CH 1: SELECTION

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Lesson 1: Defining Traits

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In animal genetics, a trait is an observable characteristic of an animal that are determined by its genetic makeup, or genotype. When a trait can be observed and possibly measured, it is referred to as a Phenotype (P)

Traits (or Phenotypes) are the result of interactions between genes (G) and the environment (E).

P = G + E

G represents the Genotype of the animal, which is the collection of the genes possessed by the animal. E actually represents all the non-genetic conditions that can influence the phenotype.

We can think of the Genotype conferring a particular value on the trait in the individual and the environment causing a deviation from this value in one direction or the other.

Mendelian Traits: Some traits follow Mendelian inheritance patterns, where a single gene controls the phenotype. These traits typically exhibit simple dominant-recessive relationships, such as eye color in humans.

Polygenic Traits: Many traits are influenced by multiple genes and environmental factors. These are called polygenic traits. Examples include height, skin color, and intelligence. Polygenic traits often show a continuous range of variation in a population.

Alleles: Genes exist in different forms called alleles. Alleles can be dominant or recessive, and their combination determines the phenotype. For example, in Mendelian inheritance, a dominant allele will mask the expression of a recessive allele.

Gene Interaction: Sometimes, multiple genes interact to produce a trait. This interaction can be additive, where the effects of each gene add up, or epistatic, where one gene masks the expression of another.

Environmental Influence: Environmental factors, such as nutrition, temperature, and exposure to toxins, can also influence the expression of traits. This is particularly true for traits with a polygenic basis.

Qualitative and Quantitative Traits

Qualitative traits are also known as discontinuous traits. These are traits that exhibit distinct, non-overlapping categories or variations within a population. These traits are typically controlled by one or a few genes and are often influenced less by environmental factors. While the environment can have some impact, the genetic control is more predominant in determining the expression of qualitative traits.

Qualitative traits typically have distinct categories or variations that are easily observable and do not blend into one another. Variation in qualitative traits is discrete, meaning individuals can be clearly categorized into distinct groups based on their phenotypes. Examples include flower color in plants (e.g., purple vs. white), blood type in humans (e.g., A, B, AB, O), and coat color in animals (e.g., black vs. brown).

Mendelian Inheritance: Many qualitative traits follow Mendelian inheritance patterns, with distinct dominant and recessive alleles.

Genetic Disorders: Some genetic disorders are determined by qualitative traits, such as cystic fibrosis and sickle cell anemia. These disorders typically result from mutations in single genes, leading to distinct phenotypic outcomes.

Quantitative traits, also known as continuous traits, are traits that exhibit a range of phenotypic variation within a population. Unlike qualitative traits, which have distinct categories, quantitative traits show a continuum of phenotypes.

Quantitative traits exhibit continuous variation, meaning that individuals within a population vary along a spectrum rather than falling into distinct categories. Examples include height, weight, blood pressure, and yield in crops.

Phenotypic variation in quantitative traits often follows a normal distribution curve, also known as a bell curve.

Quantitative traits are typically influenced by multiple genes, (polygenic) each gene causing small effects on the traits, as well as environmental factors. This polygenic inheritance contributes to the continuous range of variation observed in these traits.

Environmental factors such as nutrition, climate, and stress can significantly impact the expression of quantitative traits. Unlike qualitative traits, which are more genetically determined, environmental factors play a larger role in shaping the phenotype of quantitative traits.

Many complex traits, such as intelligence, disease susceptibility, and behavioral traits, are quantitative in nature. These traits are influenced by a combination of genetic and environmental factors, making them challenging to study and predict.

Selection for quantitative traits often results in gradual changes in the population over multiple generations. Response to selection for quantitative traits is typically slower than for qualitative traits due to the polygenic nature of the traits.

Lesson 2: Genetic Variation

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Genetic variation in animals refers to the diversity of genetic material present within a population or species. This variation arises from differences in the DNA sequences of individuals and can manifest as differences in phenotypes such as disease susceptibility, productivity and other performance traits.

