Fish genetics BY: DAUDI NKUKURAH

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Genetics of the cultured fish species

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Fish genetics:

Fish genetics NKUKURAH, D.K nkukurahd@yahoo.com

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The goal of every selective breeding programme is to improve the breeding value of the population. The breeding value is determined by the fish's genes. Improved breeding value of the population will improve monetary value, which is determined by the fish's phenotypes. Select (save) fish that possess certain phenotypes and cull (remove) those that do not. The fish in the next generation will be more valuable because their genes will enable them to grow faster or to exhibit a more desirable colour. Introduction

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The goal of a selective breeding programme is to manipulate a population's genes thus to produce better fish. It is impossible to examine and manipulate the genes directly. Instead, a fish's genes are examined indirectly by examining its phenotypes /traits. Important is to understand how the genes are transmitted from a parent to its offspring and how the genes produce the phenotypes. This helps explain how selection works. This ensures success.

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The material in this chapter, especially that dealing with quantitative phenotypes, is intended for extension agents and for highly educated aquaculturists.

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Difference between Meiosis and Mitosis

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Meiosis I Interphase Prophase I Metaphase I Anaphase I Telephase I

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Meiosis II Prophase II Metaphase II Anaphase II Telephase II

Spermatogenesis:

Spermatogenesis

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Oogenesis in the Ovary

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Oogenesis

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Phenotype and genotype Phenotype: The phenotype is the physical expression of what the gene or set of genes produce, and this is what we describe (for example, colour or sex) or measure (for example, length or weight). Breeders divide phenotypes into two major categories: qualitative phenotypes and quantitative phenotypes . A gene or set of genes contains the blueprints or chemical instructions for the production of a protein. This protein either forms or helps produce various phenotypes.

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The genotype: is the genetic make-up of the fish. It is the gene or genes that controls a particular phenotype. Because chromosomes occur in pairs, genes also occur as pairs but there are some exceptions. The genotype is a paired entity. A gene can occur in more than one form. Alternate forms of a gene are called “alleles.” In a population, a gene may exist in only one form, which means that there is only one allele at a given locus (locus = gene), or there may be up to a dozen alleles at a locus.

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Genetics of qualitative phenotypes Qualitative phenotypes are the phenotypes that are described, such as colour, sex, or scale pattern. The genetics of qualitative phenotypes is simple and is often called “Mendelian genetics” . These phenotypes are usually controlled by one or two genes. The alternate forms of a phenotype (for example, blue vs yellow) are produced by the alternate forms of a gene (alleles). Often, the normal phenotype is called the “common” or “wild-type” phenotype, while the others are referred to as “mutant” phenotypes.

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Qualitative phenotypes are often called “cosmetic” because they primarily affect an individual's appearance. But this does not mean that they are unimportant. These phenotypes can improve health or make the product more acceptable to consumers. For example: dwarf is a desired phenotype in many varieties of wheat because short stalks are stronger than the normal tall stalks; polled (hornless) is a desired phenotype in many varieties of cattle for safety and health reasons . Fish farmers need only look at the ornamental fish farming industry to see the importance of qualitative phenotypes. The value of an ornamental fish is determined by its colour, colour pattern, fin shape, eye shape, etc .

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Qualitative phenotypes can be divided into two major categories: autosomal and sex-linked . Autosomal phenotypes are those that are controlled by genes located on an autosome (a chromosome other than a sex chromosome). Sex-linked phenotypes are controlled by genes located on the pair of chromosomes that determines sex. (There are some exceptions; some fish have more than one pair of sex chromosomes, while other species have an odd number-either one or three sex chromosomes. All important aquacultured food fish have a single pair of sex chromosomes.)

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Autosomal genes are inherited and expressed identically in males and females (unless a sex hormone is needed for phenotypic expression). Sex-linked genes are inherited and expressed differently in males and females. To date, all qualitative phenotypes that have been deciphered in food fish are autosomal. Sexlinked genes are known only in ornamental fish. Because all qualitative phenotypes that have been discovered in cultured food fish are autosomal, this section will describe only the genetics of autosomal phenotypes. Sex-linked phenotypes will not be discussed.

