New genetic conditions identified that affect dairy cattle fertility

Researchers have identified four new genetic conditions, referred to as haplotypes impacting fertility. A total of 9 haplotypes are now being reported by artificial insemination organizations and breed associations.

With increasing availability of information about the dairy cattle genome, researchers continue to identify new genetic conditions. Among these conditions are nine haplotypes that impact fertility in four dairy breeds. Five haplotypes have been reported since Aug. 2011 and four new haplotypes have recently been identified. 

A haplotype is a sequence of DNA on a chromosome that is inherited as a unit from the sire or dam. When the haplotypes impacting fertility are in the homozygous state, early embryonic death or stillbirth occurs. Homozygous means that the DNA in the specific haplotype is the same in each chromosome. In other words, the DNA in the haplotype from the dam is the same as the haplotype of the sire. 

Haplotypes impacting fertility have different frequencies and are specific to a given breed. The stage of gestation in which the pregnancies are lost vary among the haplotypes. The frequencies of the haplotype and the approximate timing of the pregnancy losses are listed in the table below.

Haplotype frequency
Timing of pregnancy loss


4.5 percent

All stages


4.6 percent

Before Day 100


4.7 percent

Before Day 60


0.7 percent



4.8 percent

Before Day 60


23.4 percent

Before Day 60


14.0 percent

Before Day 100


20.5 percent

Stillborn Calves


26.1 percent



The first letter in the name designates the breed (H=Holstein, J=Jersey, B=Brown Swiss, A=Ayrshire). The second letter “H” stands for Hapolotype. The third character is the number of the haplotype within the given breed. Lists of animals that have been identified as carriers of these haplotypes through genomic testing are available from the artificial insemination (AI) organizations and the dairy breed associations. 

Animals that are carriers of a given haplotype impacting fertility also can be referred to as heterozygous for the genetic condition. Heterozygous means that the DNA sequence is different at a specific site on the two corresponding chromosomes of the animal.

Conception rates will be reduced for matings in which both the cow and bull are heterozygous for a given haplotype affecting fertility. When a heterozygous cow is bred to a heterozygous bull, 25 percent of the embryos are expected to be homozygous for the haplotype and the pregnancies will be lost. As a consequence PTAs (predicted transmitting abilities) for Daughter Pregnancy Rate (DPR) and Sire Conception Rates (SCR) will account for the negative impact of these haplotypes impacting fertility.

Should dairy producers avoid using service sires that are carriers of one or more haplotypes impacting fertility? The answer is no. If no carrier (heterozygous) sires are used in a herd, some bulls with exceptional genetic merit for production and/or other health and fitness traits may be eliminated from the herd breeding program. Rather than totally avoiding the use of these bulls, efforts can be made to avoid matings of heterozygous cows to heterozygous bulls. This can be accomplished most effectively by using a computerized mating program. Accurate sire and dam identification is essential to successfully minimize the negative effects of these haplotypes impacting fertility as well as manage overall inbreeding levels in future matings in the herd. 

When making semen purchases, Michigan State University Extension recommends being aware of which bulls have been designated as carriers of any haplotypes impacting fertility. This information can be used to make optimum herd mating decisions.

For more information about haplotypes impacting fertility in dairy cattle, contact me at or 231-839-5850.

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