College of Agriculture, Guizhou University, Guiyang, 550003, China.
Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, China.
BMC Genomics. 2023 Aug 8;24(1):445. doi: 10.1186/s12864-023-09528-6.
Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations and widely distribute across the genomes in plant. Development of SNP and InDel markers is a valuable tool for genetics and genomic research in radish (Raphanus sativus L.).
In this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome resequencing between 'YZH' and 'XHT'. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome sequencing. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. The 100 polymorphic InDels markers generated 207 alleles among 200 Chinese radish germplasm, with an average 2.07 of the number of alleles (Na) and with an average 0.33 of the polymorphism information content (PIC). Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 11,003 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained.
The large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The SNPs and InDels within flowering time-related DGEs provide fundamental insight into for dissecting molecular mechanism of bolting and flowering in radish.
单核苷酸多态性（SNPs）和插入/缺失（InDels）是最丰富的遗传变异，广泛分布在植物基因组中。SNP 和 InDel 标记的开发是萝卜（Raphanus sativus L.）遗传和基因组研究的一种有价值的工具。
在这项研究中，基于'YZH'和'XHT'之间的基因组重测序，共鉴定出 366679 个单核苷酸多态性（SNP）和 97973 个插入缺失（InDel）标记。通过转录组测序，在两个品种中总共检测到 53343 个 SNP 和 4257 个 InDel。在 InDel 变异中，新开发并验证了 85 个基因组和 15 个转录组 InDel。100 个多态性 InDel 标记在 200 份中国萝卜种质资源中产生了 207 个等位基因，平均等位基因数（Na）为 2.07，多态性信息含量（PIC）平均为 0.33。群体结构和系统发育关系表明，来自中国北方的萝卜品种聚集在一起，来自中国西南的品种聚集在一起。RNA-Seq 分析表明，在两个品种之间鉴定出 11003 个差异表达基因（DEGs），其中 5020 个上调，5983 个下调。总共检测到 145 个与开花时间相关的 DGEs，其中大多数涉及开花时间整合因子、昼夜节律/光周期自主和春化途径。在开花时间相关的 DGEs 区域，获得了 150 个转录组 SNP 和 9 个 InDels。
本研究中鉴定的大量 SNP 和 InDels 将为萝卜遗传和基因组研究提供有价值的标记资源。开花时间相关 DGEs 中的 SNP 和 InDels 为解析萝卜抽薹和开花的分子机制提供了基础。
