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♦ Haplotypes Impacting Fertility
♦ Haplotypes Impacting Fertility

Haplotypes Impacting Fertility 

Over the years, genomic technology has proven to be a powerful tool in the area of genetic advancement. It has provided dairy producers avenues to greater genetic progress through use of young bulls with higher genetic levels. 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.

USDA researchers have now identified 10 haplotypes that appear to inhibit fertility when these haplotypes occur in a homozygous state; in other words, when a specific DNA sequence is inherited from both parents. Five of these haplotypes are found in the Holstein breed, two occurring in each of the Jersey and Brown Swiss breeds, and a newly-discovered haplotype in the Ayrshire breed. Research is ongoing to further describe this genetic condition, confirm its mode of inheritance and determine the overall economic impact.

Since the exact genetic conditions in producing an unviable embryo have not been directly observed and the biological causes are yet unknown, the haplotypes have been given the simple names of Holstein Haplotypes 1 through 5 (HH1, HH2, HH3, HH4, HH5), Jersey Haplotypes 1 and 2 (JH1, JH2), Brown Swiss Haplotypes 1 and 2 (BH1, BH2) and Ayrshire Haplotype 1 (AH1.) These haplotypes appear to be inherited in a recessive nature where animals with one or no copies of the haplotype are completely normal. Descendants that inherit two copies of the haplotype are lost as embryos or are stillborn.

To elaborate further, each haplotype represents a distinct genetic condition; they are not related to each other. For instance, the haplotypes have no impact when a bull that is heterozygous for HH1 is mated to a cow that is heterozygous for HH2. The risk only occurs when animals are heterozygous for the same haplotype.

The impacts of these haplotypes on fertility vary and their effects depend on the frequency in which they occur within each breed. 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 rate (CR) and the approximate timing of fertility loss on carrier x carrier matings


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.  

It's important to realize the negative impact of these haplotypes is already accounted for in traits like Daughter Pregnancy Rate (DPR) and Sire Conception Rate (SCR). Furthermore, the five Holstein haplotypes impacting fertility have been included within the Fertility and Fitness (FYFT$) sub-index of the Ideal Commercial Cow (ICC) index developed by Genex. FYFT$ recognizes the economic impact of these haplotypes affecting fertility and stillbirths, and the magnitude in which bulls are penalized within this sub-index is based on the frequency of the haplotype in the population. Therefore, producers using DPR, SCR or the ICC index in choosing sires are already negatively selecting for these genetic conditions. Click here to read more about the ICC sub-indexes.

Fertility and Fitness
(FYFT$) Sub-Index


Excluding bulls or females that possess one or more of the haplotypes from a breeding program may have minimal impact on improving overall herd conception rate and also result in reduced net genetic gain. Table 2 summarizes a scenario detailing the potential economic loss from these haplotypes and their impact on breeding programs.

Table 2. Scenario for Economic Loss from Haplotypes Impacting Fertility 
• If 20% of cows in herd carry the haplotypes 
• For every 100 matings, 20 cows carry a haplotype 
• 1/2 or 10 of their eggs carry a haplotype 
• 1/2 or 5 of the resulting embryos are mated to a carrier bull and are homozygous for the haplotype
• Homozygous embryos are 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 = $2 

Total economic loss per 100 matings:
5 cows x 30 days per cow x $2 per day
= $300 or about $3 per mating

For example, assume a desired bull's ICC evaluation is +$900. However, because he is a haplotype carrier, a producer decided to buy semen from a non-carrier bull instead. The non-carrier was +$800 ICC. With the replacement bull, the producer gave up $97 in an attempt to save $3. This is counterproductive as that $3 was already accounted for in the first bull's overall ICC evaluation.

Here's another way of assessing the risk. With approximately 1,400 Holstein bulls available in the industry, 14-15% carries 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% CR would only improve by 0.36% by eliminating a bull that possesses a haplotype. Again, this information is already reflected in DPR and SCR. In avoiding purchasing semen from bulls that carry these haplotypes, their effects are double-counted.

In conclusion, as technology advances more will be learned about the cattle genome and how this new information can be incorporated into precision management. As more is learned, the goal should be to identify the corresponding economic impact of these discoveries and then utilize sound common sense to develop the most profitable breeding program.

Summary Points:

  Haplotypes are sections of chromosomes and can be traced across generations with DNA genotyping.
Ten haplotypes impacting fertility have been identified with additional research ongoing to describe biological
  function and assess economic impact.
These haplotypes affecting fertility appear to have a recessive nature of inheritance.
Expected losses of these haplotypes are already accounted for with selection on DPR, SCR and within the
  ICC index.
When heterozygous males are mated to heterozygous cows, pregnancies will be lost 25% of the time.
Excluding bulls or females that possess one or more of the haplotypes from breeding programs may have
minimal impact on improving overall herd conception rate and also result in reduced net genetic gain.