Lecture 10b - Population Analysis & Marker Traits
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Questions and Answers

What is the typical frequency of recombination events per chromosome during meiosis?

  • 5-10 times
  • Once
  • 2-3 times (correct)
  • More than 10 times

    • Recombination occurs more frequently in the middle regions of the chromosome.

    False (B)

    What discovery did Thomas Hunt Morgan make regarding genes on chromosomes?

    Genes are organized in a row on the chromosome.

    The different versions of orthologous genes at a specific chromosome location are called __________.

    <p>alleles</p> Signup and view all the answers

    Match the following terms with their definitions:

    <p>Genotype = The genetic composition of an organism Phenotype = The observable traits of an organism Recombination = The exchange of genetic material between chromosomes Genetic marker = A trait associated with specific alleles</p> Signup and view all the answers

    What is the main purpose of meiosis?

    <p>To produce gametes for reproduction (B)</p> Signup and view all the answers

    Genetic recombination occurs during the formation of diploid cells.

    <p>False (B)</p> Signup and view all the answers

    What term describes a cell with only one copy of a genome?

    <p>haploid</p> Signup and view all the answers

    During meiosis, _________ is the process where new combinations of alleles are created in haploid cells.

    <p>recombination</p> Signup and view all the answers

    What type of recombination involves the exchange of chromosome segments between homologous chromosomes?

    <p>Intrachromosomal recombination (D)</p> Signup and view all the answers

    What is the result of independent assortment during meiosis?

    <p>Unique combinations of alleles (B)</p> Signup and view all the answers

    Most animals and plants are haploid organisms.

    <p>False (B)</p> Signup and view all the answers

    What can individuals be considered as regarding their genetic makeup?

    <p>A mosaic of all generations in their pedigree (B)</p> Signup and view all the answers

    Ancestral recombination events can be identified from a pedigree with low genotyping resolution.

    <p>False (B)</p> Signup and view all the answers

    Name one method used to capture population structure.

    <p>Structure or principal component analysis</p> Signup and view all the answers

    An individual is often regarded as a mixture of the genes from its maternal and paternal __________.

    <p>parent</p> Signup and view all the answers

    Match the following terms with their appropriate descriptions:

    <p>Genome Mosaic = An individual composed of genes from multiple ancestors Population Structure = Imbalance in allele frequency due to non-random mating Pritchard’s Structure = A program that infers sub-populations from genotype data Polymorphism = The occurrence of different alleles in a population</p> Signup and view all the answers

    What is the primary function of Pritchard's Structure program?

    <p>To infer sub-populations based on genomic data (D)</p> Signup and view all the answers

    Non-random mating can result from random chance.

    <p>True (A)</p> Signup and view all the answers

    What is one potential consequence of a prevalent polymorphism in a population?

    <p>It may be erroneously associated with a specific trait.</p> Signup and view all the answers

    What is one limitation of Quantitative Trait Loci (QTL) mapping?

    <p>It can only genetically map traits that differ between two parents. (D)</p> Signup and view all the answers

    Association mapping populations can easily be created using closely related individuals.

    <p>False (B)</p> Signup and view all the answers

    What is the typical size of populations used for QTL mapping?

    <p>In the hundreds.</p> Signup and view all the answers

    Association mapping populations can have sizes greater than _____ individuals in some human studies.

    <p>100K</p> Signup and view all the answers

    Match the following population characteristics with their descriptions:

    <p>QTL Mapping = Limited to traits differing between two parents Association Mapping = Easy to construct and can include traits that vary among members Population Size in QTL Mapping = Typically in the hundreds Population Size in Association Mapping = Can exceed 100K individuals</p> Signup and view all the answers

    Who developed the first genetic map in 1911?

    <p>Alfred Sturtevant (A)</p> Signup and view all the answers

    The distance between markers in a genetic map is measured in physical base pairs.

    <p>False (B)</p> Signup and view all the answers

    What is the term used to describe the percentage chance of recombination occurring between two markers?

    <p>centimorgans</p> Signup and view all the answers

    A genetic map is created from the __________ that differ in the traits under investigation.

    <p>bi-parental populations</p> Signup and view all the answers

    Match the types of mapping populations with their descriptions:

    <p>Bi-parental populations = Cross of two parents differing in traits Genome-wide association panels = Individuals with variability in many traits from the same species Multi-parent populations = Crossing of several well-characterized individuals NAM = Nested Association Mapping</p> Signup and view all the answers

    What does a distance of 1 centimorgan (cM) mean in terms of recombination likelihood?

