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GWAS GAPIT

Determining what is the favorable allele for your trait based on the + or - effect in GAPIT

For example, you want a lower stripe rust score:
If you have a - negative effect from your GWAS, the second allele in your SNP is what is giving the lower rust score
If you have a + positive effect from your GWAS, the first allele in your SNP is what is giving the lower rust score
The negative or positive value refers to the slope if you were to graph the phenotype in the y axis and 0,1,2 allele in the x-axis … and what you are determining.. is which allele (0 or 2) to recommend for selection for your favorable allele (the lower rust rating)
The + and - has nothing to do with major and minor allele.