Kapuscinski, A. R., M. Hove, W. Senanan, and L. M. Miller. 1996. Selective breeding of walleye: 

building block for closed-system aquaculture. Pages 331 -338 in R. C. Summerfelt, editor. Walleye 

culture manual. NCRAC Culture Series 101. North Central Regional Aquaculture Center Publications Office, Iowa State University, Ames. 

Selective Breeding of Walleye: 

Building Block for ClosedSystem Aquacu Itu re 

Anne R. Kapuscinski, Mark Hove, Wansuk Senanan, and Loren Ad. Miller, Department of Fisheries and 

Wildlife, 200 Hodson Hall, University of Minnesota ,Sf. Paul, MN 55108 

Introduction 

This chapter begins with a brief introduction to some 

basic genetic concepts involved in selective breedmg, 

then illustrates these concepts with some data on 

walleye, and ends with general advice to aquaculturists 

who might be interested in conducting a breeding 

program. If you are looking for a quick fix to increase 

production or to reduce variability in yield, this chapter 

may &sappoint you. In terrestrial agriculture, selective 

breedmg has been an effective method of improving 

production, but the improvements came from long-term 

commitments to breeding programs. 

The ideas and recommendations in this chapter apply 

only to walleye breeding programs for aquaculture in 

contained systems; i.e. systems where fish have a 

negligible risk of escape into natural waters. Also, we 

strongly discourage aquaculturists from undertaking 

selective breeding or other genetic modifications of 

walleye that are destined for intentional stocking into 

natural waters. In any breedng program, there is a 

trade-off between improved performance in the selected 

environment and reduced performance in other environments. If you start with a wild-type or nearly wild-type 

broodstock and practice artificial selection for improved 

performance in an aquaculture environment, offspring 

of the selected parents will exhibit reduced performance 

in wild environments. Intentional, selective breeding of 

walleye in an aquaculture system selects for improved 

performance within that artificial, captive environment. 

This necessarily reduces the selectively bred strain’s 

performance in environments of natural bodies of water. 

We particularly caution the reader against stocking 

selectively bred walleye into waters containing wild 

walleye populations. This could adversely affect wild 

genetic diversity and, thus, jeoparhze the long-term 

sustainability of walleye populations. It is in the best 

interest of aquaculturists to protect wild gene pools, 

because these are irreplaceable sources of future genetic 

material that may be needed to improve captive 

populations. For instance, if a new disease were to 

sweep through progressively inbred, domesticated 

walleye broodstocks, wild gene pools of walleye could 

be the source of a gene that confers disease resistance. 

Because all artificial breeding programs inevitably 

reduce the broodstock’s genetic variation over time, a 

periodic infusion of wild walleye genetic material is 

one of the best ways to avoid problems such as inbreeding depression. 

Basic genetic concepts involved in selective 

breeding 

Quantitative traits 

Many production traits of interest to aquaculturists are 

called quantitative traits. Quantitative traits are described by a measurement, such as grams of body 

weight, and are controlled by many genes. Figure 1 

shows the frequency distribution of the quantitative 

trait, body weight at 247 days, in a captive walleye 

population which was raised in a series of indoor flowthrough tanks. In any interbreeding population, quantitative traits vary among individuals due to the different 

genetic make-up of each fish and the different environmental conditions experienced by each fish over its 

NCRAC Culture Series 101 - Walleye Culture Manual 331 
I 

where: 

50 1 Number 

2o of fish 

F req u e ncy 

0.1 

10 

15 35 55 75 95 115 

247-d Weight (9) 

Figure 1. Frequency distribution of individual weight (9) 

at age 247 days for the founder generation of a pedigreed walleye broodstock that was raised in flowthrough indoor tanks at the University of Minnesota. 

lifetime. Data in Figure 1 represent fish belonging to 12 

dfferent families; these families were propagated by 

crossing gametes collected from adults of one wild 

population. Each family was first raised in a separate 

tank, and then fish of each family were evenly distributed among two grow-out tanks. Although we tried to 

keep culture condtions similar in the entire facility, 

&fferent fish still experienced different environments. 

Heritability and artificial selection 

Heritability provides a way to measure the degree of 

genetic control over a particular quantitative trait. 

