Major crops are all survivors of domestication bottlenecks. Studies have focused on the genetic loci related to the domestication syndrome, while the contribution of ancient haplotypes remains largely unknown. Here, an ancestral genomic haploblock dissection method is developed and applied to a resequencing dataset of 386 tetraploid/hexaploid wheat accessions, generating a pan-ancestry haploblock map. Together with cytoplastic evidences, we reveal that domesticated polyploid wheat emerged from the admixture of six founder wild emmer lineages, which contributed the foundation of ancestral mosaics. The key domestication-related loci, originated over a wide geographical range, were gradually pyramided through a protracted process. Diverse stable-inheritance ancestral haplotype groups of the chromosome central zone are identified, revealing the expanding routes of wheat and the trends of modern wheat breeding. Finally, an evolution model of polyploid wheat is proposed, highlighting the key role of wild-to-crop and interploidy introgression, that increased genomic diversity following bottlenecks introduced by domestication and polyploidization.

主要农作物都是驯化瓶颈的幸存者。研究重点是与驯化综合症相关的遗传位点，而古代单倍型的贡献仍然很大程度上未知。在这里，开发了一种祖先基因组单倍体解剖方法，并将其应用于 386 个四倍体/六倍体小麦种质的重测序数据集，生成泛祖先单倍体图谱。结合细胞质证据，我们揭示了驯化多倍体小麦是由六个创始人野生二粒小麦谱系的混合产生的，这为祖先嵌合体奠定了基础。与驯化相关的关键基因座起源于广泛的地理范围，通过一个漫长的过程逐渐形成金字塔。鉴定了染色体中心区多种稳定遗传的祖先单倍型群，揭示了小麦的扩张路线和现代小麦育种的趋势。最后，提出了多倍体小麦的进化模型，强调了野生作物和间倍体渗入的关键作用，在驯化和多倍化引入的瓶颈之后增加了基因组多样性。