An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments
An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments
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DOI：
10.1101/gr.2479404
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发表时间：
2004-09-01
期刊：
影响因子：
7
通讯作者：
Paterson, AH
中科院分区：
文献类型：
--
作者：
Feltus, FA;Wan, J;Paterson, AH
用多态DNA标记密集覆盖水稻基因组是DNA标记辅助育种、位置克隆和广泛进化研究的宝贵工具。我们对比了两个水稻亚种--籼稻和粳稻的草案，并分析了遗传多样性的水平和模式。在筛选多拷贝和低质量序列后，在两个亚种之间发现了408,898个候选DNA多态(SNPs/Indels)。这些过滤器的结果是，我们的数据集只包括可用SNPs的一个子集(特别是排除了可能出现在重复DNA等位基因之间的大量SNPs)，但增加了这个子集有用的可能性：直接测序表明，79.8%的+/-7.5%的硅胶SNPs是真实的。我们数据库中的SNP样本并不是随机分布在基因组中的。事实上，566个水稻基因组区域具有异常高的多态频率(328个重叠群/48.6Mb/13.6%的基因组)或低(237个重叠群/64.7Mb/18.1%的基因组)。许多缺乏SNP的区域比大多数SNP丰富的区域要长得多，覆盖范围高达4Mb，可能反映了数百年前可能发生的各自基因库之间的相互渗透。尽管46.2%+/-8.3%的SNPs可以区分其他类型的水稻和水稻，但水稻中的SNP频率并不能预测另一种草本植物高粱中相应基因的进化速度。该数据集可在http://www.plantgenome.uga.edu/snp.上免费获得
Dense coverage of the rice genome with polymorphic DNA markers is an invaluable tool for DNA marker-assisted breeding, positional cloning, and a wide range of evolutionary studies. We have aligned drafts of two rice Subspecies, indica and japonica, and analyzed levels and patterns of genetic diversity. After filtering Multiple copy and low quality sequence, 408,898 candidate DNA polymorphisms (SNPs/INDELs) were discerned between the two subspecies. These filters have the consequence that our data set includes only a subset of the available SNPs (in particular excluding large numbers of SNPs that may occur between repetitive DNA alleles) but increase the likelihood that this subset is useful: Direct sequencing suggests that 79.8% +/- 7.5% of the in silica SNPs are real. The SNP sample in Our database is not randomly distributed across the genome. In fact, 566 rice genomic regions had unusually high (328 contigs/48.6 Mb/13.6% of genome) or low (237 contigs/64.7 Mb/18.1% of genome) polymorphism rates. Many SNP-poor regions were substantially longer than most SNP-rich regions, covering up to 4 Mb, and possibly reflecting introgression between the respective gene pools that may have occurred hundreds of years ago. Although 46.2% +/- 8.3% of the SNPs differentiate other pairs of japonica and indica genotypes, SNP rates in rice were not predictive of evolutionary rates for corresponding genes in another grass species, sorghum. The data set is freely available at http://www.plantgenome.uga.edu/snp.