Statistical genetics in traditionally cultivated crops

• We study how crop properties can be extracted from genotype data.
• Our method uses statistical tests built upon Monte Carlo simulations.
• We apply the method to C. lanatus var. lanatus cultivated in Ivory Coast.
• This method allows us to clearly assess the significance in hypothesis tests.

Traditional farming systems have attracted a lot of attention over the past decades as they have been recognized to supply an important component in the maintenance of the genetic diversity worldwide. A broad spectrum of traditionally managed crops has been studied to investigate how reproductive properties in combination with husbandry characteristics shape the genetic structure of the crops over time. However, traditional farms typically involve populations of small size whose genetic evolution is overwhelmed with statistic fluctuations inherent to the stochastic nature of the crossings. Hence there is generally no one-to-one mapping between crop properties and measured genotype data, and claims regarding crop properties on the basis of the observed genetic structure must be stated within a confidence level to be estimated by means of a dedicated statistical analysis. In this paper, we propose a comprehensive framework to carry out such statistical analyses. We illustrate the capabilities of our approach by applying it to crops of C. lanatus var. lanatus oleaginous type cultivated in Côte d׳Ivoire. While some properties such as the effective field size considerably evade the constraints from experimental data, others such as the mating system turn out to be characterized with a higher statistical significance. We discuss the importance of our approach for studies on traditionally cultivated crops in general.