Introduction to Veterinary Genetics

Frank W. Nicholas is Emeritus Professor of Animal Genetics in the Sydney School of Veterinary Science at the University of Sydney, NSW, Australia. He is an Honorary Member of the International Society for Animal Genetics. In 2022 he was awarded Doctor Medicinae Veterinariae Honoris Causa from the University of Bern and was appointed Member (AM) of the Order of Australia. His work includes co-authoring Charles Darwin in Australia and creating the global reference website for inherited diseases in animals: Online Mendelian Inheritance in Animals (OMIA; omia.org).

• PrefaceAcknowledgements1 Basic geneticsChromosomes Meiosis and mitosis        The biochemistry of inheritanceWhat is a gene?Gene regulation              Mutation            Simple or Mendelian inheritance             LinkageInactivation       Types of DNASummaryWebsites            Further readingAppendix 1.1 Banded karyotypes of domestic species2 Molecular biology       Restriction enzymes      DNA cloning and Recombinant DNA        DNA sequencing              Complementary DNARNA sequencingPolymerase chain reaction (PCR)              Microsatellites Single nucleotide polymorphisms (SNPs)Gene mappingReference genome assembliesWhole-genome sequencing (WGS)Whole-exome sequencing (WES)Beyond SNP chipsComparative genomicsProduction of polypeptide from cloned DNATransgenesisAntisense technologyCRISPR-CasSummaryWebsitesFurther reading3 Single-gene disordersInborn errors of metabolism      Sex-limited inheritanceGenetic heterogeneity of disease            Type of gene action and type of diseasePhenocopiesCongenital and non-congenital disorders              A sample of single-gene disorders           A revolution in identifying the likely causalvariant of single-gene disordersSummaryWebsites            Further readingAppendix 3.1 Online Mendelian Inheritance in Animals (OMIA): a compendium of single-gene traits and their likely causal variants  4 Chromosomal aberrations       Abnormal chromosome numberAbnormal chromosome structure            Chromosomal aberrations in cancer        Evolution of karyotypesInterspecific hybridization           Freemartins      Biological basis of sex    Classification of intersex              A sample of chromosomal aberrationsSummary            Further readingAppendix 4.1 A sample of chromosomal aberrations in animals   5 Single genes in populations     Allele and genotype frequencies              Random matingThe Hardy–Weinberg law            Extensions to the Hardy–Weinberg law Selection and mutationGenetic drift and the founder effect       Extending population genetics to more than one locusSummaryWebsites            Further reading6 Familial disorders not due to a single gene       Liability and threshold  The multifactorial model              More than one thresholdHeritabilityPenetrance and expressivityFuture resolution of multiple factorsRecurrence risks              Summary            Further reading7 Is it inherited?              General evidence for a genetic aetiology              The four types of simple, Mendelian inheritanceStudying and analysing the dataSummaryWebsites            Further reading8 Immunogenetics         Antibodies         Red-cell antigens             The major histocompatibility complex (MHC)SummaryWebsites            Further reading9 Pharmacogenetics and Pharmacogenomics     Genetic polymorphisms affecting drug reaction Genetics and anaesthesia            Warfarin resistance        Multifactorial pharmacogeneticsSummaryWebsites            Further reading10 Hosts, parasites, and pathogens         Host–pathogen interactions       Resistance in hosts         Resistance in parasites and pathogens   Control of parasites and pathogens         Increasing the level of resistance in hostsIncreasing the level of resilience in hostsSummaryWebsites            Further reading11 Single genes in animal breeding         Coat colour        Carpet wool       Prolificacy in sheep        Polledness         Muscular hypertrophy in cattle and sheep           Dwarf poultry   Genes for sexing chickens           Parentage testingSummaryWebsites            Further reading12 Relationship and inbreeding The inbreeding coefficient          RelationshipGenomic relationship    The inbreeding coefficient revisited        General expressions for relationship and inbreeding       The base population      Inbreeding in populationsRuns of homozygosity   Inbreeding depressionSummaryWebsites            Further reading13 Quantitative variation             Quantitative traits           The performance of an individual animal               The differences between animals            Heritability         Correlations between traits        Quantitative trait loci (QTL)SummaryWebsites            Further reading14 Selection between populations          Comparison between populations           Genotype–environment interactionComparing breeds of companion animals             Further reading15 Selection within populationsEstimated breeding values and accuracy of selection       Phenotypic clues to a candidate’s breeding value for a trait          Combining clues from more than one source      Best linear unbiased prediction (BLUP)  Correlated traits              Selection for more than one trait              The importance of inbreeding and genetic drift  Genomic selection          Polygenic Risk Scores: genomic clues to a candidate’s phenotypic valueUltimate genotypesSummaryWebsites            Further reading16 Breed structure         The traditional pyramidClosed-nucleus breeding schemes           Open-nucleus breeding schemes             Community-based breeding programmesSummaryWebsites            Further reading17 Crossing        Regular crossingCrossing to produce a syntheticDesigner dogs   Grading-upSummaryWebsites            Further reading18 Selection and regular crossing             Selection            Selection and regular crossingSummary            Further reading19 Biotechnology            Artificial insemination (AI)           Multiple ovulation and embryo transfer (MOET)In vitro maturation (IVM) and in vitro fertilization(IVF) of ova        Control of sex ratio         Recombinant proteins  TransgenesisUses of CRISPR-Cas        Animal cloningAnimal forensicsBarcode of lifeSummaryWebsites            Further reading20 Conservation genetics            Measurement of genetic diversity within populations     Measurement of genetic diversity among populations    Importance of genetic diversity Loss of genetic diversityConservation of genetic diversityTargeted genetic interventionSummaryWebsitesFurther reading21 Genetic and environmental control of inherited disorders      Environmental control of inherited disorders      Genetic control of single-gene disordersGenetic control of multifactorial disorders           Genetic control – some final points         Crossing: thinking outside the squareSummaryWebsites            Further reading22 Cancer genetics and genomicsMutational basis of cancerGenome screens of cancersGenetic variation in susceptibility to cancerSummaryWebsitesFurther readingIndex