Principles of Genetics and Breeding

12.1.1 Inbreeding and its consequences

Inbreeding is also one of the breeding programme that can have a tremendous impact on productivity. As recently as 200 years ago there were laws forbidding consanguineous matings even in livestock, because it was considered immoral and against the laws of God and Nature. But according to plant breeders, inbreeding is one of the most important breeding techniques; without its use, agricultural productivity would decline.

• Inbreeding is simply the mating of related individuals. Inbreeding does not imply, nor does the definition mention, anything about viability, growth, or productivity. (A mating between relatives is often referred to as Consanguineous mating).
  
• Inbreeding is neither good nor bad.
• Genetically, all inbreeding increases homozygosity in the offspring (this means inbreeding also decreases heterozygosity in the offspring by an equal amount).
• The increase in homozygosity occurs because related fish share alleles through one or more common ancestors, i.e. the parents may carry a copy of an allele that both inherited from a common ancestor.
• When relatives mate, the alleles that they share because of their common ancestor(s) can be paired in their offspring. This produces offspring that are more likely to be homozygous at one or more loci.
• The mating of unrelated fish also produces offspring that have homozygous genes. Additionally, an inbred fish looks the same as one with no inbreeding; there is no distinguishing mark that separates fish into inbred vs non-inbred categories.
• The two types of homozygosity are identical; there is no genetic difference.
• The only difference between inbred and non-inbred fish is that the homozygosity of each is created in different ways, but this distinction is most important.
• Inbred fish are homozygous because they have genes where the two alleles are identical by descent ; non-inbred fish are homozygous because they have genes where the two alleles are identical because they are alike in kind.
• Inbred fish are homozygous at a locus because they inherited identical copies of an allele from both parents that the parents, in turn, inherited from a common ancestor. Non-inbred fish are homozygous at a locus because they just happened to inherit an identical pair of alleles from their parents.
• This difference in the type of homozygosity is not physical or chemical. The only difference is the paths that the alleles took before they were paired to create the homozygosity ,i.e., how the alleles were inherited.
• The mating of relatives produces offspring that tend to be more homozygous than the population average.

• This increase in homozygosity is called “inbreeding”, and the coefficient of inbreeding (F) is a measure of how much more homozygous a fish is than the population average.

• The coefficient of inbreeding does not measure how many homozygous loci the fish has; it simply quantifies the percent increase in homozygosity.
• On a gene-by-gene basis, F is the probability that the two alleles will be identical by descent. Since F measures the percent increase in homozygosity, the same level of inbreeding can produce different amounts of homozygosity in different populations, depending on the level of homozygosity that has occurred over a specific time interval (number of generations) due to identity by descent (due to the mating of relatives).
• Additionally, F is based on probability, so a given value of F is an average value; consequently, a given value of F means more homozygosity will have been produced in some fish, while less will have been produced in others.
• Because inbreeding increases homozygosity, it changes genotypic frequencies, increasing the percentage of homozygous genotypes, while shrinking the percentage of heterozygous genotypes.
• If regular systems of inbreeding are conducted, the breeding programme creates a series of inbred families which do not interbreed. This subdivides a population into numerous lines, which further increases genotypic variance.

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 x DD; Dd x Dd; dd x 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 be no heterozygotes. Although this mating pattern changes genotypic frequency, the frequencies of the two alleles do not change.

• While inbreeding changes genotypic frequency, it does not change gene frequency.
• Selection, genetic drift, migration, and mutation are the evolutionary and breeding forces that change gene frequency. Inbreeding itself does not alter gene frequency, but by altering genotypic frequency inbreeding can, theoretically, accelerate selection.

During an inbreeding programme, genotypic frequencies can be drastically altered if relatively few inbred families are maintained (a type of selection). When this occurs, gene frequencies will also change. In many domesticated animals it is possible to estimate the level of inbreeding in an individual if the pedigree of the animal is known. In most fish species this is almost impossible because of the numbers involved, the difficulties in identifying broodstock and the expense involved in keeping different families of fish separate. However, as a simple basic, it is possible to calculate an average level of inbreeding from year to year for any hatchery stock.

Inbreeding is estimated from the following equations (Falconer, 1981).

1

ΔF= 2 N_e

ΔF = rate of inbreeding per generation

4 (♂) (♀)

N_e =

(♂) + (♀)

N_e = effective breeding number

♂ = number of males contributing offspring to the next generation

♀ = number of females contributing offspring to the next generation

In order to obtain a low value of ΔF then N_e has to be increased by increasing the total number of fish being bred and by bringing the sex ratio in the stock as close to 1: 1 as possible, assuming all individuals contribute offspring equally to the next generation.