Department of Horticultural Crop Research, National Institute of Horticultural and Herbal Science, RDA, Suwon, 441-440, Republic of Korea.
Mol Genet Genomics. 2010 Feb;283(2):135-45. doi: 10.1007/s00438-009-0504-0. Epub 2009 Dec 19.
Single nucleotide polymorphisms (SNPs) and/or insertion/deletions (InDels) are frequent sequence variations in the plant genome, which can be developed as molecular markers for genetic studies on crop improvement. The ongoing Brassica rapa genome sequencing project has generated vast amounts of sequence data useful in genetic research. Here, we report a genome-wide survey of DNA polymorphisms in the B. rapa genome based on the 557 bacterial artificial clone sequences of B. rapa ssp. pekinensis cv. Chiifu. We identified and characterized 21,311 SNPs and 6,753 InDels in the gene space of the B. rapa genome by re-sequencing 1,398 sequence-tagged sites (STSs) in eight genotypes. Comparison of our findings with a B. rapa genetic linkage map confirmed that STS loci were distributed randomly over the B. rapa whole genome. In the 1.4 Mb of aligned sequences, mean nucleotide polymorphism and diversity were theta = 0.00890 and pi = 0.00917, respectively. Additionally, the nucleotide diversity in introns was almost three times greater than that in exons, and the frequency of observed InDel was almost 17 times higher in introns than in exons. Information regarding SNPs/InDels obtained here will provide an important resource for genetic studies and breeding programs of B. rapa.
单核苷酸多态性（SNPs）和/或插入/缺失（InDels）是植物基因组中常见的序列变异，可以作为作物改良遗传研究的分子标记。正在进行的芸薹属基因组测序计划产生了大量有用的遗传研究序列数据。在这里，我们根据芸薹属白菜亚种白菜 cv. Chiifu 的 557 个细菌人工克隆序列，对芸薹属基因组中的 DNA 多态性进行了全基因组调查。我们通过对 8 个基因型的 1398 个序列标记位点（STSs）进行重测序，鉴定和表征了芸薹属基因组基因空间中的 21311 个 SNPs 和 6753 个 InDels。将我们的发现与芸薹属遗传连锁图谱进行比较，证实 STS 位点随机分布在芸薹属整个基因组中。在对齐的 1.4 Mb 序列中，平均核苷酸多态性和多样性分别为 theta = 0.00890 和 pi = 0.00917。此外，内含子中的核苷酸多样性几乎是外显子的三倍，内含子中观察到的 InDel 频率几乎是外显子的 17 倍。这里获得的 SNPs/InDels 信息将为芸薹属遗传研究和育种计划提供重要资源。