Heritability of a trait quantifies the degree to which the 

performance of offspring resembles the performance of 

their parents because of genetic control over the trait. 

The value of heritability, symbolized by h2, can range 

from 0 to 1. If h2 = 0, there is complete environmental 

control and no additive genetic control over the observed trait. If h2 = 1, there is complete genetic control 

and no environmental control over the trait. The closer 

the value is to 1, the more offspring tend to predctably 

resemble their parents and the more easily can the trait 

be modified by artificial selection. 

Even when there is no change in the genetic control of a 

trait, the measured heritability for a trait withn a 

broodstock will decrease if the fish experienced high 

environmental variability in their culture conditions. 

This is because heritability is a ratio that reflects both 

genetic and environmental variation that affect the trait: 

h2 = V, / (Vc + V, + VG-E) 

V, = additive part of genetic variance affecting 

V, = total genetic variance affecting expression of 

V, = environmental variance affecting expression of 

V,., = interaction of genetic and environmental 

expression of the trait'; 

the trait; 

the trait; 

variance affecting the trait 

The terms in the denominator of equation (1) for 

heritability add up to the phenotypic variance (V,) of 

the trait in the population. Phenotype refers to the 

detectable property of a trait, for example, the measured 

wet weight of fish; so V, is the variance of wet weight 

among all fish measured in a given population. 

Thus, 

v, = v, + v, + VGxE 

and 

h" = V, /V, (3) 

Rearing environment injZuences heritabizity. 

An increase in environmental variability-for example, 

increased differences in fish stochng or in feedmg rates 

among tanks at one fish farm-will likely increase the 

value of the denominator of the ratio in equation (1) 

and, therefore, will decrease the h2. 

Aquaculturists must also beware that hfferent rearing 

environments may change the value of heritability of 

I 

m 

X parental 

Parental I - 'L 3 

Progeny 

Figure 2. An illustrative example of response to mass 

selection. S is the selection differential imposed in 

the parent generation, h2 is the heritability of the 

selected trait, and R is the response to selection in 

the progeny generation. 

332 NCRAC Culture Series 101- Walleye Culture Manual 
the same trait, so that heritabilities estimated at one 

facility may not be directly transferable to a population 

cultured at another facility. For example, studies have 

shown that heritabilities of fish survival and growth 

differed under different rearing temperatures and in 

dfferent rearing facilities (reviewed by Tave 1993: 13 1 

and 148). 

Importance of heritability in application of selection. 

To understand the central role of heritability in selective 

breeding, consider the simplest form of selection, called 

“mass selection” (Figure 2). The upper curve shows the 

normal distribution of trait X in a population being 

raised at a fish farm. The selection bfferential, (S) is 

the difference between the mean phenotypic value of 

the entire parental population (X parental) and the mean 

phenotypic value of the select broodstock (% selected). 

The select parents, whose values for trait X are denoted 

by the shaded portion of the distribution, are the only 

parents that are mated to produce the next generation. 

The lower curve shows the altered distribution of trait X 

in the progeny generation. The response to selection (R) 

is the difference between the mean of the progeny and 

parental generations. 

Breeders can estimate heritability at one of two points 

in a selective breeding program: 

(1) In the parent generation, before actually imposing selection. 

This approach involves actually estimating the 

values of the variances in Equation (3). It allows 

breeders to determine whether a breeding 

program is likely to be worthwhile. If selection 

appears worthwhile, it allows breeders to plan the 

most effective way to apply artificial selection on 

one or more traits and to obtain the desired 

response in the next generation. It also permits 

improved forecasting of costs and benefits of the 

breeding program. But it requires greater up-front 

costs of producing the parental population 

through a specific mating scheme and keeping 

performance records on individually marked fish. 

(2) After imposition of selection. 

This approach involves actually measuring S, R, 

and then estimating heritability as: 

h2=R/S (4) 

This approach is cheaper at the outset. It precludes, 

however, good forecasting of costs and benefits because 

one lacks the information to predict the response to 

selection. It also involves taking the risk that the 

breeding program will be a waste of effort due to low 

heritabilities for your population or in your rearing 

environment. For a review of two real cases where this 

happened, see Tave (1993: 148-149). 

