There is much interest in predicting the impact of global warming on the genetic diversity of natural populations and the influence of climate on biodiversity is an important ecological question. Since Holocene, we face many climate perturbations and the geographical ranges of plant taxa have changed substantially. Actual genetic diversity of plant is a result of these processes and a first step to study the impact of future climate change is to understand the important features of reconstructed climate variables such as temperature or precipitation for the last 15,000 years on actual genetic diversity of forest. We model the relationship between genetic diversity in the European beech (Fagus sylvatica) forests and curves of temperature and precipitation reconstructed from pollen databases. Our model links the genetic measure to the climate curves. We adapt classical functional linear model to take into account interactions between climate variables as a bilinear form. Since the data are georeferenced, our extensions also account for the spatial dependence among the observations. The practical issues of these methodological extensions are discussed.