Radish ( Raphanus sativus L.) is a representative root crop of the Brassicaceae family and is important to the vegetable seed industry in East Asia. Due to its agronomic importance, various molecular markers, genetic maps, genomic resources, and genome assemblies of radish have been developed during the past decade. Marker integration and comparative mapping using these resources will accelerate genetic improvements in radish cultivars. With the goal of establishing a marker-based high-throughput genetic analysis tool, we integrated 3765 nonredundant genetic markers into the Rs1.0 reference genome and converted them into 1182 single nucleotide polymorphism (SNP) markers via whole-genome resequencing data of the mapping parents ‘WK10039’ and ‘WK10024’. A genetic map covering 721.3 cM with 768 framework loci was constructed by analyzing these SNP conversion markers in the F 2 mapping population, which was composed of 93 individuals. Comparison of this map with the Rs1.0 reference genome and other linkage maps showed the physical and genetic correlations of the markers. To develop a high-throughput genotyping system for large accessions or populations with smaller numbers of SNPs, 674 Fluidigm and 68 kompetitive allele-specific PCR (KASP) markers were validated. Application of the 68 KASP assays to 127 commercial cultivars enabled successful identification and classification of genotypes; 11 KASP markers constituted the minimum marker set. The SNP markers used to construct the genetic maps will be a useful resource in research on radish and should lead to low-cost, accurate, and high-throughput genotyping platforms.

中文翻译：

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用于萝卜高通量基因分型的 Fluidigm/KASP 检测的标记整合和开发

萝卜（ Raphanus sativus L. ）是十字花科的代表性块根作物，对东亚的蔬菜种业很重要。由于其农艺学的重要性，在过去十年中已经开发出萝卜的各种分子标记、遗传图谱、基因组资源和基因组组装。使用这些资源进行标记整合和比较作图将加速萝卜品种的遗传改良。为了建立基于标记的高通量遗传分析工具，我们将3765个非冗余遗传标记整合到Rs1.0参考基因组中，并通过作图的全基因组重测序数据将它们转化为1182个单核苷酸多态性（SNP）标记父母'WK10039'和'WK10024'。覆盖721的基因图谱。通过分析由93个个体组成的F 2 作图群体中的这些SNP转换标记，构建了具有768个框架位点的3 cM。该图与 Rs1.0 参考基因组和其他连锁图的比较显示了标记的物理和遗传相关性。为了为大样本或 SNP 数量较少的群体开发高通量基因分型系统，验证了 674 个 Fluidigm 和 68 个竞争性等位基因特异性 PCR (KASP) 标记。将 68 种 KASP 检测应用于 127 个商业栽培品种，成功识别和分类基因型；11个KASP标记构成了最小标记集。用于构建遗传图谱的 SNP 标记将成为萝卜研究中的有用资源，并应导致低成本、准确和高通量的基因分型平台。