Genetic variations can be caused or attributed to several processes such as:

• Mutation: Mutations are the ultimate source of genetic variation. They can occur spontaneously during DNA replication or in response to environmental factors such as radiation or chemical exposure. Mutations can range from single nucleotide changes to large-scale chromosomal rearrangements.
• Recombination: Recombination during sexual reproduction shuffles genetic material between homologous chromosomes, leading to new combinations of alleles in offspring. This process increases genetic diversity within populations by generating novel genetic combinations.
• Gene Flow: Gene flow occurs when individuals migrate between populations, introducing new alleles into the gene pool. It can occur through dispersal of individuals or through movement of gametes (e.g., pollen or sperm). Gene flow can homogenize genetic variation between populations or introduce new variation.
• Natural Selection: Natural selection acts on genetic variation within populations, favoring individuals with traits that enhance survival and reproduction in a given environment. Over time, natural selection can lead to changes in allele frequencies, resulting in adaptation to specific ecological niches.
• Genetic Drift: Genetic drift refers to random fluctuations in allele frequencies due to chance events, particularly in small populations. Genetic drift is a significant driver of evolution in small or isolated populations and can lead to loss of genetic variation over time.
• Balancing Selection: Balancing selection occurs when multiple alleles at a gene locus are maintained in a population over time. This can occur through mechanisms such as heterozygote advantage, where individuals heterozygous for a particular allele have a selective advantage.
• Artificial Selection: Humans have selectively bred animals for specific traits for thousands of years, leading to the creation of diverse breeds within species. Artificial selection can rapidly change allele frequencies and phenotypic traits within populations.

Genetic diversity is important for the long-term viability and adaptability of populations. Higher levels of genetic diversity can provide a reservoir of adaptive potential in response to environmental changes and reduce the risk of inbreeding depression and genetic diseases. Animal breeders utilize this genetic variation to improve traits of economic or ecological importance within livestock and companion animal populations.

Case Study: The Belgian Blue Cattle Breed

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Belgian Blue cattle, also known as BBB or Belgian Blue-White, are a breed of beef cattle originating from Belgium. They are renowned for their distinctive appearance, characterized by their heavily muscled bodies, often referred to as "double-muscling." The double-muscling phenotype is a heritable condition resulting in an increased number of muscle fibres (hyperplasia), instead of the (normal) enlargement of individual muscle fibres (hypertrophy).

The double-muscling phenotype is results from a naturally occurring mutation known as "double-muscling" mutation in the myostatin gene which codes for the protein, myostatin. Myostatin is a protein that inhibits muscle development. This mutation also interferes with fat deposition, resulting in very lean meat. The truncated myostatin gene causes accelerated lean muscle growth mainly due to physiological changes in the animal's muscle cells (fibres) from hypertrophy to a hyperplasia mode of growth. The Belgian Blue's bone structure is the same as normal cattle, albeit holding a greater amount of muscle, which causes them to have a greater meat to bone ratio. These cattle have a muscle yield around 20% more on average than cattle without the genetic myostatin mutation.

The birth weight and width of the calf is usually higher than in animals without the double-muscling gene. Calves are commonly born by Caesarean section. Natural calving is always associated with dystocia.

Belgian Blue cattle require modified diets because of this breed's increased muscle yield. A diet containing higher protein is required to compensate for the altered mode of weight gain. During finishing, this breed requires high-energy (concentrated) feeds, and will not yield the same results if put on a high-fibre diet which reflects the role of the environment in influencing the expression of phenotypes.

Breeding programs for Belgian Blue cattle focus on maintaining and improving desirable traits, such as muscling, while also addressing potential health concerns associated with the double-muscling mutation. Selective breeding and careful genetic management are essential for ensuring the long-term sustainability and welfare of the breed.

Lesson 3: Phenotypic Variation

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Phenotypic variation refers to the observable differences in traits or characteristics among individuals within a population. These differences can arise from genetic variation, environmental influences, or interactions between genes and the environment. Phenotypic variation is a fundamental aspect of biological diversity and plays a crucial role in evolution, adaptation, and the functioning of ecosystems.

Phenotypic variation occurs due to the following factors:

Genetics: Genetic variation among individuals is a primary determinant of phenotypic variation. Genes encode the instructions for the development and functioning of organisms, influencing traits such as height, coloration, behavior, and physiological processes. Allelic variation, gene interactions, and gene-environment interactions contribute to the diversity of phenotypes within a population.

