A whole-genome approach can unlock value for pork industry
By Jim Carlton
| Tuesday, February 01, 2005
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Scientists believe genomics technology can play a big part in improving the quality and consistency of pork-meat products for consumers. |
Editor’s note: This is the first in a two-part series of articles.
What is the value from learning more about the pig genome?
Researchers and geneticists who participated in an industry roundtable discussion titled Creating Value from Genomics in the Pork Industry, held in conjunction with the 2004 American Association of Animal Science meeting, agreed there are definite benefits from learning more about the pig genome.
Monsanto Choice Genetics sponsored the roundtable. Roundtable participants included geneticists and researchers Jack Dekkers, PhD, Iowa State University; Bill Muir, PhD, Purdue University; Sue DeNise, PhD, MMI Genomics; Floyd McKeith, PhD, University of Illinois; Rodger Johnson, PhD, University of Nebraska and Albert Paszek, PhD, Cargill Corporation.
“People got very excited when they saw the covers of Science and Nature about the human genome being sequenced,” says Max Rothschild, PhD, CF, Curtiss Distinguished Professor of Agriculture and co-director of the Center for Integrated Animal Genomics at Iowa State University. Rothschild’s comments were made while addressing the participants of the roundtable.
“We read about the value of unlocking the power of the human genome; some of the secrets include determining genetic reasons for disease or growth and development. It begs the question, is there a similar opportunity possible from learning about the pig genome and is there value from the knowledge?”
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Jack Dekkers, professor of animal breeding and genetics at Iowa State University, says that molecular genetics are now providing tools to enhance rates of genetic improvement in pigs. |
Rothschild says that one of the main expected outcomes of this technology is increased discovery. “It will certainly yield better products throughout the entire pork chain. We’ll see better genetic lines that will yield better products for producers, packers and consumers. But genomics are only going to modify the base product, which must be good to start with.”
According to Sue DeNise, PhD, vice president of genomic research for MetaMorphix, Inc., livestock breeding companies have been highly successful in the past using quantitative genetics. “We have a very good way of estimating the genetic potential of individuals by knowing an individual’s own phenotypic value and those of their relatives. The challenge is combining information obtained at the DNA level to understand the underlying genetic causes of the phenotypes. Therefore, there are a number of steps between DNA and the expression of the phenotypes, and that is where many challenges are going to lie for the future.
“As we get down to the gene level to understand the sequence that influences quantitative traits, we are going to require a map that is much denser than currently available, and those markers are single nucleotide polymorphisms,or SNPs (pronounced “snips”),” she adds.
“Single nucleotide polymorphism is a single base substitution at a location in the genome. They are highly abundant. We found them in roughly one per 200 base pairs. They are distributed throughout the genome, including genes, and, unlike microsatellites, are genetically very stable. With SNP markers, we can do approximately 180,000 genotypes a day,” says DeNise.
More markers
Rothschild says that when you look at all the markers currently available, there are only 20 to 50 being used by breeding companies. “But the exciting thing is that somewhere between 100,000 and 700,000 markers are being developed. We have to realize we are at the beginning of this technology. There are more new discoveries yet to deliver.”
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Purdue University geneticist Bill Muir describes genome-wide, marker-assisted, selection as a holistic approach because it will work for any trait regardless of heritability or type of trait. |
Currently, pork producers have to make random choices on which animals to move into their breeding program, according to Jack Dekkers, PhD, professor of animal breeding and genetics in the Department of Animal Science at Iowa State University. “Molecular genetics are now providing tools to enhance rates of genetic improvement by being able to select on quantitative trait loci (QTL) or on linked markers,” he says. “Sophisticated statistical methods have been developed to estimate the effects of QTL in complex pedigrees.
“However, if you have QTL information, you could select individuals that have the favorable QTL genotypes and move those into your testing program. Depending on the effect of the QTL, you can expect to get an increase in the genetic level of the pigs that go into your testing program.”
The process that DeNise and Dekkers describe is a whole-genome approach to genomics. DeNise simplifies the difference between the whole-genome approach to selection and current technologies:
“To give you an idea of the resolution between microsatellite markers and SNP markers, if we have a map of California from Sacramento to Reno and if we think about our DNA being a linear piece of real estate, then the interstate highway is similar to a strand of DNA,” she explains. “If we are interested in getting to the Sugar Bowl Ski Resort, it could be rather difficult if we only have the major exits to choose to exit the interstate. That might be like microsatellite markers.
“On the other hand, if we saturate that region with a number of different exits, which are like SNP markers, then we have a pretty good chance of getting to the point at which we want to be. In designing our research strategy, we knew that we had to be able to saturate the genome in order to have a chance of finding some of the important QTLs in a commercial population.”
