Holstein Cow Genomes Project - Department of Primary Industries, Victoria

10,000 Holstein Cow Genomes Project

Background

The 10,000 Holstein Cows Genomes Project was funded by the Dairy Futures Cooperative Research Centre (CRC), a large-scale partnership between dairy farmers, pasture and cattle breeding companies, government and researchers. The project included a $1.2 million grant from Regional Development Victoria.

Genomics is a new technology that can take advantage of DNA information to assist in the calculations of breeding values for animals. The use of genomic information can increase reliability of Australian Breeding Values (ABV’s) for young unproven Holstein bulls by 10-28 % (depending on trait) over parent average ABVs. The reliability of ABV’s can be increased by collecting more genomic data from animals with good herd records.

As part of Dairy Futures CRC’s “Breeding with Genomics “ program a team of Department of Primary Industries (DPI) researchers used genomics information from thousands of animals to provide new options for increasing the rate of genetic gain in the Australian dairy herd. It was one the largest undertakings of its kind in the world. A total of 91 farms were identified, mainly in Victoria, that were doing an excellent job of recording these traits, and farmers were asked if they would collaborate with DFCRC in the project.

Aims of The Project

The 10,000 Holstein Cow Genomes Project is an ambitious project which aims to improve the rate of genetic gain for profitability in the Australian dairy herd by 100 per cent by increasing the accuracy of genomic selection. Genetic gain is a major productivity driver for the dairy industry, and the outputs will have a significant impact through greater accuracy of selection (Impact $54 million) and will contribute to a reduction in generation interval of cattle (Impact $8 million).

To achieve this aim, the project has made use of next generation sequencing technology to sequence key ancestor bulls, in combination with a very large cohort of 10,000 cows with high quality phenotypes for fertility production and other key drivers of profitability. The “10,000 cow genomes” project will deliver an improved set of SNP-based markers for traits of economic importance to the Australian dairy industry.

The project will substantially improve how well the DNA markers predict the value of bull and cow genetics for 40 key dairy traits including;

• milk yield
• protein
• resistance to mastitis
• Australian Profit Ranking (APR) – the estimated genetic merit for profit calculated by combining traits

Genomics enhanced Australian Breeding Values - ABV(g)s – will enable more rapid genetic change over time leading to improved genetic merit and ultimately enhanced productivity and profitability in the dairy industry.

The collection of DNA information from 10,000 Holstein cows conducted by DPI within the Dairy Futures CRC has doubled the size of the national database of DNA information. This has led to a more reliable estimate of genetic merit for both bulls and cows. The 10,000 Cow Genome Project has resulted in a significant increase in reliability for genomic breeding values which has been reflected in the reliability of published Australian breeding values in 2012 in the Good Bulls Guide from the Australian Dairy Herd Improvement Scheme (ADHIS).

The genetic sampling involved collecting tail hairs and other samples from selected cows from 91 dairy farms, which had kept cow performance records over many years. Then 10,000 cows were profiled for 50,000 DNA markers. By combining the trait records and the DNA marker data, it meant that is now possible to make much better predictions of the breeding merit of young bulls or heifers and the impact that genetics have for milk production, fertility, and other traits that affect farm profitability.

What are the key benefits of the project ?

DNA markers are now used routinely in the dairy industry to select the best bulls and heifers to breed from to improve production and profitability.

The main benefits of the project are industry wide.

• Dairy bulls, which are marketed by Artificial Insemination companies (such as Genetics Australia), can now be selected for use in the industry with a high degree of reliability, and at a young age, using the DNA marker technology.
• Following the 10,000 cows research project, these DNA marker profiles are much more accurate, so farmers can have greater confidence using these bulls.
• The result will be a very considerable industry wide lift in genetic gain (up to 50%), increasing production and improving profitability of the dairy industry.
• The potential economic value of this new technology is estimated at $100m over the next 12 years.
• The research will be delivered to all Dairy Farmers by the Australian Dairy Herd Improvement Scheme,(ADHIS) through their “Good bulls guide”.

“Selective breeding is a fundamental driver of farm productivity that has allowed dairy farmers to measure and improve a broad range of traits. New genomic technologies, using DNA marker information, are set to double the rate of genetic improvement.”
Quote from Dr Ben Cocks, Deputy Chief Scientist DFCRC

Collaborative Research

Key collaborators in the 10,000 Holstein Cows Genomes Project project include:

• Dairy Futures CRC
• The Australian Dairy Herd Improvement Scheme (ADHIS)
• The Gardiner Foundation
• Department of Primary Industries (DPI)

Contacts

Dr Ben HayesResearch Leader, Computational BiologyVABC, BundooraDepartment of Primary Industries(03) 9032 7013
ben.hayes@dpi.vic.gov.au

@ Holstein Cow Genomes Project - Department of Primary Industries: