Discovery of pod shatter-resistant associated SNPs by deep sequencing of a representative library followed by bulk segregant analysis in rapeseed.
Discovery of pod shatter-resistant associated SNPs by deep sequencing of a representative library followed by bulk segregant analysis in rapeseed.
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DOI：
10.1371/journal.pone.0034253
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Wang H
中科院分区：
文献类型：
--
作者：
Hu Z;Hua W;Huang S;Yang H;Zhan G;Wang X;Liu G;Wang H
单核苷酸多态(SNPs)是一类重要的靶基因定位的遗传标记。到目前为止，还没有快速有效的方法来鉴定油菜籽和其他作物中与农艺性状连锁的SNPs。我们展示了一种新的方法，通过对有代表性的文库进行深度测序和批量分离分析来鉴定油菜种子中的SNP标记。利用该方法，发现了与油菜抗角果相关的SNPs。首先，使用了油菜籽基因组的简化表示法。从感病植株(10个抗角果破碎指数为0.10的F2植株)和抗性植株(10个抗角果破碎指数为0.90的F2植株)和Solexa测序产生的90bp读数中提取了450-550bp的基因组片段。这些序列读数中大约有5000万个被组装成重叠群，覆盖深度为20倍。其次，确定了60396个“简单SNPs”，并用Fisher‘s精确检验评价了其统计学意义。选择-log10p值大于16的70个关联SNPs进行进一步分析。这些SNP的分布呈现紧密的聚集性，在A09染色体上396kb的区域内有14个相关的SNPs。我们的证据表明，该区域包含一个主数量性状基因座(QTL)。最后，将来自该区域的两个相关SNPs定位在一个主要的QTL区域。利用我们的新方法，在A09染色体上发现了70个相关的SNPs，并找到了一个主效抗结荚QTL。利用这些SNP标记对油菜的QTL进行了定位，通过分子标记辅助选择和图位克隆，可能有助于提高油菜的抗角果能力。这一方法将加速油菜和其他作物重要农艺性状的主效QTL的发现和功能基因的克隆。
Single nucleotide polymorphisms (SNPs) are an important class of genetic marker for target gene mapping. As of yet, there is no rapid and effective method to identify SNPs linked with agronomic traits in rapeseed and other crop species. We demonstrate a novel method for identifying SNP markers in rapeseed by deep sequencing a representative library and performing bulk segregant analysis. With this method, SNPs associated with rapeseed pod shatter-resistance were discovered. Firstly, a reduced representation of the rapeseed genome was used. Genomic fragments ranging from 450–550 bp were prepared from the susceptible bulk (ten F2 plants with the silique shattering resistance index, SSRI <0.10) and the resistance bulk (ten F2 plants with SSRI >0.90), and also Solexa sequencing-produced 90 bp reads. Approximately 50 million of these sequence reads were assembled into contigs to a depth of 20-fold coverage. Secondly, 60,396 ‘simple SNPs’ were identified, and the statistical significance was evaluated using Fisher's exact test. There were 70 associated SNPs whose –log10 p value over 16 were selected to be further analyzed. The distribution of these SNPs appeared a tight cluster, which consisted of 14 associated SNPs within a 396 kb region on chromosome A09. Our evidence indicates that this region contains a major quantitative trait locus (QTL). Finally, two associated SNPs from this region were mapped on a major QTL region. 70 associated SNPs were discovered and a major QTL for rapeseed pod shatter-resistance was found on chromosome A09 using our novel method. The associated SNP markers were used for mapping of the QTL, and may be useful for improving pod shatter-resistance in rapeseed through marker-assisted selection and map-based cloning. This approach will accelerate the discovery of major QTLs and the cloning of functional genes for important agronomic traits in rapeseed and other crop species.
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DOI：
10.1006/jaer.1996.0091
发表时间：
1996-11-01
期刊：
JOURNAL OF AGRICULTURAL ENGINEERING RESEARCH
影响因子：
--
作者：
Price, JS;Hobson, RN;Bruce, DM
通讯作者：
Bruce, DM
通过454转录组测序发现SNP。
影响因子：
7.2
作者：
Barbazuk, W Brad;Emrich, Scott J;Chen, Hsin D;Li, Li;Schnable, Patrick S
通讯作者：
Schnable, Patrick S
影响因子：
3.1
作者：
Feng, Hui;Li, Yuefei;Liu, Jing
通讯作者：
Liu, Jing
影响因子：
64.8
作者：
Altshuler, D;Pollara, VJ;Lander, ES
通讯作者：
Lander, ES
影响因子：
7
作者：
Feltus, FA;Wan, J;Paterson, AH
通讯作者：
Paterson, AH