Selection in segregating populations: phenotypic vs genotypic
Genotype is more precise, but only if the marker being used is a perfect one (i.e. it lies inside the gene being selected for.
Phenotype is typically more relevant, and sometimes cheaper (but note that this equation is changing as the cost of genotyping falls).
If heritability is high, phenotypic selection should almost always be preferred. But the lower it gets, the more genotyping starts to be worthwhile.
Genotypic (MAS) is particularly suited to:
- Traits which are difficult to assay
- Stacking (pyramiding) genes which each on their own give a similar phenotype (particularly disease resistances)