Cultivated peanut (Arachis hypogaea L.) is a widely grown oilseed crop worldwide; however, the events leading to its origin and diversification are not fully understood. Here by combining chloroplast and whole-genome sequence data from a large germplasm collection, we show that the two subspecies of A. hypogaea (hypogaea and fastigiata) likely arose from distinct allopolyploidization and domestication events. Peanut genetic clusters were then differentiated in relation to dissemination routes and breeding efforts. A combination of linkage mapping and genome-wide association studies allowed us to characterize genes and genomic regions related to main peanut morpho-agronomic traits, namely flowering pattern, inner tegument color, growth habit, pod/seed weight and oil content. Together, our findings shed light on the evolutionary history and phenotypic diversification of peanuts and might be of broad interest to plant breeders.

栽培花生（ ArachishypogaeaL .）是世界范围内广泛种植的油籽作物；然而，导致其起源和多样化的事件尚不完全清楚。在这里，通过结合来自大型种质收集的叶绿体和全基因组序列数据，我们表明A.hypogaea的两个亚种（ hypogaea和fastigiata ）可能起源于不同的异源多倍化和驯化事件。然后根据传播途径和育种工作对花生遗传簇进行区分。连锁图谱和全基因组关联研究的结合使我们能够表征与主要花生形态农艺性状相关的基因和基因组区域，即开花模式、内皮颜色、生长习性、荚/种子重量和含油量。总之，我们的发现揭示了花生的进化历史和表型多样化，可能会引起植物育种者的广泛兴趣。