INTERPRETING OFFICIAL GENETIC CODES
Animals who have had a specific gene test performed for the condition in question will have a two- or three-character label, indicating whether they have been tested free or found to be a carrier for the condition. Following are examples of official genetic codes you may see;
- CVM – TV (tested free) or CV (tested carrier)
- Brachyspina – TY (tested free) or BY (tested carrier)
- BLAD – TL (tested free) or BL (tested carrier)
- DUMPS – TD (tested free) or DP (tested carrier)
- Mulefoot – TM (tested free) or MF (tested carrier)
- Cholesterol Deficiency – TC (tested free) or CD (tested carrier)
- Horned/Polled – TP (tested free), PC (tested heterozygous, one copy of the polled allele), or PP (tested homozygous, two copies of the allele); additionally, animals may have the official genetic code of PO, meaning the breeder reported the animal as being Observed Polled, but the animal has not had the official test to confirm.
- Dominant Red – DR1 (tested heterozygous, one copy of Dominant Red allele), DR2 (tested homozygous, two copies of the allele). Animals who are not carriers for Dominant Red (DR0) will not be labelled.
- Recessive Red – TR (tested free) or RC (tested carrier)
UNDERSTANDING HAPLOTYPE CODES
A haplotype is a combination of alleles (DNA sequences) at different locations on a chromosome that are transmitted together as a group (linked). Genomics is giving us more insight into the genetics of our cattle than ever before, leading more informed, better decision-making on the farm.
In the past 10 years, 7 different haplotypes have been discovered and future research will likely uncover more haplotypes. These haplotypes are believed to cause embryonic or foetal death when present in homozygous form, i.e., the offspring inherits the haplotype from both the sire and dam. In a herd, this would appear as if a cow did not conceive, resulting in greater days open and lower conception rates.
It is good to point out that the presence of a specific haplotype does not interact with haplotypes of different classes: for instance, matching HH1 sire and HH2 dam, do not cause probability of lethal condition for the embryo.
Research in Italy has shown the following results -
In July 2015, dairy researchers identified a new deleterious haplotype, called Holstein Haplotype Associated with Cholesterol Deficiency (HCD). This is a more serious defect than the Haplotypes Impacting Fertility, as animals who are homozygous for the unfavourable haplotype only survive a few months from birth. There are two versions of the haplotype, one which is lethal in homozygous form. The two haplotype versions look identical when examining only the surrounding marker genotypes. Pedigree information, combined with having knowledge of the haplotype status of earlier ancestors, allows for an accurate determination. The haplotype carrying the defect is difficult to track because both the normal version and the defected version occur frequently Codes of 0 to 4 are being used to denote an animal’s status on Holstein Association USA’s reports, as noted below.
CODES FOR HAPLOTYPE ASSOCIATED WITH CHOLESTEROL DEFICIENCY (HCD)
Haplotype results can be useful for identifying animals that are good candidates for further genetic testing and can also be used in conjunction with known genetic codes to trace different genetic conditions through the pedigree of an animal.
It is important to note that haplotype results are not a 100% accurate indicator of whether or not an animal is a carrier or free of a condition. In the case where an animal has an actual gene test result and a haplotype result, the actual gene test result should always be considered official.
Most haplotypes have simple result reporting: “T” indicates the animal is tested free of that haplotype and “C” indicates the animal is a carrier of the haplotype. For example, the haplotype associated with CVM is abbreviated as HHC; HHCT indicates an animal has tested free of that haplotype, and HHCC would indicate that an animal was found to carry that particular haplotype.
With three potential genotypes, the haplotype associated with Polled has an addition to the codes above, and can be interpreted as follows:
CODES FOR HAPLOTYPE ASSOCIATED WITH POLLED (HHP) CODES
Dominant Red and Recessive Red also have more possible genotypes, and they are coded as follows:
CODES FOR HAPLOTYPE ASSOCIATED WITH RECESSIVE RED (HRR)
