Australian researchers are leading the creation of international library of cattle genetics data.

Summary

• The ‘1000 Bull Genomes Project’ is an international collaboration to create a reference library of the complete genomes of key ancestor bulls.
• This library has an important role in improving the accuracy of the Australian Breeding Values (ABVs) of young dairy bulls.
• DairyBio’s world leading status attracts top research talent to Australia, providing a rich training ground for PhD students.

Imagine a library of 1000 dictionaries in languages from around the world. Combined, they’d contain millions of words and provide an understanding of the spelling, meaning and derivation of each word.

Now imagine that instead of dictionaries, the library contains the entire DNA sequences of the bulls that are the forefathers of today’s dairy herds. This is the library that geneticists around the world are creating. Called the ‘1000 Bull Genomes Project,’ their library contains details of genetic markers, the variations in the DNA that influence animal performance. The key ancestor bulls include Holstein, Jersey, Fleckvieh, Angus, Brown Swiss, Ayrshire, Brahman and Simmental breeds.

A collaboration of about 40 international partners has created the genome library, which has surpassed the original target and now contains whole genome DNA sequences from 3817 bulls. Of these, about half are dairy bulls.

Such an important international project is surely run by a team from the USA or another leading producer of dairy bulls? No; it is driven by Australian geneticists and the full genome data supplied by the other partners is processed and analysed by our researchers.

DairyBio is a joint initiative between Agriculture Victoria, Dairy Australia and the Gardiner Dairy Foundation. The DairyBio team works in purpose-built facilities at the AgriBio Centre for AgriBioscience near Melbourne, as well as at Agriculture Victoria’s research facilities in regional Victoria. The AgriBio research facility is home to Agriculture Victoria’s molecular scientists and quantitative geneticists, as well as industry organisations such as DataGene, Holstein Australia, Jersey Australia and NHIA. Being co-located creates a unique mix of great scientific minds, cutting edge technology and real-world perspective.

Agriculture Victoria Research Leader Computational Biology, Dr Hans Daetwyler, leads the 1000 Bull Genomes Project.

“We can compare the DNA of young bulls with the complete genomes of the key ancestor bulls to develop more accurate Australian Breeding Values – ABVs,” said Dr Daetwyler.

The project would not be possible without international collaboration to provide the human and physical resources required for such a huge project. In return all partners share the evaluated genomic data.

“The combination of our team’s vision, track record and breadth of experience, together with infrastructure provided by Agriculture Victoria and the support of the industry has established a level of trust in Australia’s genetic research capabilities,” said Dr Daetwyler.

“Having the project led by the DairyBio team allows us to build crucial collaborations with the leading global cattle genetics researchers to achieve better research outcomes for the Australian cattle industries.

“It also builds research capacity in Australia, attracting top research talent to Australia, including PhD students who will be our next generation of researchers.”

The ‘1000 Bull Genomes Project’ aims to identify as many genetic markers as possible by comparing and contrasting the complete genomes of bulls in the library. So far, more than 100 million markers have been identified.

As genetic markers are not influenced by environment and many occur in several breeds, this international genomic data is relevant to dairy and beef herds across the globe.

“Having the whole genome sequence, we have the actual DNA variants; that is the actual gene or section of DNA controlling a trait.”

Central to the project is a huge advanced scientific computer capable of processing the massive volumes of data required to evaluate the DNA sequence.

“The super computer can run one of my analyses in three days; that would take over three years on your best desktop computer,” said Dr Daetwyler.

Practical outcomes

Like many of his DairyBio colleagues, Dr Daetwyler is focused on achieving practical outcomes from the investment in genetic research. These outcomes are in the form of new and improved ABVs which are published regularly by DataGene.

“I come from a dairy farming family and for six years worked fulltime in my family’s Canadian dairy operation. I understand that our research needs to provide solutions that help farmers choose the best genetics to meet on-farm production, breeding and health objectives.”

The 1000 Bull Genomes Project should enable researchers to identify multiple genes linked to a performance trait. For example, fertility is thought to be influenced by thousands of separate genes.

Quantitative geneticists use statistical analyses to map incomplete genetic sequences against the whole genome of this reference bull herd. The gaps can then be filled by using a technique called imputation.

“It’s a bit like doing a crossword where you have clues and some letters in a word and from those letters the whole word can be recognised.”

The technology enables researchers to identify both ‘good and bad’ DNA variations; that is variations linked with desirable traits and traits the industry wants to avoid, for example, gene variations related to embryonic death (early miscarriage), and dwarfism.

Australian dairy farmers were the first in the world with the tools to breed for improved feed conversion efficiency and heat tolerance. With projects like this, Australia is well-placed to continue to be step ahead of the dairy genetics game.

Photo: Agriculture Victoria’s Dr Hans Daetwyler is leading a global research team to create a library of complete genomic sequences of key ancestor bulls.