Environment: Environmental factors, including temperature, humidity, nutrient availability, and social interactions, can significantly impact phenotypic expression. Environmental conditions during development can shape phenotypic traits and may induce phenotypic plasticity, where individuals with the same genotype exhibit different phenotypes in response to environmental cues.

Interaction between Genes and Environment: Phenotypic variation often results from complex interactions between genetic and environmental factors. Genes provide the potential for trait expression, while environmental conditions determine how genes are expressed. Genotype-environment interactions can result in phenotypic differences among individuals with the same genotype exposed to different environments.

Phenotypic Plasticity: Phenotypic plasticity refers to the ability of a single genotype to produce different phenotypes in response to environmental variation. Phenotypic plasticity allows organisms to adjust their phenotype to optimize fitness in different environments, enhancing their capacity to survive and reproduce in diverse conditions.

Phenotypic variation can be continuous or discontinuous. Continuous variation refers to traits that show a range of values across a population, such as height or weight, and are influenced by multiple genes and environmental factors. Discontinuous variation involves distinct categories or states, such as blood type or flower color, and may be controlled by one or a few genes.

Lesson 4: Genetic Response

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Genetic response refers to the changes in the genetic composition of a population in response to selective pressures or environmental factors over time. These changes occur as a result of natural selection, artificial selection, or other evolutionary forces acting on the genetic variation within a population.

A genetic response may arise from the following factors:

Natural Selection: Natural selection is the primary driver of genetic response in natural populations. It occurs when individuals with certain heritable traits have greater reproductive success or survival rates than others, leading to the increased frequency of advantageous alleles in subsequent generations. Over time, natural selection can result in the adaptation of populations to their environments.

Artificial Selection: In artificial selection, humans deliberately choose individuals with desired traits to breed, leading to changes in allele frequencies within populations. Artificial selection has been widely used in agriculture to improve traits such as yield, disease resistance, and quality of agricultural products. It can lead to rapid genetic responses compared to natural selection.

Selective Breeding Programs: Selective breeding programs aim to enhance specific traits in plants and animals through controlled mating. These programs typically involve identifying individuals with desirable traits, such as high productivity or disease resistance, and using them as parents for the next generation. Over successive generations, this process can lead to significant genetic changes in populations. This course focuses on genetic changes arising from selective breeding.

Response to Environmental Changes: Genetic response can occur in response to environmental changes, such as shifts in climate, habitat loss, or the introduction of new predators or pathogens. Populations may evolve traits that confer resistance or tolerance to environmental stressors, allowing them to persist in changing conditions.

Gene Flow: Gene flow, the movement of genes between populations through migration, can influence genetic responses by introducing new genetic variation or altering existing allele frequencies. High rates of gene flow can homogenize populations genetically, while low rates can lead to genetic divergence and local adaptation.

Genetic Drift: Genetic drift, the random fluctuation of allele frequencies in small populations, can also influence genetic responses, particularly in small or isolated populations. Genetic drift can lead to the fixation of alleles or the loss of genetic variation over time, affecting the potential for adaptation to changing conditions.

Genetic change from Selective Breeding

Selective breeding, also known as artificial selection, can elicit specific genetic responses within populations over successive generations.

Selective Breeding involves the following process:

Trait Selection: Selective breeding involves deliberately choosing individuals with desirable traits to serve as parents for the next generation. These traits can vary depending on the breeding goals, such as increased yield, improved disease resistance, enhanced flavor, or altered appearance.

Consider the trait's heritability: The success of selective breeding relies on the heritability of the target traits, which determines the extent to which they are passed from parent to offspring genetically. Traits with high heritability are more responsive to selective breeding, as their phenotypic expression is strongly influenced by genetic factors.

Genetic Variation: Genetic variation within the breeding population provides the raw material for selection to act upon. Initially, the breeding population may exhibit a range of phenotypic variation for the target traits. Selective breeding aims to increase the frequency of alleles associated with desirable traits while decreasing the frequency of alleles associated with undesirable traits.

Breeding Strategies: Selective breeding programs employ various breeding strategies to achieve desired genetic responses. These strategies may include inbreeding, line breeding, crossbreeding, or hybridization, depending on the goals of the breeding program and the genetic characteristics of the target species.

