The high- tech chip that may halt the scourge of PRRS
Tuesday, April 2, 2013
In a collaborative research effort, a consortium of pig breeders is working to develop a credit-card-sized chip that will enable them to analyze DNA for health and disease-resistance traits and other desirable qualities tailored to their customers' needs
by DON STONEMAN
The solution to ending, or at least minimizing, the effects of the scourge of PRRS and other diseases via genetic improvement may lie with a high-tech chip the size of a credit card and unparalleled collaboration in the pork breeding industry. (In 2008, the cost of PRRS alone in Canada was estimated at $100 million annually.)
The card is called an SNP chip. The acronym is a short form for single nucleotide polymorphism. SNPs occur throughout an animal's DNA and can act as biological markers. The chip is a tool used to analyze DNA from a pig for about 60,000 of these SNPs, spread out across the genome of the pig. "It effectively gives you a map that you can use to relate what you see to the genetics in the individual pig," says geneticist Brian Sullivan, head of the Canadian Centre for Swine Improvement (CCSI) and also vice-president of PigGen Canada.
The PigGen consortium (http://piggencanada.com/) represents one of the reasons that progress is expected to be made quickly. Just about every pig-breeding entity in Canada is involved, including the big three – PIC, Hypor and Topigs. Seven of nine members are companies and CCSI and Canadian Swine Breeder represent the independent breeders. PigGen Canada's members share the cost of funding the research projects.
Along with health and disease resistance, priorities include meat quality and lean meat deposition, production efficiency and animal welfare. "It is an example of how big this project is that these competitors have come together. It has never happened before," Sullivan says.
Tim Nelson, executive director of PigGen, describes two types of projects as "pre-competitive" and "competitive." The pre-competitive projects include developing the technologies that help genomics to work in the swine industry and, first of all, using those tools to identify traits that will enable them to make better decisions about animal health. The swine industry lives and dies on exports, both of purebred genetics and of meat, and Canada's high health reputation is critical to its export status. "Everybody benefits" from improving the health status of pigs in Canada, Nelson says.
The competitive projects would be development of swine genetic lines that individual companies could sell to producers to meet their needs and the needs of their customers.
Governments like to see this collaboration and PigGen Canada has been very successful in leveraging "hundreds of thousands of dollars" of industry money "into millions" because of the collaboration, Nelson says, including through the Swine Health Advisory Board.
PigGen will be looking for funds out of the five-year Growing Forward 2 and its AgriInnovation program, recently signed onto by provincial and federal governments, and which comes into effect April 1.
One of the independent breeders involved in this program is Rod de Wolde, operator of a 120-sow breeding stock supplier herd near Millbrook, south of Peterborough. His BMR Genetics is one of 24 herds across Canada taking part in a project where about 3,300 gilts are being tested for their natural resistance to disease, Sullivan says.
De Wolde farrows 120 sows – Yorkshire, Landrace and Durocs – and partially finishes the offspring, mostly breeding stock, as purebred boars and gilts and F1 gilts. De Wolde is part of Alliance Genetics Canada, the recently formed breeder group led by Dave Vandenbroek. Its members place a lot of boars into Ontario Swine Improvement's boar stud.
De Wolde supplies high-health gilts to customers, some of whom may have health challenges in their barns. For this project, de Wolde's gilts, having already been DNA tested, are blood-tested before they go into the customer's herd and again 30 days later. The same animals will be blood-tested for disease again after each weaning, for up to four parities.
"This particular project is just looking at sow health," de Wolde says. "The intention is to discover gene markers on pigs that have a higher resistance to health challenges."
In human health, the markers identified by SNPs help scientists locate genes that are associated with disease. In this high-tech pork industry program, these SNPs help scientists locate genes that are associated with resistance to disease. The goal is to develop a pattern of which genetic variations are common to pigs that stay robust when they face disease challenges. In the future, DNA testing can be used to select the pigs and get the most desirable traits. Part of breeding selection can be based on a robustness score.
"You can see what combinations of SNPs are in the pigs with the best outcomes versus those with the least desirable outcomes," says PigGen's Sullivan. To make these determinations, he says, "you've got to test a lot of pigs. Around 1,000, you start to get meaningful results that will start to allow you to use the markers for selection."
Mohsen Jafarikia, a genomicist with CCSI, says pigs can be genotyped at any age, even as embryos, to estimate their genomic breeding values. The plan is to genotype pigs after birth and return the genomic breeding values to breeders within two weeks. They can then choose males they want to keep for breeding and castrate the rest.
