Article for Centralia Swine Update
January, 1998

Moving Into A Molecular Era

J.P. Gibson
Centre for Genetic Improvement of Livestock
Animal & Poultry Science
University of Guelph

Genetic improvement of pigs has been remarkably successful. Indeed, it has been estimated that over the past 15 years, approximately 60% of all the improvements in growth rate and about 90% of all the reduction in backfat of pigs in Canada has been due to genetic improvement. Yet, all of this improvement has come from a black box approach (see Figure 1).

Inside the black box are the genes that pig breeders are trying to improve. Until recently, we have known almost nothing about these genes and had no way of accessing them directly. Genetic improvement has, therefore, taken place indirectly by recording the performance of the animal itself which is in part due to the genes inside the black box. As outlined in Figure 1, the performance information is gathered, collected into data bases, analyzed statistically to obtain estimated breeding values (EBV), and these EBV are then used to select parents of the next generation. A new generation of animals is then born, each containing their own genetic black box, and the process repeats.

This traditional process of genetic improvement has limitations in that each cycle takes a long time because of the necessary steps involved. Also, many potentially useful genes are either lost along the way or not used very effectively. This explains the increasing interest in a wide range of new molecular genetic technologies which are giving us our first glimpse inside that genetic black box. We are still a very long way from being able to open the box completely to reveal its full contents, but we can begin to locate some of the genes of interest with sufficient accuracy to be able to use the information in genetic improvement programs.

While Canada was a world leader in the development of genetic evaluation techniques and genetic improvement programs generally, we have fallen badly behind in development of molecular applications to pig improvement. Several groups in Canada are now trying to change that, including a major new initiative at the University of Guelph.

In broad terms, there are two general approaches when using molecular markers to find genes that are of economic importance. The first approach is referred to as the candidate gene approach. A candidate gene is a gene for which there is some prior evidence that it might be involved in the performance of the animal. For example, studies in mice have shown that there is a mutation in the leptin gene which causes extreme obesity in one particular strain of mice. It is therefore possible that more mild mutations might contribute to genetic variation in fatness in other species such as pigs, for example. Thus, the leptin gene is a candidate for controlling genetic variation in fatness. The second approach to finding genes of interest is referred to as the anonymous marker approach. Anonymous markers are genetic mutations that are not expected to have any effect on the animal, but which can be recorded on individual animals through a variety of laboratory techniques. Anonymous markers can act as bookmarks for other genes that might cause genetic mutations. Because genes tend to be passed from parents to progeny in very large blocks, if we can follow the inheritance of an anonymous marker gene, we are also following the inheritance of a large number of unknown genes in the region of the marker. With specially constructed populations, by following the inheritance of these markers and recording individuals for their performance, we can begin to relate the inheritance of markers to performance and thereby track regions in which there seem to be genes of interest. Once we have found such genes, we can then use the marker information in selection to help make more rapid genetic improvement.

The Centre for Genetic Improvement of Livestock has teamed up with the Guelph Molecular Super Centre at the University of Guelph to apply both candidate gene and anonymous marker techniques to pig improvement. We are currently developing a number of initiatives in the area of sow productivity, and in the area of growth and carcass quality. We already have a considerable number of candidate genes for both sow productivity and carcass quality traits, and plan to apply these to a number of test populations over the next couple of years. We have also had considerable success with preliminary testing of a new type of anonymous marker known as amplified fragment length polymorphisms or AFLP. This is an exciting new molecular marker technology which is already widely applied with plants but has been relatively untested with animals, but has the potential to generate a very large number of markers in a fairly short period of time. The current system we are using generates about 1,200 AFLP markers and we hope to expand this to about 3,000 or 4,000 markers over the coming year. Our hope is that this technology will allow us to do much more detailed and precise QTL mapping than microsatellite markers, which are the type of marker most commonly used today.

All DNA work requires animal resource populations. We have just reached agreement with the research group in Edinburgh, Scotland to house a second copy of their DNA bank on their population of pigs which are crosses between the highly prolific Meishau breed and the Large White breed. We plan to use this population in collaboration with researchers in Edinburgh to locate genes controlling litter size and other sow productivity traits. We also have a minor collaboration with a research group at Nanjing University in China who are working with another highly prolific Chinese breed, the Erhualian. We are also currently working towards developing markers for the acid meat gene which is primarily a problem in the Hampshire breed, but is believed to also be present in other breeds. We have a DNA bank from about 2,200 pigs that went through the Ontario Pork Carcass Appraisal Project (OPCAP) where we are currently testing a variety of candidate genes for carcass quality traits. We hope to put into place a specific resource population to study carcass quality genes in collaboration with one or more industry partners later this year.

As we enter the research and development phase, it is obviously difficult to predict how long it will take to develop tests that can be used in practice. We have, however, just discovered our first genes of major economic effect in a similar project in Canadian Holsteins (in collaboration with the Saskatchewan Research Council), indicating that the time from commencing research to discovering economically important genes need not be particularly long. One advantage of the group we have set up in Guelph is that the Guelph Molecular Super Centre has a commercial division and we can therefore guarantee that any commercially useful results that we do discover will be made available to the industry immediately.

Acknowledgments

We gratefully acknowledge the financial support for these projects from Ontario Swine Improvement, Ontario Pork and the Ontario Ministry of Agriculture, Food and Rural Affairs.