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.
Autosomal gene - A gene located on an autosome, which are the non-sex chromosomes.
Autosomal phenotype - A qualitative phenotype produced by an autosomal gene. Autosomal phenotypes are expressed identically in males and females, unless a sex hormone is needed for phenotypic expression.
Autosome - A non-sex chromosome. The autosomes are the pairs of chromosomes that are the same in males and females.
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.
Chromosomal manipulation - Biotechnical manipulation of eggs, sperm, or zygotes by temperature or pressure shocks or with chemicals either to alter chromosome set number or to create fish with only a single parent. This is used to create triploid (3N) or tetraploid (4N) fish and to create fish that have only a mother (gynogens) or only a father (androgens). The creation of triploids is done to produce a population of sterile fish.
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.
Cohort - A sub-population. If a population is divided into several groups based on spawning date, the population is divided into age cohorts.
Common phenotype - The normal qualitative phenotype. This is the phenotype that most individual's have. A common phenotype is also called a “wild-type phenotype.”
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.
Control population - A population of fish where no selection occurs. The select population is compared to this population to quantify the gain that occurred as a result of selection.
Crossbreeding - A breeding programme where fish from different populations or species are mated to produce hybrids. Crossbreeding is used to exploit dominance genetic variance. In some cases, it can be used to produce monosex populations (e.g., tilapia) or sterile populations (e.g., baitfish). The terms “crossbreeding” and “hybridization” are synonymous.
Crossing over - The exchange of sections of chromosomes (and thus genes) during meiosis. This occurs during tetrad formation.
Cryopreservation - The freezing and storage of gametes (usually sperm) so they can be used at a later date.
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.
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; instead, it is recreated in new and in different combinations every generation at fertilization. It is exploited by crossbreeding.
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.
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 (Vl) - 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 division of the replicated homologs that exist in the secondary gametocytes into the gametes. This is final step of meiosis.
F1, F2, etc. - The names of the generations that are produced during a breeding programme. The F1 generation is the first generation of select brood fish, which are chosen from the P1 generation; F1generation select fish are the offspring that are produced by the initial (F1) generation of select brood fish. The F2 generation (second generation of selection) is the descendants of 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.
Fix - To make the frequency 100%. The goal of a selective breeding programme that works with qualitative phenotypes is to fix the desired phenotype by fixing the allele that produces it. This will produce a true-breeding population.
Gamete - An egg or a sperm. Gametes are haploid (N).
Gametogenesis - The process by which gametes are produced. The portion of gametogenesis that deals with the reduction of the chromosome complement from the diploid (2N) to the haploid (N) state is called “meiosis.”
Gene - The basic unit of inheritance. Genes contain the 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. In nature, it is the time it takes fish to become sexually mature and spawn. In aquaculture, this time period can be lengthened or shortened, either by retaining the brood fish for a longer period before they are replaced or by speeding up maturity in the offspring via culture techniques. Progress, in terms of gain per year, is partially determined by the generation interval.
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 (V,).
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.
Haploid (N) - A fish or cell that contains only one chromosome from each chromosome pair. Gametes are haploid. Haploid fish will not survive, but they can be created by chromosomal manipulation.
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 heritabilities ≥O.25 can be improved efficiently by individual selection; those with heritabilities, ≤ 0.15 are difficult to improve by individual selection, and family selection is usually used. A heritability ≥0.3 is considered to be large.
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.
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.
Homologues - The two chromosomes that combine to form a chromosome pair. One of the homologues 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.
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.
Importance factor - A value derived by dividing the phenotypic mean by the relative importance of the phenotype. Importance factors are used in a modified selection index to establish the I value (the breeding value) for a fish when conducting a selective breeding programme that incorporates two or more quantitative phenotypes.
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 when inbreeding reaches certain levels.
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 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.
Independent culling - A selective breeding programme that is used to simultaneously select for two or more quantitative phenotypes. Cut-off values are created for all phenotypes, and a fish must meet or exceed all cut-off values in order to be saved.
