Aquaculture Magazine

February/March 2015

Genetic Improvement Considerations for Small Producers

By C. Greg Lutz

A review of aquaculture industry publications over the past decade might suggest that much of the expansion in global production has been attributable to high-profile, large- scale, highly capitalized operations.

By Greg Lutz 

Nonetheless, most of the world’s aquaculturists are small-scale producers. Principles of genetic improvement are often fairly easily applied in industrial-scale aquaculture, but small operations typically face numerous difficulties in terms of genetic improvement of production stocks. And, while large-scale breeding programs are being expanded to develop improved lines of many species in many parts of the world, these lines may not always be available or suitable for many small-scale operations.

Small producers wishing to improve the quality of their production stocks typically face one of two common situations. They either obtain their fry, post-larvae or spat from outside sources, or they rely on on-farm production for their seedstock needs. In each situation, an understanding of basic genetic fundamentals and methods can result in improved efficiency and profitability.

Evaluating available varieties is perhaps the simplest form of selection, and this is usually the first step in genetic improvement for most aquaculturists. For those producers who obtain their stocks from outside sources, the best place to start is to develop an understanding the basic methods involved in comparing available varieties. Record-keeping skills are essential for meaningful comparisons of various genetic lines. While growth rate is usually the attribute of greatest interest to aquaculturists, attention must also be paid to survival (and resultant effects on stocking density), feed conversion, and marketing attributes such as conformation and coloration. Fortunately for mollusk producers, side-by-side comparisons with these species are often fairly straightforward. They can, however, be extremely complicated with some crustaceans and finfish.

When species such as shrimp, prawns or finfish are being evaluated, it may be desirable to utilize communal stocking and rearing, wherein all individuals are cultured in a common environment. In such situations, however, it may be difficult or impossible to identify the origins of individual animals without some sort of practical marking system. Techniques such as cold-or heat branding, fin clipping and other approaches can provide sufficient identification of many types of finfish, at least on a short-term basis, but they are often logistically difficult and time-consuming. Some of these methods are reviewed in my book, Practical Genetics for Aquaculture.

Feed conversion efficiency cannot be easily compared, if at all, among strains or varieties that are reared communally. Other problems with evaluations based on communal rearing can arise if behavioral interactions bias overall performance. A variety that might grow and convert feed quite well in monoculture may perform poorly in the presence of more aggressive individuals from another genetic background. Such situations have been documented for a number of aquatic species.

The alternative to communal rearing may involve increasingly artificial culture conditions to allow for identification and evaluation of strains or varieties. Perhaps the simplest approaches involve separate containment of groups of animals in cages or pens within the same pond, tank or raceway. In the case of recirculating systems, individual tanks connected to common filtration can be used to minimize environmental differences among groups of animals being evaluated. The problem with this approach, from a small producer’s perspective, is that it usually requires additional equipment, labor, time, and facilities.

So, for small producers trying to locate the best available source of seedstock, maybe the simplest approach is to evaluate one source at a time. Complicating influences such as changes in feed, production management, system configurations, etc. must be avoided if comparisons are to be meaningful. Eventually, it should be possible to identify the strain or variety that performs best in relation to the management practices and facilities available. Of course, there is no guarantee that the genetic quality of any particular source will not deteriorate (or improve) over time, as we will see below.

For small producers who produce their own seedstock on-site, either by choice or necessity, all the above considerations apply in terms of conducting meaningful evaluations and comparisons. However, the concepts of selection, inbreeding and crossbreeding must also be understood and utilized in a program of genetic improvement. Small producers are generally forced to obtain breeders from within their own production stocks, often for many generations at a time. This presents the opportunity to select for a line of fish, crustaceans, or mollusks that is highly adapted to the facilities and management being utilized.

One unavoidable result of selection, however, is inbreeding. Limiting reproduction to a relatively small portion of a population, selected for particular traits, will result in mating more and more closely related individuals over time.  Inbreeding depression is usually associated with a general decline in fitness. Breeding between more closely related individuals tends to increase the number of loci that are homozygous, which often tends to reduce fitness (for complex reasons beyond the scope of this discussion).

