The Applied Genetics of Plants, Animals, Humans and Fungi

The following sections are included:

• ACKNOWLEGEMENTS, AND COPYRIGHT OF PHOTOS

• DEDICATION

• WHY A BOOK ON APPLIED GENETICS?

• CONTENTS

The following sections are included:

• Introduction

• The aims of applied genetics in plants, animals, humans and fungi; the use of genetic variation ; improving the harvest index

• Revision of basic genetic concepts, definitions and symbols
  • Alleles, genes, loci, wild-types and mutants
  • Ploidy
  • Genotype and phenotype; homozygotes and heterozygotes; hemizygotes
  • Dominance and recessiveness; incomplete dominance and additive action; primes; overdominance; co-dominance; pure breeding
  • Additive and multiplicative gene action
  • Mutation
  • Recombination; linkage; syntenic and non-syntenic loci; coupling and repulsion arrangements
  • Allelism and the cis/trans test
  • Heritability
  • Selection
  • Populations and population structure
  • Polymorphism
  • Random mating

• Suggested reading

The following sections are included:

• Single-locus qualitative characters: autosomal loci with complete dominance, partial dominance, additive action, overdominance; X-linked and holandric loci
  • Qualitative characters
  • Autosomal loci: complete dominance
  • Autosomal local with partial dominance, additive actions or overdominance
  • X-linked and holandric loci

• Multiple-loci qualitative characters: dihybrid ratios and gene interactions such as epistasis causing modified ratios
  • Standard dihybrid ratios
  • Gene interactions such as epistasis causing modified dihybrid ratios

• Quantitative characters; quantitative trait loci and polygenes Suggested reading

The following sections are included:

• Genetic and environmental causes of regression and transgression

• Environmental effects on phenotypes
  • Sex-limited characters
  • Phenocopies, conditional mutants and environmental effects
  • Phenotype plasticity
  • Variable expressivity
  • Incomplete penetrance

• Narrow and broad sense heritabilities; equations, estimation and use; correlations between characters

• Genotype value, phenotype value and breeding value

• Suggested reading

The following sections are included:

• Introduction

• The Hardy-Weinberg equilibrium for one locus and two loci; linkage disequilibrium, and population mixing
  • One locus, two alleles
  • One locus, more than two alleles
  • Allele segregation at two loci and the importance of recombination frequencies
  • What happens when two pure-breeding but different populations mix?

• Genetic drift, fixation and effects of population size

• Gene flow and population structure

• Effects on allele frequencies of selection, mutation, migration and gene conversion; equilibria between forces in populations
  • Selection
  • Migration
  • Mutation

• Suggested reading

The following sections are included:

• Natural, artificial and sexual selection

• Stabilising selection, towards uniformity

• Directional selection, favouring one extreme

• Cyclic selection, alternatively favouring different extremes

• Disruptive selection, selecting against the average type

• Pedigree selection

• Progeny testing

• Half-sib and family selection

• Selecting for correlated characters

• Selecton for more than one character: tandem selection, independent culling levels and index selection
  • Tandem selection
  • Independent culling levels
  • Index selection, including PTA, PIN and £PLI

• Selection intensities and rates of response to selection

• In vitro selection

• Selection for meat charateristics

• Suggested reading

The following sections are included:

• Positive and negative assortative mating

• Inbreeding and outbreeding, and their consequences; inbreeding depression

• Wright's inbreeding coefficient, F; Wright's equilibrium for genotype frequencies under inbreeding; calculation of F from pedigrees

• Suggested reading

The following sections are included:

• Molecular types of mutation and their revertibility; mutation frequencies
  • Revertibility
  • Germ-line and somatic mutations
  • Base substitutions
  • Frame shifts
  • Large deletions
  • Unstable length mutations

• Spontaneous and induced mutation; mutagenic agents
  • Spontaneous mutations
  • Induced mutations

• Mutation control and repair systems
  • Mutagen access
  • Repair systems
  • Suppressor mutations
  • Optimum mutation rates

• How different types of mutation can complicate population genetics calculations

• Using induced mutations

• Suggested reading

The following sections are included:

• Recombination, genetic distances and the numbers of progeny needed to get particular recombinants

• Types of recombination and their effects; meiotic and mitotic crossovers;. interference and map functions

• Numbers of types of gamete, and of offspring genotypes and phenotypes, for different numbers of segregating loci

• Calculation of the frequencies of particular genotypes and phenotypes

• Mapping, including physical mapping

• Locating genes on particular chromosomes, including the use of pseudodominance, parasexual methods and hybridisation probes
  • Pseudodominance
  • Parasexual methods
  • Hybridisation probes

• A practical use of molecular markers in agriculture

• Suggested reading

The following sections are included:

• Introduction

• Deletions

• Inversions, paracentric and pericentric; their effects on fertility

• Duplications and the origin of new genes

• Translocations, single and multiple

• Suggested reading

The following sections are included:

• Background

• Changes in ploidy

• Monoploids

• Diploids

• Triploids

• Tetraploids

• Higher polyploids

• Loss or gain of single chromosomes: aneuploids, monosomics and trisomics

• Chromosome manipulations and substitutions

• Suggested reading

The following sections are included:

• Definition, origins, numbers and size
  • Origin
  • Numbers
  • Size

• Effects on phenotype and fertility

• Suggested reading

The following sections are included:

