Technical information - selection

On tap - 150 new DNA markers discovered by Beef CRC


New technologies have advanced the Beef CRC’s discovery of new gene markers from a trickle to a flood - and that introduces a whole new set of questions for researchers.

Now it is being asked whether BREEDPLAN can be the vehicle for the wealth of new information emerging from a rapidly accelerating gene discovery process.

For much of the CRC’s existence, just identifying a single gene marker with potential commercial relevance to the beef industry was a milestone, usually reached after a long and rigourous research process.

But technologies introduced in the past 18 months have ramped up the process of gene marker discovery, to the point that Beef CRC researchers have identified nearly 150 markers in the last 12 months alone.

By comparison, it took about five years for CSIRO and Beef CRC researchers back in the 90’s to produce TG5 and then CAST3, the first and second commercialised gene markers for marbling (commercialised in July 2000) and tenderness (commercialised in November 2002) respectively. But as the new markers roll in, the focus is shifting from gene discovery to what happens next.

The Beef CRC has a definite goal for its gene marker discovery program: to obtain enough markers for key traits to explain at least 50 per cent of the genetic variation between cattle.

For instance, the TG5 marbling gene was found to only explain about six per cent of the variation in marbling. Other genes, some since identified by the Beef CRC, also influence how an animal marbles. Finding enough genes to explain at least 50 per cent of the genetic variation means a DNA test using several genes that gives a far more accurate assessment of an animal’s ability than a single gene alone.

Traits being fleshed out by the gene discovery program include meat quality, fertility, Net Feed Intake (NFI) and tick resistance. The CRC databases will also be exploited to look at new commercially significant traits, such as fat distribution (intramuscular vs. carcass) and total carcass fatness.

Professor Mike Goddard, program manager for the Beef CRC’s Underpinning Sciences program, says that the CRC hopes to identify at least 10 markers for each of the six significant traits, and by 2012 to have about 100 commercially significant gene markers available or in the commercialisation pipeline.

But at this point, the Beef CRC enters new and interesting territory.

How to make all this information available to the beef producers who need it, given that Beef CRC is only one of several research organisations worldwide undertaking gene discovery for the beef industry? “The last thing we want is for cattle breeders having to send DNA samples to half a dozen different labs to get a picture of the potential of their animal,” Professor Goddard said.

“It all has to be bundled into a single tool, and we’ll be pressing hard for that tool to be BREEDPLAN.”

DNA data can be used on its own as a predictive tool, Professor Goddard says, but that leaves cattlemen caught between two rival systems, gene markers and BREEDPLAN Estimated Breeding Values (EBVs). “If you’re a breeder and you’ve got access to an EBV for marbling, and a DNA marker, what do you choose?” Professor Goddard says. “If we don’t develop this properly, we face the possibility that we’ll be confusing the cattle industry, not helping it.”

For successful uptake of the gene discovery work, choosing the right method of presentation will also be vital.

“I think DNA markers are best rolled into current EBVs, where those EBVs exist,” Professor Goddard says. “Again, for a gene like marbling, it’s not helpful to cattlemen to have a traditional EBV, and a markerderived EBV.”

He points out that traits that can only be assessed on the carcass pose challenges for stud breeders, as do traits like NFI - which is very expensive to test for - and female fertility.

“If there is already an EBV for days to calving, then it would be crazy to throw it away. But we can enhance it with genetic markers for fertility.”

But there is some work ahead before this puzzle needs to be solved.

First, there are the technical and political hurdles to be negotiated before DNA markers can be integrated into BREEDPLAN; not least, the DNA testing and analysis needed to ease the integration of molecular information into conventional breed evaluation.