Managing Genetic Conditions

Managing Wagyu Recessive Genetic Conditions

Recessive genetic conditions are an inherent part of all species, including Wagyu.  Some conditions have been proven to be detrimental to economic production and so need to be managed carefully through DNA testing and the use of tools such as GeneProb to estimate carrier status.

The GeneProb analysis interrogates the pedigree of each animal and calculates the probability that the animal is a carrier for each genetic condition from the known DNA information of their relatives. For example, if an animal’s dam had been tested free of the genetic condition but the sire was a tested carrier, the animal would be reported as having a 50% chance of being a carrier.

The gene probability analysis includes all known DNA information for animals recorded on the Australian Wagyu Association (AWA) database.  Genetic test results are based on samples provided by breeders.

In July 2012 it was discovered that the trial Wagyu GeneProb analysis was not effectively “solving” for 3 out of the 4 recognised recessive genetic conditions. This was identified when the GeneProb software was upgraded to a new version with enhanced diagnostic capabilities.  The AWA, in conjunction with technical support from the ABRI, have recently resolved this issue with the GeneProb analysis now solving for all 4 recognised recessive genetic conditions.  This involved undertaking several test runs on subsets of animals recorded on the AWA database. Once one run solved another run was undertaken including a broader group of animals. The most recent Wagyu GeneProb analysis includes 77,540 animals out of a possible 78,389 animals (i.e. only excluding 849 animals).

The main reasons for a GeneProb analysis not effectively “solving” are (1) pedigree inconsistencies or (2) inconsistencies in the recessive genetic condition DNA test results recorded on the AWA database. As 98.9% of the possible animals are now included in the GeneProb analysis the AWA have released results based on this group of animals. At this stage no further work will be undertaken to try and identify the individual inconsistencies within the 849 excluded animals.

 

AWA Recognised Recessive Genetic Conditions

There are currently four recessive genetic conditions that are recognised by the AWA and for which GeneProb results are available:

Spherocystosis (B3) – This is a disorder of the surface membrane of the erythrocyte (red blood cells). The protein from the B3 gene makes up the basic structure of the erythrocyte. Cattle that are homozygous (have two copies of the recessive allele) have pernicious anaemia (bleeding caused by the abnormal red blood cells). Death normally occurs within the first 7 days after birth. Some cases live to adulthood but there is a severe retardation in growth.

Chediak Higashi Syndrome (CHS) – CHS is a macrophage disorder (a white blood cell that has an important role in the immune response to disease). If cattle have a malfunctioning immune system, this makes them unable to resist bacterial challenge. Blood is slow to coagulate so often the first indicator is unusual umbilical cord haemorrhage at parturition (calving). Cattle with this syndrome often have an unusually pale coat colour.

Claudin 16 Deficiency  (CL16) – CL16 (also known as RTD or Renal tubular dysplasia) is a gene disorder on chromosome 1 and causes kidney failure (chronic interstitial nephritis often with zonal fibrosis or excess of fibrous connective tissue). This disorder results in terminal kidney failure and the onset can occur any time from late adolescence. Cattle are unlikely to live more than 6 years.

Factor XI deficiency (F11)F11 is a plasma protein that participates in the formation of blood clots. Factor XI deficiency is an autosomal disorder that is associated with mild bleeding in Wagyu. Affected animals show prolonged bleeding time and abnormal plasma coagulation after trauma or surgical procedures such as castration or dehorning. It is also possible that Carrier x Carrier matings have increased difficulty producing viable fertilized embryos or  full‐term pregnancies and may be repeat (return to cycle) breeders. Note – this is generally a non-lethal recessive condition with affected animals being able to live and breed as normal.

Note – There are other recessive genetic conditions known to exist in Wagyu cattle (e.g. F13) however they have not been identified in the Australia Wagyu population and therefore are not included in the GeneProb analysis at this point in time.

 

Putting Undesirable Genetic Recessive Conditions in Perspective

All breeds of cattle, in fact all mammals including humans, have undesirable genetic conditions. Fortunately, advances in molecular genetics have facilitated the development of DNA tests for their management. Breed Societies are at the forefront of development of strategies to manage undesirable genetic conditions and seedstock members are leading the industry with their uptake of this technology.

 

How are the conditions inherited?

Research from Japan indicates that B3, CHS, CL16 and F11 are simply inherited recessive conditions. This means that a single pair of genes controls each condition. For this mode of inheritance two copies of the undesirable gene need to be present before the condition is seen; in which case you may get a calf with the symptoms of B3, CHS, CL16 or F11.

