Given the wealth of raw genomics data, the challenge is now to get the most of observations and to decipher the phenotypes – genotypes relationships, including the Genotype x Environment component. Reliable phenotypic data (at the ‘macro’ level such as breading quality or plant’s fitness, ‘micro’ level such as cellular response or pathogen colonization, or ‘molecular’ level such as gene expression levels or metabolite profiling) are thus a must for in-depth genetic studies thanks to high-throughput phenotyping methods. High-Quality phenotypic data rely on proven and accurate experimental designs, and make use of covariates. Genetic relationships among individuals ought also to be included in the models. The matrix form of the Linear Mixed Model allows an unprecedented and successful jump into this task, due to its extraordinary flexibility and the improvement of computational resources.