Data from: Geography and end use drive the diversification of worldwide winter rye populations

In order to meet the current challenges in human food production, an improved understanding of the genetic diversity of crop species that maximizes selection efficacy in breeding programs is needed. The present study offers new insights into the diversity, genetic structure and demographic history of cultivated rye (Secale cereale L.). We genotype 620 individuals from fourteen worldwide rye populations with different end use (grain, forage) at 32 genome-wide SSR markers. We reveal the relationship among these populations, their sizes and the timing of domestication events using population genetics analyses and model-based inference with Approximate Bayesian Computation (ABC). Our main results are: 1) a high within-population variation and genetic diversity, 2) the unexpected absence of reduction in diversity with increasing improvement level, and 3) evidence for multiple independent domestication events. The estimated domestication events are in agreement with archaeological studies. We suggest that the main drivers of diversification of winter rye are the end use of rye in two early regions of cultivation: rye forage in the Mediterranean area and grain in North Eastern Europe. The lower diversity and stronger differentiation of North Eastern European populations is most likely due to more intensive cultivation and breeding of rye in this region, in contrast to the Mediterranean region where it was considered a secondary crop or even a weed. We discuss the relevance of our results for management of gene bank resources, and the pitfalls of inference methods applied to crop domestication due to violation of model assumptions and model complexity.