Genetics, Genex
For the past two years, we have described genomic technology as a powerful tool; it has provided dairy producers avenues to greater genetic progress through use of young bulls with higher genetic levels and the ability to optimize semen choices on genomic-tested heifers. As our ability to analyze the cattle genome has grown, so has our curiosity and understanding. In addition to deriving genomic PTAs, research is ongoing to describe and explain the function of specific genes or chromosome segments, also referred to as haplotypes. By better understanding how haplotypes function, there is greater opportunity to utilize this information in breeding decisions.
Through research, animal scientists at USDA-AIPL have identified five haplotypes that are inhibitors of fertility when occurring in a homozygous state, or in other words, a specific DNA sequence is inherited from both parents. Three of these haplotypes are found in the Holstein breed, with one haplotype occurring in each Jersey and Brown Swiss breeds. Research is on-going to further describe this genetic condition, confirm its mode of inheritance and determine the overall economic impact. Since the exact genetic or biological cause is yet unknown, the haplotypes have been given the simple names of Holstein Haplotypes 1 through 3 (HH1, HH2, HH3), Jersey Haplotype 1 (JH1) and Brown Swiss Haplotype 1 (BH1).
The discovery of haplotypes impacting fertility is not cause for alarm; rather it is advancement in information. In today's world of genomic research, it is expected that cattle follow a pattern much like humans, where each individual possesses a gene or haplotype that could result in an undesirable genetic condition if mated to another with the same haplotype. Now armed with more information, we can use it to our advantage to assess the risk of potential matings.
Table 1, below, lists the known source ancestors for each haplotype and provides the frequency of occurrence within the genotyped population. Furthermore, the table indicates the overall reduction on conception rates (CR) and 60-day non-return (NR) rates for carrier x carrier matings at the current frequency level.
Table 1. Analysis of Five Haplotypes Affecting Fertility
| Haplotype | Chromosome | Frequency | Earliest Known Ancestor(s) | Impact on CR | Impact on 60-day NR |
| BH1 | 7 | 14.0% | West Lawn Stretch Improver | -3.4% | -2.5% |
| HH1 | 5 | 4.5% | Pawnee Farm Arlinda Chief | -3.1% | -1.1% |
| HH2 | 1 | 4.6% | Willowholme Mark Anthony | -3.0% | -1.7% |
| HH3 | 8 | 4.7% | Gray View Skyliner Glendell Arlinda Chief | -3.2% | -3.1% |
| JH1 | 15 | 23.4% | Observer Chocolate Soldier | -3.7% | -3.7% |
While these haplotypes impacting fertility appear to be inherited in a recessive nature - similar to selecting for red coat color and polled condition or against defects like mulefoot and CVM - they should be treated differently in breeding programs than these other conditions. To a large degree, the economic impact of this genetic condition is already accounted for in traits like Daughter Pregnancy Rate (DPR) and Sire Conception Rate (SCR). Excluding bulls or females that possess one or more of the haplotypes from your breeding programs may have minimal impact on improving overall herd conception rate and also result in reduced net genetic gain.
As stated by Dr. Kent Weigel, in a recent article detailing the haplotypes impacting fertility and their impact on breeding programs, "...The Lifetime Net Merit (LNM) index weights every trait according to its economic value; (therefore) bulls that carry BH1, HH1, HH2, HH3 or JH1 have already been penalized in LNM. The magnitude of this penalty depends on the frequency of the haplotype within the breed." Table 2, explaining the potential economic impact, is adapted from this article.
Table 2. Scenario for Economic Loss from Haplotypes Impacting Fertility
If 20% of cows in the herd carry the haplotypes |
For every 100 matings, 20 cows carry haplotype |
1/2 or 10 of their eggs carry haplotype |
1/2 or 5 of the resulting embryos mated to a carrier bull and are homozygous for haplotype |
Homozygous embryos lost at 5-10 days of gestation |
Each of 5 cows will have an increase of approximately 30 days open |
Cost per extra day open is $2 |
Total economic loss per 100 matings: 5 cows x 30 days per cow x $2 per day = $300, or about $3 per mating |
Weigel continues, "Now assume this bull's LNM evaluation is +$600, and we decided to buy semen from another bull that was +$500 instead - we just gave up $97 in our attempt to save $3. Plus, that $3 was already included in the first bull's LNM evaluation." To read the complete article visit http://genex.crinet.com/haplotype.
Here's another way of assessing risk. With approximately 1,400 Holstein bulls available in the industry, 14-15 percent carry one or more haplotypes. With the current frequency, the likelihood of mating two carrier animals together is seven times in every 1,000 breedings. A herd with an average of 31 percent CR, would only improve by 0.36 percent by eliminating a bull that possesses a haplotype. Again, this information is already reflected in DPR and SCR, and if we avoid purchasing semen of bulls that carry these haplotypes, we double-count their effects.
In conclusion, we are only at the cusp of learning about the cattle genome and how we can incorporate the information into breeding programs and precision management. As we learn more, the goal should be to identify the corresponding economic impact. From there, good common sense should always prevail.
Summary Points:
- Haplotypes are sections of chromosomes and can be traced across generations with DNA genotyping.
- Five haplotypes impacting fertility have been identified with additional research on-going to describe biological function and assess economic impact.
- In Holsteins, frequency of random mating of two carrier animals is seven in every 1000 breedings.
- Expected losses are already accounted for with selection on DPR and SCR, and LNM is a good measure of net economic gain.
- For a list of haplotype status of Genex bulls, visit http://genex.crinet.com/haplotype.
