Table 1 Features of different approaches aiming to link genotype and phenotype
E&R | Classic GWAS | GWAS in reference panel | Pool-GWAS | Linkage mapping | |
|---|---|---|---|---|---|
Analysis of heterozygous individuals | + | + | − | + | + |
Repeated phenotyping | Every generation | − | + | − | − |
Sensitivity to environmental noise | Low because of repeated phenotyping in every generation and replication | High | Low because of repeated phenotyping of identical genotypes | Moderate because of replication | High |
Well-established analysis strategies | − | + | + | − | + |
Mapping resolution | High | High | High | High | Moderate (cost effective), high (expensive) |
Genetic diversity analyzed | High | High | Moderate–high | High | Limited to parental genotypes |
Inference of effect size | Selection, coefficient | + | + | − | + |
Randomized genetic background | +, in starting population and repeated mixing by sexual reproduction during the experiment | +, but sensitive to population structure that can be accounted for in analysis | +, but sensitive to population structure that can be accounted for in analysis given a sufficient sample size | +, but sensitive to population structure that can be accounted for in analysis | + |
Genotyping/sequencing costs | Low because of Pool-Seq | High for establishment, no costs for follow-up experiments | High for establishment, no costs for follow-up experiments | Low because of Pool-Seq | Low because of the use of genetic markers (Rad-Tag sequencing) |
Sampling effort | High because of maintenance of experimental populations | Depends on species | High for establishment, low later on | Moderate | Moderate |
Analysis of multiple traits from the same genotypes | − | + | + | − | + |
Replication | Yes, is common practice | Only across different populations | Requires an independent reference panel | Yes, it is common practice. Easy to expand to multiple populations | Requires independent mapping families |
Influence of allele frequency (conditional on presence in the sample) | Low power for high-frequency alleles, low-frequency alleles are often lost | Yes | Yes | Yes | No |
Trajectories of selected variants | + | − | − | − | − |
Identification of adaptive variants in a defined environment | + | − | − | − | − |