• Using hybrid vigour
  • Definition of hybrid vigour (heterosis)
  • Explanations of hybrid vigour
  • Typical F1 hybrid breeding programmes
  • Hybrid maize production
  • Hybrid sprout production
  • Hybrid animals

• Selection methods for inbreeders
  • Single line selection
  • Using a mixture of lines, with agricultural mass selection
  • Bulk population breeding
  • Pedigree breeding

• Selection methods in outbreeders or random-maters

• Recurrent backcrossing for gene transfer

• Interspecific and intergeneric hybrids
  • Interspecific hybrids
  • Intergeneric hybrids

• Making polyploids

• Examples of plant and animal breeding programmes
  • Semi-dwarf wheats
  • Broad beans
  • Semi-leafless combining pea
  • Sheep, including cross-breds and Border Leicesters
  • Cattle, including Ayrshires

• Breeding for shows

• Breeding programmes from crosses to selection, to local and national trials, possible commercial release, and approved lists

• Suggested reading

The following sections are included:

• Introduction

• Finding out how or whether characters are inherited: pedigree studies; twin studies; Hardy-Weinberg analysis; familial incidence
  • Pedigree studies
  • Twin studies
  • Hardy- Weinberg analysis of populations
  • Familial incidence

• Single gene characters and disorders, and their treatments
  • Autosomal genes
  • X-linked genes

• Polygenic and multifactorial disorders

• X-inactivation and Barr bodies

• Sex differences in disease susceptibility
  • X-linked diseases
  • Non-X-linked diseases

• Causes of human mutation; cancer
  • UV light
  • Chemicals
  • Ionising radiations
  • Temperature
  • Infection

• Chromosome number abnormalities and chromosome aberrations
  • Human chromosome methods
  • Autosomal abnormalities
  • Sex chromosome abnormalities

• Selection before and after birth

• Blood groups, especially ABO and Rhesus
  • The ABO blood group
  • The Rhesus blood group
  • Blood groups in farm animals

• The major histocompatibility complex

• Prenatal, neonatal and adult screening
  • Amniocentesis
  • Early amniocentesis
  • Chorionic villus sampling
  • Ultrasound screening
  • Maternal blood sampling
  • Foetal DNA screening
  • Neonatal screening
  • Adult or adolescent screening

• Effects of human inbreeding

• Genetic counselling

• Suggested reading

The following sections are included:

• Genetic engineering
  • Introduction
  • Restriction endonucleases and ligases
  • Vectors
  • Getting a particular piece of DNA into a vector, and recognising a clone containing it
  • Site-directed mutagenesis
  • Gene targeting
  • Genetic engineering in plants
  • Genetic engineering in animals
  • Genetic engineering in micro-organisms
  • Some dangers of genetic engineering; the amount of genetically engineered crops grown

• Human gene therapy
  • Introduction
  • Methods for somatic gene therapy
  • Progress

• Suggested reading

The following sections are included:

• The forces controlling the amounts of variation in a population
  • The forces or processes which increase or maintain genetic variation within a population
  • The forces or processes which reduce genetic variation within a population
  • The interactions of forces or processes affecting the amount of variation within a population

• Using a knowledge of the origins of genetic variation to solve a practical problem

• The maintenance of polymorphism in populations

• The need for genetic conservation; methods of conservation
  • The need for genetic conservation and the value of some old varieties
  • Conservation programmes and methods of genetic conservation

• Suggested reading

The following sections are included:

• Introduction

• The release of sterile insects

• The breeding of insect-resistant varieties

• Suggested reading

The following sections are included:

• Plants
  • Plant sexual reproduction
  • Incompatibility in higher plants
  • Crossing methods
  • Getting uniform fruit, seed or bud ripening
  • Somaclonal variation and vegetative propagation
  • Plant protoplast fusion
  • Gene expression and natural and artificial selection at the haploid stage

• Animals
  • Sex ratios
  • Anatomy, progeny per pregnancy, and temperature effects
  • Breeding seasons and oestrous cycles
  • Sperm; natural and artificial insemination
  • Egg transplantation, embryo freezing and animal cloning

• Humans

• Suggested reading

The following sections are included:

• General fungal genetics: life cycles; wild-types and mutants; spore types; control of sexual and vegetative fusions
  • Life cycles
  • Wild-types and mutants
  • Spores
  • The control of vegetative and sexual fusions

• The commercial importance of fungi

• Recombination and sexual mapping

• The parasexual cycle and parasexual mapping

• The induction and isolation of mutants, including auxotrophs

• Obtaining improved strains for industry
  • Aims and methods
  • Different aims in different yeasts
  • Penicillin production

• Suggested reading

The following sections are included:

• Basic economics: economic systems; price theory; factors affecting supply and demand; perfect and imperfect competition; monopolies; inflation
  • Factors of production; types of economic system
  • Price theory
  • Types of competition
  • Inflation

• Economics applied to agriculture
  • Gluts and shortages; how governments intervene in agriculture; European Union policies
  • Seasonal and perishable produce
  • The value of rarities
  • “Health foods”
  • Discounted cashflow assessment of breeding programmes
  • Breeders' rights

• Suggested reading

The following sections are included:

• Colour Plates

• Index