Pedigree information is of fundamental importance in breeding programs and related genetics efforts. However, many individuals have unknown pedigrees. While methods to identify and confirm direct parent–offspring relationships are routine, those for other types of close relationships have yet to be effectively and widely implemented with plants, due to complications such as asexual propagation and extensive inbreeding. The objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes (referred to in this study as “summed potential lengths of shared haplotypes”, SPLoSH). A custom Python script, HapShared, was developed to generate SPLoSH data in apple and sweet cherry. HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops. These distributions were then used to estimate previously unknown relationships. Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data. For cherry, a full-sib relationship was deduced for ‘Emperor Francis, and ‘Schmidt’, a half-sib relationship for ‘Van’ and ‘Windsor’, and the paternal grandparents of ‘Stella’ were confirmed. For apple, 29 cultivars were found to share an unknown parent, the pedigree of the unknown parent of ‘Cox’s Pomona’ was reconstructed, and ‘Fameuse’ was deduced to be a likely grandparent of ‘McIntosh’. Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets, integrated genetic maps, and previously identified pedigree relationships. Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.

中文翻译：

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在无性繁殖的远交作物中使用共享的单倍型长度信息进行谱系重建，苹果和甜樱桃得到证明

谱系信息在育种计划和相关遗传学工作中至关重要。然而，许多人的血统不详。虽然识别和确认直接亲子关系的方法是常规方法，但由于无性繁殖和广泛近亲繁殖等并发症，其他类型的密切关系尚未在植物中有效和广泛实施。本研究的目的是开发和展示支持复杂谱系重建的方法，这些方法通过状态单倍型相同的总长度（在本研究中称为“共享单倍型的总潜在长度”，SPLoSH）。开发了一个自定义 Python 脚本 HapShared，以在苹果和甜樱桃中生成 SPLoSH 数据。HapShared 用于为这些作物中的已知关系建立 SPLoSH 数据的经验分布。然后使用这些分布来估计以前未知的关系。每种作物的案例研究展示了使用 SPLoSH 数据的各种谱系重建场景。对于樱桃，推断出“弗朗西斯皇帝”和“施密特”是同胞关系，“范”和“温莎”是半同胞关系，并证实了“斯特拉”的祖父母。对于苹果，发现29个品种有一个未知亲本，重建了“Cox's Pomona”未知亲本的谱系，推断“Fameuse”可能是“McIntosh”的祖父母。促成这项实证研究的关键遗传资源是大型全基因组 SNP 阵列数据集、综合遗传图谱、和先前确定的谱系关系。具有类似资源的作物也有望从使用 HapShared 进行谱系重建中受益。