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Genetic expert Sue DeNise equates current swine genetic technology to panning for gold, where after a lot of work you can begin to find a few nuggets. |
Like panning gold
This new SNP technology is allowing geneticists to put the whole piece of the puzzle together and figure out exactly what combination of markers provides the optimum phenotype. “If you equate this technology to panning for gold, it’s like panning for a little bit at a time,” DeNise offers. “After a lot of work, you will find a few small nuggets. That is what the current selection process produces with the number of markers that we currently have — a lot of work to find a few nuggets of value.
“But with the whole-genome approach, you find the genes and the traits that interact with each other, and you immediately discover traits that can be used in commercial populations. The whole-genome approach allows us to discover all of the gold at once.”
DeNise believes there are several valuable opportunities with this new whole-genome approach to selection.
“We think that breeders and pro-ducers will utilize this technology as a unique breeding tool where they can increase the accuracy of selection and be able to target traits that are difficult to measure with traditional selection,” DeNise says. “For producers and feeders, perhaps they will be able to sell individual animals into a marketing program (such as the Japanese market) that’s really designed for their genetics.
“They might also be able to sort and manage individual animals to optimize their genetic potential,” she adds. “Finally, for the packers and processors, they might be able to make purchasing decisions or guarantee palatability characteristics or meat quality characteristics. They might be able to forward market products, and they might be able to create new branded products. So, we think that there are a number of different opportunities, and it remains to be seen exactly how the industry and the research will combine to create these new products.”
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University of Illinois meat scientist Floyd McKeith believes that genomics will play a huge role in the future of branded pork products. |
Quality and consistency
“We just finished a quality audit and product consistency was one of the biggest economical issues brought up by the meat industry,” says Floyd Mc-Keith, PhD, a University of Illinois meat scientist. “The meat industry sees traits such as size, color, shape and taste as part of consistency. The industry is putting a lot more emphasis on quality and consistency.”
McKeith adds, “There is no doubt, genomics will play a huge role in the future of branded products. Economics will dictate the speed at which they are adopted and utilized. The industry is also looking closely at genomics to help them more efficiently market the entire animal more profitably.
“They are looking at how they can utilize genomics to help the pork chain capture additional value for the entire animal. We have to look beyond one or two meat choices to carry the load
financially. We feel genomics can help us reach that ability quickly.”
Rothschild adds, “We need to take a portfolio approach to genomics and utilize all the science and tools available. There are varieties of approaches that will work in genomics. We need to look at this hard and develop some value strategies for the industry.”
Bill Muir, PhD, Purdue University geneticist, sums up the new technology: “I call genome-wide marker-assisted selection a holistic approach because this method will work for any trait regardless of heritability or type of trait and the same genome scan for all traits. Thus, the same selection indexes used in breeding programs can still be used.
“The only difference is the equations are augmented with genomic information. In addition, it will be possible to make meaningful advances for traits that are difficult or impossible to measure on live animals, such as disease resistance or meat quality. It is very exciting technology that will complement our other technologies to unlock the genetic potential of pigs.”
Next: How genomics is creating a new standard of meat quality.
Four major advantages of genomics
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Iowa State University genomics expert Max Rothschild believes that genomics discoveries will yield better products throughout the entire pork chain. |
Max Rothschild, PhD, CF, co-director of the Center for Integrated Animal Genomics at Iowa State University believes there are four major advantages of genomics for the pork industry. They include:
1. Speed of discoveries will be increased. “There’s no doubt in my mind it would be a lot easier if I had the whole sequence to figure out where I, as a scientist, am headed. You can use positional candidates or biological candidates more rapidly. You can compare gene sequences from different phenotypes more quickly. You can use comparative genomics and examine genetic structure and look for causative mutations more easily. Therefore, those all fit into speed of discoveries. The downside is they require more investment.”
.2 Ability to verify discoveries in different genetic backgrounds. “One of the big lies that I think geneticists told themselves was that if a gene didn’t work in all backgrounds, then it wasn’t the right gene. In fact, we now know that is not correct. We needed to go back and look at how genes interacted in pathways so we could verify the value of each gene in different backgrounds and look for different mutations in the same gene. Of course, knowing the sequence would really speed this along. Gene discoveries can be applied to all commercial lines in a much more rapid fashion. Moreover, additional mutations can be discovered. This requires considerably more investment in phenotyping.”
3. Variety of traits affected can be increased. “There is no doubt that sequencing cost will go down. But, phenotyping costs will probably go up. This technology will allow us to more quickly target key traits like disease resistance, healthiness and longevity. Moreover, there are some large marketing advantages with these traits. This will require more accurate description of phenotypes.”
4. Greater speed at which genetic improvement can be implemented. “That offers an opportunity to leapfrog over past, existing selection programs. Accuracy is increased. Of course, you may have an excellent pig-breeding program for the gene improvements to be valuable. The expected outcomes are faster delivery through marker- or gene-assisted selection, definitely better genetic lines and better-branded products or better-directed products.
