Additive gene action: The type of gene action whereby each of two alleles contributes equally to the production of qualitative phenotypes; neither allele is dominant. The heterozygous genotype produces a phenotype that is intermediate between those produced by the homozygous genotypes.
Additive genetic variance (VA): The portion of phenotypic variance for a quantitative phenotype that is due to the additive effects of all alleles across all loci. This is the heritable component of variance, and it is exploited by selection. The proportionate amount of phenotypic variance due to additive genetic variance is called “heritability.”
Allele: An alternate form of a gene.
Androgen: 1) A fish that has only a male parent; all genes in an androgen come from the father. 2) Anabolic steroid hormone that causes the production of male traits.
Ancestor: A fish that appears in a previous generation in a fish's pedigree. For inbreeding purposes, it is a relative that contributed genes to the individual, either directly or via another fish.
Autosome: A chromosome that is not a sex chromosome.
Between-family selection: A selective breeding programme for quantitative phenotypes where selection occurs at the family rather than at the individual level. In this type of selective breeding programme, whole families are either culled or saved, and that decision is based on family means.
Bottleneck: A severe restriction in a population's effective breeding number.
Centromere: The constricted region of a chromosome that holds sister chromatids together.
Character: A synonym for phenotype. See phenotype.
Chromatid: One copy of a homologue that is joined to the other by the centromere. The joined pair is called “sister chromatids.”
Chromosomal manipulation: Biotechnical manipulation of eggs, sperm, or zygotes by temperature or pressure shocks either to alter chromosome set number or to create fish with only a single parent. This procedure can be used to create highly inbred fish that have only a mother (gynogens) or only a father (androgens).
Chromosome: The structure on which the genes are located. Chromosomes reside in the nucleus of each cell and, in most species, they occur in pairs. There are two types of chromosomes: autosomes and sex chromosomes.
Coefficient of inbreeding (F): The measure of inbreeding. It is the probability that the two alleles at a locus are identical by descent.
Cohort: A sub-population.
Common ancestor: A fish that is an ancestor of both parents. A common ancestor appears on both sides of a fish's pedigree. Parents that share a common ancestor produce inbred offspring.
Complete dominant gene action: A type of gene action whereby one allele is expressed more strongly than the other in the production of qualitative phenotypes: the allele that is expressed more strongly is called the “dominant allele,” and the other is called the “recessive allele.” A gene that exhibits complete dominance produces two qualitative phenotypes: a dominant phenotype and a recessive phenotype. The dominant allele always produces the dominant phenotype and suppresses phenotypic expression by the recessive allele in the heterozygous state; consequently, homozygous dominant and heterozygous genotypes both produce the dominant phenotype. The recessive phenotype is produced only when a fish is homozygous recessive.
Consanguineous mating: A “blood related” mating; i.e., a mating between relatives. A consanguineous mating produces inbred offspring.
Control population: A population of fish where no inbreeding occurs. The inbred population is compared to this population to quantify inbreeding depression.
Crossbreeding: A breeding programme where fish from different populations or species are mated to produce hybrids. Crossbreeding is used to exploit dominance genetic variance, and it can also be used to produce offspring with no inbreeding. The terms “crossbreeding” and “hybridization” are synonymous.
Crossing over: The exchange of chromosomal segments between homologues. This occurs during meiosis.
Cull: The removal of fish from the population during selection. Culled fish are not allowed to spawn.
Cut-off value: The minimum acceptable phenotypic value during selection for a quantitative phenotype. Fish that meet or exceed the cut-off value are saved; those that fall below the cut-off value are culled.
Diploid (2N): A fish or cell where chromosomes occur in pairs. Although there are naturally occurring triploid (3N) and tetraploid (4N) species, all fish are considered to be diploids is this manual.
Di-hybrid: A hybrid produced by mating two F1 hybrids.
Domestication: The selection process by which the farm (the culture environment and the management programme) and the farmer alter the genetic and phenotypic make-up of a population. This unplanned, non-directed process usually produces faster growing, healthier, calmer, and less aggressive animals that are easier to raise.
Dominance genetic variance (VD): The portion of phenotypic variance for a quantitative phenotype that is due to the interaction between the two alleles at all loci. This portion of genetic variance is not heritable because it is destroyed during meiosis. It is recreated in new and in different combinations every generation at fertilization. It is exploited by crossbreeding, and helps explain inbreeding depression.
