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.为应对当前人类粮食生产领域的现存挑战，亟需更深入地解析作物物种的遗传多样性，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.）的多样性、遗传结构及种群历史动态提供了全新研究视角。我们对来自全球14个不同用途（粮用、饲用）黑麦种群的620个个体，采用32个全基因组简单序列重复（Simple Sequence Repeat, SSR）标记开展基因分型。通过种群遗传学分析与近似贝叶斯计算（Approximate Bayesian Computation, ABC）的模型推断，我们揭示了这些种群间的亲缘关系、种群规模以及驯化事件的发生时序。本研究的核心结果如下：1）种群内部存在高水平的遗传变异与遗传多样性；2）出乎预料的是，随着改良程度提升，黑麦的遗传多样性并未出现下降；3）存在多次独立驯化事件的遗传学证据。估算得到的驯化事件时间与考古学研究结论相一致。我们提出，冬黑麦种群分化的主要驱动因素为两个早期种植区域的黑麦用途差异：地中海地区的饲用黑麦，以及东北欧的粮用黑麦。东北欧种群较低的遗传多样性与更强的种群分化程度，大概率源于该区域更为集约化的黑麦种植与育种实践；与之形成鲜明对比的是，地中海地区将黑麦视为次要作物甚至杂草。本研究还讨论了所得结果对于基因库（gene bank）管理的参考价值，以及作物驯化研究中因违背模型假设与模型复杂度问题，导致所采用推断方法存在的局限性。