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Qualitative phenotypes produced by single autosomal genes Most qualitative phenotypes that have been deciphered genetically in food fish are controlled by single autosomal genes with two alleles per locus. In general, genes express themselves either in an additive or in a non-additive manner. In additive gene action, each allele contributes equally to the production of the phenotypes and the heterozygous phenotype is intermediate between the two homozygous phenotypes. In non-additive gene action, one allele (the dominant allele) is expressed more strongly than the other (the recessive allele), and it has a greater influence on the production of the phenotypes.

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COMPLETE DOMINANT GENE ACTION INCOMPLETE DOMINANT GENE ACTION ADDITIVE GENE ACTION

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Because the mode of gene action is incomplete dominance, the heterozygous (Bb) genotype produces a unique phenotype (light-black), one that resembles but that is slightly different than the dominant phenotype (black), which is produced by the homozygous dominant (BB) genotype; white is the recessive phenotype, and it is produced by the recessive genotype (bb). Gene C produces black and white colours by additive gene action. Because neither allele is dominant, the heterozygous (CC') genotype produces a unique phenotype (gray) that is intermediate between the phenotypes (black and white) produced by the two homozygous genotypes (CC produces black and and C'C' produces white). When the mode of gene action is additive, there is no dominant or recessive allele or phenotype.

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Complete dominant gene action occurs when the dominant allele is so strong that it produces its phenotype, regardless of the genotype. Only a single dominant allele is needed to produce the dominant phenotype. This means the homozygous dominant and heterozygous genotypes both produce the dominant phenotype; thus, the phenotypes produced by these genotypes are identical. The recessive allele can produce the recessive phenotype only when no dominant allele is present. Complete dominant gene action:

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Nile tilapia blond normal pigmentation syrup normal pigmentation light-coloured (pink) normal pigmentation caudal deformity syndrome normal tail normal pigmentation red Species Recessive phenotype Dominant phenotype Examples of phenotypes in cultured food fishes that are controlled by single autosomal genes with complete dominant gene action. All phenotypes in this table are body colours except caudal deformity syndrome, which is a tail deformity.

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Common carp blue normal pigmentation gold normal pigmentation grey normal pigmentation normal pigmentation light yellow band on dorsal fin; yellow on head Grass carp albino normal pigmentation Channel catfish albino normal pigmentation Rainbow trout albino normal pigmentation iridescent metallic blue normal pigmentation

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PHENOTYPE GENOTYPE NORMAL PIGMENTATION NORMAL PIGMENTATION PINK

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Inheritance of normally pigmented and pink body colours in Nile tilapia. These phenotypes are controlled by a single autosomal gene with complete dominant gene action called the B gene: the dominant B allele produces normal pigmentation, while the recessive b allele produces pink. Because the B allele is completely dominant over the b allele, the BB and Bb genotypes both produce the dominant normally pigmented phenotype. The recessive pink phenotype is produced only when a fish is homozygous recessive (bb).

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Incomplete dominant gene action: Incomplete dominant gene action occurs when the dominant allele expresses itself more strongly than the recessive allele, but it is not strong enough to completely suppress the recessive allele in the heterozygous genotype. Because of this, the dominant phenotype can be produced only when a fish has two copies of the dominant allele (homozygous dominant). Since the recessive allele is not completely suppressed by the dominant allele, the heterozygous genotype produces a phenotype that resembles, but is not identical to, the dominant phenotype.

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For example, black (normal pigmentation), bronze, and gold body colours in Mozambique tilapia are controlled by the G gene. The dominant G allele produces melanistic (dark-coloured) fish, but because the G gene exhibits incomplete dominance, the G allele does not completely suppress the expression of the recessive g. allele in the heterozygous state. The homozygous dominant and heterozygous genotypes produce unique phenotypes: GG fish are black, while Gg. fish are bronze. Gold fish are produced by the homozygous recessive genotype (gg.)

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When phenotypes are controlled by additive gene action, there is no dominant or recessive allele. Both alleles contribute equally to the production of the phenotypes, so the heterozygous genotype produces a phenotype that is intermediate between those produced by the two homozygous genotypes. Consequently, when the mode of inheritance is additive gene action, there are three genotypes and three phenotypes, a unique phenotype for each genotype. Additive gene action:

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The phenotypic ratios for phenotypes controlled by incomplete dominance and by additive gene action are identical. The only difference is the appearance of the heterozygous phenotype-does it resemble the dominant phenotype (incomplete dominance), or is it intermediate between the two homozygous phenotypes (additive)?

