Population genetics by Knud Christensen - RTH

1 1 Population genetics by knud Christensen Division of Animal genetics Population genetics by knud Christensen .. 1 introduction .. 3 References.. 4 Chapter 1. introduction , quantitative versus qualitative genetics .. 5 Domestic animals in Denmark, quantitative traits .. 5 quantitative versus qualitative inheritance .. 5 The terms phenotype, genotype and heritability .. 6 Effect of animal breeding (evolution) .. 7 Qualitative traits, Mendelian genetics .. 8 Data base on Mendelian inheritance in domestic animals .. 9 Chapter 2. Hardy-Weinberg law for gene frequency stability in large populations.

2 10 Gene counting method for calculation of gene frequencies .. 10 Hardy-Weinberg equilibrium and statistical tests .. 12 Sex-linked inheritance .. 13 Examples of application of gene frequencies .. 14 Gamete frequencies under linkage .. 17 Chapter 3. Deviations from Hardy-Weinberg equilibrium .. 21 Systematic deviations from H-W equilibrium .. 21 Selection against the recessive .. 22 Selection for heterozygotes .. 24 Selection against heterozygotes .. 25 Random deviations from Hardy-Weinberg equilibrium .. 26 Effective Population size .. 27 Chapter 4.

3 Relationship and inbreeding .. 29 Relationship and inbreeding, definition .. 29 Relationship and inbreeding, calculation examples and formulas .. 30 Simple forms of close inbreeding .. 31 Segregation of the recessive by inbreeding .. 31 Calculation of inbreeding and relationship, the tabular method .. 32 Chapter 5. Test of simple genetic hypotheses, experimental or field data .. 36 Genealogy and formulating genetic hypotheses .. 36 Autosomal recessive inheritance .. 36 2 Autosomal dominant inheritance .. 37 Sex-linked recessive inheritance .. 37 Sex-linked dominant inheritance.

4 38 Test mating, statistical tests .. 38 Field data, statistical tests .. 40 Definition of a quantitative trait .. 42 The terms genotype value, breeding value and dominance deviation .. 42 The terms additive variance and heritability .. 45 Estimating the heritability and common environmental effect .. 46 Chapter 7. Estimation of breeding values .. 49 Estimation of breeding values, general .. 49 Formulas for calculating estimated breeding value based on uniformly related phenotypes .. 49 Direct update of breeding values .. 52 Estimation of breeding values in animal breeding, and use of gene markers.

5 53 Chapter 8. genetic changes by selection .. 56 Difference of and intensity of selection .. 56 Selection response .. 56 Selection of threshold traits .. 57 genetic correlation, changes in secondary traits .. 60 Chapter 9. Inbreeding, crossing and bred structure .. 65 Effect of inbreeding on individual and on Population level .. 65 Effect of crossbreeding .. 66 Minimum systems of inbreeding .. 69 Inbred lines in laboratory animals .. 70 Population structure, breeding pyramid .. 70 Chapter 10. Chromosomes and chromosome aberrations .. 72 Preparation of chromosomes.

6 72 Normal karyotypes in domestic animals .. 72 Chromosome aberrations in domestic animals .. 74 Identification of chromosomes by means of chromosome paint .. 78 Chromosome aberrations identified by means of DNA-content in sperm cells .. 79 Chapter 11. genetics on hair and coat colour in mammals .. 81 Hair coat types in mammals .. 81 Coat colour types in mammals, colour genes .. 82 The biochemical function of the colour genes .. 84 Colour genes in domestic animals .. 85 3 Chapter 12. Estimating- and biotechnology and disease resistance .. 91 Technology for breeding value estimation.

7 91 The significance of artificial insemination for estimation of breeding values .. 92 Transgene and transgenic animals .. 93 Utilization of DNA markers .. 94 Detection of DNA markers for disease genes or QTL's .. 95 Results of experimental selection for disease resistance.. 97 14. genetic calculation applets and other programs .. 101 Critical Values of the Chi-Square Distribution .. 101 Calculation of Chi-square test for deviation from Hardy-Weinberg equilibrium .. 102 Calculation of Chi-square test for a 2 by 2, 3 by 3 or 2 by 3 table .. 103 Calculation of mating type frequencies in H-W Population .

8 104 Linkage, Calculation of gamete and genotype frequencies generation after generation .. 104 Selection: Change in gene- and genotype frequencies by selection .. 105 Selection: Change in gene- and genotype frequencies, and effect of Population size .. 106 An Applet for general matrix handling and calculating relationship and inbreeding .. 107 Calculation of Chi-square test for deviation from Mendelian ratios .. 110 Calculation of corrected segregation ratio according to Singles method .. 110 Applet for calculation of mean, Genotypic and Breeding values and Dominance deviations.

9 111 Estimating simple forms of breeding values .. 112 Estimating animal model breeding values .. 113 Estimating breeding values and selection response .. 116 Applet for calculating heritability for threshold traits (diseases) .. 117 introduction The present genetics notes are produced as a substitute for 'Veterinary genetics ' by , Oxford University Press, 1989. This book was not available after 1995. The notes are produced for a course for veterinary students. Therefore, efforts have been made to adjust the notes for students with a biological background, and at the same time supply a minimal set of formulas to describe the relationship between practical observations and genetic theory.

10 In addition to the description of traits with simple Mendelian inheritance, the description of the genetics for traits (diseases) with multifactoriel aetiology has also been emphasized, here the application of correct breeding plans make it possible to significantly lower the frequency of the disease. The genetics notes are available on the www server, which can be reached from the address: Both an English and a Danish version is available. The online voice version includes a slide show with more than 350 slides. The voice in the voice version 4 belongs to Anne Asp Poulsen who study English at the Copenhagen University, she also gave comments on the English style in the text and figures.