Table 1.
Characteristics of methods in GAPIT3.
| Method | Testing marker | No. of steps | Model | Kinship |
|---|---|---|---|---|
| GLM | Single locus | One | Fixed | NA |
| MLM | Single locus | One | Mixed | All markers |
| CMLM | Single locus | One | Mixed | Individuals clustered into groups |
| ECMLM | Single locus | One | Mixed | Individuals clustered into groups by enrichment |
| SUPER | Single locus | Two | Mixed | All marker except pseudo QTNs |
| MLMM | Multiple loci | Iterative | Mixed | All markers |
| FarmCPU | Multiple loci | Iterative | Fixed and mixed | Pseudo QTNs |
| BLINK | Multiple loci | Iterative | Fixed | NA |
| gBLUP | NA | One | Mixed | All markers for all individuals |
| cBLUP | NA | One | Mixed | Individuals clustered into groups with all markers |
| sBLUP | NA | One | Mixed | Pseudo QTNs |
Note: NA, not applicable; GLM, general linear model; MLM, mixed linear model; CMLM, compressed MLM; ECMLM, enrichment CMLM; SUPER, settlement of MLMs under progressively exclusive relationship; MLMM, multiple loci MLM; FarmCPU, fixed and random model circulating probability unification; BLINK, Bayesian-information and linkage-disequilibrium iteratively nested keyway; gBLUP, genomic best linear unbiased prediction; cBLUP, compressed BLUP; sBLUP, SUPER BLUP; QTN, quantitative trait nucleotide.