Genetic change in farm stocks: Should there be concern? NICK ELLIOTT1 AND BRAp EVANS2 The genetic histories and relationships of commercial aquaculture cohorts are generally poorly understood. Unlike traditional livestock industries, few commercial aquaculture operations have controlled breeding programs with full pedigree information on the farm stock. Therefore, managers have no knowledge of genetic changes occurring between cohorts and the natural populations to which they are likely to be comparing performance. We have examined genetic Fig. 1. Handful of cultured Australian abalone. variation in farmed populations (Photo by Peter Whyte) of abalone (Figure 1) and compared this with the variation observed in wild populations from which the broodstock were obtained. Our results demonstrate the potential for use of molecular markers to monitor genetic variation in farm stocks and, thus, enable remedial action to be taken if required. Our aim was to quantify genetic change over the first generation of domestication. Major losses of genetic variation were observed. Why Might This Be of Concern? Aquaculture species are highly fecund, with individual broodstock producing many thousands to millions of gametes. The survival of the resulting larvae under controlled hatchery and nursery operations is now much higher than under natural conditions. It is therefore easy to produce large numbers of commercial stock, for harvest and future broodstock, from few breeding animals. This can lead to a small genetic base and low genetic diversity in the farm stock. Commercial fertilizations are often mass or uncontrolled events. There6 MARCH 2007 fore, the proportional gamete contribution of particular individuals is unknown. So, despite the use in some instances of large numbers of broodstock, it is unknown how many actually contribute to the next generation. If only a few, again this will result in a small genetic base and low genetic diversity. Likewise, use of closely related broodstock can result in low genetic diversity of the farm stock. A small genetic base and low diversity in a farm stock can result in high rates of inbreeding or unintentional selection, which may lead to poor commercial performance due to lower growth, fitness or higher instances of deformities. The aim for many farm managers is to improve the performance of their farm stock to gain a commercial advantage. They can achieve this through better management of the environment and the genetics on their farm. To make appreciable genetic gains in a farm stock there needs to be genetic diversity and little genetic improvement will be possible without sufficient genetic diversity. Our Studies Given that abalone farmers were starting to use domesticated broodstock without pedigree knowledge and the need for sustainability of farm stocks, we were interested in knowing how much the genetic diversity differed between a first generation of farmed abalone and a wild cohort from which the farm broodstock had been collected. In other words, what was the genetic change in one generation due to the actions of farming? It is relatively easy to see and measure phenotypic variation in such traits as size or color. This variation is controlled by the interaction of an individual's genes and the enviromnent. So while we could easily measure and compare growth rate between cohorts, we could not easily, without pedigree lines, say how much of the difference is under genetic control and, so, how much genotypic change had occurred. We could, however, examine specific regions of the DNA and compare this between individuals in the different cohorts. For our studies, we chose to examine genetic change using non-coding regions of nuclear DNA called microsatellites. An example of a microsatellite is GATCGATCGATCGATCGATC. It is a region of DNA in which two to five DNA bases are repeated a number of times, in this example GATC is repeated five times. As microsatellites are nuclear DNA, each individual carries two copies, generally one inherited from each parent. Each copy is termed an allele for that microsatellite locus.
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