In the walleye genetics research done at the University 

of Minnesota, we chose the first approach and measured 

h2 for many traits in the parental generation. Our 

original goal was to obtain the best planning information for a long-term breedmg program. 

Using the first approach, we estimated the heritability 

of wet weight at age 247 days to be 0.93. This was 

based on data collected from indwidually marked fish 

belonging to 12 families of a parental generation and 

raised in a flow-through indoor tank system. This high 

heritability value is a welcome result because the closer 

the value is to 1, the more offspring tend to predictably 

resemble their parents and the more easily can we 

modify the trait by artificial selection. 

Now that we know the heritability value for this trait, 

we can predict the average weight of progeny from 

select parents for any S that we might consider imposing in the parental generation. Figure 3 illustrates this 

point for the following example: By relying on our 

inhvidual performance records and the fact that 

parental generation fish are indwidually marked with 

passive integrated transponder (PIT) tags, we could 

choose to mate only those fish which weighed more 

than 53 g at age 247 days. According to the calculations 

shown below, we predict the average weight of offspring at 247 days to be 64.1 g, an increase of 35.5 g: 

Response to selection for wet weight at 247 days 

8 S = 66.3 g - 35.5 g = 30.8 g 

h2 = 0.93 (estimated from University of Minnesota 

8 R = S x h = 30.8 g x 0.93 = 28.6 g 

Progeny average weight: x progeny = 

parental data) 2 

x parental + R = 64.1 g. 

These calculations predict a gain of 80.5% per generation, which is very large. If we were to actually impose 

the selection bfferential of this example, the realized 

response will likely be lowe?, but these results show 

NCRAC Culture Series 101 - Walleye Culture Manual 333 
03 

0.2 

Frequency 

01 

I 

X parental = 35.5 n 

~fS+ 

X select = 66.3 

50 

40 

3o Number 

2o of fish 

10 

15 35 55 75 95 115 wt(g) 

X progeny = 64.1 g I 

I 

IT 

+R+ 

Figure 3. Example of how breeders can use a measured 

trait heritability to predict the response to selection for 

any selection differential, S, that they might consider 

imposing in the parental generation. If a breeder mates 

only those fish which weighed more than 53 g at age 247 

days, predicted average weight of progeny is 64.1 g 

based on the following calculations: Selection differential, S = 66.3 g - 35.5 g = 30.8 g. Heritability, h2 = 0.93 

(estimated from data on parental fish raised at the 

University of Minnesota). Response, R = S x h2 = 30.8 g x 

0.93 = 28.6 g. Progeny average weight: X progeny = 

X parental + R = 64.1 g. 

the potential for rapid gains through selective breedmg 

of walleye for food fish aquaculture. 

Potential for selective breeding of walleye 

Collective experience of animal 

breeders leads to the following 

general recommendations 

about the effectiveness of 

artificial selection depending 

on a trait’s value of h2. Traits 

with h2 > 0.25 respond well to 

selection, while traits with h2 

e 0.15 are hard to change by 

selection, although certain 

selection strategies more 

complex than mass selection 

can improve response in such 

cases. Traits with h2 between 

0.15 and 0.25 will respond to 

selection, but may require more 

generations of selection to 

Examples of juvenile traits amenable to selection 

Following these general guidelines, a number of 

juvenile walleye traits should be amenable to selection. 

Table 1 shows some of the trait heritabilities which 

were estimated using 12 families of fry raised at Iowa 

State University (Summerfelt and Bristow 1994). Table 

2 shows some of the growth-related heritabilities which 

were estimated using a different set of 12 families 

reared at the University of Minnesota. The families 

raised at Iowa and Minnesota were founded from the 

same source population-gametes collected from wild 

fish caught in the Mississippi River near Genoa, 

Wisconsin. In Table 1, the relatively hgh h2 for gas 

bladder inflation and cannibalism indcate that these 

traits should respond well to selection. This is good 

news because tank-reared walleye have shown poor 

performance in these traits. In Table 2, the high heritabilities inQcate that a selective breeding program 

should be able to improve growth in walleye with good 

to excellent rates of gain per generation. Note that these 

heritabilities of weight and length increase as age 

increases. 

