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

To meet the current challenges in human food production, improved understanding of the genetic diversity of crop species that maximizes the 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 genotyped 620 individuals from 14 global rye populations with a different end use (grain or forage) at 32 genome-wide simple sequence repeat markers. We reveal the relationships among these populations, their sizes and the timing of domestication events using population genetics and model-based inference with approximate Bayesian computation. Our main results demonstrate (i) a high within-population variation and genetic diversity, (ii) an unexpected absence of reduction in diversity with an increasing improvement level and (iii) patterns suggestive of multiple domestication events. 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 northeast Europe. The lower diversity and stronger differentiation of eastern European populations were 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 the management of gene bank resources and the pitfalls of inference methods applied to crop domestication due to violation of model assumptions and model complexity.

为应对当前人类粮食生产面临的挑战，亟需深化对作物物种遗传多样性的认知，以最大化育种项目中的选择效能。本研究针对栽培黑麦（*Secale cereale* L.）的遗传多样性、群体遗传结构及种群历史提供了全新见解。我们对来自全球14个不同终端用途（粮用或饲用）黑麦群体的620份个体，利用32个全基因组范围的简单序列重复（simple sequence repeat, SSR）标记开展了基因分型。借助群体遗传学方法与基于近似贝叶斯计算的模型推断，我们解析了这些群体间的亲缘关系、群体规模及驯化事件的发生时间。本研究主要结果显示：(i) 群体内部存在高水平的遗传变异与遗传多样性；(ii) 令人意外的是，随着改良程度提升，黑麦的遗传多样性并未出现下降；(iii) 群体演化模式暗示存在多次驯化事件。我们提出，冬黑麦多样性分化的主要驱动因素为两个早期种植区域的黑麦终端用途差异：地中海地区的饲用黑麦与东北欧的粮用黑麦。东欧群体较低的遗传多样性与更强的遗传分化，大概率源于该地区更为集约化的黑麦种植与育种实践，这与地中海地区将黑麦视为次要作物甚至杂草的情况形成鲜明对比。我们讨论了本研究结果对基因库资源管理的参考价值，以及因模型假设违背与模型复杂性导致的作物驯化研究推断方法所存在的局限性。