Inbreeding in Fish

Inbreeding

Inbreeding is breeding between close relatives, or the mating of fish more closely related than the population average .

If practiced repeatedly,

It leads to an increase in homozygosity of a population.
A higher frequency of recessive, deleterious traits in homozygous form in a population can, over time, result in inbreeding depression.
This may occur when inbred individuals exhibit reduced health and fitness and lower levels of fertility.

Inbreeding may result in a far higher phenotypic expression of deleterious recessive genes within a population than would normally be expected. As a result, first-generation inbred individuals are more likely to show physical and health defects, including:

# reduced fertility in sperm viability

# increased genetic disorders

# fluctuating facial asymmetry

# lower birth rate

# higher infant mortality

# slower growth rate

# smaller adult size

# loss of immune system function.

Uses of inbreeding

-Inbreeding is a breeding programme that can be used to produce superior animal and plant brood stock, and it can also be used to produce genetically improved animals and plants for grow-out.

-Inbreeding is the breeding programme that is often used to create new breeds or varieties that breed true for “type”; i.e., a particular body conformation or set of qualitative phenotypes.

-Line-breeding is a form of inbreeding that is used to increase an outstanding animal’s contribution to a population.

-Inbreeding can be used as a type of progeny testing to create defect-free animals.

-Inbreeding is often combined with crossbreeding to increase hybrid vigour.

Inbreeding depression

As inbreeding increases, it often causes a decrease in productivity which is termed “inbreeding depression.”
Inbreeding depression is a decrease in growth rate, fecundity, etc. that is observed in the inbred group when it is compared to a control population where there is no inbreeding.
Inbreeding depression is what gives inbreeding its bad reputation.
The most common explanation is that inbreeding depression occurs because of the pairing and expression of detrimental recessive alleles.

Although the terms “dominant” and “recessive” do not mean that one allele is good and the other undesirable, most of the alleles that produce abnormal phenotypes or that lower viability are recessive. Most of the mutant alleles are recessive.

Since recessive alleles can be expressed only when a fish is homozygous, these mutations tend to accumulate in a population. Consequently, many fish carry “hidden” copies of these mutant alleles in the heterozygous state.

Mutations do not have to be bad; some increase fitness or lead to the evolution of new species by creating new or improved phenotypes. But most mutations lower fitness, because they cause random changes in a phenotype.

Each fish carries a number of these detrimental recessive alleles, and inbreeding uncovers them. When relatives mate, they produce offspring with an increased level of homozygosity; consequently, some of the detrimental recessive alleles that the parents carry in the unexpressed heterozygous state are paired and expressed in the offspring.

The effect of inbreeding on genotypic and gene frequencies. In the P1 generation, all fish are heterozygotes (Dd). In every generation, the following matings are made: DD × DD; Dd × Dd; dd × dd. These matings reduce the percentage of heterozygotes and increase the percentage of homozygotes. In the F3 generation, only 12.5% of the fish are heterozygotes, while 87.5% are homozygotes. Eventually, there will no heterozygotes. Although this mating pattern changes genotypic frequency, the frequencies of the two alleles do not change.

CALCULATING AVERAGE INBREEDING VALUES IN HATCHERY POPULATIONS

# Most farmers and hatchery managers cannot calculate individual inbreeding values for fish that they culture, because individual fish cannot be identified.

#This does not mean that inbreeding values cannot be determined for hatchery fish. Even though individual inbreeding values cannot be calculated, population averages can be and should be determined.

# Average inbreeding values should be determined for all hatchery populations every generation, and the acquisition and use of these data should be an integral part of hatchery management.

# The average inbreeding value of a population is determined from the population’s effective breeding number (Ne). Effective breeding number is one of the most important bits of information that can be gathered about a hatchery population, and Ne should be determined every generation for all hatchery populations.

# Effective breeding number is traditionally calculated by counting the number of males and number of females that produce viable offspring.

#Effective breeding number and the average inbreeding value are important population descriptors, because they help explain trends in yield, fecundity, and other important production phenotypes. These values also enable a farmer to predict if problems will occur as a result of inbreeding depression or the loss of genetic variance. Proper brood stock management cannot be accomplished without this information

EFFECTIVE BREEDING NUMBER (Ne)

# Effective breeding number is one of the most important concepts in brood stock management, because it gives an indication about the genetic stability or genetic health of the population. This is because N_e is inversely related to inbreeding and to genetic drift.

# If hatchery populations were infinitely large, an understanding of N_e would be unnecessary. However, hatchery populations are usually small and are often closed. A closed population is one where immigration (the introduction of fish from another population) is not allowed; consequently, fish from other populations are not allowed to mate with or hybridize with fish from a closed population.

