GeneProb

Genetic Conditions

Genetic conditions or defects are caused by DNA abnormalities and are present in all species, including beef cattle. The incidence of genetic conditions is normally low within a population but increases in inbreeding or the rapid dissemination of genes through artificial breeding, can lead to a rapid escalation in the prevalence of a condition.

The symptoms of genetic conditions can be quite nonspecific, such as:

  • Poor growth and fertility performance. For example, calves with Protoporphyria (photosensitivity) develop scabs and open sores when exposed to sunlight and have reduced liver function, which in turn decreases their overall performance.
  • Structural unsoundness. For example, animals with Snorter Dwarfism have a short, blocky appearance with deformed bone growth in the nose, causing difficulty breathing.
  • Semi-lethal - Not all affected individuals survive to maturity. For example, many calves affected by Contractural Arachnodactyly (CA) will die shortly after birth because they are unable to stand and suckle. Those calves who are able to stand will often survive to maturity but have poor growth performance.
  • Lethal - No affected animals survive to maturity. For example, animals affected by Pompes will typically die between 6 to 12 months of age after displaying progressive muscular weakness.

When large numbers of calves are dying or being born with similar abnormalities, both environmental and genetic causes are suspected. Consequently, there is a need for the surveillance and reporting of abnormal calves to breed societies, veterinarians or beef technical officers if genetic conditions are to be identified. Photographs and DNA samples from affected animals should be collected to aid in the identification of the condition.

GeneProb Technology

GeneProb amplifies the use of DNA test results to create breed wide benefits and management solutions for genetic conditions and simple qualitative traits. It utilises the basic principles of inheritance to estimate the probabilities of specific genes being present in a wider, related population than the animals with DNA test results available. GeneProb allows registered breeders to focus on animals that need testing, instead of blanket-testing all animals, which can be an unnecessarily expensive exercise.

GeneProb uses known DNA test results for a nominated gene and combines this with pedigree information stored on Breed Society databases to calculate the probability of alleles (different forms of the gene) being present in untested animals. GeneProb is commonly used to:

  • Track recessive genetic conditions, such as Osteopetrosis (OS), Contractural Arachnodactyly (CA), Protoporphyria, Snorter Dwarfism and Neuropathic Hydrocephalus (NH).
  • Report the probability of the animal being a carrier of the nominated gene mutation.

GeneProb allows individual herds to better identify animals within their herd that need testing, instead of blindly testing all animals, and manage the spread of undesirable or desirable genes within their herd.

It also enables each Breed Society to monitor the prevalence of genetic conditions within their breed and maximise the usefulness of the DNA test results stored on Breed Society databases, whilst minimising the number of extra animals that need testing.

Display of Results

GeneProb results can be provided to both Breed Societies and individual seedstock herds in a number of paper and electronic forms. Many Breed Societies currently using GeneProb software display results for each animal on their online database facility while providing members with specific csv files that contain the results for all animals owned or bred within their herd.

_ _F Indicates that the sample submitted for this animal has been tested and found to be free of the causative mutation responsible for the indicated genetic condition. This animal is homozygous free, meaning that it has two copies of the normal variant (or allele) of the gene. Eg. AMF

_ _C Indicates that the sample submitted for this animal has been tested and found to be a carrier of the causative mutation responsible for the indicated genetic condition. This animal is heterozygous for the mutation, meaning that it has one mutant allele and one normal allele. This animal could pass the mutation to approximately half of its progeny. Eg. AMC

_ _ _% Indicates that, based on pedigree information supplied by the breeder of the animal, the animal has a chance to be a carrier of the mutation responsible for the indicated genetic condition but has not been tested. The higher the indicated percentage, the larger the chance the animal may be a carrier. Breeders are recommended to test this animal for the genetic condition prior to using this animal in a breeding program. Eg. AM45%

_ _FU Indicates that, based on pedigree information supplied by the breeder of the animal, the animal is expected to be free of the mutation responsible for the indicated genetic condition but has not been tested. Eg. AMFU

_ _A Indicates that the sample submitted for this animal has been tested and found to be affected by the genetic condition. This animal is homozygous for the mutation responsible for the indicated genetic condition and has two copies of the mutant variant of the gene. Eg. AMA

Contacts

Your first point of contact regarding GeneProb is the GeneProb operator. They can be contacted via email or phone:
Email: breedplan@abri.une.edu.au
Phone: +61 2 6773 3555

For general GeneProb queries, you can also contact BREEDPLAN staff or the relevant SBTS or TBTS Technical Officer for your breed.

Attribution

The GeneProb software was developed by Prof Brian Kinghorn and Dr Richard Kerr at the University of New England in Armidale, Australia and is licensed for commercialisation to the Agricultural Business Research Institute.

For more information about algorithms, user notes and licensing click here.

For further reading, please see the relevant papers below.