The pear ( 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 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 potentially enhance sepal shedding in ‘Xuehuali’ which is vital for pear quality. 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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梨基因组显示出显着的遗传多样性，为果实品质性状差异提供了新的见解


梨 (spp.) 因其多样化的口味、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被探索。在这里，我们组装并注释了杂交“玉露香”梨的母本（PsbM）和父本（PsbF）系的基因组，并通过将这两个基因组与先前发表的代表栽培和野生梨的五个基因组相结合，构建了1.15 Gb的梨全基因组。种质。利用构建的泛基因组，我们在非参考基因组中鉴定出了 PsbM 参考基因组中不存在的 21 224 个基因 PAV（存在-不存在变异）和 1 158 812 个 SNP（单核苷酸多态性）。与 SNP 标记相比，基于 PAV 的分析提供了对梨种群结构的更多见解。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中出现频率和基因表达存在差异。此外，我们对梨全基因组的分析揭示了一个突变的 SNP 和该基因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。可能在 IAA 途径中发挥作用，通过异源过度表达该基因，导致植物中观察到的独特的低生长素表型。这项研究有助于捕获梨种群的遗传多样性，并为加速育种提供基因组资源。