Animal Genetics

Population and Quantitative Genetics

Overview

• Population and quantitative genetics study allele and phenotype frequencies.
• They analyze changes in these frequencies over space and time under evolutionary forces.
• Quantitative genetics: Focuses on the genetics of complex traits.
• Population genetics: Focuses on the study of genetic variation within and among populations.

Terminology

• Phenotype: The physical expression of an organism's genes.
• Characters: Features of a phenotype (e.g., eye color).
• Trait: A heritable, specific form of a character (e.g., brown, blue, or green eyes).
• Genotype: The genetic constitution of an individual.
• Locus: A specific location on a chromosome.
• Allele: An alternate form of a genetic character at a given locus.
• Gene Pool: All the different alleles of all the genes existing in all individuals in a population.

Molecular Markers

• Molecular markers are genes, DNA/RNA fragments, or proteins used to characterize individuals or species.
• They reveal the amount of genetic variation.

Types of Molecular Markers

• Protein:
  • Allozymes (or alloenzymes): different molecular forms of an enzyme corresponding to different alleles of a common gene (locus). These are rarely used anymore.
• Genetic or Genomic: single locus or multi-locus.
• DNA:
  • Gene or fragment (e.g., cyt b).
  • Intron (e.g., ITS1).
  • Microsatellites.
  • SNPs (Single Nucleotide Polymorphisms).
  • RFLP (Restriction Fragment Length Polymorphism).
  • AFLP (Amplified Fragment Length Polymorphism).
  • RAPD (Randomly Amplified Polymorphic DNA).
  • From mitochondrial, chloroplast, or nuclear DNA.
• RNA:
  • mRNA.
  • microRNA (small, ≈22 nt, regulatory RNAs) - for gene expression studies (RNAseq).
• Most markers require PCR (or a variation) to generate millions of copies of a target DNA sequence.
• ITS1 = Internal transcribed spacer

DNA Sequencing

1. Traditional Sanger sequencing
2. High-throughput DNA

• Process involves chromatograms, sequence editing, sequence alignment, and analysis.

Genotyping

1. Microsatellites: AKA Simple Sequence Repeats (SSRs) or Short Tandem Repeats (STRs) are used to determine the genetic make-up of individuals (nuclear DNA).

• Microsatellite markers: simple sequence repeats consisting of repetitions of very short nucleotide motifs (usually 1–5 nucleotides) and can occur in perfect repetition, as interrupted repeats or together with another repeat type.

1. Single Nucleotide Polymorphisms (SNPs)

• Example:

  • An heterozygote AAT7/AAT3

    • 5’-GCTTACCG AAT AAT AAT AAT AAT AAT AAT GGACCTAC-3’ Or, (AAT)7

  • 5’-GCTTACCG AAT AAT AAT GGACCTAC-3’ Or, (AAT)3

Paternity Testing

• Microsatellite markers can be used for paternity testing.
• Example: If the maternal marker passed to the child is 6, and the child also has marker 7, then the father must have contributed marker 7.
• If the alleged father has marker 7, it supports paternity.

Studies on Single Populations

• Genetic analysis treats single populations as isolated.
• This is the starting point for studying multiple populations.
• Used to assess long-term viability, e.g., in reintroduction programs or invasive species.
• Requires quantifying genetic variation using molecular markers.
• Genetic diversity estimates are based on allele, genotype, and haplotype frequencies.

Hardy-Weinberg Equilibrium

• Hardy-Weinberg equilibrium (H-W Equilibrium) describes a population with no evolution occurring.
• Principle: Allele and genotype frequencies remain constant from generation to generation without evolutionary influences.
• Equations:
  • $p^2 + 2pq + q^2 = 1$
  • $p + q = 1$
  • $p^2$: dominant homozygous frequency (AA)
  • $2pq$: heterozygous frequency (Aa)
  • $q^2$: recessive homozygous frequency (aa)

Assumptions of Hardy-Weinberg Equilibrium

1. Infinitely large population (no genetic drift).
2. No mutation.
3. No gene flow (no migration with reproduction).
4. Equal chances of survival and reproduction (no selection).
5. Random mating (no sexual selection of a certain genotype).

Estimates of Genetic Diversity for DNA Sequences

• Haplotype diversity: average number of haplotypes.
• Nucleotide diversity: the number of nucleotide differences in a DNA sequence.
  • $\pi = \sum f<em>i f</em>j$
    • $f<em>i$ and $f</em>j$ are the frequencies of the $i^{th}$ and $j^{th}$ haplotypes.
    • is the sequence divergence between sequences
• Haplotype: A set of DNA variants along a single chromosome inherited together due to their proximity.

Estimates of Genetic Diversity for Genotype Data

• Allelic diversity (A): average number of alleles per locus.
• Proportion of polymorphic loci (P): number of polymorphic loci divided by number of loci studied.
• Observed heterozygosity ($H_o$): average number of heterozygotes.
• Gene diversity (h): Also known as $H_e$.
  • $h = 1 - \sum<em>{i=1}^m x</em>i^2$
    • $x_i$ is the frequency of allele i in one locus.
    • $m$ is the number of alleles.
    • h is then averaged over all loci.

Studies with Multiple Populations

• Population genetics are influenced by intra- and inter-population processes.
• Gene flow and geographical isolation influence species and population evolution.
• Most natural populations are subdivided into subpopulations: metapopulations.
• We quantify the level of subdivision and the amount of gene flow.

