TABLE 1.

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

	Linkage analysis	Admixture mapping	Joint linkage and LD mapping (and inbred-by-outbred cross)	Nested association mapping	Association mapping
Allele richness	Low	Low	Intermediate	High	High
Inference from markers in identity-by-state to quantitative trait nucleotides in IBD	Low	Low to intermediate	Intermediate	High	High
No. of SNPs required for whole-genome scan	Low	Low	Intermediate to high	Low (only high for founders)	High
Efficiency in using sequence information	Low	Low	Intermediate	High	Intermediate
Mapping resolution	Poor	Intermediate	Intermediate	Good	Good
Designed mapping population	Yes or no	Yes or No	Mostly no	Yes	No
Sensitivity to genetic heterogeneity	Low	Moderate	High	Low	High
Repeated phenotyping	Possible	Possible	Possible	Yes	Possible
Statistical power	Low to intermediatea	Highb	Intermediate	High	High

^aWith designed mapping populations such as F₂, BC, or RIL, the power of linkage analysis is generally higher in plants than in humans.

^bPower diminishes to zero with equal allele frequencies in the ancestral population (Darvasi and Shifman 2005).