Data from: Combined use of molecular markers and high resolution melting (HRM) to assess chromosome dosage in potato hybrids

In plants, the most widely used cytological techniques to assess parental genome contributions are based on in situ hybridization (FISH and GISH), but they are time-consuming and need specific expertise and equipment. Recent advances in genomics and molecular biology have made PCR-based markers a straightforward, affordable technique for chromosome typing. Herein we describe the development of a molecular assay that uses single-copy conserved ortholog set II (COSII)-based SNPs and the high resolution melting (HRM) technique to assess the chromosome dosage of interspecific hybrids between a Solanum phureja-S. tuberosum diploid (2n=2x=24) hybrid and its wild relative S. commersonii. Screening and analysis of 45 COSII marker sequences allowed S. commersonii-specific SNPs to be identified for all 12 chromosomes. Combining the HRM technique with the establishment of synthetic DNA hybrids, SNP markers were successfully used to predict the expected parental chromosome ratio of five interspecific triploid hybrids. These results demonstrate the ability of this strategy to distinguish diverged genomes from each other, and to estimate chromosome dosage. The method could potentially be applied to any species as a tool to assess paternal to maternal ratios in the framework of a breeding programme or following transformation techniques.目前植物研究中用于评估亲本基因组贡献的主流细胞学技术基于原位杂交（in situ hybridization，FISH与GISH），但此类技术耗时耗力，且需配备特定的专业实验设备与技术人员。近年来基因组学与分子生物学的进展，使基于PCR的分子标记成为一种简便易行、成本可控的染色体分型技术。本研究详述了一种分子检测方法的开发流程：该方法依托单拷贝保守同源基因集II（single-copy conserved ortholog set II, COSII）的单核苷酸多态性（Single Nucleotide Polymorphism, SNPs），结合高分辨率熔解曲线（High Resolution Melting, HRM）技术，用于评估Solanum phureja与Solanum tuberosum的二倍体杂种（2n=2x=24）与其野生近缘种S. commersonii之间的种间杂种的染色体剂量。通过对45个COSII标记序列的筛选与分析，我们在12条染色体上均鉴定到了S. commersonii特异性的SNP位点。结合高分辨率熔解曲线技术与人工合成DNA杂种的构建，SNP标记成功实现了对5个种间三倍体杂种的预期亲本染色体比例预测。本研究结果证实，该策略可有效区分分化程度各异的基因组，并准确估算染色体剂量。该方法有望在育种项目或转基因操作后，作为评估父本与母本染色体比例的工具应用于任意物种。