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PHENOTYPE GENOTYPE BLACK BRONZE GOLD incomplete dominance

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Figure above : Inheritance of black, bronze, and gold body colours in Mozambique tilapia. These phenotypes are controlled by a single autosomal gene with incomplete dominant gene action called the G gene. Because the dominant G allele is not completely dominant over the recessive g. allele, the heterozygous genotype produces a phenotype that is similar to but distinct from that produced by the homozygous dominant genotype.

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Examples of phenotypes in cultured food fishes that are controlled by single autosomal genes with incomplete dominant gene action. Species Dominant phenotype Heterozygous phenotype Recessive phenotype Common carp death light coloured normal pigmentation Blue tilapia death saddleback ( abnormaldorsal fin) normal Mozambique tilapia black (normal pigmentation) bronze gold

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Qualitative phenotypes controlled by two autosomal genes Some qualitative phenotypes are controlled by two autosomal genes. When two genes control the production of a set of phenotypes, there is usually some sort of interaction, and one gene influences the expression of the other. This means one gene alters the production of the phenotypes that are produced by the second gene. This gene interaction is called “epistasis.” Most of the examples of epistasis that have been found in fish were discovered in ornamental fish, but several have been found in important cultured food fishes. The two most important are scale pattern in common carp and flesh colour in chinook salmon.

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The four scale pattern phenotypes in common carp-scaled (normal scale pattern), mirror, line, and leather are controlled by two genes (S and N) with what is called “dominant epistasis.” The S gene determines the basic scale pattern via complete dominance. The dominant S allele produces the scaled phenotype (SS and Ss genotypes), while the recessive s allele produces the reduced scale phenotype called “mirror” (ss genotype). The N. gene modifies the phenotypes produced by the S gene. There are two alleles at the N locus. The dominant N allele modifies the phenotypes as follows: in the homozygous state (NN). the N allele kills the embryo; in the heterozygous (Nn) state, the N allele changes the scaled phenotype into the line phenotype and changes the mirror phenotype into the leather phenotype.

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The recessive n allele has no effect on the phenotypes produced by the S gene. The five phenotypes (one is death) and the underlying genetics are illustrated in the following Figure . A set of qualitative phenotypes may be controlled by more than two genes. Body colour in the Siamese fighting fish is an example of a set of phenotypes that is controlled by the epistatic interaction among four genes. Working with these phenotypes is far more complicated because of the number of genes involved. Fortunately, in food fish, no qualitative phenotype controlled by more than two genes has been discovered.

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In the above illustrations Inheritance of scale pattern in common carp. Scale pattern is determined by the epistatic interaction between the S and N genes. The S gene determines whether the fish has the scaled phenotype (SS and Ss genotypes) or the mirror phenotype (ss genotype). The N gene modifies those phenotypes. The NN genotype kills the fish (SS, NN, Ss, NN, and ss, NN genotypes); the Nn genotype changes the scaled phenotype into the line phenotype (SS, Nn and Ss, Nn genotypes) and changes the mirror phenotype into the leather phenotype (ss, Nn). The nn genotype does not alter the phenotypes produced by the S gene, so scaled fish have the SS, nn or Ss, nn genotypes, while mirror fish have the ss, nn genotype.

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Quantitative phenotypes are the phenotypes that are measured, such as length, weight, eggs/kg female, or feed conversion. Quantitative phenotypes differ from qualitative phenotypes in that individuals do not fall into discrete, non-overlapping categories. Genetics of quantitative phenotypes

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Because an individual's phenotypic value is determined by measurement (for example, length in millimeters) rather than by descriptive category (for example, colour), the differences between two individuals is a matter of degree (millimeter) rather than of kind (colour). Because the differences among individuals are matters of degree, in a population quantitative phenotypes form what are called continuous distributions, which can be described graphically, as shown below.

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Distribution exhibited by a quantitative phenotype in a population. Graph a illustrates a perfect distribution, which creates what is called a “bell-shaped curve” with the mean bisecting the curve at its peak. Graph b is the distribution of 7-month length in a population of common carp.

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. Quantitative phenotypes are controlled by dozens to hundreds of genes. The exact number is usually never known. The genes are shuffled like a deck of cards during meiosis due to crossing over and the independent assortment of chromosomes; the combination of these events ensures that each offspring will receive a slightly different genetic message.

