Abstract Background Persimmon (Diospyros kaki Thunb.) is the most widely cultivated species of the genus Diospyros. In this study, genetic diversity and variations in persimmon genotypes were investigated using single nucleotide polymorphism (SNP) markers identified by genotyping-by-sequencing (GBS) analysis. Results Ninety-five persimmon accessions grown in the Pear Research Institute, National Institute Horticultural and Herbal Science, were sequenced using the Illumina Hiseq2500 platform and polymorphic SNPs were detected to develop molecular markers. These reliable SNPs were analyzed using the Kompetitive Allele Specific PCR (KASP) assay to discriminate among persimmon genotypes. GBS generated a total of 447,495,724 trimmed reads, of which 89.7% were raw reads. After demultiplexing and sequence quality trimming, 108,876,644 clean reads were mapped to the reference transcriptome. An average of 1,146,070 genotype reads were mapped. Filtering of raw SNPs in each sample led to selection of a total of 1,725,401 high-quality SNPs. The number of homozygous and heterozygous SNPs ranged from 1,933 to 6,834 and from 846 to 5,927, respectively. Conclusions Of the 49 SNPs selected for development of an identification system for persimmons, 15 SNPs were used in the KASP assay to analyze 32 persimmon accessions. These KASP markers discriminated among all accessions.

中文翻译：

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使用基因分型测序技术鉴定柿子品种的竞争性等位基因特异性 PCR 标记的开发

摘要背景柿子(Diospyros kaki Thunb.)是柿属(Diospyros)中栽培最广泛的物种。在这项研究中，使用通过基因分型测序 (GBS) 分析鉴定的单核苷酸多态性 (SNP) 标记研究了柿子基因型的遗传多样性和变异。结果 使用 Illumina Hiseq2500 平台对梨研究所、国家园艺和草药科学研究所种植的 95 个柿种进行测序，并检测到多态性 SNP 以开发分子标记。使用竞争性等位基因特异性 PCR (KASP) 测定法分析这些可靠的 SNP，以区分柿子基因型。GBS 总共生成了 447,495,724 个修剪读取，其中 89.7% 是原始读取。解复用和序列质量修整后，108,876，644 个干净的读数被映射到参考转录组。平均绘制了 1,146,070 个基因型读数。过滤每个样本中的原始 SNP 导致总共选择了 1,725,401 个高质量 SNP。纯合和杂合 SNP 的数量分别为 1,933 至 6,834 和 846 至 5,927。结论 在为开发柿子鉴定系统而选择的 49 个 SNP 中，15 个 SNP 用于 KASP 分析以分析 32 个柿子种质。这些 KASP 标记区分所有种质。结论 在为开发柿子鉴定系统而选择的 49 个 SNP 中，15 个 SNP 用于 KASP 分析以分析 32 个柿子种质。这些 KASP 标记区分所有种质。结论 在为开发柿子鉴定系统而选择的 49 个 SNP 中，15 个 SNP 用于 KASP 分析以分析 32 个柿子种质。这些 KASP 标记区分所有种质。