In his talk at the 2016 British Cattle Breeders Conference, Dr Donagh Berry explained why he would like to see all Irish cattle (a population exceeding two million) genotyped at birth.
While some audience members would have considered such a daunting task impossible, he reminded delegates that existing data recording systems, such as electronic recording of sheep, would once have been considered unfeasible. Therefore contemplating an all-encompassing genotyping mission should not be regarded as such.
Universal genotyping would provide a great deal of advantages to the Irish cattle industry, not least the ability to correct the estimated 17% of pedigrees that are incorrectly recorded.
In light of recent controversies surrounding meat contamination, it is unsurprising that the issue of traceability was the first touched upon by Dr Berry. If all cattle were genotyped then meat could be analysed and traced back to the cow that it came from, therefore giving a degree of transparency across the supply chain. As well as the obvious food safety considerations, this also provides a unique marketing opportunity. Retailers would be able to use this data to not only report on the provenance and rearing history of a product but to do so with the assurance that the information they provide is correct and trustworthy. This would increase the sales value of beef because the consumer would be able to trust in the origin of their food, with the additional marketing ploy of selling a particular breed or production system.
Genotyping of all cattle could provide crucial information about carriers of lethal gene mutations. In the dairy industry, these mutations have already been identified in Holstein cattle and information is available to breeders in order to avoid breeding calves carrying two copies of these genes, and therefore expressing the unwanted phenotype. Without genotyping it is impossible to know whether a phenotypically normal animal is a carrier of a recessive lethal mutation, whereas with universal genotyping all carriers would be identified. Similarly haplotypes, a stretch of DNA variants known as polymorphisms that tend to be inherited together and negatively influence fertility values, have been identified in Holsteins and widespread genotyping could identify similar genes for beef cattle. This could have a massive impact on reducing calving intervals and the early culling of fertility challenged cattle.
Inbreeding coefficients based on pedigree information show an assumed proportion of shared DNA ( 50% between parents and full siblings, 12.5% between half siblings and grandparents and their grandchildren), but genotyping can provide more accurate information on the degree of inbreeding that exists. The percentage of shared DNA may be smaller or larger than that expected from the pedigree. Breeders who genotype can therefore make more informed decisions about breeding or not breeding related animals. Inbreeding in stretches of DNA referred to by geneticists as “junk DNA, may have little impact on animal health and performance and therefore genotyped animals with shared stretches in these non-important regions of the DNA strand could be crossed with little potential of harm. This information is not currently available, but with universal genotyping and future research it may become a key tool for breeders.
High value meat markets are often influenced by the breed of the animal that a cut of meat came from. The breed recorded on an animal’s passport is not always accurate and cross bred cattle derived from multiple crosses can result in an unequal division of breed-specific DNA. Genotyping may be useful to accurately determine the breed of an animal in these situations. As this technology relies on the different influences of genes in separate breeds a large population of cattle would need to be genotyped; another call for universal screening of animals.
In spring 2016, data will be released from the 2014 Beef Genomic Scheme, a financially incentivised project in Ireland that targeted herds to genotype 15% of cows and all natural mating bulls. This should provide multi-breed genomic evaluations. In 2015 the scheme was extended to record an additional 200,000 cows and 150,000 heifers with no previous recorded data.
The scheme highlights the importance of collaboration across the cattle industry with a strong reliance on using major genes and individual SNPs already identified as performance indicators in dairy cows. Four lethal mutations and over eight thousand research SNPs will be included in the analysis.
Dr Berry concluded that the beef industry should take heart that genomic selection is already working well for the dairy sector and that evaluations look profitable for beef. Universal genotyping could work to clean up poorly recorded pedigrees, assign breeds, provide mating advice and ensure full traceability of meat products.