# When working with a closed, finite population, the best way to describe it is not by total number of fish, but by N_e. Effective breeding number is determined by the number of male and female brood fish that produce viable offspring, the sex ratio of the brood fish that spawned, the variance of family size, and the mating system that is used.

# In most situations where fish cannot be identified and where mating is random, N_e can be determined by using the following formula:

Where number of males and number of females are the number of male and female brood fish that produce viable offspring. If all offspring for a brood fish die, that male or female is not included when determining N_e.

# If mating and offspring production cannot be monitored, N_e cannot be determined.

# The formula shows that N_e is determined both by the number of male and female brood fish and by the sex ratio.

# For example, if 53 female brood fish produced eggs and if 25 males were used to fertilize those eggs and if all brood fish produced viable offspring, N_e is:

Ne = 67.95

# This example illustrates a fundamental concept of brood stock management: The genetic size of the population (Ne) and the number of fish that produce offspring are not always the same; the genetic size is usually smaller. Seventy-eight brood fish produced offspring, but Ne was only 67.95. The reason Ne was smaller is because the sex ratio was skewed; in this example, the sex ratio was 2.12 females: 1 male (53 females:25 males).

# Effective breeding number and the number of brood fish that produce offspring will be the same only when the sex ratio is 1:1. In the above example, there were 78 total brood fish, so a 1:1 sex ratio would have been 39 females:39 males. If these numbers were used to produce offspring, Ne would have been:

Effective breeding numbers produced by various combinations of males and females.

Once N_e has been determined, a simple formula can be used to calculate the average inbreeding value in the population:

where F is the average inbreeding value in the population. For example, if N_e = 100, the average inbreeding value for the fish in the population is:

F=0.005

This value is assigned to every offspring produced by those brood fish.

The formula shows that F is inversely related to N_e: a large N_e produces a small F; a small N_e produces a large F.

Figure shows how much inbreeding will be produced by various N_e‘s for a single generation. The relationship between F and N_e in this formula clearly demonstrates why it is important to calculate N_e and why management of N_e is of paramount importance in the management of hatchery populations.

Effective breeding numbers produced by various combinations of males and females.

GENETIC DRIFT

# Genetic drift is the second important genetic concept that is a function of Ne.

# Genetic drift is random changes in gene frequency; it is a major factor in evolution and population biology.

# The effects of genetic drift can be devastating.

# Genetic drift can irreversibly alter gene frequencies and eliminate alleles, which can decrease a population’s ability to survive or to adapt to an altered environment, and it can preclude future selection.

# The effect that genetic drift can have on a population’s gene pool can make many management goals impossible to achieve.

EFFECTIVE BREEDING NUMBER AND GENETIC DRIFT

# Genetic drift is random changes in gene frequency that occur because of sampling error.

# Sampling error can be natural, or it can be manmade.

# Natural sampling errors are those which occur when earthquakes, floods, landslides, or other natural disasters subdivide a population and isolate small groups of organisms. This process is a major force in the evolution of new species.

# Manmade sampling errors are inaccurate collections: sampling only a portion of the population, sampling only a single age class, sampling only fish that possess a certain phenotype or that spawn on a particular day, etc.

# When a population is sampled, there is a chance that the sample does not accurately reflect the make-up of the population. This inaccuracy can include length, sex ratio, body colour, and gene frequencies. The smaller the sample, the greater the likelihood that inaccuracies in the sample will occur.

# Changes in gene frequency that occur as a result of sampling error are called “genetic drift.”

When culturing fish, the important changes that can occur in gene frequency as a result of genetic drift occur during the creation of the next generation (during spawning season) or during the acquisition of the population.

This is when the genes are transferred from parents to offspring (the transfer of genes across time; from one generation to the next) or when they are transferred from one hatchery to another (the transfer of genes across space).

As was the case with inbreeding, Ne is the factor that determines the magnitude of genetic drift. The relationship between Ne and genetic drift is:

where: σ²_Δq is the variance in the change of gene frequency, and p and q are the frequencies of alleles p and q for a given gene. The variance of the change in gene frequency is the way genetic drift is measured.

Like average inbreeding value, genetic drift is also inversely related to Ne.

The probability of losing an allele by genetic drift is determined by using the following formula:

P = (1.0 – q)2Ne

where: P is the probability of losing an allele, and q is the frequency of the allele.

