Validation of a haplotype test for polled in Australian cattle

Summary

As with previous MLA funded projects of this type, the major objective of this project was to decrease the need for dehorning in the Australian beef cattle herd. Currently, dehorning is routinely practiced, as horns are an important cause of bruising, hide damage and other injuries, particularly in yards, feedlots and during transport. Although it is advisable to dehorn at a young age, as a result of mustering practices and especially in northern Australia, dehorning is frequently carried out in older calves between 3 and 10 months of age. Dehorning in older calves is labour intensive and causes more pain to the animal. The wound takes longer to heal, is prone to secondary infection, with mortality rates in dehorned cattle estimated to be as high as 2% in extensively managed research herds [1], and potentially higher in commercial herds. 
The best long term alternative to dehorning is to have naturally polled cattle. The transition to a 100% polled breeding herd will be quicker if it is possible to distinguish between homozygous polled animals and heterozygous carriers of the allele responsible for horns; cattle of both these genotypes are usually hornless. In previous projects we developed a single marker gene test that was able to make this distinction in many animals, but not all animals. 
To improve the assignment rate, we subsequently developed a test that used additional markers in the vicinity to the gene affecting polled, we call this test the haplotype test. In a small test population the haplotype test had far higher assignment rates than the single marker test; in Limousin 169 out of 198 samples that could not be assigned with the single marker test were assigned with the haplotype test. However, these animals were from a selected sample and so these results could not be generalised to the wider population. 
The objective of this project was to validate the haplotype test in a much larger sample, across a wider range of breeds. This objective was completely satisfied. Haplotypes were estimated for almost 2,000 animals with poll/scur/horn records. Once haplotypes was observed in 3 or 4 animals we were usually able to determine whether the haplotype was associated with polled or horned. We observed that certain common haplotypes occurred across breeds, and that the associations between the haplotypes and polled were also consistent across breeds. This makes a haplotype test useful in crossbred animals and sometimes even in breeds where we currently have no data. 
In Brangus, Limousin and Shorthorn, where the original single marker test was able to assign genotype in fewer than 50% of animals, the haplotype test assigned genotypes in over 97%, 95% and 93% of animals respectively. Across all breeds the assignment rate was 85%. On the basis of the results from this project, a new, improved test for polled was launched in November 2013.