Unordered parent-offspring (PO) relationships are an outstanding issue in pedigree reconstruction studies. Resolution of the order of these relationships would expand the results, conclusions, and usefulness of such studies; however, no such PO order resolution (POR) tests currently exist. This study describes two such tests, demonstrated using SNP array data in the outcrossing species apple (Malus × domestica) on a PO relationship of known order ("Keepsake" as a parent of "Honeycrisp") and two PO relationships previously ordered only via provenance information. The first test, POR-1, tests whether some of the extended haplotypes deduced from homozygous SNP calls from one individual in an unordered PO duo are composed of recombinant haplotypes from accurately phased SNP genotypes from the second individual. If so, the first individual would be the offspring of the second individual, otherwise the opposite relationship would be present. The second test, POR-2, does not require phased SNP genotypes and uses similar logic as the POR-1 test, albeit in a different approach. The POR-1 and POR-2 tests determined the correct relationship between "Keepsake" and "Honeycrisp". The POR-2 test confirmed "Reinette Franche" as a parent of "Nonpareil" and "Brabant Bellefleur" as a parent of "Court Pendu Plat". The latter finding conflicted with the recorded provenance information, demonstrating the need for these tests. The successful demonstration of these tests suggests they can add insights to future pedigree reconstruction studies, though caveats, like extreme inbreeding or selfing, would need to be considered where relevant.

中文翻译：

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利用SNP阵列数据重建亲子二重关系方向的新方法及其在古代和现代异交物种苹果×家养品种中的示范。


无序亲子（PO）关系是谱系重建研究中的一个突出问题。解决这些关系的顺序将扩大此类研究的结果、结论和有用性；但是，目前尚不存在此类 PO 订单解析 (POR) 测试。本研究描述了两项此类测试，使用异型杂交物种苹果 (Malus × Domestica) 中的 SNP 阵列数据证明了已知顺序的 PO 关系（“Keepsake”作为“Honeycrisp”的亲本）和先前仅通过出处排序的两个 PO 关系信息。第一个测试 POR-1，测试从无序 PO 二人组中一个个体的纯合 SNP 调用推导出来的一些扩展单倍型是否由来自第二个个体的精确定相 SNP 基因型的重组单倍型组成。如果是这样，第一个人将是第二个人的后代，否则就会出现相反的关系。第二个测试 POR-2 不需要分阶段的 SNP 基因型，并使用与 POR-1 测试类似的逻辑，尽管方法不同。 POR-1 和 POR-2 测试确定了“Keepsake”和“Honeycrisp”之间的正确关系。 POR-2 测试确认“Reinette Franche”是“Nonpareil”的父母，“Brabant Bellefleur”是“Court Pendu Plat”的父母。后一个发现与记录的出处信息相冲突，表明需要进行这些测试。这些测试的成功演示表明它们可以为未来的谱系重建研究增加见解，尽管需要在相关时考虑诸如极端近亲繁殖或自交等警告。