Dominant allele: An allele that is expressed more strongly than its partner allele. When the mode of gene action is complete dominance, the dominant allele completely suppresses the recessive allele in the heterozygous state. When the mode of gene action is incomplete dominance, the dominant allele only partially suppresses the recessive allele in the heterozygous state.
Dominant gene action: The type of gene action whereby one allele is expressed more strongly than the other. There are two types: complete dominant gene action and incomplete dominant gene action.
Dominant phenotype: The qualitative phenotype produced by the dominant allele.
Effective breeding efficiency (Nb): The ratio of the effective breeding number (Ne) to the breeding population (N): Nb = Ne/N.
Effective Breeding Number (Ne): The breeding (genetic) size of a finite population. Inbreeding and genetic drift are inversely related to Ne.
Electrophoresis: A biochemical technique that determines protein phenotypes and genotypes.
Environmental variance (VE): The portion of phenotypic variance for a quantitative phenotype that is due to environmental factors (e.g., spawning date, age of mother, temperature).
Epistasis: A type of gene action where one gene suppresses or alters the qualitative phenotypes produced by a second gene. This interaction usually results in the production of new qualitative phenotypes.
Epistatic genetic variance (VI): The portion of phenotypic variance for a quantitative phenotype that is due to the interactions of alleles across loci. This portion of genetic variance is difficult to exploit, and most is non-heritable as a result of the reduction division during meiosis; consequently, it is usually ignored.
Equational division: The second meiotic division. The division of the replicated homologues (sister chromatids) that exist in the secondary gametocytes into the gametes. This is final step of meiosis.
Estrogen: Anabolic steroid hormone that causes the production of female traits.
F: The symbol for coefficient of inbreeding. It is a measure of the percent increase in homozygosity that has been created by inbreeding over the population average. For each gene, it is the probability that the two alleles are identical by descent.
F1 hybrid: A hybrid produced by mating two unrelated groups.
F1, F2, etc.: The names of the generations that are produced during a breeding programme. The F1 generation is the first generation of fish produced during a breeding programme; the F1 generation is produced by the P1 (parental) generation. The F2 generation is produced by the F1 generation, etc.
Family: A group of fish that have the same mother and father.
Family selection: A selective breeding programme for quantitative phenotypes where selection occurs at the family, rather than at the individual level. Selection is based on family means rather than on individual values. There are two types of family selection: between-family selection and within-family selection.
Founder effect: The loss of genetic variance that occurs when a population is started with a small effective breeding number.
Gamete: An egg or a sperm. Gametes are haploid (N).
Gene: The basic unit of inheritance. Genes are the chemical blueprints that determine the production of phenotypes. Genes are located on chromosomes.
Generation: The length of time it takes to replace brood fish with their offspring.
Genetic drift: Random changes in gene frequency caused by sampling error (shipment of fish from one station to another; brood stock selection). The ultimate effect of genetic drift is the loss of genetic variance. Genetic drift is inversely related to effective breeding number.
Genetic-environmental interaction variance (VG-E): The portion of phenotypic variance for a quantitative phenotype that is due to the interactions between the fish's genes and the environment. It is due to genes that are expressed differently in different environments.
Genetic variance (VG): The portion of phenotypic variance for a quantitative phenotype that is due to the genes. There are three sub-components of genetic variance: additive genetic variance (VA), dominance genetic variance (VD), and epistatic genetic variance (VI).
Genome: A fish's entire genetic make-up.
Genotype: The genetic make-up of a fish at the locus (or loci) that produces a specific phenotype. Fish are either homozygous or heterozygous at each locus.
Gynogen: A fish that has only a female parent; all genes in a gynogen come from the mother.
h2: The symbol for heritability.
Haploid (N): A fish or cell that contains only one chromosome (homologue) from each chromosome pair. Gametes are haploid.
Heritability (h2): The portion of phenotypic variance for a quantitative phenotype in a given environment that is due to additive genetic variance (h2 = VA/VP). Heritability describes the percentage of phenotypic variance that is heritable. Phenotypes with h2's >0.25 can be improved efficiently by individual selection; those with h2's <0.15 are difficult to improve by individual selection, and family selection is usually used. Inbreeding can be used to improve the results of family selection when h2>0.15.
Heritable: Something that is transmitted from a parent to its offspring.
Heterozygote: A fish with two different alleles at a locus.
Heterozygous: The genotype that occurs when the pair of alleles at a locus are not identical. Inbreeding decreases the percentage of heterozygous loci.