For example, if Ne is 50, the probability of losing an allele whose frequency is 0.1 (q = 0.1) is:

P = (1.0 – 0.1)2(50)

P = (0.9)100

P = 0.0000265

If Ne is 10, the probability of losing the same allele is:

P = (1.0 – 0.1)2(10)

P = (0.9)20

P = 0.12158

These examples clearly show that the probability of losing an allele is inversely related to Ne; the probability of losing the allele was 4,588 times greater when Ne decreased from 50 to 10

USING INBREEDING TO IMPROVE GROWTH AND OTHER PHENOTYPES

To manage the genetic aspects of a population, one must know how inbreeding can be used to improve productivity and profits.
Inbreeding is one of the three major traditional breeding programs that breeders have used for centuries to improve animals and plants.
While it is not as important as selection or crossbreeding, inbreeding is used to produce genetically improved livestock, plants, and laboratory animals. Inbreeding might be the most important breeding technique used in the production of laboratory animals, because genetically uniform lines of rats, mice, etc. are desired for biological and medical research.
Inbreeding has been used to create better, faster growing livestock, and new technologies have improved the ability to create and use highly inbred fish to improve a population or for research purposes.
Inbreeding programs should be far easier with fish than with livestock, because many species can be stripped, which enables fish culturists to create mating combinations. Additionally, fish are highly fecund when compared to livestock, so different types of inbreeding programs can be used.

INBREEDING PROGRAMS: Although selection and crossbreeding are the breeding programs that are usually considered to improve a population genetically, inbreeding is a third option that can be used to produce good results.

Inbreeding is generally shunned because it is a two-edged sword that can mortally wound a population. However, when used properly, inbreeding can be an effective and efficient breeding program.
Inbreeding programs are used when you have superior animals. If you inbreed average animals, you produce average animals. But if you inbreed superior animals, you can create outstanding animals.

Some of the ways inbreeding programs can be used

Creation of new breeds

Inbreeding is often used when a new breed, strain, or variety is founded. In many cases it is inevitable and unavoidable. New breeds can be formed as the result of a fortuitous hybrid, or they can originate from a single individual with an unusual or desirable phenotype. When breeds or strains are first created, there may be only a few males in the breed, and one is considered to be far superior to all others. When this happens, that male is bred to many females and to a good percentage of his daughters and granddaughters in order to produce a population of animals that resembles him. This is how a breed “type” (a particular body conformation) is created. A second round of inbreeding can occur if only one or two of the male’s sons are used.

Linebreeding

Linebreeding is an inbreeding program whereby an individual is mated to its descendants. Traditionally, a single male is bred to many females. Most linebreeding programs that are used in livestock husbandry only linebreed males, because fecundity is low and gestation periods are long. However, in aquaculture the fecundity of fish should enable farmers and hatchery managers to use females as well as males in linebreeding programs. Linebreeding can be used when the breed is in its infancy to develop the breed, or it can also be used in an established breed or strain when an outstanding animal is discovered. Linebreeding is used to increase an outstanding individual’s contribution to a population, especially when a farmer thinks that the animal is so superior that it is unlikely that he will ever find a better one.

Inbreeding to expose and cull detrimental recessive alleles

Inbreeding can be used as an extreme form of progeny testing to expose detrimental recessive alleles and eliminate families that carry these undesired genetic bombs. Progeny testing is a selective breeding program that is often used to accomplish this, but progeny testing is usually used to eliminate only one recessive allele. Progeny testing is a breeding program where fish with the dominant phenotype are mated to a test fish (one that is homozygous recessive) to identify and cull the heterozygotes and to identify and save the homozygotes.

Inbreeding to improve the results of between-family selection

Inbreeding can be used to improve the results of selection when the h2 for a trait is small. When h2 is small, inbreeding can be used to create inbred families which will further magnify the heritable differences among the families. Inbreeding makes it easier to assess the heritable differences among families, by minimizing some of the non-heritable sources (V_D, V_I, and V_E). Inbreeding does not change the absolute amount of V_A; it changes relative amount, which improves the breeder’s ability to identify and save families which are superior because of V_A.

Creation of inbred lines for crossbreeding programmes

Once a breed is established, perhaps the most important use of inbreeding is to develop inbred lines that will be used in crossbreeding programmes to produce outstanding hybrids for grow-out. Crossbreeding and inbreeding are mating extremes along a continuum: inbreeding is the mating of animals that are more closely related than the average in a population, and crossbreeding is the mating of animals that are less related than the average in a population.

PREVENTING INBREEDING DEPRESSION AND LOSS OF GENETIC VARIANCE IN HATCHERY POPULATIONS

Unless a farmer is going to conduct a selective breeding program or use inbreeding to improve the results of selection or crossbreeding, a population should be managed genetically to prevent unwanted inbreeding from causing inbreeding depression and to prevent genetic drift from robbing the population of alleles and genetic variance.