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Quantitative phenotypes are also strongly influenced by environmental variables , and this helps produce a continuous distribution. These variables range from the obvious ones, such as stocking density, to ones not often considered, such as size and age of the mother. Some of these variables are felt at the family level (for example, date of birth and age of mother), while others are felt at the individual level (for example, access to food).

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The simultaneous actions of these genetic and environmental factors results in the creation of single phenotypic categories where the only way an individual can be described is by measuring it. Quantitative phenotypes are single categories with continuous distributions, that can be analyzed by calculating populational values and compare individual or family phenotypic values to the population's values. In a population, quantitative phenotypes are described by the mean, which is the arithmetic average, and by the standard deviation , which is the square root of the variance. The mean describes the central tendency and the standard deviation describes how the values in the population are distributed about the mean.

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For practical breeding work on medium-sized fish farms, it is important to know how to calculate the mean, so that a farmer can assess the effect of his selective breeding programme. A farmer really does not need to know how to determine the standard deviation; scientists and researchers, on the other hand, must know how to determine the standard deviation .

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Because quantitative phenotypes are controlled by dozens to hundreds of genes, the simultaneous and/or sequential expression of these genes makes it impossible to identify individual genes and to decipher their modes of inheritance. Consequently, a different approach is needed to work with and to understand these phenotypes. Because quantitative phenotypes are more complicated genetically, it is more difficult to work with these phenotypes, but quantitative phenotypes are the most important phenotypes in agriculture or aquaculture-weight, fecundity, etc.--so the breeding value of a farmed population of food fish is mainly determined by the genes that control quantitative phenotypes. Their importance is underscored by the fact that quantitative phenotypes are often called “production phenotypes.”

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Step 1. Obtain individual lengths to the nearest millimeter. Thirty fish are measured. 98 , 103, 106, 111, 104, 91, 87, 103, 114, 107, 101, 104, 97, 105, 108, 100, 110, 113, 104, 105, 95, 97, 107, 108, 99, 111, 112 , 113, 105, 103, How to calculate the mean for a quantitative phenotype. In this example, we will calculate mean length. In general, you determine the mean from a random sample of 30–200 fish. Step 2. Determine the sum of the measurements; that is, add the phenotypic values. 98 + 103 + 106 + 111 + 104 + 91 + 87 + 114 + 103 + 107 + 101 + 104 + 97 + 105 + 108 + 100 + 103 + 113 + 105 + 95 + 97 + 107 + 108 + 99 + 111 + 112 + 105 + 113 + 103 = 3,120 Step 3. Divide the total value derived in Step 2 by the number of fish that were measured. In this case, 30 fish were measured, so you divide by 30. The mean length in this population is 104 mm.

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Phenotypic variance Phenotypic variance is the variability that a phenotype exhibits in a population; the mean describes the average phenotypic value, while the variance describes how individuals are distributed around the mean (the standard deviation, which was mentioned earlier, is the square root of the variance). Phenotypic variance (VP) is the sum of three components: genetic variance (VG), environmental variance (VE), and genetic-environmental interaction variance (VG-E). This can be represented by the following formula: VP = VG + VE + VG-E

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Genetic variance (VG) is the sum of additive genetic variance (VA), dominance genetic variance (VD), and epistatic genetic variance (V1). As before, this can be represented by a formula: Genetic variance VG = VA+ VD + VI The words “additive,” “dominance,” and “epistatic” do not refer to specific types of gene action as they do when discussing the modes of inheritance for qualitative phenotypes. The correct terms are “additive genetic variance,” “dominance genetic variance,” and “epistatic genetic variance” (not gene action), and they refer to specific components of variance that are produced by the entire genome, not by one or two genes.

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Additive genetic variance is the genetic component that is due to the additive effects of all the fish's alleles. Additive genetic variance is the sum of the values that each allele makes to the production of the phenotype. Some alleles will make a large contribution; some will make a small contribution; some will make no contribution; and some may even make a negative contribution. The contribution made by every allele is added, and the sum is the additive genetic variance component for each fish.

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Dominance genetic variance is the genetic component that is due to the interaction that exists between the pair of alleles at every locus. Because of this, dominance genetic variance cannot be inherited .

