Joining the DNA dots to improve dairy breeding

DNAScientists from Agriculture Victoria, in collaboration with the University of Melbourne, have developed a world-first customised single nucleotide polymorphism (SNP) chip designed with the latest known genes that affect dairy cattle traits.

The work involves the customisation of a small piece of plastic – an SNP chip – with 50,000 small dots that bind DNA to detect genetic variations on the bovine genome, with the potential to improve dairy breeding worldwide.

Agriculture Victoria Research Scientist and Research Fellow with the University of Melbourne Dr Ruidong Xiang said SNP chips help breeders select animals with genetics of interest by testing tens of thousands of genetic variants to find the genes for important traits in each animal for the purposes of breeding.

“The information obtained from an SNP chip can be used to make genetic predictions for a trait of interest, such as milk production, so breeders can quickly narrow down which animals they are interested in breeding.

“The new customised SNP chip will have better predictions for a trait of interest compared to existing chips currently used in the industry and ultimately improves breeding decisions,” Dr Xiang said.

The research team started with 16 million genomic variants from 44,000 Australian dairy cattle and moved along the bovine genome, picking the next best variant until they narrowed it down to 50,000 genetic variations for inclusion on the customised SNP chip.

Dr Xiang said by screening genes of interest to the Australian dairy industry, the team was able to customise the SNP chip to reflect the most up-to-date biological information.

“This method included using more genes associated with 37 dairy traits, which was a huge improvement on the standard chips, as most genetic variants used in the standard chip were not supported by biology,” Dr Xiang said.

Agriculture Victoria Research’s high throughput sequencing capabilities and the Biosciences Advanced Scientific Computing facility at AgriBio was used to analyse the vast amount of data. It was also used to develop the methodology and statistical methods utilised in the research, such as incorporating Bayesian modelling.

The research findings showed the customised biology-informed chip outperformed the standard chip in predicting the genetic value of multiple traits across datasets from 90,000 dairy cattle by up to 10 per cent.

Dr Xiang said by translating big genomic data, we’ve been able to develop an industry-usable product that will help farmers select and breed the best animals more accurately and efficiently.

“This research has the potential to benefit both the Australian dairy industry as well as other key global dairy regions such as New Zealand and the United States.”

The research aligns with the Grow, Modernise and Promote themes of the Victorian Agriculture Strategy. It is part of DairyBio, a research and innovation initiative of Dairy Australia, Gardiner Foundation and Agriculture Victoria Research, and further supported by the Australian Research Council, and in collaboration with Dairy New Zealand.

You can read more about the research findings in the open access scientific journal Nature Communications.

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