Other traits potentially amenable to selection 

A growing body of data indcates that many production 

traits show sufficiently high heritabilities across various 

fish species, which means that they can be modified by 

artificial selection (Chevassus and Dorson 1990; Tave 

1993: 132-147). So far, we have mentioned the potential for selection on fry traits, weight-at-age, and lengthTable 1. Examples of walleye fry 

traits amenable to selection, 

based on pedigreed families 

raised at Iowa State University 

(Summerfelt and Bristow 1994). 

Trait Sire h2 

Hatching length 0.47 

Gas bladder inflation (14 d) 0.83 

Gas bladder inflation (21 d) 0.60 

Cannibalism 0.55 

at-age. Other traits may show 

adequate heritabilities in walleye. 

Traits worthy of future genetic 

investigation in walleye include: 

carcass traits-gutted weight, 

dressing percentage, belly 

thickness, percent fat; 

reproductive traits-age at 

sexual maturity, age at spawning, 

egg size, egg number; 

disease resistance traitssurvival from exposure to 

specific pathogens; and 

physiological traits-oxygen 

consumption, food conversion, 

tolerance of sub-optimal temperatures, 

reach desired values for the modified trait. 

Through proper planning and appropriate application of 

systematic selective breeding, fish breeders have 

334 NCRAC Culture Series 101- Walleye Culture Manual 
experienced good to excellent 

rates of change in average values 

of traits per generation. To get a 

sense of the rates of change per 

generation obtained from selective 

breedmg of other fish species, 

Table 3 presents reported gains in 

weight or growth rate for four 

selective breeding programs. 

Gains can be expected for many 

generations of continuous 

selection in the same direction on 

a given trait. However, selection 

will likely reach a plateau 

possibly after 30 to 100 generations of selection. The number of 

generations it takes to reach the 

selection plateau 

depends, in part, on 

the amounts of V, for Table 3. 

Table 2. Examples of growthrelated traits amenable to 

selection, based on pedigreed 

walleye families raised at the 

University of Mi n n esot a. 

Trait Sire h2 

25-d length 

47-d weight 

115-d length 

1 15-d weight 

247-d length 

247-d weight 

270-d weight 

0.30 

0.41 

0.42 

0.62 

0.74 

0.93 

0.90 

Reported gains in fish weight or growth 

of yield due to genetic causes. 

Genetic variation decreases over 

time through a process geneticists 

call “random drift” or “genetic 

drift.” This leads to loss of some 

alleles that have beneficial effects 

on economically important 

production traits. Also, inbreeding accumulates over generations. 

If inbreeding levels get too high, 

it can cause inbreeding depression, whch might cause reductions in survival, growth, or 

disease resistance or detrimental 

changes in other traits. The 

second lowest curve depicts the 

case where genetic factors have 

the trait. Thus, it is 

desirable to start a 

rate from different selective breeding programs. 

Species Ga i n/Ge n e rat i o n Reference breeding program 

with a population that 

has good overall 

levels of genetic Rainbow trout 10% 

choose the Genoa, Coho salmon 10% 

variability. This was Atlantic Salmon 30% 

one criterion used to Atlantic salmon 10-1 4% 

Wisconsin wild 

population, compared 

to other candidates, as the source of founders for the 

walleye families raised at Iowa State University and 

University of Minnesota (NCRAC 1993: 31). 

What do different breeding programs offer? 

If you are contemplating embarlung on a breeding 

program, it is important to understand the different 

opportunities and constraints offered by different types 

of breeding programs3

. Figure 4 compares the effects on 

yields of no breeding, systematically choosing the best 

strain, selective breeding, hybridzation, and certain 

combinations among these options. 

Walleye farming with no deliberate breeding program 

might follow one of two trajectories depicted by the two 

lowest curves in Figure 4. The lowest curve depicts the 

situation where the number of parents used to propagate 

each generation of offspring is too low, leadng to loss 

Kincaid et al. 1977 

Gjedrem 1979 

Kinghorn 1983 

Hershberger et al. 1990 

no effect on yield. The 

number of parents per 

generation is sufficient 

to keep levels of genetic 

drift and inbreeding low 

enough to avoid 

adverse effects on 

yields. This independence from genetic 

factors, however, 

cannot go on forever. 

