A practical guide to quantifying the effect of genes underlying adaptation in a mixed genomics and evolutionary ecology approach

Abstract In adaptation studies, approaches in genomics investigate the genetic, cellular and biochemical mechanisms involved in adaptation using model organisms. In study systems such as Arabidopsis, the demand is high to test for the effect of genes which polymorphism is known on the ability of plants to cope with adverse environmental conditions. In evolutionary ecology, understanding how selection and environmental heterogeneity shape the diversity of organisms is crucial. In that regard, tools to decipher how the architecture of standing genetic variation affects the evolutionary potential of plants to adapt are required. Quantitative genetics provide a range of statistical methods that could be used to study those questions but are generally neglected as a consequence of their scary name, as for example for the pedigree based random regression method used in our approach. Here, we provide a practical guide for researchers from multiple domains who would like to use such methods. We begin by providing an overview of some of the challenges in plant sciences, such as understanding the role of regulatory genes in adaptation that could gain from using such approach. We then illustrate the “how to” of the method by applying it to an imaginary example. We also provide a complete tutorial in the supplementary online material under the form of a protocol and data that can be used to train researchers and students by replicating entirely our approach. We conclude by highlighting the advantages and limits of such approach.