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DNA of 58,000 cattle examined in massive global study

Teagasc took part in collaborative project looking into genetic trait of height in cattle

The analyses undertaken by the Teagasc geneticists were based on more than 5,000 dairy animals and more than 20,000 beef animals
The analyses undertaken by the Teagasc geneticists were based on more than 5,000 dairy animals and more than 20,000 beef animals

A massive global study involving Teagasc has examined the DNA of 58,000 cattle from around the world in order to identify the genes that influence the complex genetic trait of height in cattle. The findings open the door for researchers to pinpoint the genes involved in other high-value traits that are important for Irish beef and milk production.

The study was a collaboration between 31 academic institutes and industry partners from 13 countries. Each country performed its own analyses with the results combined in a meta-analysis based on 25.4 million DNA fragments from 58,265 cattle representing eight different cattle breeds.

Stature was chosen as it is under strong genetic control, is measured relatively consistently globally in cattle, and is also a topic of active research in human genomics. The analyses undertaken by the Teagasc geneticists were based on more than 5,000 dairy animals and more than 20,000 beef animals.

A paper on the study entitled Meta-analysis of genome-wide association studies for the stature of cattle reveals numerous common genes that regulate size in mammals, which was co-authored by Teagasc quantitative geneticists, Dr Deirdre Purfield and Dr Donagh Berry, has just been published by Nature Genetics.

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Known as the 1000 Bull Genomes Project, Dr Purlfield explains that it was modelled on a previous study known as the 1000 Genomes Project, which ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. It was the first project to sequence the genomes of a large number of people, to provide a comprehensive resource on human genetic variation.

“The power of international collaboration for elucidating the genomic architecture of traits is now well-recognised,” says Dr Purfield. “We are seeing strong growth in open access data and software, as well as greater multi-institution consortia in pursuit of advancing science, in particular advancing genetic gain in domesticated species and using these as model organisms for human genomics research. The strength of such initiatives in unravelling the genomic construction of traits is particularly strong when data from diverse breeds are used.”

Similiar to humans

Interestingly, the results from the combined analyses revealed that the genetic architecture of height in cattle is quite complex and is influenced by a very large number of DNA variants and is more similar to that in humans than it is to dogs.

The study did not involve full genetic sequencing for every animal in the study. Rather it looked at different regions of the DNA. “DNA is inherited in chunks,” Purfield explains. “We can look at a number of these chunks and through a process known as imputation fill in the blanks for the rest of the DNA with 97 per cent accuracy.”

The study found that 163 different DNA regions or chunks are significantly involved in variations in the stature of cattle. This is less than, but of a similar level of magnitude to the level of variability in human height explained by significant DNA variants. On the other hand, the results are substantially different to that reported in dogs, for example, where just six DNA variants were sufficient to explain between 25 per cent and 72 per cent of height variations within different breeds.

Size and fatness

These results support the hypothesis that there are numerous common genes affecting size and other traits such as fatness in mammals. Teagasc geneticists are already part of similar large global initiatives for other complex performance traits with the aim of developing value-added tailored management strategies as well as possibly improve the accuracy of predicting the future performance of an animal using DNA technology.

There are also very practical implications for farmers. As things stand now, a hair sample can be taken from a newborn calf and within six to eight weeks Teagasc can come back with a pretty accurate prediction as to how that animal will perform in future, including what height it will grow to, how fertile it might be, and its likely milk production performance.

“This will enable farmers to select the best of the best animals for their herds,” says Purfield. “For example, the trend in dairy farming now is towards smaller, more efficient cows. This study will help select for those traits.”

The six to eight week waiting period has nothing to do with technology and everything to do with demand. As Purfield explains, the great majority of calves in Ireland are born during the spring months and this places huge demand on testing services at that time of the year.

For the future, the collaborative big data approach used by the 1,000 Bull Genome Consortium could also be applied to identify genes associated with high-value complex traits such as feed efficiency and methane emissions with very important implications for both profitability and environmental sustainability.

Barry McCall

Barry McCall is a contributor to The Irish Times