Bulk segregant analysis using single nucleotide polymorphism microarrays.
Bulk segregant analysis using single nucleotide polymorphism microarrays.
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DOI：
10.1371/journal.pone.0015993
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发表时间：
2011-01-27
期刊：
影响因子：
3.7
通讯作者：
Baxter I
中科院分区：
文献类型：
--
作者：
Becker A;Chao DY;Zhang X;Salt DE;Baxter I
使用微阵列的批量分离子分析（BSA）和极端阵列作图（XAM）最近已被用于快速鉴定多个物种中与表型相关的基因组区域。然而，这些实验需要鉴定每个新的基因型组合的杂交亲本之间的单特征多态性（SFP），这提高了实验成本。拟南芥基因组多态性数据的可用性，加上单核苷酸多态性（SNP）基因分型阵列的有效设计，消除了对SFP检测的要求，降低了每个阵列的成本，从而降低了每个实验的总成本。为了证明这些方法将在SNP阵列上起作用并确定置信区间，我们分析了天然加入物与拟南芥ATSNPTILE阵列的杂交，并模拟了BSA或XAM，给出了各种基因模型，群体和批量选择参数。我们的研究结果显示了两种方法的基因分型输出之间的显著相关性，这表明在BSA背景下SFP基因分型的益处可以通过更便宜、更有效的SNP阵列获得。作为概念的最后证明，我们将来自硫和硒遗传学突变体的F2作图群体的DNA与拟南芥ATTILE1R和ATSNPTILE阵列杂交，其产生几乎相同的结果。我们制作了R脚本，提示用户输入所需参数，并使用ATSNPTILE1阵列执行BSA分析，并将其作为补充数据文件提供。
Bulk segregant analysis (BSA) using microarrays, and extreme array mapping (XAM) have recently been used to rapidly identify genomic regions associated with phenotypes in multiple species. These experiments, however, require the identification of single feature polymorphisms (SFP) between the cross parents for each new combination of genotypes, which raises the cost of experiments. The availability of the genomic polymorphism data in Arabidopsis thaliana, coupled with the efficient designs of Single Nucleotide Polymorphism (SNP) genotyping arrays removes the requirement for SFP detection and lowers the per array cost, thereby lowering the overall cost per experiment. To demonstrate that these approaches would be functional on SNP arrays and determine confidence intervals, we analyzed hybridizations of natural accessions to the Arabidopsis ATSNPTILE array and simulated BSA or XAM given a variety of gene models, populations, and bulk selection parameters. Our results show a striking degree of correlation between the genotyping output of both methods, which suggests that the benefit of SFP genotyping in context of BSA can be had with the cheaper, more efficient SNP arrays. As a final proof of concept, we hybridized the DNA from bulks of an F2 mapping population of a Sulfur and Selenium ionomics mutant to both the Arabidopsis ATTILE1R and ATSNPTILE arrays, which produced almost identical results. We have produced R scripts that prompt the user for the required parameters and perform the BSA analysis using the ATSNPTILE1 array and have provided them as supplemental data files.
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影响因子：
4.2
作者：
Kaczorowski, Karen A.;Kim, Ki-Seung;Hudson, Matthew E.
通讯作者：
Hudson, Matthew E.
影响因子：
7
作者：
West, Marilyn A. L.;van Leeuwen, Hans;Michelmore, Richard W.
通讯作者：
Michelmore, Richard W.
ATHKT1的天然变体可增强拟南芥两种野生种群的Na+积累。
影响因子：
4.5
作者：
Rus, Ana;Baxter, Ivan;Muthukumar, Balasubramaniam;Gustin, Jeff;Lahner, Brett;Yakubova, Elena;Salt, David E.
通讯作者：
Salt, David E.
影响因子：
56.9
作者：
Winzeler, EA;Richards, DR;Davis, RW
通讯作者：
Davis, RW
DOI：
10.1073/pnas.88.21.9828
发表时间：
1991-11-01
影响因子：
11.1
作者：
MICHELMORE, RW;PARAN, I;KESSELI, RV
通讯作者：
KESSELI, RV