Haplotypes Impacting Fertility


With our growing knowledge about the bovine genome, experts have predicted for some time that we'd likely discover numerous cattle genetic defects. Human genetic researchers estimate that we each carry four or five genetic defects. It's reasonable to expect that these exist at a similar level in cattle. So, it should not be surprising that we are beginning to uncover some information about a number of new genetic conditions in the Holstein, Jersey, Brown Swiss and Ayrshire breeds.

USDA researchers along with international collaborators have now identified nine haplotypes that appear to cause embryo loss or stillbirths when these haplotypes exist in the homozygous state. These were discovered by taking the full SNP50 genotype database of cows and bulls used for genomic evaluations and studying the frequency of the various haplotypes. Those haplotypes that meet two conditions, 1) there are no live individuals that are homozygous for this haplotype and 2) there is an observed reduction in conception rate or increase in stillbirths when carrier sires were mated to cows sired by carrier bulls are added to the list of haplotypes that are labeled and tracked. Five haplotypes impacting fertility have been labeled since August 2011. In August 2013, four additional haplotypes were added to the list of those to track.

List of Carriers

These genetic conditions have not been directly observed and we do not know the exact genetic or biological cause of why the embryos or fetuses are not viable. Because of this, they've been given simple names of Holstein Haplotype 1 (HH1), Holstein Haplotype 2 (HH2), Holstein Haplotype 3 (HH3), Holstein Haplotype 4 (HH4), Holstein Haplotype 5 (HH5), Jersey Haplotype 1 (JH1), Brown Swiss Haplotype 1 (BH1), Brown Swiss Haplotype 2 (BH2) and Ayrshire Haplotype 1 (AH1). These haplotypes appear to have a recessive mode of inheritance where animals with zero or one copy of the haplotype are completely normal. Those that inherit two copies of the haplotype are lost as embryos or are stillborn.

The impacts of these haplotypes vary and are dependent on their frequency in the population and at what stage of gestation the pregnancies are lost. The table below shows the frequency of each of these haplotypes and when the pregnancies are lost. Haplotypes with a higher population frequency and those that cause pregnancy loss later in gestation lead to larger losses of profitability. It's important to realize that the negative impact of these haplotypes is already accounted for in the routinely published sire conception rate (SCR) evaluations and daughter pregnancy rate (DPR) genomic evaluations. So, if you are using these traits in selecting you're A.I. sires you're already avoiding or compensating for these new genetic conditions

The haplotypes each represent a distinct and unique genetic condition. They are not related to each other. 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 is only experienced when animals are heterozygous for the same haplotype.

Select Mating Service™ (SMS™) is an excellent tool for managing these genetic conditions. By using the SMS program, herds with at least one generation of pedigree information on their cows can use heterozygous bulls with less than 1 percent chance of lost pregnancies from known conditions. SMS herds that do a good job of complying with the recommended matings should continue to use the A.I. sires that best deliver the traits desired in their breeding program regardless of their status for these new haplotypes.

The Select Mating Service™ (SMS™) is an excellent tool for managing these genetic conditions, as well as for avoiding inbreeding which may result in recessive conditions. By using the SMS program, herds with at least one generation of pedigree information on their cows can include heterozygous bulls in their breeding program with less than a 1 percent chance of lost pregnancies from known genetic conditions. SMS herds that do a good job of complying with the recommended matings should continue to use the A.I. sires that best deliver the traits desired in their breeding program, regardless of their status for these new haplotypes.


Name Key Sire Fathers Haplotype Frequency Timing of Pregnancy Loss
HH1 Chief, Mark, Lindy, Formation, Finley, Throne, Jordan-Red, Palemo 4.5% All Stages
HH2 Outside, Boulet Charles, Colby, Million, Mr Burns 4.6% Before Day 100
HH3 Glendell, Rotate, Emory, O Man, Boss Iron, Snowman 4.7% Before Day 60
HH4 Besne Buck, Jocko Besne 0.7% Unknown
HH5 Thornlea Texal Supreme 4.8% Before Day 60
JH1 Top Brass, Sooner, Beretta, Hallmark, Paramount, Jace, Louie 23.4% Before Day 60
BH1 Stretch Improver, Emory, Prelude, Even, Earnest T, Peeless, Vigor 14.0% Before Day 100
BH2 Rancho Rustic My Design 20.5% Stillborn Calves
AH1 Sellwood Betty's Commander 26.1% Unknown


All herds should avoid making inbred matings in their breeding programs. Avoiding recessive conditions is the main reason why this is important. Avoiding inbreeding is a good strategy for avoiding both the known and the unknown genetic conditions.

In Summary

  • A number of haplotypes that impact fertility have been identified and are routinely tracked in animals that are genomic tested.


  • They appear to have a recessive mode of inheritance.


  • When heterozygous bulls are mated to heterozygous cows, pregnancies will be lost 25 percent of the time.


  • The impacts of these haplotypes are already accounted for in genomic evaluations for DPR and in SCR evaluations for bulls.


  • Following SMS mating recommendations is a good way to take advantage of the outstanding genetics found in sires that are heterozygous for these haplotypes without experiencing the pregnancy loss that they cause.


  • Continued use of some heterozygous sires will provide a greater opportunity for higher overall genetic improvement. As industry programs gradually reduce the frequency of these haplotypes in the population, their impact will also be reduced.


What is a haplotype?

A haplotype is a stretch of chromosome or DNA that is transmitted as a unit from one generation to the next. In this case, we are talking about a set of single-nucleotide polymorphisms (SNPs) on a single chromosome that is inherited together. We often think about genes or SNPs as individual units but SNPs that are located next to each other on an individual chromosome are almost always inherited together as a unit.

What are homozygous and heterozygous?

Cattle have two versions of each chromosome. One chromosome was inherited from the sire and one was inherited from the dam. The words homozygous and heterozygous are used to describe the DNA, genes or SNPs at specific points along the chromosome. Homozygous describes the situation when the DNA on each chromosome is the same. Heterozygous means the DNA on each chromosome is different at a specific site.

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