🧫 Canovas Lecture 2

Polymorphisms in Genes

Definition
 Polymorphisms = variations in DNA sequence between individuals

Location
 Can occur within a gene (coding or regulatory regions) or outside genes

Effect
 Some polymorphisms change how a gene works
 Others have no effect and are used as markers

Use in QTL
 Polymorphisms help identify genetic differences linked to traits

QTL Detection: Marker Genotyping

Genotyping
 Genotype individuals at the marker locus to see which alleles they carry

Visualization
 Develop a method to visualize DNA sequence
 Use primer and enzyme combinations to target the sequence with polymorphisms
 DNA is cleaved into fragments of different molecular weights to see differences

Challenge
 Increase the number of loci tested while reducing cost per genotype

Genotyping by PCR

DNA Sequence Differences
 Restriction endonuclease = enzyme that cuts DNA at a specific sequence
 Differences in DNA sequences are coded as alleles

Process
 PCR amplifies the DNA region of interest to see which alleles an individual has

Genotyping by Sequencing Specific Genes/Markers

Purpose
 Identify polymorphisms = differences in DNA sequence between individuals

Schematic
 Shows how DNA from a specific gene or marker is sequenced to detect polymorphisms

Genotyping by High Density Marker Panels

High Density Marker Panels
 Use many markers = 50,000, 100,000, 500,000, or 1,000,000

Anonymous Marker Approach
 Markers are "unimportant" polymorphisms used to locate QTL

Process
 Photo-etch a glass slide, build Velcro-like tags
 Tags "grab" matching animal DNA
 Grabbed DNA lights up spots = shows genotype

Genotyping by Whole Genome Sequencing

Purpose
 Genotype individuals by reading the entire DNA sequence of their genome

Sequence Example
 Shows a section of DNA from an individual
 Nucleotides (A, T, C, G) represent the genetic code

Process
 Use a genome sequencer to read all DNA
 Every nucleotide is detected to find polymorphisms and determine genotype

Summary of Genotyping Methods 1. Candidate Gene Approach and 2. Anonymous Marker Panel Approach

PCR
 Candidate Gene approach = genotype individuals by PCR
 Target specific gene and identify polymorphisms

Sequencing
 Candidate Gene approach = sequence specific genes or markers
 Whole Genome Sequencing = sequence entire genome

High-Density SNP Chip
 Anonymous marker panel approach = genotype individuals by High Density Marker Panels
 SNP = Single Nucleotide Polymorphism

Summary
 Candidate Gene approach → PCR or Sequencing specific genes/markers
 Anonymous marker panel approach → High Density Marker Panels or Whole Genome Sequencing