Ability to predict genetic response accurately: Over successive generations of selective breeding, individuals with the desired traits with known heritability and genetic variation lead to predictable changes of favorable alleles in the breeding population.

Lesson 5: Breeding Goals

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Animal breeding goals or objectives may vary depending on the specific objectives of the breeding program and the characteristics desired in the animals being bred. These goals can differ widely between different sectors of animal agriculture, and across individual farms. Generally, breeding goals might fall under one or more of the following areas:

Improving Production Efficiency: One of the primary goals of animal breeding is to enhance production efficiency by increasing the quantity and quality of products obtained from animals. This may include improving traits such as growth rate, feed conversion efficiency, milk yield, egg production, and meat quality.

Enhancing disease resistance, resilience and general health: Breeding programs often aim to improve the resistance and/or resilience of animals to diseases and health issues. This can involve selecting for associated traits such as immune response, resistance to specific pathogens, and overall robustness and resilience to environmental stressors.

Optimizing Reproductive Performance: Reproductive traits are critical for the success of animal breeding programs. Breeding goals may include improving fertility, reproductive lifespan, reproductive rate, high conception rates and high offspring survival rates - superior maternal traits.

Enhancing Animal Welfare and Behavior: Breeding programs may prioritize traits related to animal welfare and behavior, such as temperament, docility, stress tolerance, and adaptability to different management systems. Animals with calm temperaments and low stress levels are easier to handle and less prone to behavioral issues.

Improving Environmental Sustainability: Sustainable animal production systems aim to minimize environmental impact while maintaining profitability and productivity. Breeding goals may include selecting for traits that reduce resource inputs (e.g., feed, water) and environmental emissions (e.g., methane from enteric fermentation), as well as promoting traits associated with resilience to climate change and resource scarcity.

Enhancing Product Quality and Marketability: Breeding programs may focus on improving product quality attributes that are valued by consumers, such as flavor, texture, color, and nutritional content. Animals with desirable product quality characteristics can command premium prices in the market.

Preserving Genetic Diversity and Adaptation: In some cases, breeding goals may include preserving genetic diversity within populations and maintaining traits associated with local adaptation and resilience to specific environments. This is particularly important for conserving rare or endangered breeds and for promoting biodiversity in agricultural systems.

Lesson 6: Breeding Programs

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An animal breeding program is a systematic and structured approach to improving the genetic characteristics of a population of animals over time. These programs aim to enhance desirable traits.

A breeding program consists of the following components/steps:

Setting breeding goals: The first step in developing an animal breeding program is defining clear and achievable breeding goals. These goals are determined based on the specific objectives of the program, which may vary depending on the industry sector (e.g., dairy, beef, poultry), market demands, and production system.

Selection of Breeding Stock: Once breeding goals are established, suitable breeding stock is selected to serve as parents for the next generation. Selection criteria may include performance records, pedigree information, genetic evaluations, and physical characteristics relevant to the breeding goals.

Develop a Breeding Strategy: Breeding strategies outline how mating decisions will be made to achieve the desired genetic improvements. This may include:

• Inbreeding and Line Breeding: Used to concentrate desirable traits within a population and fix desired alleles.
• Outcrossing: Introducing genetic diversity into a population by mating unrelated individuals to reduce the risk of inbreeding depression.
• Crossbreeding: Mating individuals from different breeds or lines to capitalize on breed complementarity and heterosis (hybrid vigor).

Selection Intensity: Determining the proportion of individuals selected as parents based on their genetic merit.

Genetic Evaluation: Genetic evaluation involves estimating the genetic merit of animals for specific traits of interest using statistical models and performance data. This helps identify superior animals for selection as parents and informs breeding decisions.

Estimating Breeding Value: Breeding values quantify the genetic merit of animals for specific traits, accounting for genetic and environmental factors. Breeding values are used to rank animals and guide mating decisions to maximize genetic progress.

Recording and Data Management: Accurate and comprehensive records of pedigree, performance, and genetic information are essential for the success of an animal breeding program. Data management systems facilitate the collection, storage, analysis, and utilization of breeding data.

