7 Genetics Rex Dunham

7 Genetics Rex Dunham 7.1 INTRODUCTION to improve these traits. Genetic enhancement programs are Genetic intervention has been used to enhance animal and then the plans that we use to accomplish these goals and plant agriculture production for centuries and has intensi- objectives. The primary purpose of this chapter is to fied during the last two centuries. These techniques are review these genetic enhancement programs to show how now being applied to aquatic organisms to improve pro- effective they have been with the focus on production duction traits. Aquaculture genetics has tremendous poten- traits of foodfish and shellfish. tial for enhancing aquaculture production. Modern research on aquaculture genetics began sporadically 80 years ago 7.2 BASIC GENETICS and became commonplace in the 1970s. During the last 7.2.1 Gene action three decades, research in this area has steadily grown, and There are two basic types of gene action, dominant/ now research on traditional selective breeding, genetic recessive and additive. In the case of dominance, only one biotechnology, transgenics, and genomics is quite active. copy of the dominant allele (A) in a diploid organism is Knibb et al. (1998) considered that in their genetics needed for expression of the associated trait. In the case most marine fish production remains equivalent to the use of the recessive allele (a), two copies of the allele are of undomesticated wild ancestral cattle, chicken, etc. in needed for the recessive phenotype to be observed. In a ancient terrestrial agriculture. This may be true for marine completely dominant system (Table 7.1a), a large unit of fish, many molluscs and crustaceans, and new aquaculture phenotypic change occurs when going from the species in general. But after 40–50 years of genetics and homozygous recessive genotype (aa) to the heterozygous breeding research, coupled with genetic biotechnology, genotype (Aa) and no unit of change when going to the this is no longer true for established species such as carps, homozygous dominant genotype (AA). For additive gene catfish, salmonids, tilapias and oysters. The best available action, the alleles, of course, act in an additive fashion with genotypes may have performance levels of up to 10-fold equal units of change when comparing the different geno- that of poor performing wild genotypes, and the rate of types (aa → Aa → AA) (Table 7.1b) or, like mathematical progress and genetic gain certainly rivals that for terrestrial addition, the stronger allele will make a greater contribu- livestock. Regardless of the species and the genetic gain tion to the phenotype (Table 7.1c). The alleles at one locus made as of today, much greater genetic progress can con- can affect the expression of alleles at a second locus. This tinue to be accomplished. type of gene interaction is termed epistasis. Effective programs have goals and plans, and this is also true for genetic enhancement programs. Goals are the 7.2.2 Qualitative traits important traits of economic importance that we want to Qualitative traits are phenotypes that are expressed in an improve, and the extent to which we consider it feasible all-or-none fashion. For example, albino or normal colora- Aquaculture: Farming Aquatic Animals and Plants, Second Edition. Edited by John S. Lucas, Paul C. Southgate. © 2012 Blackwell Publishing Ltd. Published 2012 by Blackwell Publishing Ltd. 138 7 / Genetics 139 Table 7.1 Basic types of gene expression. (a) Complete dominance. (b) Incomplete dominance. (c) Overdominance. (d) Co-dominance (additive gene expression). Unit of phenotypic change Genotypes Phenotypes between genotypes (a) Complete bb red large dominance Bb black none BB black (b) Incomplete bb white large dominance Bb dark grey small BB black (c) Over- ss malaria prone large dominance Ss healthy (best) large SS sickle cell (sick) (d) Co-dominance rr white large equal Rr pink units of change RR red tion is usually a result of gene expression from a single or only a few loci. Coloration and deformities are examples of qualitative traits. Qualitative traits such as changes in color, finnage, scale pattern or deformities can be desirable or detrimental in homozygous homozygous heterozygous aquaculture. Obviously, qualitative traits are important and the primary basis for the ornamental aquaculture industry. Parental type 1 Parental type 2 F1 genotype Deformities can be valuable in the ornamental trade, but are usually undesirable in the foodfish industries. If these Fig. 7.1 Co-dominance: both alleles are expressed qualitative traits are a result of dominant gene action, they equally. DNA or protein banding patterns illustrate the concept. can be easily eliminated as all homozygous dominant and heterozygous (carrier individuals) phenotypes are obvious, and