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The idea that some form of genetics cannot be inherited usually causes confusion , but it is a simple concept. Dominance genetic variance is due to the interaction of the pair of alleles at each locus, which means that dominance genetic variance is a function of the diploid state (2N). The reason that dominance genetic variance is not heritable is that each parent contributes a haploid (N) gamete to the production of each offspring. Gametes do not contain pairs of alleles (2N); the diploid state is reduced to the haploid state during meiosis.

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During reduction division, all allelic pairs are separated when the chromosomes undergo independent assortment, which means that a parent's dominance genetic effects are destroyed during meiosis. Since an individual's dominance genetic variance is destroyed during reduction division, it cannot be transmitted via a gamete to an offspring-thus, it is not heritable. Dominance genetic variance effects are recreated at fertilization when a haploid sperm fertilizes a haploid egg to produce a diploid zygote. At fertilization, genes once again exist in the paired state, which means that an interaction exists between the pairs of alleles at each locus which, in turn, means that dominance genetic variance exists. Consequently, dominance genetic variance effects are destroyed and then recreated in new and in different combinations each generation.

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Epistatic genetic variance is the genetic component that is due to the interaction(s) of alleles between or among loci; in other words, it is the interaction(s) that an allele has with alleles other than its own pair. Epistatic genetic variance is a mixture of heritable and non-heritable variance. The portion of the interaction that is between and among the alleles that were included in a gamete is heritable, but the portion that is between or among alleles that were parcelled to other sperm or to the polar bodies is not heritable.

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The percentage of epistatic genetic variance that is heritable varies from gamete to gamete because of crossing over and independent assortment. Independent assortment and crossing over tends to disrupt most epistatic genetic variance during meiosis, so only a small random sample is transmitted from a parent to its offspring; consequently, only a small random portion of epistatic genetic variance is heritable .

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The differences among additive genetic variance, dominance genetic variance, and epistatic genetic variance and how they are transmitted is important on a practical level because different kinds of breeding programmes are needed to exploit these components of genetic variance. The relative amount of phenotypic variance that can be attributed to these components of genetic variance determines the type of breeding programme that can be used and how effective it will be in improving the phenotype.

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The two important genetic components are additive genetic variance and dominance genetic variance. Most breeders assume that epistatic genetic variance is not important. This assumption is made because it is difficult to try and select for combinations of alleles when you do not know what combinations are desirable. Additionally, the improvement that can be gained by selection for epistatic effects is rather small, and it plateaus quickly.

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Additive genetic variance and dominance genetic variance are essentially opposites. Additive genetic variance is a function of the alleles, so it is function of the haploid state; dominance genetic variance is a function of allelic pairs, so it is a function of the diploid state. A parent produces haploid gametes, so it can transmit its additive genetic effects to its offspring, but it cannot transmit its dominance effects, which are destroyed during meiosis.

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Dominance effects are created in each zygote after fertilization. Thus, the additive effects are a function of each parent, while the dominance effects are a function of specific matings. Because the additive effects are transmitted from a parent to its offspring, additive genetic variance is often called the “variance of breeding values.”

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Because additive genetic variance is transmitted from a parent to its offspring, selection is the breeding programme that is used to exploit this component of variance and to improve the population. Because dominance genetic variance is not heritable but a function of the mating, hybridization is the breeding programme that is used to exploit this component of variance and to improve the population.

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Because additive genetic variance is transmitted from a parent to its offspring in a predictable and reliable manner, if the percentage of phenotypic variance that is due to additive genetic variance is known, a farmer can predict the amount of improvement that can be made as a result of selection, and he can even customize selection to achieve a pre-determined amount of improvement per generation. Heritability

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The proportionate amount of additive genetic variance is called “heritability,” and it can be represented by the following formula: h2 = VA/VP where: h2 is the symbol for heritability, VA is additive genetic variance, and VP is phenotypic variance. Heritability is expressed as a percentage (0–100% or 0.0–1.0). Thus, heritability quantifies the percentage of phenotypic variance that is inherited in a predictable and reliable manner .

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The major reason for determining the heritability of a quantitative phenotype is that it can be used to predict the results of a selective breeding programme by using the following formula: R = Sh2 where: R is the response to selection (gain per generation), S is the selection differential (the superiority of the select brood fish over that of the population average; to determine this, you simply subtract the population average from the average of the select brood fish), and h2 is heritability.

