2 To my family, friends and colleagues Acknowledgements I would like to acknowledge my colleagues and collaborators in the United States, Israel and Russia with whom I obtained data on fish genetics used in this book. My special thanks to Nina Cherfas, my teacher and long-term collaborator, and Robert Durborow for the help in preparation of this book. I would like to acknowledge all authors whose data I mentioned and considered in this book and whose figures and tables have been reproduced. In order to follow a textbook format, I was obligated to omit formal citations for some presented materials. 3 Table of Content Page Chapter 1. Fish Chromosomes and Cytogenetics of Fish Reproduction 7 1.1. Variability and Evolution of Fish Karyotypes 7 1.1.1. Introduction: Chromosomes and Karyotypes 7 1.1.2. Variability of Fish Karyotypes 8 1.1.3. Evolution of Fish Karyotypes 10 1.2. Sex Chromosomes and Genetics of Sex Determination 15 1.3. Formation of Reproductive System and Sex Differentiation 18 1.4. Gametogenesis and Fertilization 21 1.4.1. Introduction: Gametogenesis and Meiosis 21 1.4.2. Oogenesis 22 1.4.3. Spermatogenesis 28 1.4.4. Fertilization 30 1.5. Natural Gynogenesis and Hybridogenesis 33 Chapter 2. Inheritance of Qualitative Morphological Traits in Fish 37 2.1. Introduction: Main Features of Qualitative Traits 37 2.2. Inheritance of Color Traits in Fish 37 2.2.1. Basic Principles of Color Development and Inheritance 37 2.2.2. Albinism and Its Inheritance 38 2.2.3. Color Modifications in Some Aquaculture and Sport Fish Species 41 2.2.3.1. Rainbow Trout 41 2.2.3.2. Tilapias 43 2.2.3.3. Koi 47 2.2.3.4. Crappie 51 2.3. Inheritance of Scale Cover in Common Carp and Koi 52 2.4. Inheritance of Other Qualitative Morphological Traits in Fish 58 Chapter 3. Inheritance of Quantitative Traits in Fish 61 3.1. Quantitative Traits: Main Features and Principles of Inheritance 61 4 3.2. Genetic Analysis of Quantitative Traits. Concept of Heritability 64 3.3. Methods of Heritability Determination 67 Chapter 4. DNA Genetic Markers and Their Application 71 4.1. Genetic Markers: Definition and Basic Types 71 4.2. DNA Markers and Methods of Molecular Genetics 72 4.3. Types of DNA Markers 74 4.3.1. Restriction Fragment Length Polymorphism (RFLP) of Nuclear and Mitochondrial DNA 74 4.3.2. Multilocus Minisatellites 75 4.3.3. Microsatellites or Simple Sequence Repeats 79 4.3.4. Random Amplified Polymorphic DNA (RAPD) 83 4.3.5. Amplified Fragment Length Polymorphism (AFLP) 84 4.3.6. Single Nucleotide Polymorphism (SNP) 85 4.4. Application of DNA Markers in Aquaculture and Fisheries 87 4.4.1. Evaluation of Within-Population and Between-Population Genetic Variability 88 4.4.2. Monitoring the Level of Genetic Variability in Cultured Fish Stocks 92 4.4.3. Identification of Species and Interspecies Hybrids 93 4.4.4. Parentage Determination 95 4.4.5. Genetic Mapping 97 4.4.6. Identification of Quantitative Trait Loci 99 4.4.7. Marker-Assisted Selection 100 4.4.8. Identification of Genetic Sex 100 Chapter 5. Selective Breeding and Hybridization 102 5.1. Introduction: Methods of Genetic Improvement of Fish 102 5.2. Fish Selection 102 5.2.1. Artificial Selection and Its Forms 102 5.2.2. Peculiarities of Fish as Objects of Selection 103 5 5.2.3. Directions and Objectives of Fish Selection 105 5.2.4. Methods of Fish Selection 111 5.2.4.1. Individual or Mass Selection 111 5.2.4.2. Selection Based on Relatives 119 5.3. Inbreeding and Methods of Its Reduction 126 5.3.1. Inbreeding: Definition and Methods of Its Determination 126 5.3.2. Expression of Inbreeding Depression in Fish 131 5.3.3. Methods of Inbreeding Reduction 132 5.4. Intraspecies and Interspecies Hybridization 133 5.4.1. Intraspecies Hybridization or Crossbreeding 133 5.4.2. Interspecies Hybridization 137 Chapter 6. Chromosome Set Manipulation and Sex Control 144 6.1. Induced Gynogenesis 144 6.1.1. Methods of Production of Gynogenetic Fish. Types of Induced Gynogenesis 144 6.1.2. Properties of Gynogenetic Fish 149 6.2. Induced Androgenesis 152 6.3. Induced Polyploidy 153 6.3.1. Production of Triploid Fish by Suppression of 2nd Meiotic Division in Eggs 154 6.3.2. Properties of Triploid Fish 155 6.3.3. Production of Triploids by Crossing of Tetraploids 159 6.4. Hormonal Sex Reversal and Genetic Sex Regulation 162 6.4.1. Hormonal Sex Reversal in Fish 162 6.4.2. Application of Hormonal Sex Reversal for Sex Control 165 Chapter 7. Gene Engineering and Genomics 169 7.1. Gene Engineering and Production of Transgenic Fish 169 7.1.1. Introduction: Gene Engineering and Transgenic Animals 169 6 7.1.2. Methods of Transgenic Fish Production 169 7.1.3. Properties of Transgenic Fish Valuable for Aquaculture 171 7.1.4. Future Prospective of Using Transgenic Fish in Aquaculture 173 7.2. Fish Genomics 174 