Red raspberry is an economically important horticultural crop that is known for its fruit's sweet flavour and nutritional value. A reliable and economic genotyping platform is needed to facilitate clonal/variety identification. Previous attempts for clonal identification utilized morphological traits or low-throughput, difficult to score dinucleotide-containing simple sequence repeat molecular markers. Single nucleotide polymorphisms (SNPs), despite having lower allelic diversity, are numerous across the genome and more easily converted to high-throughput assays restoring differential power. In this study, we use the kompetitive allele-specific PCR (KASP™) chemistry, an affordable and high-throughput platform, to develop a panel of SNPs to distinguish a diverse collection of red raspberry accessions for clonal identification. The panel consists of 48 KASP assays that show high concordance with whole genome sequencing, allelic balance, and recovery rate and a minimal set of 24 assays that distinguished the same accessions differentiated by the larger panel.

中文翻译：

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开发用于红树莓 (Rubus idaeus L.) 克隆鉴定的 KASP 指纹图谱组合

红树莓是一种重要的经济园艺作物，以其果实的甜味和营养价值而闻名。需要一个可靠且经济的基因分型平台来促进克隆/品种鉴定。先前的克隆鉴定尝试利用形态特征或低通量、难以对含有二核苷酸的简单序列重复分子标记进行评分。单核苷酸多态性 (SNP) 尽管具有较低的等位基因多样性，但在整个基因组中数量众多，并且更容易转换为高通量测定，以恢复差异能力。在本研究中，我们使用竞争性等位基因特异性 PCR (KASP™) 化学（一种经济实惠的高通量平台）来开发一组 SNP，以区分不同的红树莓种质，以进行克隆鉴定。该面板由 48 个 KASP 测定组成，这些测定与全基因组测序、等位基因平衡和回收率高度一致，以及最小的 24 个测定集，可区分由较大面板区分的相同种质。