Article supplied courtesy of The Waikato Times
A Silicon Valley software company spun out of Hamilton developer NetValue is helping the Livestock Improvement Corporation find the links between genetic variations and production traits in top producing cattle.
The enhanced genetic sequencing project is intended to help improve productivity in the national herd.
Andrew Scott, who is managing the research and development project for LIC, said the Hamilton-based herd improvement co-operative had set up research facilities and already carried out a trial run using DNA analysis software from Real Time Genomics, based in San Francisco.
"We did an extensive comparison, " Scott said. "We sequenced a small number of animals. We did 25 cross breeds to test our capabilities."
Most cells contain a complete copy of an organism's genome, the complete genetic material encoded in the DNA of an organism.
In bovine and human cells this consists of about 3 billion base pairs, the basic building block of the genetic code.
DNA is extracted from the blood of cows or semen of bulls and is then fragmented into short lengths of 200-500 base pairs so the sequencing technology can read it.
Each of these three billion bases is a potential site for variation that may affect an animal's characteristics. Each base must be read and recorded on average 10 times to allow for any potential errors in the process.
Now LIC has completed the initial trial phase, where in- house expertise and infrastructure has been developed, Scott said he expected the next phase to begin in March with the sequencing of 250 animals. The process involves the generation, storage and analysis of 7500 billion data points. Assembling the raw data takes several weeks, and processing it takes another few weeks.
The research will cost $22.4 million and is being jointly funded by LIC, dairy giant Fonterra and the Government's Primary Growth Partnership fund through the Ministry of Agriculture and Fisheries. The research is being administered by DairyNZ, also in Hamilton.
Scott said he expected the sequencing of hundreds of animals a year to become routine.
"As understanding and technology advances the tools being developed will be used to answer ever more complicated questions such as how the environmental factors interact with the genome, which genes are turned on and off in various tissue types, or even what effect the environment the parent was subject to may affect the way their offspring's genes are expressed, " he said.
LIC chief executive Mark Dewdney said the Primary Growth Partnership funding would accelerate LIC's research programme significantly.
"In effect it means we'll be able to understand significantly more about the effect of variations in the genome sequence of animals for which we have good physical production datasets . . . What this means for farmers, is faster genetic progress in their herds from breeding more productive and profitable cows."
Real Times Genomics was founded by NetValue chief executive Graham Gaylard, backed by Silicon Valley venture capital firm Catamount Ventures, in 2009.
Gaylard, speaking from San Francisco, said LIC tested a beta, or prototype, version of the software to which Real Time Genomics added extra functionality, in the form of a pedigree module.
About 200 individuals and companies use the software.
"We are working with leading organisations in the US. The market (for such software) is going to expand out and the price of sequencing is coming down so a lot of people can afford to do it. A lot of smaller businesses can do it . . . it will be used for diagnostics."
Human genome sequencing now costs $4000 and was expected to come down to about $1000 by next year.
"Two years ago that cost was $100,000."