Large-scale identification of single-feature polymorphisms in complex genomes
Large-scale identification of single-feature polymorphisms in complex genomes
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DOI：
10.1101/gr.541303
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发表时间：
2003-03-01
期刊：
影响因子：
7
通讯作者：
Chory, J
中科院分区：
文献类型：
--
作者：
Borevitz, JO;Liang, D;Chory, J
我们已经开发了一个高通量的基因分型平台，通过杂交基因组DNA从拟南芥加入到RNA表达基因芯片（AtGenomel）。使用新开发的分析工具，大量的单特征多态性（SFPs）被确定。两个加入，参考菌株哥伦比亚（Col）和菌株兰茨贝格直立（Ler）的比较，确定了近4000个SFP，这可以可靠地评分在5%的错误率。Ler序列用于确认121个SFPs中的117个，并确定阵列杂交的灵敏度。包含序列重复的特征，以及来自高拷贝基因的特征，表现出更高的多态性率。开发了线性聚类算法，以5%的错误发现率（FDR）鉴定代表III基因中潜在缺失的SFP簇。潜在的缺失包括转座子、抗病基因和参与次生代谢的基因。通过对重组近交系进行基因分型证明了该技术的适用性。可以清楚地定义突变断点，并且在一种情况下，将其限定为29kb的间隔。我们进一步证明，阵列杂交可以与批量分离分析相结合，以快速定位突变。将这些工具扩展到具有复杂基因组的生物，如拟南芥，将大大提高我们定位和克隆数量性状基因座（QTL）的能力。
We have developed a high-throughput genotyping platform by hybridizing genomic DNA from Arabidopsis thaliana accessions to an RNA expression GeneChip (AtGenomel). Using newly developed analytical tools, a large number of single-feature polymorphisms (SFPs) were identified. A comparison of two accessions, the reference strain Columbia (Col) and the strain Landsberg erecta (Ler), identified nearly 4000 SFPs, which could be reliably scored at a 5% error rate. Ler sequence was used to confirm 117 of 121 SFPs and to determine the sensitivity of array hybridization. Features containing sequence repeats, as well as those from high copy genes, showed greater polymorphism rates. A linear clustering algorithm was developed to identify clusters of SFPs representing potential deletions in III genes at a 5% false discovery rate (FDR). Among the potential deletions were transposons, disease resistance genes, and genes involved in secondary metabolism. The applicability of this technique was demonstrated by genotyping a recombinant inbred line. Recombination break points could be clearly defined, and in one case delimited to an interval of 29 kb. We further demonstrate that array hybridization can be combined with bulk segregant analysis to quickly map mutations. The extension of these tools to organisms with complex genomes, such as Arabidopsis, will greatly increase our ability to map and clone quantitative trait loci (QTL).