    <p>1% chance of recombination (B)</p> Signup and view all the answers

    Modern mapping populations are typically not genotyped for analysis.

    <p>False (B)</p> Signup and view all the answers

    What are the two key outcomes of identifying genes involved in controlling traits through genetic mapping?

    <p>Creation of new drugs and treatments or development of improved plant varieties.</p> Signup and view all the answers

    What does the eigenvalue represent in a PCA?

    <p>The amount of variance explained by a principal component (B)</p> Signup and view all the answers

    Kinship matrices are only relevant for analyzing populations with no related individuals.

    <p>False (B)</p> Signup and view all the answers

    What rule of thumb is used to determine the number of populations in PCA modeling?

    <p>The PC number where the curve starts to flatten out (the 'elbow').</p> Signup and view all the answers

    A kinship matrix captures the relationships among individuals as a __________ value.

    <p>numerical</p> Signup and view all the answers

    Why is it important to account for kinship in population analysis?

    <p>To reduce the probability of false associations (B)</p> Signup and view all the answers

    A heat map can visually represent kinship values among individuals in a population.

    <p>True (A)</p> Signup and view all the answers

    What does IBD signify in the context of a kinship matrix?

    <p>It means that the allele has been inherited from a common ancestor.</p> Signup and view all the answers

    The __________ along the top and side of a heat map shows how individuals cluster together by kinship.

    <p>dendrogram</p> Signup and view all the answers

    What can happen if relatedness among individuals is not accounted for in analysis?

    <p>False associations between markers and traits (A)</p> Signup and view all the answers

    Flashcards

    Meiosis

    Specialized cell division creating haploid gametes for reproduction, shuffling genetic material into four daughter cells.

    Recombination

    Process creating new allele combinations in haploid cells, involving interchromosomal and intrachromosomal methods.

    Haploid cell

    A cell with only one copy of each chromosome.

    Interchromosomal recombination

    Process of shuffling whole chromosomes to create new genetic combinations in haploid cells.

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    Intrachromosomal recombination

    Exchange of chromosome segments between homologous chromosomes.

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    Independent assortment

    Random distribution of chromosomes to daughter cells during meiosis.

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    Genetic relationship

    Measure of how related individuals are in a population.

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    Marker-trait association

    Study of how genetic markers are linked to specific traits or characteristics in a population.

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    Recombination frequency

    The likelihood of two genes being separated during meiosis due to their physical proximity on a chromosome.

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    Genetic markers

    Genotypes associated with a specific trait.

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    Alleles

    Slightly different versions of genes at a specific location on a chromosome.

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    Chromosome location of genes

    The position of genes on a chromosome, impacting recombination likelihood.

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    Crossovers

    Events where chromosome segments exchange during recombination; a specific type of recombination.

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    Ancestry

    An individual's genetic makeup is a combination of their parents' genes, ultimately representing a mosaic of all past generations.

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    Population Structure

    When allele frequencies deviate from what's expected in a random-mating population, signifying non-random mating driven by factors like geographical isolation, migration, or selective pressures within the group

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    Genome Mosaic

    An individual's genome, (genetic code), is a combination of genetic material inherited from different ancestors with recombination events incorporated

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    Allele Frequency

    The proportion of a specific form (allele) of a gene within a population.

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    Non-random mating

    Mating among members of a population in a way that deviates from random chance.

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    Population Structure Methods

    Techniques like "Structure" and Principle Component Analysis (PCA) are used to identify and quantify genetic differences within subgroups of a population.

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    Recombination Events

    Reshuffling of genetic material during reproduction, leading to new combinations of traits in offspring, these events occur in each new generation.

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    Phylogenetic Trees

    Visual representations showing evolutionary relationships among individuals or groups based on shared ancestry.

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    QTL

    Regions on a chromosome associated with a specific trait, often spanning large intervals of 5-10 cM. They are identified through quantitative trait loci (QTL) mapping, which involves analyzing the genetic makeup of a population and comparing it to the trait of interest.

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    QTL Mapping

    A technique used to identify regions on chromosomes that are associated with specific traits. This involves analyzing the genetic makeup of a population and comparing it to the trait of interest.

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    Association Mapping

    A technique that identifies associations between genetic markers and specific traits in a population. It relies on historical recombination events within the population to correlate markers with traits, enabling high resolution mapping.

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    Benefits of Association Mapping

    It's an efficient way to map many traits, it doesn't require constructing special populations, and allows for large population sizes, which can improve the accuracy of mapping.

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    Limitations of Association Mapping

    It's less effective in finding regions that contribute minimally to a trait and struggles with identifying polymorphisms with low frequency in the population.

