Fish Breeding Programs

• There are a number of breeding programs that can be used to improve a population of fish genetically
• A fish farmer can increase fish production by increasing the size of the fish farm, and increasing the yield per volume

Breeding Approaches

• Selective breeding and crossbreeding (hybridization) are traditional approaches used for improving crops and livestock
• Additional approaches that have been developed recently are:
  • Chromosomal manipulation
  • Production of sex-reversed brood stock
  • Genetic engineering

Selective Breeding

• This is a breeding program to improve the breeding value of a population
• Selecting and mating the best fish (largest, heaviest, desired color, etc.) to transmit their superiority to their offspring
• Selective breeding increases yields, increases efficient growing, and lowers feed costs
• The result is fish with more desirable body color and increased market value

Crossbreeding

• This a breeding program that finds mating combinations that produce superior offspring that exhibit hybrid vigor
• It is a hit-or-miss proposition because results can't be predicted unless the mating has been made previously
• Many mating combinations must be evaluated to find one that produces offspring with hybrid vigor
• Can involve different strains within a species (intraspecific hybridization), or different species (interspecific hybridization)

Selective Breeding Goal

• The ultimate goal of every selective breeding program is to improve the breeding value of the population
• Breeding value is determined by the fish's genes
• Breeding is the applied science of genetics
• A farmer who conducts a selective breeding program is a breeder
• A breeder selects fish with certain phenotypes and culls fish that do not, hoping to create a genetically improved population

Genes

• Improving fish species is about manipulating the Genes
• Genes cannot be directly manipulated
• Genes are examined indirectly by examining phenotypes (traits)
• A gene or set of genes contains the blueprints or chemical instructions for the production of a protein
• The genotype is the genetic make-up of the fish
• It is the gene or genes that controls a particular phenotype

Phenotypes

• A phenotype is the physical expression of what the gene or set of genes produce
• What we describe (color/sex) or what we measure (length/weight)
• Breeders divide phenotypes into two major categories
  • Qualitative
  • Quantitative

Qualitative phenotypes

• Qualitative phenotypes are described, such as color, sex, or scale pattern
• Qualitative phenotypes are the easiest to observe because an individual falls into one discrete, descriptive, non-overlapping category or it falls into another

Quantitative phenotypes

• Quantitative phenotypes are important production traits, such as length, weight, feed conversion, and eggs/kg female
• A farmer does not separate fish into descriptive non-overlapping categories as he does with qualitative phenotypes

Quantitative Phenotypes Selection

• Selective breeding programmes that are used to improve quantitative phenotypes are more sophisticated than those that are used to fix qualitative phenotypes
• These programs are open-ended and continue year after year because it is not possible to produce true-breeding populations for these phenotypes
• Programs are designed to improve the population's mean each generation
• Selective breeding programs that are used to improve quantitative traits are open-ended
• If abandoned, gains that were realized will be lost
• Improving growth rate is the major goal of selective breeding programs related to quantitative phenotypes
• This will improve yield
• Selective breeding programs are expensive, so accurately assessing the effects of selection via phenotype's mean over time, is important

Individual Selection

• In individual selection, individuals are measured and the decision to select or cull a fish is based on its phenotypic value
• Each fish is compared to the "cut-off value“
• Fish whose phenotypic value is equal to or larger than the cut-off value are saved
• Fish whose phenotypic value is smaller than the cut-off value are culled
• The cut-off value is a pre-determined phenotypic value that is often expressed as the "top 10%" or "top 5%"
• Fish that are saved become the first generation (F1) of select brood fish

Environmental Effects

• Environmental variables have a significant influence on the production of quantitative phenotypes
• Environmental influence on phenotypic variance would be of minimal concern during selection if they were the same for all fish
• Sufficient heritable variance would be needed to enable selection to work
• Many sources of environmental variance have a differential effect on individuals or families
• Farmers must control these environmental variables when selection is used, or they will give some individuals or families an advantage

Cut-Off

• In order to create a population of select brood fish, a farmer needs to decide where to place the cut-off value.
• It can be expressed as a percentage or a minimum size
• Measure a random sample of 100-200 fish to determine the cut-off value
• Measurements are ranked, and the value to the desired percentile is the cut-off value
• For example, if the top 20% will be saved, the cut-off value is the 80th percentile

Sexual Dimorphism

• A farmer must determine if selection will be conducted in the population as a whole or separately in both sexes
• Sexual dimorphism in some species means that one sex grows to a larger size or grows faster
• If the species does not exhibit sexual dimorphism, or if selection will occur before sexual dimorphism begins, then a single cut-off value can be created for the entire population

