The power of both single and multi-locus probes diminishes rapidly if the sample is old or degraded by sunlight and weather.

However, the future approaches for GWAS should be based on the multi-locus genetic model, QTN-by-environment interaction, epistatic detection and multivariate analysis.

Then, the main approaches and their softwares for GWAS in plants were reviewed, including a single-locus model, a multi-locus model, epistasis, and multiple correlated traits.