De Wolde says DNA samples can be taken when pigs' tails are cut shortly after birth, or later in life when an Allflex tag is put in sows' ears. The tag produces a sealed sample suitable for DNA testing, linked to the tag number on the sow.
Robustness isn't the only gene for which testing is being done, only the biggest of the projects. De Wolde notes that a gene has already been discovered for IGF2, a marker indicating higher lean yield and higher growth rate.
Sullivan anticipates that, this year, PigGen Canada will use this technology on boars going into AI centres to get evaluations on traits they are already evaluated on "and evaluations on new traits like marbling and the colour of meat that you couldn't practically evaluate in new boars in the past." Ultimately, he says, geneticists and producers will work with packers to tailor pork to match consumer demands and market opportunities.
There are benefits for even the larger companies to work together on the application, Sullivan says, stressing that "you have to keep on measuring the animals."
De Wolde believes that "this type of thing is really going to change how we select animals." Currently, most selecting for genetic improvement is done on the estimated breeding value system. A lot of that is based on phenotypical data: back fat days, loin eye area, mothering ability, and thus number born, number weaned and weaning weight. "Maybe eventually we can get to the point where we take a DNA sample of the pigs and decide which ones have the best genetic value based on the criteria that we put out."
As examples, de Wolde sees producers with disease-challenged herds selecting boars with gene markers for disease resistance. Over time, that would build up resistance in the herd. Use of the same genomic technology may allow for differentiation of products for different markets.
De Wolde sees a bright future ahead for swine breeders, including some breeders like him. "We still have to do our due diligence on the farm in terms of testing and verifying information, whether it be our typical back fat in days and mothering ability. It will all be intertwined. It is all going to be related. Multi-systems can be used in conjunction with one another to make a selection."
Selection "will be more complex," de Wolde predicts, but the farmer's role will still be key. Good record-keeping "is still very essential to the whole system," de Wolde notes. That includes record-keeping in the barn for mothering ability traits and scanning for back fat days. Performance in the barn "will always be our verification process. Will that ever change? I find it hard to believe that it would."
Asked how long it will be before this type of selection will be possible, de Wolde laughs. "I ask Brian (Sullivan) that all the time." De Wolde expects this project will last for a couple of years. "In reality, in some cases we already can do some genomic selection for pigs." Some gene markers have already been discovered "and we can select for gene markers as we speak."
One that comes to de Wolde's mind is IGF 2, a marker indicating higher lean yield and higher growth rate. "We've also discovered that with the opposite, the absence of that gene, the animals will have better mothering ability. There is a place for that particular one on both sides of the spectrum."
De Wolde believes that this is ground-breaking research. "We are at the leading edge of technology and that is where you want to be." BP
PigGen Canada board of directors
President: Benny Mote, Fast Genetics
Vice-President: Brian Sullivan,
Canadian Centre for Swine Improvement
Secretary-Treasurer: Daniel Godbout, Génétiporc
Bob Kemp, Genesus
Dave McLaren, PIC Canada
Nicole Dion, La Co-op fédérée
Patrick Charagu, Hypor Canada
Pramod Mathur, Topigs Canada
Paul Riese, Canadian Swine Breeders Association
SNP chips herald dairy's ‘genomic revolution'
To see how breeding selection can be changed through use of genomics, take a look at the dairy industry. Dairy's genetic industry has been using SNP chips for several years, changing how they select bulls for AI units. According to Canadian Dairy Network geneticist Jacques Chenais, the use of SNPs in dairy is likely the biggest event in dairy cattle breeding since artificial insemination.
"We call it the genomic revolution," says Chenais. The rate of genetic progress for all traits has nearly doubled because the genetic interval has been reduced and selection has been intensified. About half of the young bulls currently used in North America were chosen for AI service based on genotype rather than "proving" or measuring the production of their offspring. Use of the former is rising.
While some producers prefer to use proven bulls, Chenais says proven bulls are older and "on average have a lower genetic merit than genotyped young bulls."
Traits that are hard to measure because of their low heritability, such as fertility, longevity and somatic cell score (a low score is a sign of high-quality milk and increases profitability), can be more easily measured using genomics, just as can the highly heritable traits. This opens the door for selection in traits such as milk composition, feed efficiency, and resistance to disease, Chenais says. This sounds much like the swine industry, where Brian Sullivan, head of the Canadian Centre for Swine Improvement, says the technology also allows for selection for difficult-to-measure traits. Sullivan allows, however, that "the application and the benefits will be different in pigs. It is not as straightforward" as in dairy.
"We need to do a lot of research. That said, results are coming fast. We expect it will be used in the Canadian breeding industry in the next year. It is happening very quickly," Sullivan says. BP