Broodstock will need 

periodic infusions of 

new genetic material to 

avoid detrimental levels of inbreedmg and genetic dnft. 

selection 

. followedby .. ..‘ ..’ .’ .. hybridization .. .. .. .. . _... selection on .. .. .. ... 

. .. .. . best strain 

best hybrid 

beat strain via 

yield trials 

selection, 

chosen stock 

, I I , , , , , , haphazardly 

genetic dritt 

genetic drift 

Generations 

Figure 4. Comparison of different breeding programs in 

terms of genetic gains possible over future generations 

(adapted from Tave 1993). 

NCRAC Culture Series 101 - Walleye Culture Manual 335 
Compared to these two cases, selective breeding of the 

same broodstock brings about some increase in yields 

over time. However, the broodstock may not have a 

desirable genetic make-up, compared to other possible 

sources of founders. From a breeder’s perspective, this 

broodstock is a haphazard choice for launchng a 

breedmg program. It may seriously limit the gains 

obtained from the breedmg program. 

Compared to doing nothing, a better option for increasing yields is to establish a captive broodstock from the 

best strain. To identify the best strain, breeders conduct 

carefully designed and monitored comparisons of a 

number of candidate strains under the same aquaculture 

environment(s). This approach essentially involves 

taking advantage of nature’s past work by finding the 

pre-existing gene pool that is already fairly well 

adapted to a particular aquaculture environment. For 

example, Figure 5 shows the differences in body weight 

among 19 dfferent strains of Atlantic salmon cultured 

in the same aquaculture environment. As explained 

more fully below, a breeding program aiming to 

increase size at harvest might involve application of 

selection, hybridization, or both. The number of 

generations of breeding needed to reach a specific goal 

for increased size, as well as the associated costs, would 

be reduced if breeders began with 1, the best performing strain, rather than with strain 19. Additionally, 

different strains may naturally perform better in 

dfferent aquaculture systems. Thus, systematic 

identification of the best strain for a given aquaculture 

environment is essential for having an effective breeding program. The limitation of a breeding program 

based solely on identification of the best strain is that it 

precludes additional genetic gain in future generations. 

This is depicted by the horizontal line in Figure 4. 

Strain number 

Building on identification of the best strain, breeders 

have three options for getting additional genetic gain. A 

one-time increase in genetic gain is possible by 

propagating the best hybrid. In this context, hybridization can be between different species (interspecific 

hybrid), such as the crossing of walleye and sauger to 

produce “hybrid walleye,” or between genetically 

different strains or lines of the same species (intraspecific hybrid). In either case, there is no way to predict a 

priori which hybrid will yield the greatest genetic gain. 

Note that this option is also limited by lack of additional genetic gain in future generations, as depicted by 

the correspondmg horizontal line in Figure 4. 

The two remaining types of breeding programs permit 

additional genetic gain in future generations and rely on 

the genetic concepts presented above. The simplest 

breedmg program is to practice selection on the best 

strain. Finally, a combined approach is to practice 

selection on separate strains and then cross them 

through hybridization. The two strains could be from 

the same species or two different species. Compared to 

simple hybridization, combined selection and hybridization will generate offspring exlubiting less variability 

in their performance traits; for instance, it could 

decrease size variability. This could measurably reduce 

production costs and increase yields. 

Small producers and breeding programs 

It will be difficult for most small-scale producers to 

conduct a breeding program as a peripheral activity of a 

farm primarily focused on grow-out of fish to marketable size. There are three feasible strategies for 

involvement of small producers in genetic improvement 

of walleye for indoor aquaculture. The order in which 

these are presented below does not imply any ranlung. 

First, one or a few farmers could decide to specialize in 

broodstock improvement. This would be the primary 

goal of their aquaculture operations and they would sell 

genetically improved eggs, fry, or fingerlings to farmers 

focused on grow-out. Second, a number of farmers 

could form a breeding cooperative. Members would 

pool their resources to develop 2-3 selectively bred 

strains. Offspring from the improved strains would be 

shared among cooperators. Such a cooperative could 

even coordmate multiple farm trials to identify best 

strains or to compare genetically modified strains 

propagated by selection, hybridization, or combined 

Figure 5. Ranking of strains of Atlantic salmon for 

body weight after two years in sea cages (adapted 

from Refstie 1990). 