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    Genetic Mapping

    Identifying the location of genes and the distance between them on a chromosome, using recombination frequency as a measure.

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    Centimorgan (cM)

    A unit used to measure genetic distance between markers, representing a 1% chance of recombination occurring between them.

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    Bi-parental Populations

    Individuals created from controlled crosses of two parents differing in a trait of interest, used for genetic mapping studies.

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    Genome-wide Association Panels

    Collections of individuals with variability in many traits, used for mapping studies.

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    Multi-parent Populations

    Individuals created through controlled crossings of a few well-characterized parents, providing a diverse pool for mapping.

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    High-density Genotyping

    Using techniques like DNA-sequencing or microarrays to identify millions of genetic markers across the genome, crucial for mapping.

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    Genetic Map

    A visual representation of gene locations and the distance between them, based on recombination frequency.

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    How does genetic mapping contribute to scientific advancements?

    Identifying genes linked to traits allows scientists to understand biological mechanisms, develop new drugs, treatments, and better crop varieties.

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    Scree Plot

    A graph showing how much of the total variation in data is explained by each principal component (PC) in a Principal Component Analysis (PCA). It helps determine the number of PCs needed to represent the data.

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    Eigenvalue

    A value indicating the variance explained by a principal component (PC) in PCA. Higher eigenvalues mean more variance is explained by that PC.

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    Elbow in Scree Plot

    The point on the scree plot where the curve starts to flatten out, indicating the optimal number of PCs to use for analysis.

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    Kinship Matrix

    A table showing the genetic relatedness between individuals in a population. Each cell represents the probability of sharing alleles due to common ancestry.

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    Identical by Descent (IBD)

    Alleles that are inherited from a common ancestor, not due to mutation.

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    Heat Map

    A visual representation of data with colors representing different values. Used in kinship matrices to show relatedness.

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    Dendrogram

    A tree-like diagram showing how individuals cluster together based on their genetic similarity.

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    Population Analysis

    Studying the genetic characteristics of a group of individuals to understand its structure, evolution, and relationships.

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    False Associations

    Incorrect relationships found between markers and traits due to not accounting for kinship.

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    True Associations

    Real relationships between genetic markers and traits after controlling for kinship.

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    Study Notes

    Lecture 10b - Population Analysis and Marker Trait Associations

    • Topics covered include population analysis, marker-trait associations, and bioinformatics.
    • A workflow diagram illustrates the process, starting with DNA sequencing and quality control, followed by DNA assembly, DNA read mapping, genome annotation, expression analysis, genotyping, and ending with polymorphism discovery and marker-trait associations.

    Learning Objectives

    • Understand the relationship between genome recombination and genotyping.
    • Discuss approaches for measuring individual relatedness in a population.
    • Present various machine learning approaches to assign individuals to subpopulations.
    • Discuss genetic mapping approaches and their strengths/weaknesses.
    • Understand methods for identifying and interpreting marker-trait associations.

    Meiosis

    • Meiosis is specialized cell division for gamete production, resulting in four haploid daughter cells.
    • It's a multi-stage process where homologous chromosomes are shuffled.
    • A haploid cell has one copy of a genome, while a diploid cell has two.
    • Genetic recombination occurs during the creation of haploid cells.

    Recombination

    • Recombination creates new allele combinations in haploid cells.
    • Interchromosomal recombination involves shuffling whole chromosomes.
    • Intrachromosomal recombination involves exchanging chromosome segments.
    • Recombination typically occurs 2-3 times per chromosome per meiosis.
    • Recombination frequency varies across the genome.

    Genotyping

    • Genotype states at a particular position are called "alleles."
    • Alleles are slightly different versions of orthologous genes at the same chromosomal location.
    • Alleles can be used to track chromosome segments over generations.
    • The more genotyping locations, the more accurate location of recombination events.
    • A genotype associated with a phenotype is a genetic marker.

    Ancestry

    • An individual is a mixture of genes from maternal and paternal parents.
    • Individuals are mosaics of all contributing generations.
    • Identifying shared ancestral alleles among individuals quantifies relatedness.
    • This information can be used to create phylogenetic trees.

    Individuals are Genome Mosaics

    • Individuals are genome mosaics, containing regions inherited from different ancestors in different generations.
    • This can be visualized with colourful segments, each colour representing a different parent.