7.2.1. Introduction: Genomics and Its Basic Directions 174 7.4.2. Current Status of Fish Genomics 178 References 181 7 Chapter 1. Fish Chromosomes and Cytogenetics of Fish Reproduction 1.1. Variability and Evolution of Fish Karyotypes 1.1.1. Introduction: Chromosomes and Karyotypes In fish, as in the other eukaryotic organisms, genetic material is organized into structures called chromosomes. Chromosomes consist of DNA, macromolecule coding genetic information, and specific proteins called histones. Chromosomes change their structure depending on the phase of mitosis. Chromosomes reach maximum compactness at the stage of mitotic metaphase, when they are located at equatorial plane of division forming the metaphase plate. The counting of chromosomes and investigation of their structure are performed by analysis of metaphase plates. Metaphase chromosomes consist of two chromatids joined by a centromere, a special structure, to which the mitotic spindle fibers attach. Parts of chromosomes separated by the centromere are named chromosome arms. Depending on the location of centromere the following types of chromosomes may be distinguished (Figure 1.1.1): A - metacentric - the chromosome arms are equal; B - submetacentric - the chromosome arms are different but this difference is not profound; C - subtelocentric - the chromosome arms are very different; D - acro(telo)centric - the centromere is located very close to one of the ends of the chromosome. Somatic cells of organisms reproducing by a normal sexual mode have double or diploid (2n) set of chromosomes consisting of two haploid (n) sets. One haploid set has a maternal origin and the other, a paternal origin. Diploid set consists of pairs of homologous chromosomes having the same gene composition, sizes, and structure (besides the pair of sex chromosomes). 8 The set of chromosomes from somatic cell arranged according to their size and form is called karyotype. Two main indices are determined during karyological analysis: diploid number of chromosomes (designated as 2n), and the number of chromosome arms (designated as N.F., from Latin Nombre Fondamental - basic number). Metaphase chromosomes are systematized, i.e. they are placed according to their form and size. Figure 1.1.1. Types on metaphase chromosomes based on location of centromere. 1.1.2. Variability of Fish Karyotypes Up to now karyotypes of about two thousand fish species have been described. Fish karyotypes are characterized by two specific features: • High variability - diploid number of chromosomes varies in different species from 12 to 270; • Sex chromosomes are usually not identified in karyotypes. The observed high variability in karyotypes is explained by the fact that fishes are a very ancient and highly heterogeneous group of animals, evolution of which has taken place during several hundred millions years. The distribution of fish according to diploid number of chromosomes (2n) is shown in Table 1.1.1. You can see in the table that more than 75% of fish have 42- 60 chromosomes; from this class the most common diploid numbers are 48 and 50. It is supposed that these diploid numbers were typical for the ancestors of existing 9 fish. During subsequent long-term evolution essential transformations of karyotypes occurred, which resulted in a decrease or increase in chromosome numbers. Table 1.1.2 presents data on chromosome sets of aquaculture species and some fish inhabiting natural waters. Examples of karyotypes of several fish are presented in Figures 1.1.2, 1.1.3 and 1.1.4. Table 1.1.1. Distribution of fish according to diploid number of chromosomes. Diploid number of 20 and 22-40 42-60 62-80 82-100 102 and chromosomes, 2n less more Frequency, % 0.7 11.8 76.3 4.0 4.8 2.4 Karyotype of grass carp (Figure 1.1.2) has 48 chromosomes; as was mentioned above, this number is very typical for fish karyotypes. Karyotype of rainbow trout (Figure 1.1.3), consists of 44 metacentric and submetacentric chromosomes, 14 acrocentric chromosomes, and 2 subtelocentric chromosomes. Total number of chromosomes (2n) is 60. Another index of karyological analysis, N.F., is determined based on composition of chromosomes with different structure in karyotype. N.F. is calculated by assuming that each metacentric or submetacentric chromosome has 2 arms, while subtelocentic or acrocentric chromosome has 1 arm. Therefore, for this karyotype (Figure 1.1.3) N.F. is determined as 44 (number of meta- and submetacetric chromosomes) x 2 + 16 (number of acrocentric chromosomes) = 104. In karyotypes of sturgeons some chromosomes have a very small size (Figure 1.1.4); they are called microchromosomes. The number of microchromosomes may vary; therefore for sturgeons the value of 2n is given with a range of variation (see Table 1.1.2).