Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.

中文翻译：

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用rhAmpSeq对葡萄共线核心基因组进行单倍型可提高多种属中标记的转移性。

可转移的DNA标记对于育种和遗传至关重要。葡萄（Vitis）育种者利用约2000万年以来同属物种的抗病等位基因发散，但现有的Vitis标记平台的跨物种转移率低至2％。在这里，我们应用了针对推断的葡萄属核心基因组的标记策略。结合了七个链接阅读的从头组装和三个现有组装，Vitis共线核心基因组估计收敛于39.8 Mb（占基因组的8.7％）。从40个登录件中添加散弹枪基因组序列，可以鉴定具有高信息含量的多态性单倍型侧翼的保守核心PCR引物结合位点。在这些目标区域中，我们开发了2 000个rhAmpSeq标记作为PCR多重检测，并验证了跨越葡萄属多样性的四个双亲群体中的面板，显示可转移性提高至91.9％。这种标记物开发策略应广泛适用于许多类群的遗传研究，尤其是那些距今约两千万年的物种。