Genetic Similarity(or distance)

• Estimates the genetic distance between two populations based on nucleotide differences or allele frequencies.
• $D = - ln I$
  • Where I is the proportion of genetic similarity based on the differences in allele frequencies (or DNA sequence) between populations.
• Phylogenetic trees and haplotype networks show relationships among individuals or taxa.
• F-statistics are inbreeding coefficients used to partition variation within and among populations based on heterozygosity.

F-Statistics

• Equations:
  • $F<em>{IS} = \frac{H</em>e - H<em>o}{H</em>e}$
  • $F<em>{ST} = \frac{H</em>T - H<em>S}{H</em>T}$
  • $F<em>{IT} = \frac{H</em>T - H<em>o}{H</em>T}$
• Low $F_{IS}$ = Outbreeding, if high observed heterozygosity.
• High $F_{IS}$ = Inbreeding, if low observed heterozygosity.
• Low $F_{ST}$ = no differentiation, if two subpopulations have similar allele frequencies.
• High $F_{ST}$ = differentiation, if two populations have very different allele frequencies.
• Low $F_{IT}$ = low inbreeding at the level of the population.
  • Level of inbreeding
  • Level of differentiation
  • Level of inbreeding total population

Applications of F-Statistics

• Estimate genetic differentiation among subpopulations.
• Estimate Isolation by Distance (IBD).
• Quantify gene flow among subpopulations.
• Identify barriers to dispersal.
• Estimate connectivity in the landscape.
• Assign individuals to subpopulations.
• Detect hybridization.
• Estimate genetic drift, selection, and local adaptation.

Applications of Molecular Markers in Genetics

• Population and conservation genetics: genetic variation within populations, kinship/patternity.
• Phylogeography: tracking genetic lineages through time and space.
• Systematics: classification, taxonomy, and biogeography of organisms.
• DNA barcoding: identifying species based on DNA sequences.
• Forensics: legal issues (human, illegal trade, etc.).
• Quantitative genetics: genetics of complex traits.

Quantitative Genetics

• Deals with the genetics of complex traits.
• Based on models where many genes influence a trait (phenotype), with non-genetic factors also important.
• Traits show differences on a continuous scale.
• The observed phenotype is the phenotypic value.

Phenotypic Variation

• Components of phenotypic variation:

  • $V<em>P = V</em>G + V_E$
    • $V_P$ = Total phenotypic variance
    • $V_G$ = Variance in genotype due to genetics
    • $V_E$ = Variance in genotype due to environment

• Including genotype by environment interaction:

  • $V<em>P = V</em>G + V<em>E + V</em>{GxE}$

• Further breakdown of $V_G$:

  • $V<em>P = V</em>A + V<em>D + V</em>I + V<em>E + V</em>{GE}$
    • Phenotypic variation

Heritability

• Heritability ($h^2$): the proportion of the total phenotypic variance ($V<em>P$) caused by genetic differences or variance ($V</em>G$).
• Ranges from 0 to 1.
  • $h^2 = \frac{V<em>G}{V</em>P}$ (broad-sense $h^2$)
  • $h^2 = \frac{V<em>A}{V</em>P}$ (narrow-sense $h^2$, more useful), where $V_A$ is the additive genetic variance caused by alleles inherited from parents.

Limitations of Heritability

1. Heritability does not indicate the degree to which a characteristic is genetically determined.
2. An individual does not have heritability.
3. There is no universal heritability for a characteristic.
4. Even when heritability is high, environmental factors can play a significant role in that characteristic.
5. Heritability does not indicate anything about the nature of population differences.

Application in Animal Breeding

• Can we apply selection to a population and change the phenotypic value?
• Can we predict evolutionary change in a trait?
• Methods: Breeder’s equation, correlations, linear regressions (parent/offspring), other models.

Breeder's Equation

• $R = h^2s$
  • R = response to selection
  • $h^2$ = heritability
  • s = selection differential.
• $h^2$ can be inferred by measuring the phenotypic similarity of parents to their offspring.
• Response-to-selection experiment: realized heritability.
• Example:
  • $S = \mu_s – \mu$
  • S = 12.5 – 10.0 = 2.5
  • $R = \mu’ – \mu$
  • R = 11.0 – 10.0 = 1
  • $R = h^2s$
  • then $h^2 = \frac{R}{s}$
  • $h^2 = \frac{1.0}{2.5}$
  • $h^2 = 0.40$
  • (40% of variance in trait values in the parental population was caused by genetic variation)

Quantitative Trait Loci (QTL)

• Chromosomal regions containing genes that control polygenic characteristics.
• Used to identify and determine the influence of individual genes affecting quantitative traits.
• Led to advances in genetics and animal (and plant) breeding.
• QTL mapping is very laborious!

Genome-Wide Association Studies (GWAS)

• An alternative to QTL mapping.
• Does not rely on the progeny of a cross.
• Looks for associations between traits and genetic markers in a biological population.

Single Nucleotide Polymorphisms (SNPs)

• Positions in the genome that show variation in a single base pair.

Example of GWAS

• Study: Exploring the growth trait molecular markers in two sheep breeds based on Genome-wide association studies (GWAS) by Tuersuntuoheti et al., 2023.
• Looking at growth traits and quantitative traits, controlled by multiple micro-effect genes.
• Breeds used: 100 Qira Black sheep and 84 German Merino sheep.
• Sample Collection: Blood from the jugular vein.
• Genotyping: Illumina Ovine SNP 50K Bead Chip.