Heterozygous phenotype: The qualitative phenotype produced by the heterozygous genotype. A heterozygous phenotype can be produced when the mode of gene action is incomplete dominance or additive.
Herd bull: The only male in a population. A herd bull is mated with all females.
Homologues: The two chromosomes that combine to form a chromosome pair. One homologue comes from the father, while the other comes from the mother.
Homozygote: A fish with an identical pair of alleles at a locus.
Homozygous: The genotype that occurs when the pair of alleles at a locus are identical. Inbreeding increases the percentage of homozygous loci. The coefficient of inbreeding (F) is a measure of the increase in homozygosity that has occurred because relatives mated.
Homozygous phenotype: The qualitative phenotype produced by the homozygous genotype. When the mode of gene action is complete dominance, the recessive phenotype is the homozygous phenotype. When the mode of gene action is incomplete dominance or additive, there are two homozygous phenotypes.
Hybridization: A synonym for crossbreeding. See crossbreeding.
Inbreeding: The mating of relatives.
Inbreeding depression: Declines in growth rate, fecundity, etc. and an increase in the percentage of deformed/abnormal fish that occur because of inbreeding.
Incomplete dominant gene action: A type of gene action whereby one allele is expressed more strongly than the other during the production of qualitative phenotypes, but the dominant allele cannot suppress the recessive allele in the heterozygous state. Two copies of the dominant allele are needed to produce the dominant phenotype. Because the recessive allele is able to function in the heterozygous state, that genotype produces a phenotype (the heterozygous phenotype) that is marginally different from the dominant phenotype. The recessive allele produces a third phenotype (the recessive phenotype) when the fish is homozygous recessive.
Independent assortment: The segregation of homologues of each chromosome pair (and the genes on these chromosomes) into the secondary spermatocytes or into the secondary oocyte and the first polar body. The segregation of the homologues of each chromosome pair is independent of that which occurs in all other chromosome pairs. This process destroys all dominance genetic variance and most epistatic genetic variance.
Indirect selection: Changes that occur for one phenotype when selection is placed on another. A breeding programme that improves one phenotype by selecting for another. This occurs because the two phenotypes have a positive genetic correlation.
Individual selection: A selective breeding programme for quantitative phenotypes where selection is based on individual merit. An individual whose phenotypic value is equal to or exceeds the cut-off value is saved, while those whose phenotypic value falls below the cut-off value are culled. Family relationships are ignored. Individual selection is also called “mass selection.”
Linebreeding: An inbreeding programme where an outstanding individual (usually a male) is mated with its descendants to increase its contribution to the gene pool.
Linkage: Genes are linked when they are located near each other on a chromosome. Linked genes tend to cross over together.
Locus (plural = loci): The location of a gene on a chromosome. The terms “gene” and “locus” are often used interchangeably, and they are used synonymously in this manual.
Mass selection: A synonym for individual selection. See Individual selection.
Mean: The arithmetic average.
Meiosis: The process by which the diploid (2N) complement of chromosomes is reduced to the haploid (N) state during gametogenesis. Heritable mutations, crossing over, and independent assortment occur during meiosis.
Meiotic gynogen: A gynogen that is created by chromosomal manipulation by: 1) fertilizing an egg with irradiated sperm; and 2) shocking the egg to prevent the second polar body from leaving. The haploid second polar body and haploid egg nucleus fuse to form a diploid gynogen; consequently, all genes come from the mother.
Mitotic androgen: An androgen that is created by chromosomal manipulation by: 1) fertilizing an irradiated egg; and 2) shocking the haploid zygote during first cleavage to prevent nuclear and cell division. Mitotic androgens are 100% homozygous and 100% inbred; additionally, all genes come from the father.
Mitotic gynogen: A gynogen that is created by chromosomal manipulation by: 1) fertilizing eggs with irradiated sperm; and 2) shocking the haploid zygote during first cleavage to prevent nuclear and cell division. Mitotic gynogens are 100% homozygous and 100% inbred; additionally, all genes come from the mother
Monomorphic: When there is only one allele at a given locus in a population.
Monosex population: A population composed only of males or only of females.
Mutation: A mistake that occurs during chromosomal replication. When a mutation occurs, a gene is incorrectly replicated during the creation of the new chromosome. This new allele may be capable of producing a different (mutant) phenotype. Many mutant alleles produce lethal or sub-viable phenotypes. The accumulation of recessive sub-viable and lethal mutations and their subsequent pairing and expression when relatives mate is a major factor in inbreeding depression.
