Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality.

苹果的驯化主要由种间杂交驱动。在本研究中，我们报告了栽培苹果 ( Malus domestica cv. Gala) 及其两个主要野生祖先M. sieversii和M. sylvestris的单倍型解析基因组. 在每个基因组的两个单倍型之间鉴定出大量变异。基因组祖先的推断将大约 23% 的 Gala 基因组确定为杂交起源。对 91 个种质的深度测序确定了栽培苹果中源自两个祖先中的任何一个并与重要的驯化特征相关的选择性扫描。苹果泛基因组的构建和分析揭示了数千个新基因，其中数百个是从其中一个祖先中选择出来的，并且大部分固定在栽培苹果中，这表明新基因/等位基因的渗入是通过杂交驯化苹果的标志。最后，Gala 果实在 13 个发育阶段的转录组谱揭示了约 19% 的等位基因特异性表达基因，包括许多与果实品质相关的基因。