Lecture 1: Mutations and Disease
Answer: Citrullinaemia in cattle is caused by a single base substitution (C → T) at codon 86 in the gene responsible for the urea cycle. This leads to a stop codon, which halts protein synthesis, resulting in ammonia accumulation. Only homozygous recessive (dd) individuals lack functional enzymes, leading to the disease, while heterozygous (Dd) carriers remain asymptomatic.
Answer: In incomplete dominance, heterozygotes express a phenotype that is intermediate between the two homozygous phenotypes. An example is the cream dilution gene (SLC45A2) in horses, where heterozygous individuals (N/Cr) show a diluted coat color, while homozygous individuals (Cr/Cr) display a more intense cream color.
Answer: Myostatin deficiency, caused by mutations in the MSTN gene, leads to excessive muscle growth (double muscling). While it increases carcass yield, it also results in health problems like dystocia, respiratory diseases, and reduced organ size. Economically, it provides higher meat production, but these animals require specialized care and diets due to their health vulnerabilities.
Answer: Healthy parents can produce offspring with citrullinemia if both are heterozygous carriers (Dd). In Mendelian inheritance, each parent has a 50% chance of passing on the defective allele (d). If both parents contribute the defective allele, the offspring will be homozygous recessive (dd) and express the disease.
Answer: In recessive inheritance, only homozygous recessive individuals express the disease, while carriers remain asymptomatic, making it difficult to identify and eliminate the defective allele. In dominant inheritance, both homozygotes and heterozygotes express the disease, making it easier to identify and select against affected individuals, thus eliminating the allele from the population.
Lecture 2: Genome Technologies
Answer: First-generation (Sanger) sequencing is highly accurate but slow and costly, often used for small-scale projects or detecting specific mutations. Second-generation (Illumina) is much faster and cost-effective, making it suitable for large-scale genome projects. Third-generation (Oxford Nanopore) can read long fragments in real-time but has a higher error rate, making it ideal for applications like field pathogen detection or species monitoring.
Answer: Repetitive DNA sequences make it difficult to correctly assemble genomes because the short reads generated by earlier sequencing technologies cannot differentiate between identical or similar repeats. Third-generation sequencing, which reads longer fragments, helps resolve this by providing more context for these repetitive regions, reducing assembly errors.
Answer: Genome annotation involves identifying genes and other functional elements within a genome sequence. mRNA sequencing (RNA-seq) helps by mapping expressed genes, providing insights into which parts of the genome are actively producing proteins. This is crucial in veterinary research for identifying disease-related genes and understanding how different genes are expressed in various tissues or conditions.
Answer: In 2000, sequencing a genome took years and billions of dollars, limiting its use. With the advent of second- and third-generation technologies, genome sequencing is now much faster (in as little as 24 hours) and significantly cheaper (around $1,000). This has made it accessible for more routine applications in veterinary science, such as breeding programs, pathogen detection, and personalized treatments.
Answer: Genome sequencing allows for the identification of genetic mutations that cause diseases, enabling the development of targeted treatments or vaccines. For example, sequencing the genome of pathogens like viruses or bacteria helps researchers understand their mechanisms of infection and drug resistance, leading to the creation of effective vaccines or therapies for animals.
Lecture 3: Animal Breeding
Answer: Polygenic inheritance refers to traits influenced by multiple genes, with alleles contributing in an additive manner. An example is disease resistance in livestock, where many genes each contribute small effects toward an animal’s overall resistance to infections.
Answer: Heritability measures the proportion of phenotypic variance in a trait that is due to genetic factors. It is important because it helps breeders predict how effectively they can improve a trait through selection. If \( h² \) is high, genetic selection will lead to rapid improvements in that trait.
Answer: The breeder’s equation predicts that the response to selection (R) is a product of heritability (h²) and selection differential (S). For example, if breeders select animals with a trait value much higher than the population mean, and the trait has high heritability, the offspring of these selected animals will, on average, show an improved version of that trait.
Answer: GWAS compares genetic variants (like SNPs) across individuals with different phenotypes (e.g., disease resistance vs. susceptibility) to find regions of the genome associated with the trait. This approach is especially useful for traits controlled by many genes, like body weight or fertility in livestock.
Answer: Traditional progeny testing involves evaluating an animal's genetic merit based on the performance of its offspring, which is time-consuming and costly. Genomic selection, on the other hand, uses DNA data from birth to predict an animal’s breeding value. This method is faster, less expensive, and accelerates genetic improvement by shortening the generation interval.
Lecture 4: Animal Breeding II, Companion Animals, Wildlife
Answer: Pleiotropy is when one gene influences multiple traits, potentially unrelated. In companion animal breeding, a gene affecting coat color may also impact behavior or health. For example, the gene for white fur in some dog breeds is associated with deafness, complicating breeding decisions to maintain healthy populations.
Answer: Genetic correlations measure how the genetic factors influencing one trait affect another. Positive correlations allow indirect selection, improving hard-to-measure traits by selecting a related, easily measurable trait. For instance, in sheep, selecting for a rumen microbial profile can lead to reduced methane emissions, as both traits have a positive genetic correlation.
Answer: Intense selection for breed standards leads to genetic bottlenecks, increasing inbreeding and the frequency of recessive deleterious alleles. This has resulted in various health issues such as brachycephalic syndrome in bulldogs, where breeding for short snouts causes respiratory problems, or hip dysplasia in large breeds like Golden Retrievers.
Answer: Genomic data helps preserve genetic diversity and prevent inbreeding in wildlife populations. In captive breeding programs, genomic-based relatedness estimates guide mating decisions, reducing inbreeding. For example, zoos use genomic tools to ensure marmots with dilated cardiomyopathy do not breed, maintaining healthier populations.
Answer: Linkage disequilibrium occurs when alleles at two or more loci are inherited together more frequently than expected by chance. This non-random association can make it difficult to select for one trait without affecting another. For example, if coat color and size genes are in LD in dogs, selecting for a particular color could inadvertently affect the dog's size.
Lecture 5: Molecular Diagnosis
Answer: PCR amplifies specific DNA or RNA sequences, allowing veterinarians to diagnose infections, assess disease risk, and monitor treatments with high specificity.
Answer: Primer design is crucial because mismatches could lead to nonspecific amplification. Melting temperatures (Tm) help determine when primers will bind or dissociate from the template, affecting reaction efficiency and accuracy.
Answer: Limitations include the need for prior knowledge of sequences, the risk of contamination, lack of proofreading by Taq polymerase, and inhibition by certain sample components. These issues can lead to false positives, missed amplifications, or errors in long sequences.
Answer: DNA metabarcoding can be used to analyze parasitic infections in animals by identifying multiple species from a single sample. For example, it helps in identifying gut microbiome diversity in horses.
Answer: PCR is ideal when cycling between temperatures is possible, while isothermal amplification is better for fieldwork or situations where simpler equipment is needed, such as rapid diagnostics.