Several methods of selection can be applied to aquaculture stocks. Some are designed to slow the accumulation of inbreeding, but often require more extensive procedures and facilities. Some aquatic species are more easily adapted to specific selection methods than others. Perhaps the simplest form of selection within a population involves rearing large groups of animals simultaneously and then selecting the best, based solely on their individual performance, to serve as breeding stock. This approach, referred to as mass selection, is often the only practical means of selection when facilities or labor are limited. A major problem with mass selection within many aquaculture operations involves the inability to determine the ancestry of any particular animal.

Mass selection, along with other selection methods, often has an additional uncertainty: the degree to which observed performance actually reflects genetic attributes. In many species, initial size advantages resulting from environmental, rather than genetic, advantages can be exaggerated over time, obscuring differences attributable to genetic superiority or inferiority. Some methods, however, have emerged in recent years to address this problem under the practical circumstances faced by most small producers.

One study along these lines examined the efficiency of size-specific (rather than age-specific) selection for growth in tilapia on a farm in Indonesia. Fingerlings were size graded prior to selection, in an effort to simplify the selection method for on-farm use, where equally-aged fingerlings would not normally be available in sufficient numbers. Selection response was significant, with a 2.3% increase in length after one generation (recall that a unit increase in length generally translates into a substantially greater increase in weight). Realized heritability was roughly 12%.

A more refined version of this approach, known as collimation, involves grading and culling of excessively large individuals prior to conducting mass selection. This procedure results in much better correlations between genetic and observed variation in the remaining population, and improves the efficiency of mass selection. Collimation and 2-step mass selection were applied to Nile tilapia reared in net-cages in the Philippines. The goal was to further develop low-cost, small-scale tilapia broodstock improvement programs that could be applied under very practical conditions. Positive-selected fish were 3% larger relative to controls after one generation, with a realized heritability of approximately 16% and a projected improvement of 34% over a 5-year period.

Clearly, mass selection can be a practical, powerful tool for small operations to improve their breeding stock on the short term, but the question of inbreeding still remains. In fact, inbreeding becomes even more serious in small facilities with limited capabilities to maintain broodstock in large numbers. Smaller numbers of breeding individuals lead to the mating of more closely related individuals over a number of generations, and this problem is even further exacerbated by genetic drift, the tendency for genetic diversity to be lost simply through random chance as breeding pairs are formed among a limited number of animals. One potential solution to this problem is to add new breeding stock from time to time, but this practice has its own associated problems, including the introduction of genes that are less adapted to the facilities and practices being employed, as well as the potential for introduction of pathogens.

Another approach to selection, know as within-family selection, is quite effective at slowing the rate at which inbreeding accumulates in a closed population. Within-family selection involves the retention of the best-performing males and females from each family of fish (or prawns, or oysters, etc., etc., etc.) for use as breeding stock. When every available family contributes equally to a breeding population, the effective population size (theoretically) equals twice the actual breeding population size.

The problem with within-family selection, especially from a small producer’s standpoint, is the requirement that every family must be raised separately (or marked in a more or less permanent fashion) to allow for identification of the best performing individuals within each family. Again, it may be possible to use separate cages or tanks under certain circumstances, but these approaches are normally less feasible for small operations. Additionally, arranging subsequent mating schemes to reduce the incidence of pair-mating between related animals also requires multiple spawning ponds, tanks, or hapas.

One other option that has proven useful in selection programs for small aquaculture operations involves maintaining two or more separate lines of breeding stock, each subjected to intense selection pressure. The best performing individuals from each line are then mated with animals from the other line to produce seedstock for grow-out. This type of selection can be a powerful method of eliminating the deleterious genes that manifest themselves in inbreeding depression, but it requires maintaining (and constantly selecting) two distinct populations.


C. Greg Lutz, has a PhD in Wildlife and Fisheries Science from the Louisiana State University. His interests include recirculating system technology and population dynamics, quantitative genetics and multivariate analyses and the use of web based technology for result-demonstration methods.

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