Phenotype Selection Types

• In general, the easiest and the most efficient program is one that selects for a single phenotype
• If a farmer wants to improve more than one phenotype, he can use either:
  • Tandem selection
  • Independent culling
  • A selection index
• Tandem selection is inefficient and not recommended
• A selection index is too sophisticated for most farmers
• It is appropriate for aquaculturists who work at research stations and managers who work at fingerling production centers
• Farmers who wish to select for two, or at most three, phenotypes should use independent culling

Tandem Selection

• First, several generations of selection for one phenotype is done
• Afterwards selection stops for that trait and a new breeding program is started with selection for a second phenotype

Independent Culling

• Is one of the easiest selective breeding programmes that a farmer can use to improve two or three phenotypes
• A farmer selects simultaneously for two or more phenotypes by establishing cut-off values for each phenotype independent of the others
• Each fish must reach or exceed all cut-off values in order to be saved
• A fish which fails one cut-off value is culled

Independent Culling Liabilities

• Although independent culling is more efficient than tandem selection, it has two liabilities:
• When you select simultaneously and independently for two phenotypes, you could end up with very few select fish
• If a fish excels in one phenotype it must be culled even if it is outstanding

Modified independent culling

• Fish that meet or exceed both cut-off values are saved
• Fish that exceed one cut-off value but that are just under the cut-off value for the second phenotype are also saved

Selection Index

• Two or more phenotypes are simultaneously evaluated
• An overall numerical value is assigned to each fish, and the fish are then ranked by these numerical values
• The rankings are established so that a fish that is at the 50th percentile for every phenotype receives an I value of 100.0
• Fish that have I values > 100 are considered to be above average, while those with I values <100 are considered to be below average

Family Selection

• conducted at the family level, and individual phenotypic values are important only as they relate to their family's mean
• Used when individual selection is inefficient because the heritability of the phenotype is small (generally <0.15)
• By selecting at the family level, a significant portion of environmental variance can be negated
• This makes it easier to identify genetic differences and to select the fish that are best because of heritable variance
• It is also used when environmental sources of variance are uncontrollable, making improvement by individual selection difficult or impossible
• Family selection is the only type of breeding programme that can be used when an animal must be killed in order to determine its phenotype

Family Selection Types

• There are two major types of family selection:
  • Between-family selection
  • Within-family selection

Between-Family Selection

• The mean values for each family are determined, and the mean values are then ranked
• Whole families are then either saved or culled
• When using this type of selection, a pre-determined minimal cut-off value is not determined
• Instead, the farmer decides to save the best 10 or 15 or 20 families
• Conducted at the family level, and individual phenotypic values are important only as they relate to their family's mean
• As was the case with individual selection, sexual dimorphism can complicate selection to improve growth rate
• If a species exhibits sexual dimorphism, the males and females within each family must be weighed or measured separately
• Selection can be done separately for each sex
• The males in some families will be culled while its females are saved, and vice versa
• In order to conduct family selection, a farmer must be able to assign fish to individual families
• Two ways is to culture each family in separate tanks until they can receive family marks or brands or marks
• The fish can be grown communally but must be separated at harvest

Assigning Families

• Another method is to culture the fish in separate tanks from the moment eggs are fertilized until selection occurs
• Even after selection has occurred, if fish cannot be marked, they often must be maintained in separate units
• If fish can be marked, the select brood fish can be stocked communally until it is time to spawn them
• Each family must be cultured using the same stocking density, or differences among family means will be partly due to density differences rather than to heritable differences

Within-Family Selection

• Each family is considered a temporary sub-population, and selection occurs independently within each family
• Used when individual selection is inefficient because the heritability of the phenotype is small (generally <0.15)

Determining

• When fish are measured to determine which will be saved and which will be culled, the fish in each family are ranked, and the best fish are saved from each family
• When conducting this type of selection, a farmer usually saves the best 10 or 15 or 20 fish from each of 15 or 20 or 30 families If sexual dimorphism exists, selection must be conducted independently for each sex
• Farmers saves the best 10 or 15 or 20 males and the best 10 or 15 or 20 females from each family.

Combining Family Selection

• First, between-family selection is used to select the best families
• Within-family selection is then used to choose the best fish from each of the select families
• When between-family and within-family selection are combined, all small fish should be culled, so the population of select brood fish will contain no runts Some large fish will be culled during the between-family portion of the breeding program but, as was described earlier, their large size may be non-heritable.

Spawning Select Brood Fish

• The first and simplest is to randomly spawn the select fish
• A Rotational mating scheme includes:
  • Mate the males from family 1 to the females from family 2, mate the males from family 2 to the females from family 3, mate the males from family 3 to the females from family 4..., and mate the males from the last family to the females from family 1
• This is done to prevent or minimize inbreeding

Assessing

• Assessing results of selection with a control population means selective breeding programmes are expensive, so it is important to be able to accurately assess the results of selection The best way to compare to the phenotypes mean over time to unselected control population