Unraveling the Brahman genome has been a wish-list project for geneticists like Dr Stephen Moore for a very long time, with cost the limiting factor.
Now the availability of more affordable technology enables the story to be told in great detail.
From next month the two year project will work to create a reference genome sequence under a $1.3m budget funded by University of Queensland, Australian Brahman Breeders and the MLA’s donor company program.
The ambitious approach to a breed so important to Australia’s north will be completed at a fraction of the US$50m spent unraveling the Hereford genome, undertaken by an international consortium at Miles City, Montana eight years ago.
In fact, professor Stephen Moore’s team – the engine room behind the Brahman project - has already undertaken a ‘short read’ of 50 selected animals at a cost of just $2000 each. This information has been mapped against the existing Hereford genome and already the team can see gaps and errors that will hopefully be rectified when the ‘long read’ genome is mapped in full.
“It has become less and less expensive to do this work,” said Dr Moore. “We couldn’t have contemplated this even five years ago. The genotyping resources are that much better.”
Central to the genome project will be single molecule sequencing which can analyse 10,000 bases at a time, offering a much better chance of putting the entire ‘reference’ genome sequence together, said Dr Moore.
Once completed a breeder will be able to spend just $40 to genetically test an animal and reference that against data available from the genome sequence.
“But we have to get our standard correct in the first place,” he said.
Chicken breeders employ genotyping on chicks worth only a few cents but use that data to steer breeds in new directions, with predictable market results.
“By making this technology more effective breeders can use it to decide which are the best animals and how much they are worth,” said Dr Moore. “We are hoping to make the Brahman a better breed, pure or cross, and create a better animal for the producer.”
Refining genetic traits
As an example of ‘effective’ breeders might refine how their herd takes advantage of the PLAG1 gene, which is responsible for up to 8% of the variation seen for early puberty, and is a complex Taurian gene that shows up in the Brahman breed – a fact clearly confirmed in the short read study.
With the wide range of puberty ages that exist in the Brahman breed, between 12-24 months, there are significant management challenges. It is hoped that by identifying those triggers in the genome Brahman breeders can shrink that range by selecting animals using inexpensive genotyping and referencing that data against the giant genome map of the Brahman breed.
Simply selecting by good eye and judgement doesn’t always do the trick, as Brazilian breeders found out when they selected for puberty and created a variant that matured too young and that brought with it all sorts of management challenges.
Never the less some sort of reduction in the age of puberty is a key desire for the breed, says Dr Moore, because when compared to Taurian breeders in the south, Indicus producers in the north must wait an extra two years before their female breeders start making money.
“The more you can finesse the balance of breed survival versus breed productivity the better you can manage a grazing business,” said Dr Moore.
History of the genome project
Line bred Hereford were originally chosen because geneticists rightly assumed there would not be much variation, making the genome easier to piece together.
A female was used in preference to bulls because two X chromosomes are simpler to map than an X and Y, with the latter a particularly troublesome chromosome which, says Dr Moore, tends to be largely repetitive DNA and ‘is a real trial to put together’.
When it comes to Brahman researchers are keen to compare the Taurus sequence against Indicus which has been separated in evolution for 350,000 years.
They already know that compared to the likes of Angus, the Brahman is significantly more complex with four times the number of genomes to decipher. The breed has six times the amount of genome variation compared to Holstein.
But the Australian Brahman is unique in that it includes 7-10 per cent Taurus genetics simply because the breed was originally crossed over the likes of Devon and Shorthorn before breeding up to what is today’s great northern herd.
In fact Dr Moore points out that Brahman is not a pure indicus, with the original breed formed in the US in the early 1800s from four Indian Zebu types. At the time there was some infusion of Taurus, a trend that occurred again when large numbers of Brahman were brought to Australia by a syndicate of graziers in the 1930s.
That's why there is so much variation in the breed,” he said.
To capture diversity of genetics researchers dragged out the oldest frozen semen they could find: a straw from 1953.
“I doubt the semen would have been viable for insemination but for our purposes it was perfect,” said Dr Moore. The youngest animal tested in the program was born in 2005.
“There is not a lot of evidence for strong selection in Australian Brahman cattle,” said Dr Moore. “Although fertility has created selection pressure. Graziers tend to select on size and we find a bigger frame has a negative impact on fertility.”
To complicate matters for geneticists, many genes affect the height or size of an animal. And as there is an increasing amount of data to crunch, researchers are finding computers are having trouble keeping up with the processing power required to make sense of such enormous quantities of detail.
Dr Moore said 99 per cent of mutations are not found in genes, so researches focus on the one per cent that do.
“We want to know how that signal is affected by cross breeding, which is a great tool but a blunt instrument. We want to refine that process and use this genome information to make better decisions. We know that crossing certain breeds results in an increase in performance but the question is why and when we know we will be able to perform better crosses and optimise those results.”
To source data on the Australian Brahman herd can be difficult when cattle are spread across the Top End of Australia. A nucleus herd belonging to the Brahman Society is providing a starting point, and further data is being sourced from South African breeders which will be extrapolated up to full DNA sequence.
“While this is a two year project we are hoping to have the reference sequence quicker than that,” said Dr Moore. “But the knock-on applications will have to wait. Having said that there are a lot of technologies in place for applications. Technologies for genomic breeding values are improving all the time. The statistical approach to genetics is improving, but there are concerns that we are measuring more variables than there are animals in the study, which can lead to false positives.
“These are happy times in the beef industry but it is best to look ahead rather than be complacent,” said Dr Moore.