IBC2000-3 Genetics

Livestock Genomics - Applications in Novel Farmed Species

Dr. Stephen S. Moore
Chair:  Beef Genomics
Agricultural, Food and Nutritional Science
University of Alberta

The following article was originally presented at the International Bison Conference in Edmonton, Alberta in August 2000.  The conference covered a wide array of bison topics including production, marketing, genetics, history and much more.  This article has been reprinted with the permission of the IBC2000 Chairman.

Introduction

In the second half of the twentieth century, the way we have grown food has changed dramatically. This change has been driven by improvements in farm practices due to mechanization and economies of scale, but also by the selection of animals and plants that have far greater potential for productivity than the breeds available half a century ago. The pace of change has been increasing with the last decade of the twentieth century witnessing the development of new technologies based on the analysis and, in plants, the manipulation of DNA.

An example of the pace of change can be seen in the cattle industry. Cattle have been farmed for millennia over which time the major beef and dairy breeds were developed. Many of these breeds were dual purpose, serving both a dairy and meat producing function. Beginning in the 1950’s intense selection based on production traits was adopted. This was particularly so in the dairy industry resulting in the Holstein cattle, which have been universally adopted by dairy producers worldwide.

In the beef industry, a different approach has been pursued. Many beef breeds were selected not directly on production traits, which in many cases were extremely difficult to measure in the live animal, but on traits thought to be associated with production or product quality. This approach still continues, however more precise, direct measurements are becoming possible. Beginning in the 1980’s cross breeding began to be adopted by the beef industry. This took advantage of the boost in production due to heterosis. Shortly afterward, individual animal evaluation based “breeding value” methods were developed which could assign a value to an animal based on the performance of all that animals relatives.

DNA Based Genetic Testing

A new revolution in genetics began in the 1980’s with the development of DNA based testing. By the 1990’s some cattle enterprises were using DNA marker assisted selection in their breeding programs. These strategies were best adopted in large breeding herds and so the dairy industry has taken the lead.

One may ask why the use of DNA markers is of interest in cattle, particularly when some breeds are so highly developed. The answer is in the power the technology brings. It is particularly useful for traits that are difficult or expensive to measure. Once a DNA marker has been identified for a trait, selection can be based on the marker. It thus becomes possible to assess markers linked to milk production traits in dairy bulls or meat quality traits in live animals. DNA markers also have utility in detecting and eliminating disease gene mutations, in increasing the frequency of advantageous but rare genes in the population, and in the introgression of genes from one population into another.

DNA markers have great potential in addressing one of the dilemmas of selective breeding. When selecting animals for a particular trait or traits one is trying in effect to “fix” the favourable traits within the population. At the same time one is trying to maintain as much of the other genetic diversity as possible. Intense selection based on phenotype can lead to low effective population size. This issue can be easily addressed by using DNA markers to monitor the genetic variation within a selection line.

With the potential of DNA based markers for selection of traits controlled by single genes established the next issue was that of quantitative or continuously variable traits. Such traits, for example growth rate, were thought to be controlled by a large number of genes each contributing a very small part of the variation seen in a population. This notion was challenged in the 1980’s, the new hypothesis being that far fewer genes of relatively large effect were responsible for quantitative variation. This question was tested in cattle and other species in large QTL (Quantitative Trait Loci) mapping studies undertaken in the USA, Australia and Europe. Indeed genes having large effects on quantitative traits were identified and DNA markers developed in or close to these genes are being used in breeding programs worldwide.

The Use of Markers in Novel Species

As exciting as these results are for multi-billion dollar industries such as the beef and dairy industries, what is the utility of the technology in more novel industries such as bison? I will give an example of how a very simple application of DNA markers resulted in a demonstrable benefit to one novel animal industry.

The example I will give is the farming of marine shrimp. At first glance this may seem a long way from ranching bison, however there are some parallels between the two industries. Both industries are farming animals that have until relatively recently been harvested from the wild. There is therefore a huge potential for genetic improvement, as the animals have never been selected for production traits. Both industries also rely on the differentiation of their product to gain market access. In the case of bison it is the fact that bison meat has properties not possessed by beef. In shrimp it is the value that the particular species (Karuma Shrimp) has in the Japanese market, which makes farming the animals viable. Farmers of both species are very aware that it is the difference rather than the similarities that are important for marketing.

The DNA marker application I will discuss is the use of markers for determining parentage. The mating of shrimp is usually carried out in large tanks with multiple males and females. It was therefore impossible to apply within family selection or to carry out mass selection and still monitor genetic diversity. Some species of farmed shrimp had already been shown to be approaching an unacceptable level of inbreeding due to lack of information about parentage. We applied DNA based parentage in a breeding scheme aimed at selecting for increased growth rate. It was possible to assign animals to particular families and to use a scheme of rotational mating between families in order to maximize genetic diversity.

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 Fig. 1. Size classes in grams of selected and unselected shrimp.

The results of the selection trial are shown in Fig. 1.  Frequency of unselected shrimp are shown by the bars on the left of each size class (horizontal bars and dotted line) while animals selected over 3 generations are shown on the bar on the right of each size class (gray scale and gray line). The bars in the centre (dark shade and solid line) show gains after one generation. It was clear that the selection resulted in more animals appearing in the larger classes. More important still for the producer was the fact that a higher dollar value per kilogram was achieved for the higher size classes. In other words the larger shrimp were worth more per kilogram than the smaller. This is shown in Fig. 2 where a 34% increase in value per kilogram was achieved for the selected line.

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