If fish can be marked, inbreeding depression can be prevented by creating pedigrees and by preventing consanguineous matings or by preventing matings between relatives more closely related than second cousins.

Marking fish and preventing consanguineous matings will not prevent genetic drift. Managing a population to minimize the effects of genetic drift can be accomplished only by managing Ne.

When fish are not marked (which will be the case for most hatchery populations), the only way to prevent unwanted inbreeding from accumulating and to prevent the ravages of genetic drift is to manage the population’s Ne. When a farmer is not using a breeding program to improve a population, managing a population’s Ne is probably the most important aspect of brood stock management. A population’s Ne is one of the most important pieces of information about the population, because Ne is inversely related to both inbreeding and genetic drift. Consequently, managing Ne is a key aspect of fish husbandry. There is no universal Ne that can be used to manage every population. It must be customized for each population. This chapter outlined the techniques and methods that must be used to determine the Ne that is needed. That number can be determined by answering a series of questions: One, what level of inbreeding will cause problems? Two, what is the frequency of the rare alleles that a farmer wants to save, and what guarantee does he want that the alleles have been saved? Three, how many generations does the farmer want to incorporate into the work plan before that level of inbreeding has been reached and when the guarantee will end?

The levels of inbreeding that cause problems in hatchery populations are not known, so appropriate levels must be determined by a “guesstimate.” Two values were proposed: 5% and 10%. The value chosen depends on how important the population is and what the goals are. Populations that are being cultured for food can use either 5% or 10%. Populations that are being cultured for stocking program must use 5%; if possible, lower levels should be used for these populations. The frequency of the rare alleles that should be saved depends on the population. If the fish are being farmed, the frequency should be 0.05 for most farmers who wish to manage their populations genetically, and 0.01 for those who have the ability and desire to conserve as much genetic variance as possible. If the population is being cultured for stocking program the frequency should be no greater than 0.01; if possible, the frequency should be 0.005-0.001. These frequencies are not absolute but are presented as guideline values.

When managing a population’s Ne, the major goal is to maintain Ne at a constant level every generation. If Ne drops below the desired value for a single generation, the genetic goals cannot be achieved. Maintaining Ne at the desired level generation after generation may be the most difficult aspect of brood stock management, because Ne can decline for a variety of reasons. Sudden and drastic decreases in Ne are called bottlenecks, and they can cause permanent and irreversible genetic damage.

Finally, there are a number of management techniques that can be used to increase Ne or that can be used to produce the same level of inbreeding but with a smaller number of brood fish: pedigreed mating; stretching generations; bringing the sex ratio closer to a 1:1 ratio; and altering some fertilization techniques when gametes are stripped.

Multiple Allelism

So far we have only studied traits controlled by two alleles. This is easy to visualize because diploid organisms can only possess two alleles. However, within a population, more than two alleles can exist (although any given individual only has two alleles) at a locus for a gene.

The human ABO blood groups are an example of multiple alleles, and the relationship between phenotype and genotype is depicted in the figure below. There are four possible phenotypic blood types for this particular gene: A, B, AB, and O. The letters refer to two specific carbohydrate molecules on the surface of red blood cells. Individuals can have the A carbohydrate (blood type A), the B carbohydrate (blood type B), both the A and B carbohydrates (blood type AB), or neither carbohydrate (blood type O). Here more than two alleles are present.

The ABO gene codes for an enzyme that modifies carbohydrates found linked
to proteins on the surface of red blood cells. The A allele codes for a
version of the enzyme that generates the A-antigen, which is a
carbohydrate. The B allele codes for a different version of the enzyme,
which generates the B-antigen, which is a different carbohydrate. The O
allele apparently codes for a defective or modified enzyme that doesn’t
modify the precursor to the A and B-antigens so it leaves the carbohydrate
unmodified. The reason for the dominance relationships seen among the three ABO alleles is clear from this biochemistry. The A and B alleles are co-dominant because when both are present both act to generate their respective
antigens. The O enzyme doesn’t do anything so it is recessive. There are subtypes under ABO grouping some of which are quite rare. Apart from this there is a protein which plays an important part in the grouping of blood. This is called the Rh (Rhesus antigens) factor. If this is present, the particular blood type is called positive. If it is absent, it is called negative. Most of us, for example, know our blood type in the ABO system as A-positive, A-negative, B-positive, B-negative, O-positive, O-negative, AB-positive, AB-negative.