Neutral gene: A gene where all phenotypes are equally fit; i.e., no phenotype and thus no genotype give a fish a selective advantage.
Nick: The production of superior hybrids.
Overdominance: When the heterozygous phenotype is superior to the two homozygous phenotypes. Inbreeding decreases the frequency of overdominance phenotypes, which helps explain inbreeding depression.
P1: The parental generation; the fish that are used to start a breeding programme. The P1 generation produces the F1 generation.
Pedigree: An individual's family tree.
Pedigreed mating: A system of mating in which each male leaves one son and each female leaves one daughter for the following generation's brood stock. The choice of sons and daughters must be random.
Phenotype: The physical expression of a fish's genotype. There are two phenotypic categories: qualitative phenotypes, which are described; quantitative phenotypes, which are measured. The terms “phenotype,” “trait,” and “character” are used interchangeably.
Phenotypic variance (VP): The total variance that is measured for a quantitative phenotype in a population. It is the sum of genetic variance, environmental variance, and genetic-environmental interaction variance.
Polymorphic: When there are two or more alleles at a given locus in a population. In population genetics, this means that there are at least two alleles whose frequencies are >0.01.
Population: A group of fish that have a common background.
Progeny testing: A breeding programme that is used to decipher a fish's genotype by examining its offspring's phenotypes.
Qualitative phenotypes: Phenotypes that are described: for example, colour.
Quantitative phenotypes: Phenotypes that are measured: for example, weight.
Random mating: A system of mating where fish are mated without regard to phenotype.
Recessive allele: An allele whose phenotype is expressed only when an individual has two copies of the allele (homozygous recessive). The pairing and expression of detrimental recessive alleles helps explain inbreeding depression.
Recessive phenotype: The qualitative phenotype produced by the recessive allele.
Reduction division: The first meiotic division. The separation (segregation) of replicated homologues of each chromosome pair (independent assortment) during the creation of the secondary spermatocytes or of the secondary oocyte and the first polar body during meiosis. This destroys all dominance genetic variance and most epistatic genetic variance.
Rotational mating: A mating programme where families or cohorts are mated in a staggered manner over successive generations to prevent inbreeding.
Select population: The population that is created by selection.
Selection: A breeding programme whereby a breeder saves only those individuals or families that meet or exceed predetermined phenotypic criteria for quantitative phenotypes or those individuals that exhibit the desired qualitative phenotype. Fish that do not meet these criteria are culled.
Sex chromosome: The chromosomes that determine sex. They can be morphologically different in males and females, but in most species of fish there is no obvious morphological difference.
Sex-reversed: Fish that are one sex phenotypically but the other genetically. Sex-reversed fish are created by feeding anabolic sex hormones to sexually undifferentiated fry.
Sibs: Brothers and sisters. Fish that have the same mother and father are full-sibs. Fish that have the same mother or the same father, but not both, are half-sibs.
Sister chromatids: A homologue and its replicated “twin”; they are joined at the centromere.
Standard deviation: The square root of the variance. The standard deviation is a value that describes how phenotypic values are disbursed about the mean. When combined with the mean, it is the best way to describe a quantitative phenotype.
Test fish: A fish whose genotype is known. Test fish are mated to fish whose genotypes are to be deciphered during a progeny test. Test fish are usually homozygous recessive.
Tetrad: A bundle of four chromosomes. Tetrads occur when the homologues of each chromosome pair replicate, become sister chromatids, and then pair-up during the early stages of meiosis. Crossing over occurs when the chromosomes exist as tetrads.
Tetraploid: A fish or cell where each chromosome occurs in sets of four.
Topcross: An F1 hybrid that is produced by mating an inbred line to a non-inbred or random-bred line. This technique often produces outstanding F1 hybrids.
Trait: A synonym for phenotype. See phenotype.
Triploid (3N): A fish or cell where each chromosome occurs in sets of three.
Variance: The average squared deviation of phenotypic values from the mean. It is a value that describes how phenotypes are disbursed about the mean. The square root of the variance is called the “standard deviation.”
Within-family selection: A selective breeding programme for quantitative phenotypes, whereby selection occurs at the family rather than at the individual level. In within-family selection, each family is considered to be a sub-population, and selection occurs independently within each family.
Zygote: The cell that is created when a sperm fertilizes an egg. This is often called a “fertilized egg.”
