The pear (Pyrus spp.) is well known for diverse flavors, textures, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled and annotated the genomes of the maternal (PsbM) and paternal (PsbF) lines of the hybrid ‘Yuluxiang’ pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm. Using the constructed pangenome, we identified 21 224 gene PAVs (Presence-absence variation) and 1 158 812 SNPs (Single Nucleotide Polymorphism) in the non-reference genome that were absent in the PsbM reference genome. Compared with SNP markers, PAV-based analysis provides additional insights into the pear population structure. In addition, some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations. Moreover, our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in ‘Xuehuali’ which is vital for pear quality. PsbMGH3.1 may play a role in the IAA pathway, contributing to a distinct low-auxin phenotype observed in plants by heterologously overexpressing this gene. This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.

中文翻译：

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梨基因组显示出显著的遗传多样性，并为水果品质性状的分化提供了新的见解


梨 （Pyrus spp.） 以其多样的风味、质地和全球园艺重要性而闻名。然而，导致其广泛表型变异的遗传多样性在很大程度上仍未得到探索。在这里，我们从头组装和注释了杂交种 '玉卤香' 梨的母系 （PsbM） 和父系 （PsbF） 系的基因组，并通过将这两个基因组与以前发表的代表栽培和野生种质的五个梨基因组相结合，构建了 1.15 Gb 的梨泛基因组。使用构建的泛基因组，我们在非参考基因组中鉴定了 21 224 个基因 PAVs （存在-缺失变异） 和 1 158 812 个 SNP （单核苷酸多态性），而这些基因在 PsbM 参考基因组中不存在。与 SNP 标记相比，基于 PAV 的分析为梨种群结构提供了更多见解。此外，一些与梨果实品质性状相关的基因在亚洲和欧洲人群间存在差异的出现频率和差异基因表达。此外，我们对梨泛基因组的分析显示，突变的 SNP 和在基因 PsbMGH3.1 启动子区域的插入可能会增强“雪花梨”的萼片脱落，这对梨的品质至关重要。PsbMGH3.1 可能在 IAA 通路中发挥作用，通过异源过表达该基因，导致在植物中观察到独特的低生长素表型。这项研究有助于捕捉梨种群的遗传多样性，并为加速育种提供基因组资源。