Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.).
Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.).
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DOI：
10.1186/s12864-023-09528-6
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发表时间：
2023-08-08
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
作者：
单核苷酸多态性（SNPs）和插入/缺失（InDels）是植物基因组中最丰富的遗传变异，广泛分布于植物基因组中。SNP和InDel标记的开发为萝卜的遗传学和基因组学研究提供了重要的工具。在这项研究中，共有366,679个单核苷酸多态性（SNPs）和97,973个插入-缺失（InDel）标记的基础上，基因组重测序的“YZH”和“XHT”。通过转录组测序，在两个品种中总共检测到53，343个SNP和4，257个InDel。在InDel变异中，85个基因组InDel和15个转录组InDel是新开发和验证的PCR。100个多态性InDels标记在200份萝卜种质中共检测到207个等位基因，平均等位基因数（Na）为2.07，平均多态信息含量（PIC）为0.33。群体结构和系统发育关系分析表明，来自北方的萝卜品种聚在一起，来自西南地区的萝卜品种聚在一起。RNA-Seq分析显示，在两个品种之间鉴定出11，003个差异表达基因（DEG），其中5，020个上调，5，983个下调。共检测到145个与开花时间相关的DGE，其中大部分涉及开花时间整合、昼夜节律钟/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SNPs和9个InDels。本研究中发现的大量SNPs和InDels将为萝卜遗传和基因组研究提供有价值的标记资源。这些与开花时间相关的DGEs中的SNPs和InDels为揭示萝卜抽薹和开花的分子机制提供了基础。在线版本包含补充材料，可通过10.1186/s12864-023-09528-6获得。
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. The online version contains supplementary material available at 10.1186/s12864-023-09528-6.
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影响因子：
4.6
作者：
Kawamoto N;Sasabe M;Endo M;Machida Y;Araki T
通讯作者：
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DOI：
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发表时间：
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期刊：
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影响因子：
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影响因子：
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