Monitor Genetic Progress: Genetic progress is monitored and evaluated over time to assess the effectiveness of the breeding program. Adjustments may be made to breeding strategies, selection criteria, or management practices based on evaluation results to enhance program performance

CH 2: VALUES AND MEANS

Introduction Lesson 1: Population Mean Lesson 2: Average Effect Lesson 3: Breeding Value Lesson 4: Dominance Deviation Lesson 5: Interaction Deviation

Introduction

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As discussed in the previous chapter, phenotypes can eitherbe qualitative or quantitative. Qualitative traits are categorical and discrete while Quantitative traits are continuous and individual vary in degree with no clear cut distinctions. Quantitative characters and also called Metric Characters because their study depends on measurement instead of counting.

The inheritance of metric characters can be predicted using Population genetics principles, however, it is impossible to track individual genes across different generations, and because in most cases, mating is not random, some modifications to the population genetics principles are necessary.

The branch of genetics focusing on quantitative traits is called Quanititative Genetics or Biometrical Genetics. Animal breding relies on a deep understanding of Quantitative genetic principles because most traits of economic value in plants and animals are quantitative traits.

We understand that the variation present at the genetic level, DNA level, is discrete, with categories of alleles and genotypes. How come this discrete variation in genotypes is translated into continuous variation at the phenotypic level? There are two main reasons for this. Firstly, most quantitative traits are contolled by multiple genes (polygenic) and the combined effect of many discrete variations result in what is observed as less discrete variation in the phenotypes. Secondly, quantitative traits are influenced by the superimposition of non-genetic variation on top of the genetic variation.

Consider an example, where a traits is controlled by 6 unlinked loci each with 2 alleles at frequencies of 0.5. Suppose there is complete dominance of one allele and that the dominant allele adds 1 unit to the measurement of the trait. If these alleles were the only cause of phenotypic variation, we would observe 7 discrete classes in measurement of the character ranging from 0 (where the individual doesnt have even one dominant allele), 1 (where the individual has an dominant allele at one of the 6 loci), 2, 3 (where the individual has 3 dominant alleles and 3 loci), 4, 5, 6 (where the individual has a dominant alele at all the 6 loci). Notice that in this situation, the trait will appear as discrete and we will be able to place any individual in a specific category directly correlated with the number of dominant alleles present. The frequencies of the classes would be according to the binomial expansion of (1/4 + 3/4)⁶.

The figure shows the distribution expected from the simultaneous segregation of two alleles at each of several loci: 6 loci (a) and 24 loci (b). There is complete dominance of one allele at each locus and the allele frequency is 0.5. Each locus when homozygous for the recessive allele will reduce the measurement by 1 unit in a and by 1/4 unit in b. The horizontal scale shows the number of loci homozygous for the recessive allele and the vertical axis shows the probability or the percentage of individuals expected in each class. Probabilities are derived from the binomial expansion of (1/4 + 3/4)ⁿ. Where n is the number of loci. Notice that as the number of genes increases, and each gene contributes only a small effect, it becomes more and more difficult to distinguish the classes.

Variation resulting from non-genetic factors is truly continuous and tends the blur the edges of the phenoptypic discontinuity that might have been present from the influence of genetic factors alone.

A gene whose effect is large enough to result in a detectable phenotypic discontinuity, even in the preence of other genes, or non-genetic factors can be referred to as a Major gene. Minor genes are those that influence a trait but not in a significant way and doesnt cause a discontinuity in the phenotype. Some genes may be major for a certain trait, but minor for another trait. This is called pleitropy.

As previously mentioned, polygenic traits are those that are controlled by multiple genes. The major genes involved in such traits can be called polygenes. Most traits of economic importance in livestock production are polygenic, such as anatomical measurements, lactation, fertility, growth rate etc.

If you plot a histogram with the number of individuals that fall in each class of measurement pltted in the vertical scale and the phenotypic measure or call on the horizontal axis, you will find that the histogram looks like this:

Notice that the frequency distribution of quantitative traits approximate a normal curve especially when the population being meausred is infinitely large.

The degree of resemblance between relatives can be readily observed and is the foundation of quantitative genetics to show how this degree of resembalnce can be used to predict the outcome of selective breeding and to point to the best method of carrying out selective breeding. The practical goal of selective breeding is to find out how we can use the observations made on the population to predict the outcome of any breeding method.

The properties of a population that can be used to understand metric traits are Means, variances and covariances. These form the basis for measuring the degree of resemblance between relatives.