Animals with only one copy of the undesirable gene (and one copy of the normal form of the gene), that appear normal (i.e. no symptoms), are known as “carriers”.

 

What happens when carriers are mated to other animals?

A carrier will, on average, pass the undesirable gene form to a random half (50 %) of their progeny.

When a carrier bull and carrier cow are mated:

  • There is a 25% chance that the progeny produced will have two normal genes and so will never pass on the undesirable gene.
  • There is a 50% chance that the mating will produce a carrier.
  • There is a 25% chance that the progeny will inherit two copies of the undesirable gene and hence be affected by the genetic condition.

 

When a carrier animal is mated to an animal tested free of the genetic condition:

  • All progeny will appear normal and will be unaffected by the condition.
  • There is a 50% chance that the mating will produce a carrier.
  • There is a 50% chance that the progeny produced will have two normal genes and so will never pass on the undesirable gene.

 

Note that an animal that is tested free by DNA test of the genetic condition will not pass the genetic condition to its descendants, even if it has carriers in its own ancestry. Therefore, DNA-tested free animals can be used in your breeding program with confidence that they are not transmitting the unfavourable gene to subsequent generations.

How should genetic conditions be managed?

An informative presentation on the management of genetic conditions titled “Managing Genetic Conditions with DNA” was delivered as part of the “Know Your Genes” webinar course conducted by Southern Beef Technology Services (SBTS). This presentation can be viewed from the following SBTS website:  http://sbts.une.edu.au/Webinars/webinars.html

Geneprob Results and Code Explanation

(The first two, three or four characters vary with the genetic condition – ie. B3, CHS, CL16 or F11)

_ _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.

_ _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.

_ _ __%

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

_ _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. However, this animal has not been tested for the causative mutation and the AWA gives no guarantee as to the animal’s “free” status.

_ _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 genetic condition and has two copies of the mutant variant of the gene.

 

It is important to note that the GeneProb results are only current at the date of publishing and are limited by the DNA test result and pedigree information available. The results may change as further DNA testing is performed, particularly when the level of testing that has been conducted is relatively low.

How often are the GeneProb results updated?

A GeneProb analysis will be run on a monthly basis. This will be in line with the monthly Wagyu BREEDPLAN analysis which s undertaken around the 18th of each month. Updated GeneProb results will therefore be available each month.

Where can I access GeneProb results?

GeneProb results are available in 2 areas:

  1. Restricted Member Login on the AWA Website – Files (.csv) listing the probabilities for each animal being a carrier within each AWA member herd are now available for download from the restricted login area of the AWA website. These files (a separate file for each recessive condition) enable you to investigate the likely incidence of the genetic conditions within your herd and conduct any DNA testing that you may wish to do. Members who don’t already have a username and password for the Member Login Area, or who cannot access the information in this manner, should contact staff at the AWA office for assistance.
  2. Data Search Facility on the AWA Website – The database search facility on the AWA website (colloquially known as internet solutions) will now display the GeneProb details for all animals’ with results available. When an animal enquiry is undertaken the GeneProb results for all animals listed will be displayed. The results will also be displayed on each animals detail screen. For easy interpretation, the results of animals identified as being free by DNA test will be highlighted by green text. Those that are identified as carriers by DNA will be highlighted in red text. Those with a GeneProb probability % or free but untested will be displayed in black text. Additionally, a function in the animal and EBV search facility has been added which allows the recessive condition status to be taken into account as a selection criteria (e.g. only search for animals that are B3F & B3FU).

Further information on GeneProb can be accessed from the AWA (E: office@wagyu.org.au P: 02 6773 3342) or Christian Duff, Wagyu SBTS Technical Officer (E: christian@sbts.une.edu.au P: 02 6773 2472)

Disclaimer: Information contained on the Australian Wagyu Association (AWA) web database, including but not limited to pedigree, DNA information, GeneProb values, Estimated Breeding Values (EBVs) and Selection Index values, is based on data supplied by members and/or third parties. Whilst every effort is made to ensure the accuracy of this information, the AWA and the Agricultural Business Research Institute (ABRI), their officers and employees, make no representations or warranties as to the accuracy of completeness of the information.   AWA disclaims all liability for all claims, expenses, losses, damages and costs any person may incur as a result of the information contained on the AWA web database, for any reason, being inaccurate, or incomplete in any way or incapable or achieving any purpose.