After more than a year of research aimed at identification of the mutation causing Contractural Arachnodactyly (CA; formerly Fawn Calf Syndrome), we are pleased to have finally completed our work. In review, CA is a genetic abnormality that is inherited as a simple recessive. A detailed description of the phenotype associated with CA can be found at http://www.dpi.nsw.gov.au/agriculture/livestock/health/specific/cattle/ca-angus. The genetic inheritance has been shown by several methods including experimental matings conducted by Australian researchers in 2004 as well as subsequent matings in 2008. In early 2009, a number of US breeders provided samples of affected calves that from pedigree information also demonstrated recessive inheritance and implicated the same common ancestor as in Australia. This was further established by using DNA from affected calves to map the gene responsible to a unique chromosomal position where all affected calves were homozygous for the same DNA segment.

In an effort to find the specific mutation within this chromosome segment that causes CA, numerous genes were selected for analysis based on their biological function and relationship to the pathology that had been described. In the end, DNA sequences were analyzed for more than 40 genes using DNA from known normal, known carrier and affected calves. In late summer of 2009, it was discovered that one of these genes had a large deleted DNA segment in CA-Affected calves. From that time, we have spent tremendous effort and resources to fully characterize this deletion so that an accurate DNA test could be developed. The most difficult aspect of this work was obtaining the complete and correct DNA sequence of this gene as well as sequences adjacent to the gene. Much of this sequence had to be generated de novo as both cattle genome assemblies are incomplete for this region of the genome. Furthermore, the DNA sequence is highly repetitive in content and contained a large, nearly identical duplicated segment of the gene causing CA. On June 8, 2010 we finally completed the correct assembly of the DNA sequence.

Using this DNA sequence we initiated the development of several DNA tests that were based on the specific mutation, a deletion of ~54,450 base pairs of the gene. Due to the probable mechanism behind the deletion and the high similarity of the duplicated DNA sequences, we first attempted an assay that was able to quantify the number of copies of a specific DNA sequence that an individual possesses, called a copy number variation assay. This assay was based on the fact that CA-Free (CAF) individuals would have two copies of the DNA sequence, CA-Carrier (CAC) animals would only have one copy, and affected calves would not have the DNA sequence. Initially this assay worked quite well, but as more samples were processed it was clear that many DNA samples were producing ambiguous results. Thus, although the results were 100% accurate for all unambiguous genotypes, up to 15% of the animals could not be readily genotyped.

A second more conventional assay was also developed that after several hundred animals also produced false positive test results for specific pedigrees. Finally, a third assay was developed that accomplishes our goal of 100% accurately determining the genotype of individuals for CA. This assay has been used on a total of 3,336 animals as of July 23, 2010. As with previous genetic defects we have attempted to assess the allele frequency of this mutation in the Angus breed. The best population to accomplish this is a nearly random sampling of the breed; in this case a large number of A.I. sires provided to us from members of the National Association of Animal Breeders. Although, this group of animals is not completely random it is sufficient for accurately estimating the allele frequency while at the same time providing information on many animals that have significant influence on the total population. To date, we have screened 1,256 A.I. sires and identified 39 bulls that are CA-carriers.  This corresponds to a heterozygote frequency of ~3.1% and an allele frequency of ~1.5%.

During the past year there has been some debate over how CA should be classified as a genetic defect. As described previously (see URL above), many CA-Affected calves do survive and can eventually reach reproductive age. Thus, there has been some advocacy to treat CA differently than previous abnormalities like Arthrogryposis Multiplex (AM) and Neuropathic Hydrocephalus (NH). To address this question as well as firmly establish the impact of this specific mutation, we screened an additional 2,080 animals that were specifically requested for their high pedigree risk of CA (i.e., highly biased toward an increased frequency of the mutation). Of these, 1,788 were CA-Free and 292 were CA-Carriers (~14%), none were homozygous for the mutation. Under population equilibrium, we would have expected to identify up to ten homozygous individuals if this mutation had no effect on the survivability of these individuals. Statistically, this is significantly different than expected (p=.0026) suggesting that CA behaves as a lethal genetic defect at the population level.

In regard to accuracy of the test, we believe it to be accurate from a scientific perspective. This means that when performed properly, the detection of this specific mutation will correctly classify an individual's status 100% of the time. However, this being true, we will still perform an additional blind validation test when the samples are collected and provided to us. This validation is being conducted with the assistance of Dr. Laurence Denholm and will be conducted with samples of known genotypes from Australia and New Zealand. When this is completed we will provide another update, but will reiterate that the results that accompany this description are 100% accurate.

Finally, as we complete our work, we will begin to go through the process of making the CA test commercially available. We anticipate this will be completed within the next month. Additionally, we expect that this test can be offered at a similar cost to those of AM and NH. 

Contractural Arachnodactyly (Fawn Calf Syndrome) in Beef Cattle
From the above description by Jonathan Beever, it is evident Contractural Arachnodactyly in Angus cattle is the result of a gene deletion. Genex will immediately stop marketing semen from carrier bulls designated as CAC effective July 26, 2010. Since Jonathan Beever is very certain of the nature of the mutation and we do have an accurate test to identify the carriers, we are equally certain the bulls listed as CAF do not carry the mutation and can be used with confidence. Genex has tested our entire lineup and many previously active bulls. We have results on any bulls that would impact breeding programs of today.

If you have purchased semen on any of the CA carrier bulls within the past 24 months, Genex will issue a credit on your account for these units. Contact your local representative to initiate this process and for instructions on returning the semen. Genex will not replace semen that has been used already and those calves will be eligible for registry in most breed associations. Remember only half of the offspring from these bulls will be carriers and an affected calf will occur only one in four times when two carriers are mated. If any effort has been made to avoid inbreeding, we would not expect to have any affected calves on these sires.

The identification of the gene deletion has taken a considerable amount of time to complete. As Jonathan Beever's description illustrates, it was a very complex analysis. This genetic defect will be handled as a lethal by the American Angus Association although we have seen affected animals that survive quite well to maturity. The article by Dr Laurence Denholm referenced in Jonathan Beever's article illustrates calves will improve quite rapidly. However, there are lingering effects such as lack of muscle development that will make these animals less valuable than their normal counterparts.

If you have any questions concerning this recessive and its manifestations, don't hesitate to contact the Genex Beef Department. 

Alfred L. Kuck, Vice President, Beef Programs