336 NCRAC Culture Series 101- Walleye Culture Manual 
selection and hybridization. The third option is to have 

a public research institution carry out the bulk of the 

time-consuming and expensive steps in a breeding 

program, followed by participation of different producers in on-farm trials and eventual public release of one 

or more improved strains. Obviously, variations of and 

combinations among these three options are possible. 

Each option has short-term and long-term benefits and 

disadvantages. 

A strategy relevant to any of the three options laid out 

above for the institutional structure of a breeding 

program is to integrate pedgreed, tagged families into a 

larger grow-out stock of fish (Figure 6). Selection is 

practiced only on the tagged fish in the pedigreed 

families and disruption of the grow-out operation is 

minimized. This approach has shown promise in coho 

salmon selection programs (Hershberger 1988). Tagged 

families and control fish are raised with production fish 

in a number of the production units. As selection is 

imposed, culled fish or families are placed in grow-out 

units (depicted by the arrows pointing away from the 

breeding circle in Figure 6). Currently, aquaculturists 

rely on artificial tags, inserted internally or affixed 

externally on indwidual fish. Recent research results, 

however, on characterization of naturally existing, 

genetic marks will eventually make it economically 

feasible for farmers to tag and track pedigreed families 

integrated into grow-out operations. One simple 

example of ths idea is that fish have DNA fingerprints 

similar to human DNA fingerprints used in forensic 

investigations. 

Conclusion 

ultimately, it is the collective responsibility of diverse 

parties concerned with walleye aquaculture to decide 

the role of breedmg programs in food fish walleye 

aquaculture. In this chapter, we have tried to introduce 

some essential concepts and illustrate them with 

examples of genetic data on walleye and other fish 

species. Coming full circle to the beginning of this 

essay, we close by rernindmg prospective breeders that 

they also bear the responsibility to foster environmentally safe breeding programs. 

Acknowledgments 

support for the authors while preparing ths manuscript was provided in part by the Minnesota Agricul12 families + " 'amilies ~ ~, ~I.~ ~, 275 control fish (to proaucrion) \n 

15 

age 1 to 

mature 

families 

sexual 

6 families 

3 families (to production) 

(to production) 

+ control 

la males x la females 

Figure 6. Schematic of a selective breeding program 

integrated into a grow-out operation (adapted from 

Hershberger 1990). The cycle depicts combined selection on pedigreed walleye families, in which the best 

performing individuals from the best performing 

families are crossed each generation. These families 

bear individual marks, such as passive integrated 

transponder (PIT) tags. Fish culled during application of 

selection become part of the grow-out stock. Each 

revolution around the circle is equivalent to one generation. Number of males and females crossed to propagate the families involved in the breeding program and 

size of control line keep the inbreeding rate less than 

2% per generation. 

tural Experiment Station; the Minnesota Sea Grant 

College Program supported by the NOAA Office of Sea 

Grant, Department of Commerce under Grant No. 

NOAA-NA46-RGOlO1, Project Nos. R/F-26 and R/F3 1, J.R. 41 9; the USDA, North Central Regional 

Aquaculture Center; and the Royal Thai Government 

Scholarship Program. We thank Craig Acomb, Deborah 

Brister, and Eric Sell for their capable rearing of 

walleye families at the University of Minnesota 

laboratory. This is article 22,382 of the Minnesota 

Agricultural Experiment Station Scientific Journal 

Article Series. 

Foot notes 

Additive genetic variance is one component of the total 

genetic variance affecting the trait. It appears in the 

numerator of this ratio, because it is the portion of genetic 

variance that responds to selection from one generation to 

the next in a predictable manner. 

This is due to a fairly high standard error for our estimate for 

h2. 

The following forms of genetic manipulation are beyond the 

scope of this chapter: ploidy manipulations (e.g., production 

of triploid walleye); gene transfer; and genetic modifications 

for sex control (e.g., production of monosex fish). One or 

more of these types of manipulations could be integrated 

with selective breeding, hybridization, or both. 

NCRAC Culture Series 101 - Walleye Culture Manual 337 
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