Schematic comparison of the main characteristics of different mapping strategies (following Darvasi and Shifman 2005)

Linkage analysisAdmixture mappingJoint linkage and LD mapping (and inbred-by-outbred cross)Nested association mappingAssociation mapping
Allele richnessLowLowIntermediateHighHigh
Inference from markers in identity-by-state to quantitative trait nucleotides in IBDLowLow to intermediateIntermediateHighHigh
No. of SNPs required for whole-genome scanLowLowIntermediate to highLow (only high for founders)High
Efficiency in using sequence informationLowLowIntermediateHighIntermediate
Mapping resolutionPoorIntermediateIntermediateGoodGood
Designed mapping populationYes or noYes or NoMostly noYesNo
Sensitivity to genetic heterogeneityLowModerateHighLowHigh
Repeated phenotypingPossiblePossiblePossibleYesPossible
Statistical powerLow to intermediateaHighbIntermediateHighHigh
  • a With designed mapping populations such as F2, BC, or RIL, the power of linkage analysis is generally higher in plants than in humans.

  • b Power diminishes to zero with equal allele frequencies in the ancestral population (Darvasi and Shifman 2005).