Title Page

Objective

 General Introduction

Genetic Markers

Definition
 Phenotypic Markers
 Blood Groups
 Biochemical Polymorphisms
 RFLPs
 Minisatellites or VNTR Markers
 Microsatellites or SSR Markers

SNPs

 The difficulty to fully automate microsatellite genotyping has revived interest in a new type of markers: single nucleotide polymorphisms or SNPs.

 Definition:

SNPs are polymorphisms due to single nucleotide substitutions (transitions > transversions) or single nucleotide insertions/deletions.

 Abundance:

The average heterozygosity per nucleotide site, p , has been estimated at approximately 1/1000 in man, 1/2500 in cattle.

  Informativeness:

SNPs are virtually always biallelic markers. Their heterozygosity is therefore limited at 50%.

 Examples of SNP genotyping methods:

  • Single Stranded Conformation Polymorphism (SSCP)(1 )
  • Allele specific oligonucleotides (ASO)(1 )
  • Single nucleotide polymorphic discrimination by an electronic dot blot assay (ASO) on semicnductor microchips (1 ; 1 )
  • Reverse dot blot on DNA chips (1 )
  • Dynamic allele specific hybridisation (DASH) (1 ; 1 )
  • Allele-specific PCR (=amplification refractory mutation system or ARMS test)(1 )
  • Mutation detection the ARMS test in combination with the TaqmanTM 5' exonuclease assay (exploiting the 5'->3' exonuclease activity of Taq DNA polymerase).(1 )
  • Minisequencing and analysis of the extension products by PAGE.
  • Minisequencing and analysis of the extension products on DNA chips
  • Minisequencing and analysis of the extension products using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDITOF)(1 )
  • Pyrosequencing (1 )
  • OLA (1 )
  • Invasive clivage of oligonucleotide probes (Invader technology)

 Map Construction

QTL Mapping in Outbred Half-Sib Pedigrees

References