Systematic breeding

The program has two outputs: the genetic markers identified are used to advance the LIC breeding program, while farmers' own breeding efforts benefit from commercial DNA tests for genes to improve productivity or quality, like Optimum and Quantum. LIC operates a commercial DNA testing unit.

Adam says the gene tests provide a simple way for farmers to identify elite animals and undertake more systematic breeding.

But farmers typically need only a simple yes or no answer; few are interested in detailed explanations of how Gene X contributes to productivity or quality. "This has implications for patents, but gene discovery and IP is quite a difficult field," he says.

"Our approach is to regard the function of our genes as a trade secret - our farmers are primarily interested in increased performance rather than the detail of which individual gene contributes what to that performance.

"A gene test will cost them a certain amount, and we tell them what benefit they are likely to get from a test to tell them whether their animals have that gene." The cost-benefit equation becomes tricky when the gene test relates to improving traits of low heritability, where the proportion of the phenotype determined by the genetics is quite low.

There tends to be an expectation that any commercial gene test will deliver significant benefits, when in fact the elite alleles being tested for may already be present at high frequency in the national herd. For example, many bulls in farmer's herds are already homozygous for the Optimum and Quantum genes. Farmers are unlikely to pay a premium for a test for a gene that already occurs at high frequency in their own herds.

Adam says it is unsurprising that some promising loci identified in a first pass subsequently disappear. The statistical correlation between a particular trait and a marker-defined locus turns out to be non-robust, because of complex interactions between the allele and anonymous genes at other loci - either in cis phase (on the same chromosome) or trans phase (between chromosomes).

"And some traits are more complex at a physiological level: fertility is a good example. There are many nutritional aspects that influence fertility. We know that if we don't feed our cows adequately in spring, they'll have more difficulty to get in calf. Fertility is of increasing importance on the farm - it's currently one of our prime targets."

When heritability is low, it becomes harder to find the genes, so large-scale experiments have to be conducted to provide the requisite statistical power to identify prospective loci, he says.

"There is a view in the biotechnology industry that if a breeding company has bred a bull using genetic markers, it will automatically be able to charge more for its semen.

"New Zealand farmers have made some progress in improving fertility through conventional breeding, and our fertility is a lot better than in many overseas herds, and farmers can now buy semen from bulls that will demonstrably improve fertility. In this instance, you might charge a premium.

"But we're unlikely to find an allele that occurs at a frequency of only one in a million in the 800 animals in our research herd. We can only look for very rare outliers in the national herd, using our database, and we've done that.

"We need to be realistic in our expectations, because we're really making improvements at the margins of what has been achieved through decades of conventional breeding.

"We're adding about one per cent improvement per year to what we call 'breeding worth' - a compound measure of extra genetic worth in relation to what could have been achieved through conventional breeding."