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DNA Markers under the microscope

by Beef CRC BEEF BULLETIN AUTUMN 2009

BRAHMAN NEWS SEPTEMBER 2009 Issue #164

As part of its role in delivering DNA markers to the Australian beef industry, Beef CRC has agreed to independently test new panels of DNA markers as they are commercialised by companies such as Pfizer Animal Genetics, Igenity /Merial and Metamorphix Inc.

Although the testing for these third party organizations takes time, it doesn’t mean that the Beef CRC has dropped the ball when it comes to discovering markers of its own.

In fact, gene discovery work in the area of meat quality, feed efficiency and female fertility continues to evolve and some exciting developments are being made each day.

In laboratories in Brisbane, Melbourne and Adelaide, scientists from the Beef CRC are involved in discovering new DNA markers.

Hunched over their microscopes, they’re trawling through thousands of DNA samples to detect more genes associated with traits of economic importance.

Dr Bill Barendse, CSIRO said they are currently testing the effects of a couple of new genes they’ve discovered for meat tenderness.

“Meat tenderness is one of the most prized attributes among consumers,” said Dr Barendse.

“If people are confident the beef they eat is tender, they will keep demanding it.”

But while nutrition, biology and management strategies are only part of the answer, Beef CRC scientists are also looking at the potential to genetically enhance meat tenderness.

Previous work has shown that the Calpain and Calapastatin genes play a large role in the breakdown of protein bonds within the muscle fibres, helping to produce tender meat.

If higher amounts of calpastatin are present, they reduce the ability of the calpains to break these proteins down and meat is likely to be less tender.

Dr Barendse said the role of the Calpain and Calpastatin genes is fairly well known.

“The effect of these genes is moderate, accounting for between 8 and 16 per cent of the genetic variation between cattle,” Dr Barendse said.

“We never imagined we’d find other genes which could have as large an effect on meat tenderness as these two.”

But Dr Barendse and his colleagues recently sampled more than 50,000 DNA markers in one-thousand cattle to look for the genetics associated with carcass weight, eye muscle area, intramuscular fat, meat tenderness, rump fat thickness, and retail beef yield.

“The Calpain and Calpastatin genes were not included in this set of markers, as the cattle we were using were the same ones that those markers were orginally discovered in. Therefore finding them again would not be surprising.”

Dr Barendse said what they found is what looked like two more genes with similar effects to Calpain and Calpastatin.

“One of the genes is in a genetic location that has previously been tagged as containing a gene for tenderness, but so far no gene test has eventuated,” Dr Barendse said.

“The other gene is new but its function is known to have some involvement in the breakdown of muscle tissue.”

Dr Barendse said while the discovery is important, more testing needs to be carried out.

“These new genes need to be tested on many more animals across several different breeds. We are currently doing that, but getting access to the thousands of cattle we now need, doesn’t happen overnight.”

But it’s not only genes for meat tenderness that are being discovered. Beef CRC’s work in the area of Net Feed Intake (NFI) continues to gain momentum.

Net feed intake (NFI) is a measure of feed efficiency and is the difference between actual feed intake by an animal and the expected feed intake it needs to maintain weight and growth.

All of the major beef cattle breeds in Australia would welcome being able to reduce feed costs while maintaining, or increasing, production levels.

Beef CRC’s Chief Scientist, Professor Mike Goddard, DPI Victoria and University of Melbourne said an animal with a negative NFI eats less than expected and is considered to be a high efficiency animal. An animal with a positive NFI eats more than expected and is of low efficiency.

“Although the Beef CRC is looking for the genes which control NFI, no markers have proven reliabile enough to commercialise,” said Professor Goddard.

However, Professor Goddard said they are closing in on some genes for NFI.

He said they have conducted two genome wide association studies.

The first used 8,000 SNP markers genotyped on 384 cattle from the selection lines for high and low NFI bred at Trangie research station. The second study used the 50,000 SNP panel genotyped on 852 animals from 7 pure breeds measured for NFI in CRC I.

“The first GWAS found 406 SNPs significantly associated with NFI,” Professor Goddard said.

“The second study found 615 significant SNPs. Unfortunately as the two panels used different SNPs we couldn’t directly compare the results for individual SNPs.”

Instead Professor Goddard said they wanted to see whether the two studies found significant SNPs close to each other on the chromosomes.

“In 54 cases we found that both studies had found a significant SNP in the same 1 megabase of DNA (ie close region),” he said.

Professor Goddard said they selected some candidate genes from regions of the chromosome with significant SNPs and tested them in 4 other groups of cattle (different to the cattle used for both GWAS).

“We found 7 markers that are significant in these new cattle and are also in one of the 54 close regions found in both GWAS.

Therefore, these 7 regions have been significantly associated with NFI in 3 independent studies.”

Professor Goddard said now they know the regions of the genome that contain genes for NFI they should be able to find markers in them that work consistently and can be commercialised.

Back in Brisbane, other scientists have discovered a number of DNA markers closely associated with age of puberty and post-partum anoestrus in tropically adapted cattle.

The project led by Dr Rachel Hawken, CSIRO Livestock Industries aims to improve the reproductive performance of cattle to increase the profitability of the northern Australian beef industry.

Dr Hawken and her team aim to develop a DNA-based selection tool which producers can use to genetically test their herds to find those heifers which mature more rapidly and can conceive earlier.

“One of the biggest inefficiencies in the northern beef industry is the fact that many tropically adapted cows don’t have a calf every year.

It will be a big help to industry if we can find the genes which control that inefficiency,” she said.

The project could add millions of dollars to the value of the northern beef industry which typically records reproduction rates of 50-60 percent in lactating Bos indicus and crossbred herds.

“Management and the condition of livestock have an impact, but there is good evidence of genetic links to these traits,” Dr Hawken said.

“We’ve been working with colleagues at New Mexico State University and the USDA in the USA to help explain the genetics behind these key reproductive traits in beef cattle.

“To date we’ve found about 10 markers that have the same effect in both Brahmans and Tropical Composites,” Dr Hawken said.

“But we still have to validate them in an unrelated cattle population to gain a better understanding of their accuracy and their value to industry.”

Dr Hawken believes these markers could represent the first DNA tests to be commercialised for age at puberty in the world.

“Age at puberty is an important issue for northern producers,” Dr Hawken said.

Tropical cattle can reach puberty anywhere from 10 to more than 40 months of age.

“A DNA test for puberty would allow producers to select animals which better suit their management system. The test could be done on young calves or even as an embryo.”

But Dr Hawken said before any DNA test is released to industry they have to be certain that reducing the age of puberty will not compromise the cow or the calf’s survival or the future breeding ability of the animal.

“This project is about improving the lifetime reproductive performance of the animal, not just one year in isolation,” she said.

While the research on finding the DNA markers for reproduction in female cattle was at a very promising stage, the big gains in productivity would ultimately come from identifying those bulls which will pass the desirable genotypes on to their daughters, Dr Hawken said.