those individuals can be immediately selected against, false. Most deformities observed are usually environmen- resulting in a population with none of the dominant detri- tally induced and are often related to low egg quality or mental allele. An example of this is the saddleback muta- poor water quality in the hatchery. tion in tilapia (Tave et al., 2003). On the other hand, it is There are different types of dominance (Table 7.1), as extremely difficult to eliminate a deleterious recessive discussed earlier. In the case of complete dominance, the allele from a population as heterozygous carriers cannot trait is fully expressed in the heterozygous and homozygous be identified by simple visual observation (Table 7.1a). If dominant genotypes. Albinism (in contrast to normal col- the trait was of high economic importance or damage, the oration) and saddleback are examples of complete domi- heterozygous carriers could be eliminated, by mating them nance in fish. with individuals of known genotype and examining the The heterozygous genotype allows a major, but not phenotypic ratios in the progeny, i.e., progeny testing. complete, unit of change in the phenotype in incomplete Since fish are highly fecund and produce large numbers of dominance. The homozygous dominant genotype is neces- progeny, progeny testing could eliminate the deleterious sary to make the complete, maximum shift in the pheno- allele from the population in a single generation. type. In the case of overdominance, the phenotype of the When deformities are observed, fish culturists often heterozygous genotype is outside that of the two assume that the deformities have a genetic basis and that homozygous genotypes (Table 7.1c). The phenotype asso- they are likely to be increasing because of inbreeding in ciated with each allele is observed in the case of co- the population. However, these assumptions are usually dominance (Fig. 7.1). 140 Aquaculture 7.2.3 Phenotypic variation Individual phenotypes, the appearance, characteristics and performance of individuals, are a result of three main components: 1. The environment. 2. The genotype. 3. The interaction between the genotype and the environment. Thus phenotypic variation (Vp) is a result of genetic variation (Vg), environmental variation (Ve) and variation due to the genotype–environment interaction (Vge): VVVVp= g + e + ge Genetic variation in populations has several components as well: • additive genetic variation; • dominance genetic variation; • variation due to epistasis interaction; • variation due to maternal heterosis. The type of genetic variation has a bearing on the Fig. 7.2 Mirror scale pattern in common carp. success of the genetic enhancement program being Genes for scale pattern in common carp have attempted. For selection to be successful, a trait must have epistatic interaction, pleiotropy, and semi-lethality. significant heritability and the ratio of additive genetic variation to total phenotypic variation must be high. Dominance, epistasis, and overdominance are the genetic • Epistasis is the interaction of genes at different loci. basis of heterosis; the relative performance of crossbreeds Alleles at one locus can affect the expression of alleles and hybrids compared to their parents. Thus, significant at another locus. Epistasis is the basis of some color dominance-related variation must exist for crossbreeding types in fish. For instance, it is the explanation for some and hybridization programs to be successful. red and black color variants in tilapia and scale pattern in the common carp is also influenced by epistatic gene 7.3 DOMESTICATION AND STRAIN action (Fig. 7.2). EVALUATION • Pleiotropy is when one gene affects more than one trait. Use of established, best-performing domestic strains is the The alleles and loci that affect scale pattern in common first step in a genetic improvement program, and the mech- carp are an excellent example of this phenomenon. anism to make the most rapid initial progress in genetic These genes not only affect scale pattern, but also improvement. Domestic strains of fish usually have better growth, survival, other meristic traits, tolerance of low performance in aquaculture settings than wild strains of oxygen, hemoglobin and hematocrit , and ability to gen- fish. Strain variation is also important, since strain affects erate fins. Some mutations can also have semi-lethal or other genetic enhancement approaches, such as intraspe- lethal effects, resulting in reduced viability or death. cific crossbreeding, interspecific hybridization, sex control, Again, certain alleles affecting scale pattern in common and genetic engineering. carp have semi-lethal or lethal effects and this applies to When wild fish are moved to aquaculture

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