New Holstein Haplotypes to be Labeled with August National Genetic Evaluation


New Holstein Haplotypes to be Labeled with August National Genetic Evaluation

Holstein Association USAAs the science of genomics continues to evolve and progress, new information is becoming available to help Holstein breeders make more informed mating decisions about their cattle. Inherited recessive effects on fertility and stillbirth have become much easier to discover by applying genomic methods to growing datasets from large populations. Following is new information that will be reported for all genomic-tested animals, beginning with the August 2013 national genetic evaluation.

Haplotypes Impacting Fertility
Two new haplotypes impacting fertility have been reported for Holstein cattle. They are inherited in a simple recessive manner, allowing breeders to easily include this information in their selection and mating decisions. One was discovered by AIPL, and the other in France.

“The discovery of these two new haplotypes causing the loss-of-function of an important protein involved in embryo survival is a credit to the ongoing genomic research program at USDA-AIPL and in other parts of the world,” explains Dr. Tom Lawlor, Research Director at Holstein Association USA. “Prior to transmitting an animal’s DNA to its progeny, a parent’s chromosomes routinely will break and recombine in the process known as meiosis, creating sperm and eggs. Popular breeding animals will have many small sections of their DNA in the population. By routinely monitoring the frequency and occurrence of their haplotypes, researchers can determine if they are following a normal inheritance pattern, or if a particular haplotype may be harboring a lethal condition,” Lawlor continued.

Each month, AIPL screens all haplotypes to check if both homozygotes are observed in one or more of the thousands of genotyped animals. If they are expecting to see a large number of homozygotes and none are observed, these haplotypes are flagged for further investigation. Given the heavy usage of some of our prominent Holstein ancestors, a second test involving conception rates and incidence of stillbirth from the mating of a carrier sire to the daughter of a carrier sire will be checked (VanRaden et al., 2011a). A statistical analysis is conducted at each step to be assured that a real biological effect is being analyzed. The use of bioinformatics can then be used to find the actual gene involved and the precise DNA change responsible for the loss-of-function.



1 The reported HH4 carrier matings and conception decrease are from French data (Fritz et al., 2013).

2 A genotyped embryo was homozygous and was implanted, but no pregnancy was detected 28 days later.

The frequency of HH4 carriers is 7.2% in France (Fritz et al., 2013) and could also be high in other countries that used many sons of Jocko Besne, a prominent carrier, but the frequency is only 0.7% in North America. No homozygotes were found in French genotypes even though 49 were expected; 0 were found in North America but less than 1 was expected. The frequency of HH5 carriers was less than 1% before 2000 but has increased rapidly to 5% because of one recent popular sire, the common ancestor for nearly all carrier sire by carrier MGS matings. Pedigree analysis and additional genotyping then traced the haplotype to an ancestor born six generations earlier.

Effects on conception rate for HH4 and HH5 are similar to those of previous fertility haplotypes (VanRaden et al., 2011b). The fertility losses from HH5 were estimated to all occur before 60 days of gestation; no estimates for HH4 are yet available.

These haplotypes can be discovered through all genomic testing options available from Holstein Association USA, and the results of these tests are used to designate animals as carriers or non-carriers. A complete list of tested animals (both males and females) will be available after August 13 on the Holstein USA web site (www.holsteinusa.com ), under Pedigree Information > Genetic Codes/Traits, and will be updated regularly. Also visit the web site for more information about how the haplotype information should be used, and how to reduce the negative impact on your breeding program.

Additional Haplotypes Associated with Published Genetic Conditions Also Being Reported
Additional haplotypes associated with published genetic conditions will be made available with genomic predictions in August. Included are:
· HH0 – Haplotype associated with Brachyspina
· HHB – Haplotype associated with BLAD
· HHC – Haplotype associated with CVM
· HHD – Haplotype associated with DUMPS
· HHM – Haplotype associated with Mulefoot
· HHP – Haplotype associated with the polled condition
· HHR – Haplotype associated with red coat color

Breeders are encouraged to investigate the pedigree of the animal to ensure the transmission of the genetic condition is consistent with the haplotype result. Requesting the exact gene test for these conditions is advised, and is required to have an animal officially labeled as free or a carrier of the genetic condition.

With questions, contact Holstein Association USA Customer Service at 800.952.5200. Visit the Holstein Association USA web site at www.holsteinusa.com for the latest information about Holstein genetic testing services.

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7.31.2013