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How to predict the response to selection if the heritability (h2) of the phenotype is known. In this example, we will predict response to selection for increased length and then calculate the predicted mean length of the next generation. Given: h2 for length at 12 months = 0.26 mean length at 12 months of the population = 146 mm mean length at 12 months of the select brood fish = 162 mm Step 1. Calculate the selection differential (S). S = mean length of the select brood fish - mean length of the population S = 162 mm - 146 mm = 16 mm Step 2. Calculate the predicted response to selection (R). R = Sh2 R = (16 mm)(0.26) R = 4.16 mm

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Step 3. Calculate the mean of the F, generation of select fish. mean of the F1 generation = mean of the population + R mean of the F1 generation = 146 mm + 4.16 mm = 150.16 mm The preceding formula clearly demonstrates that heritability is the factor that determines the percentage of selection differential that can be gained via selection; in other words, how much gain is possible. In general, heritabilities ≥0.25 indicate that selection will produce good gains, while those ≤ 0.15 indicate that selection will be ineffective. Heritabilities > 0.3 are considered to be large.

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Although it is advantageous to know the heritability of a quantitative phenotype before conducting a selective breeding programme, it is not necessary. If one exists, it can be used to predict the gains, to customize the selection differential that is needed to achieve a desired response to selection, or to indicate that selection will be so ineffective that the programme should be scrapped.

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It is often unnecessary to determine a heritability, because published information already exists. Several hundred heritabilities have already been determined for phenotypes such as growth rate, food conversion, disease resistance, fecundity, egg size, egg number, dressing percentage, body conformation, and pesticide tolerance in many important aquacultured species of food fish. The heritabilities that are published may not be the same as those in a farmer's population, because heritabilities are specific for the population that was evaluated and for the culture conditions that were used in the experiment, but the published values should be similar to those that exist in most populations. Table 6 lists some of the heritabilities that have been determined in common carp and tilapia.

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How to use the heritability (h2) of the phenotype to customize the selection differential in order to produce the desired response to selection. Given: h2 for length at 12 months = 0.26 mean length at 12 months of the population = 146 mm desired response to selection = 6 mm Step 1. Calculate the selection differential (S) needed to produce a response of 6 mm: R = Sh2 6 mm = (S)(0.26) 6 mm/0.26 = S 23.08 mm = S

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Step 2. Calculate the mean of the select brood fish that will be needed to produce a selection differential of 23.08 mm. S = mean length of the select brood fish - mean length of the population 23.08 mm = mean length of the select brood fish - 146 mm mean length of the select brood fish = 146 mm + 23.08 mm mean length of the select brood fish = 169.08 mm

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Role of environment in phenotypic expression Although the genes are the blueprints that are used to produce the phenotypes, they produce these phenotypes in conjunction with the environment. The environment influences the production of all phenotypes, but quantitative phenotypes are more affected by environmental variables than qualitative phenotypes.

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If a fish cannot eat the necessary nutrients, it will be unable to produce certain proteins, which means the fish will be unable to produce specific phenotypes. This is especially true for qualitative phenotypes which depend on pigments which cannot be synthesized by fish. For example, tropical fish farmers add various plant pigments to fish feed in order to enhance the body colours of ornamental fish, and salmon farmers add pigments to salmon feed so the flesh will be pink rather than white.

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Environmental factors that influence quantitative phenotypes range from obvious ones, such as stocking density and feed quality, to those which are subtle and usually not considered; these factors include: female age, female size, spawning date, feed particle size, and feeding practices. Even if the environment plays a large role in the production of a quantitative phenotype, the role it plays is not critical to the success of a breeding programme if it is the same for all fish. When conducting a selective breeding programme to improve a quantitative phenotype, it is crucial to be able to control environmental variables and to prevent them from varying among individuals, families, and ponds.

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If they are not controlled, they will differentially influence phenotypic expression, and a farmer will not know if the select fish are best because they are genetically superior or because they had the better environment. The difference is crucial, because only fish that are superior genetically will be able to transmit this superiority to their offspring, which is the goal of all selective breeding programmes .

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Heritabilities (h2) for some phenotypes in Nile tilapia, blue tilapia. Species Phenotype h2 Nile tilapia 4-week weight 0.0 4-week weight 0.06 45-day weight 0.04 8-week weight 0.0 8-week weight 0.21 10-week weight 0.0

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