SNP discovery in the bovine milk transcriptome using RNA-Seq technology.
SNP discovery in the bovine milk transcriptome using RNA-Seq technology.
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DOI：
10.1007/s00335-010-9297-z
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发表时间：
2010-12
期刊：
影响因子：
2.5
通讯作者：
Medrano, Juan F.
中科院分区：
文献类型：
--
作者：
Canovas, Angela;Rincon, Gonzalo;Islas-Trejo, Alma;Wickramasinghe, Saumya;Medrano, Juan F.
RNA的高通量测序（RNA-Seq）主要用于分析不同组织中的整体基因表达。然而，它也是发现编码SNP的有效方法。本研究的目的是使用RNA-Seq在牛奶转录组中进行SNP发现分析。使用Illumina基因组分析仪系统通过测序cDNA分析来自荷斯坦奶牛的七个乳样品。我们检测到19，175个基因在牛奶样品中表达，相当于分析的基因总数的约70%。SNP检测分析揭示了荷斯坦牛样本中的100，734个SNP，其中大量对应于荷斯坦牛品种和赫里福德牛基因组组装体Btau4.0之间的差异。荷斯坦奶牛中多态性SNP的数量为33，045。RNA-Seq SNP发现的准确性通过比较在一组42个候选基因中检测到的SNP来测试，所述候选基因在牛奶中表达，所述候选基因已经使用桑格测序技术较早地重新测序。使用RNA-Seq和桑格测序技术检测86个SNP中的70个。KASPar基因分型系统用于验证通过RNA-Seq发现但通过桑格技术未观察到的独特SNP。我们的研究结果证实，使用RNA-Seq技术分析转录组是一种有效且成本效益高的方法来识别转录区域中的SNP。这项研究创建了最大限度地提高SNP发现的准确性和预防假阳性SNP检测的指南，并提供了位于哺乳期表达基因编码区的33，000多个SNP，可用于开发基因分型平台，以在荷斯坦牛中进行标记-性状关联研究。
High-throughput sequencing of RNA (RNA-Seq) was developed primarily to analyze global gene expression in different tissues. However, it also is an efficient way to discover coding SNPs. The objective of this study was to perform a SNP discovery analysis in the milk transcriptome using RNA-Seq. Seven milk samples from Holstein cows were analyzed by sequencing cDNAs using the Illumina Genome Analyzer system. We detected 19,175 genes expressed in milk samples corresponding to approximately 70% of the total number of genes analyzed. The SNP detection analysis revealed 100,734 SNPs in Holstein samples, and a large number of those corresponded to differences between the Holstein breed and the Hereford bovine genome assembly Btau4.0. The number of polymorphic SNPs within Holstein cows was 33,045. The accuracy of RNA-Seq SNP discovery was tested by comparing SNPs detected in a set of 42 candidate genes expressed in milk that had been resequenced earlier using Sanger sequencing technology. Seventy of 86 SNPs were detected using both RNA-Seq and Sanger sequencing technologies. The KASPar Genotyping System was used to validate unique SNPs found by RNA-Seq but not observed by Sanger technology. Our results confirm that analyzing the transcriptome using RNA-Seq technology is an efficient and cost-effective method to identify SNPs in transcribed regions. This study creates guidelines to maximize the accuracy of SNP discovery and prevention of false-positive SNP detection, and provides more than 33,000 SNPs located in coding regions of genes expressed during lactation that can be used to develop genotyping platforms to perform marker-trait association studies in Holstein cattle.
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影响因子：
12.3
作者：
Cirulli ET;Singh A;Shianna KV;Ge D;Smith JP;Maia JM;Heinzen EL;Goedert JJ;Goldstein DB;Center for HIV/AIDS Vaccine Immunology (CHAVI)
通讯作者：
Center for HIV/AIDS Vaccine Immunology (CHAVI)
下一代测序：基因组以外的应用。
影响因子：
3.9
作者：
Marguerat S;Wilhelm BT;Bähler J
通讯作者：
Bähler J
DOI：
10.1051/rnd:2002013
发表时间：
2002-03-01
期刊：
REPRODUCTION NUTRITION DEVELOPMENT
影响因子：
--
作者：
Boutinaud, M;Jammes, H
通讯作者：
Jammes, H
影响因子：
48
作者：
Cloonan, Nicole;Forrest, Alistair R. R.;Grimmond, Sean M.
通讯作者：
Grimmond, Sean M.
影响因子：
7
作者：
Morin, Ryan D.;O'Connor, Michael D.;Marra, Marco A.
通讯作者：
Marra, Marco A.