    Population Structure

    • Allele frequencies in randomly mating populations should be stable.
    • Non-random mating causes population structure in allele frequencies.
    • Factors influencing non-random mating include physical separation, gene flow, evolutionary pressure, culture, and random chance.
    • Polymorphisms may be prevalent in a population with a high incidence of a trait. Correcting for population structure is crucial and should be accounted for during marker-trait association analyses.

    Pritchard's Structure

    • It's a clustering program used with genotype data to infer subpopulations.
    • It helps to model the groupings of individuals.
    • The number of subpopulations and their assignment to individuals must be defined.

    Principle Component Analysis (PCA)

    • PCA is an unsupervised machine learning technique to simplify high-dimensional data sets.
    • It finds the most varying axes (PC) in the multidimensional space (e.g., SNPs).
    • With vast amounts of genetic data, PCA identifies clusters of similar individuals.
    • It helps to visualize relationships between individuals, identify groups of high genetic similarity, and correct for population structure during marker-trait analysis.

    Linkage Disequilibrium (LD)

    • Linkage disequilibrium (LD) is a measure of non-random association between alleles.
    • It often occurs when alleles are physically close together on a chromosome segment such as in gene loci.
    • The software PLINK is often used to prune marker sets to ensure independence.

    Scree Plots

    • Scree plots are graphs displaying eigenvalues from a PCA.
    • Eigenvalues show how much of the variance is explained by each PC.
    • "Elbow" in the plot indicates the point where adding more PCs doesn't significantly improve variance explanation.
    • The "elbow" point helps determine the number of PCs to use in downstream analyses.

    Kinship Matrix

    • Kinship matrix captures relationships among individuals numerically.
    • The values represent the probability of randomly sampled alleles from individuals being identical by descent (IBD).
    • IBD means alleles are inherited from a common ancestor.
    • It is used in population analyses to control for relatedness and avoid spurious results.
    • A heat map of kinship values shows the degree of relatedness between individuals.

    Genetic Mapping

    • The first genetic map was developed by Alfred Sturtevant in 1911.
    • Genetic maps use phenotypic observations, not genotypes.
    • Genetic distances are measured in centimorgans (cM). A 1 cM difference means there is a 1% chance of recombination between two loci.
    • Genetic mapping helps determine relations between genes and markers.

    Types of Mapping Populations

    • Three main types: Bi-parental, Genome-Wide Association Studies (GWAS), and Multi-parent.
    • Bi-parental involves crossing two parents to study traits.
    • GWAS studies large populations to find associations between hundreds of genetic markers and the trait of interest.
    • Multi-parent populations involve complex crossing schemes to thoroughly shuffle parent genetics within offspring across generations.

    Bi-Parental Populations

    • Created from two parents differing in their traits.
    • A genetic map is generated from the progeny, showing the relationships between traits and genomic regions (QTL).
    • Larger populations refine the identification of genes controlling traits. Larger populations increase recombination and resolve the location of genes more precisely.

    Association Mapping Populations

    • These are collections of individuals, avoiding closely related individuals.
    • They rely on historical recombination events to understand marker-trait relationships within the population.
    • These populations are helpful for understanding complex traits that are frequently varying within a population and they can also identify genes responsible for those traits.
    • Population sizes can be large (>100,000 individuals).

    Multi-Parent Populations

    • Use complex crossing strategies to thoroughly mix parental genetics into offspring.
    • Populations have a fixed number of parents.
    • Better for mapping traits than bi-parental populations.

    Genome-Wide Association Study (GWAS)

    • Uses a large population to relate the genotype to a phenotype.
    • Creates a graph showing -log(P) scores for various points.

    NAM (Nested Association Mapping) Populations

    • Involve controlled crossing of a few parents and involves culling and genotyping for multiple generations.

    MAGIC (Mulit-parent Advanced Generation Inter-Cross) Populations

    • Involve complex crossing schemes.
    • Shuffles genetics across multiple generations.
    • Provides better association mapping resolution than bi-parental and GWAS, similar to NAM populations.

    Genomic Selection (GS)

    • Uses high-density genotyping to predict breeding trait values of individuals.

    Future of Marker-Trait Association

    • Current methods (e.g., bi-parental mapping, GWAS, genomic selection) often assume linear, additive relationships.
    • There is a growing interest in deep neural networks to identify non-linear, and complex relationships between genes and traits.

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    Lecture 10b - Marker Trait Associations PDF

    Description

    This quiz focuses on population analysis and marker-trait associations within the context of bioinformatics. It covers the workflow from DNA sequencing to polymorphism discovery, emphasizing the role of meiosis and genomic recombination in genetic mapping and individual relatedness. Explore how machine learning integrates into genetic research methodologies.

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