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New tool could replace need for progeny testing"It will have an almost immediate impact on enhanced genetic improvement without any real negative repercussions," said Dr. Curtis Van Tassell. By Doug Rich Progeny testing is time consuming, expensive and it might soon be as antiquated as black and white television. Research being done at the University of Missouri, the Agricultural Research Service (ARS), and the University of Alberta in Canada has the potential to enhance genetic selection and do away with the need and expense of progeny testing. Jerry Taylor, research geneticist at the University of Missouri, said the research involves taking a really high density look at what is going on in the genome. He is looking at markers that are spaced over only about 50,000 DNA bases instead of similar studies that have been done on markers spaced over 20 million DNA bases. "We know from gene mapping experiments that have been done in different populations, Holsteins in particular, that there are genes of large effect that influence nearly all of the traits that we are interested in," said Taylor. In Angus for instance at least 18 genes influence marbling score. "There are a large number of genes, most of them independent, that are responsible for creating variation in these production traits," Taylor said. "We know this from mapping studies we have done." There are currently DNA tests for homozygous black and polled animals, but these are single gene traits. The traits for which we compute Expected Progeny Difference (EPD) scores are influenced by as many as 30 different genes. While researchers know the approximate locations of these genes within the genome they do not know the identities of these genes, or just what variation in those genes causes the genetic effects on EPDs. "What we do know is that there are a lot of genes, 300 to 400 genes in the genome, that create the variation in all of the EPDs that we compute for all of the production traits in beef and dairy cattle," Taylor said. The question is can researchers figure out a way to select on all of those genes simultaneously without having to identify the specific identities of the genes? The approach that researchers have taken to this point is to try and identify the genes and the variable points within the genes that cause effects on production traits. However, this has proven to be a really difficult process and relatively few of these causal genes have been discovered. Taylor said a paper published by a Dutch researcher a few years ago suggested a different approach that involves estimating an animal's EPD using DNA markers. This approach requires scoring a very large number of DNA markers in a huge population of animals that is representative of a breed and using the markers to estimate EPDs. Taylor and his colleagues at the ARS and the University of Alberta are building a tool that will allow the genotyping of 50,000 single nucleotide polymorphism (SNP) markers in a single test. "We are going to use this high resolution tool to come in and find the markers that are really predictive of all the genes that would influence a trait within the breed of interest," Taylor said. For example take a group of 1,800 registered Angus bulls and all the data that has been collected on them over a 50-year period. If we genotype all of these bulls for 50,000 SNPs evenly spread out across the genome, researchers should be able to find out which of these markers are predictive of marbling genetic merit. To validate that this approach works they need to get another group of Angus bulls that have marbling EPDs, genotype them and check to see if their EPDs computed from progeny records and from DNA markers agree with each other. "If we can do a precise job of estimating EPDs using only DNA marker information, we will have a new tool that we can use for selection that is based on our ability to genotype individuals for a huge number of markers simultaneously," Taylor said. "This will allow many more bulls to have carcass trait EPDs with moderate to high accuracy." Dr. Curtis Van Tassell, research geneticist at the Agriculture Research Service, said one of the practical applications of this new tool will be accelerated genetic progress through reduced generational intervals. In genetics there always has been a natural antagonism between generational interval and the accuracy of selection decisions. "This technology should allow us to increase the intensity and accuracy of selection without increasing the generation intervals," Van Tassell said. "It will have an almost immediate impact on enhanced genetic improvement without any real negative repercussions. "If this approach allows for accurate estimates of genetic merits using only DNA markers, it means there will be no further need for progeny testing. Van Tassell said that currently in the dairy industry they are spending $25,000 to $50,000 per animal to do progeny testing. "What you are looking at is anywhere from a quarter million to half a million dollars per bull that eventually goes into an active lineup," Van Tassell said. Basically producers will be able to take a DNA sample at birth, apply the new genome selection tool and estimate EPDs for the desired traits. It is possible that this new genetic selection tool will be even more accurate for low heritability traits. Things like daughter fertility, somatic cell score and other traits have been difficult for the industry to measure. "The gene markers could give us a better handle on those as well as carcass traits, milk production, dairy form, and reproductive longevity." Moore said they also are very interested in looking at gene markers for feed efficiency in cattle. "What will happen with these gene markers is that they will be incorporated into the system that already exists and improve the accuracy of those predictions," Moore said. "If we can examine all of the genes together rather than one at a time, then we can get a better handle on which areas of the chromosome affect some of the production and quality traits that we are interested in." Even though this new selection tool has great potential for beef and dairy producers there is a small downside risk, that risk is accelerated inbreeding. "We will need to manage inbreeding at a much higher level," Van Tassell said. "One of the risks is that everyone picks the same family and we accelerate inbreeding and end up with a catastrophic result. That is the potential negative for this new technology." Unlike other research projects where the benefits are years away, this research could be commercialized and available to the beef and dairy industries within six months. Taylor, Moore and Van Tassell all agree that this new selection tool should be ready within six months to a year. The three groups plan to genotype over 11,000 DNA samples at the three study sites. The majority of these samples will be on Angus and Holstein cattle. Taylor said it will take about two months to genotype 7,000 of these samples at the University of Missouri and another six months to do the statistical analysis of those samples. "We could see the dairy industry jump all over this," Taylor said. Those 7,000 DNA samples analyzed at the University of Missouri will be collected from 4,000 Angus, 1,000 Holstein, 1,000 Limousin cattle, small groups from lots of different breeds, ancient DNA samples from bison and Auroch. Auroch cattle are the ancestors of all of the modern Bostaurus livestock breeds. The last Auroch cow died on a Polish game farm in 1627 but some DNA samples from this species have been retrieved from ancient bone samples found in archeological digs. "We want to see how much of those genes have survived or more importantly what got lost in the domestication of the breeds," Taylor said. Think of this new genetic selection tool as high definition television. It is the same picture just much, much clearer. Doug Rich can be reached by phone 785-749-5304 or by email at richhpj@aol.com. Date: 12/21/06
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