Indirect selection - 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.”
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.
Modified independent culling - A variation of independent culling. In modified independent culling, fish that are superior for one trait can be saved, even if their other phenotype's value falls below the cut-off value.
Monosex population - A population composed only of males or only of females.
Mutant allele - An allele that is created when a portion of a chromosome is replicated incorrectly during meiosis.
Mutant phenotype - A qualitative phenotype that is produced by a mutant allele; a qualitative phenotype that is different from the normal or common phenotype.
Mutation - A mistake that occurs during chromosomal replication. When a mutation occurs, a gene is incorrectly replicated on 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 mutation rate for each gene is very low.
P1 - The parental generation. F1 select brood fish are chosen from the parental generation.
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” and “trait” are used interchangeably.
Phenotypic variance (Vp) - The 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.
Pleiotropy - Secondary effects that occur when fish have a particular qualitative phenotype. Many alleles that control the production of qualitative phenotypes can also affect traits such as growth and survival. If growth and survival are affected, the pleiotropic effects can be of greater economic importance than the phenotype (colour or scale pattern) itself.
Population - A group of fish at a fish farm that have a common background.
Progeny testing - A breeding programme that is used to decipher a fish's genotype by examining it offspring's phenotypes.
Qualitative phenotypes - Phenotypes that are described: for example, colour, scale pattern, and sex.
Quantitative phenotypes - Phenotypes that are measured: for example, weight, length, eggs/kg female, and dressing percentage.
Recessive allele - An allele whose phenotype is only expressed when an individual has two copies of the allele (homozygous recessive).
Recessive phenotype - The qualitative phenotype produced by the recessive allele.
Reduction division - The separation (segregation) of homologues of each chromosome pair during the creation of the secondary spermatocytes or of the secondary oocyte and the first polar body during meiosis. This phase of meiosis destroys all dominance genetic variance and most epistatic genetic variance.
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.
Selection differential - The difference between the mean of the select brood fish and the mean of the population from which they were chosen.
Selection index - A selective breeding programme that can be used to simultaneously select for two or more quantitative phenotypes. A selection index assigns a numerical value to each fish (I), based on the individual's phenotypic values relative to the population means and on how important the phenotypes are. Once each fish has received its overall numerical value, the fish are ranked, and selection is based only on these values.
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-linked gene - A gene located on a sex chromosome. These genes are inherited and expressed differently in males and females.
Sex-linked phenotype - A qualitative phenotype produced by a sex-linked gene.
Sex-reversed - Fish that are one sex phenotypically but the other genetically. Sex-reversed fish are created by feeding sex hormones to sexually undifferentiated fry. Sex-reversed fish can be used to produce monosex populations.
Sexual dimorphism - This occurs when there are marked phenotypic differences between the sexes. The differences can be qualitative in that phenotypes are present or absent, such as colour or breeding tubercles; or they can be quantitative, in that one sex grows faster and is larger. If sexual dimorphism exists for body size, selection for growth rate must be conducted independently in males and females.
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.
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.
Tandem selection - A selective breeding programme that can be used to improve two or more quantitative phenotypes. Initially, you select for only one phenotype for several generations; then you stop selecting for that phenotype and select for the second 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 and then pair-up during the early stages of meiosis.
Trait - A synonym for phenotype. See Phenotype.
Triploid (3N) - A fish or cell where each chromosome occurs in triplicate (the cells contain three sets of chromosomes). Triploids are usually created by temperature or pressure shocks; this type of breeding programme is used to produce sterile fish.
True-breeding - A population that is capable of producing only one qualitative phenotype, because only one allele exists at the locus in question. When working with qualitative phenotypes, the goal of a selective breeding programme is to produce a true-breeding population.
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.”
Wild-type phenotype - A synonym for common phenotype. See Common phenotype.
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.”