Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology.
Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology.
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DOI：
10.1186/1471-2164-12-77
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发表时间：
2011-01-27
期刊：
影响因子：
4.4
通讯作者：
Jackson EW
中科院分区：
文献类型：
--
作者：
Oliver RE;Lazo GR;Lutz JD;Rubenfield MJ;Tinker NA;Anderson JM;Wisniewski Morehead NH;Adhikary D;Jellen EN;Maughan PJ;Brown Guedira GL;Chao S;Beattie AD;Carson ML;Rines HW;Obert DE;Bonman JM;Jackson EW
遗传标记是现代基因组学研究的关键;然而，燕麦中分子标记的发现和基因分型受到基因组大小和复杂性以及序列数据稀缺的阻碍。本研究的目的是产生燕麦表达序列标签（EST）信息，开发SNP发现的生物信息学管道，并建立一种快速，经济，简单的SNP标记基因分型方法在复杂的多倍体基因组，如燕麦。基于四种栽培燕麦基因型的cDNA文库，从大约一百万个Roche 454序列读段组装了大约127，000个重叠群。通过一种新的生物信息学管道过滤重叠群，以消除由亚基因组同源性引起的模糊多态性，并从9，448个候选基因座中选择96个计算机模拟SNP，用于使用高分辨率解链（HRM）分析进行验证。其中52个（54%）在Ogle 1040 × TAM O-301（OT）作图群体的双亲间具有多态性，48个为单一孟德尔分离，44个位于现有的OT连锁图上。对来自12个引物的Ogle和TAM扩增子进行测序以进行SNP验证，揭示了7个扩增子中的复杂多态性，但SNP位点内的一般序列保守性。HRM的全扩增子询问显示插入，缺失和杂合子在二级燕麦种质库，在一些引物靶产生多个等位基因。为了验证标记的实用性，使用36种SNP测定来评估34种不同燕麦基因型的遗传多样性。树状图聚类一般对应于已知的基因组组成和遗传祖先。本文提出的高通量SNP发现流水线是一种快速有效的鉴定燕麦基因组中多态性SNP等位基因的方法。当前一代HRM系统是用于SNP基因分型的简单且高度信息化的平台。这些技术提供了一个模型，SNP的发现和基因分型在其他物种的复杂和不良特征的基因组。
Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM) analysis. Of these, 52 (54%) were polymorphic between parents of the Ogle1040 × TAM O-301 (OT) mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry. The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide a model for SNP discovery and genotyping in other species with complex and poorly-characterized genomes.
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影响因子：
12.3
作者：
Huse SM;Huber JA;Morrison HG;Sogin ML;Welch DM
通讯作者：
Welch DM
DOI：
10.1101/sqb.2003.68.69
发表时间：
2003-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
Fan, JB;Oliphant, A;Chee, MS
通讯作者：
Chee, MS
影响因子：
2.5
作者：
Manly, KF;Cudmore, RH;Meer, JM
通讯作者：
Meer, JM
影响因子：
3.1
作者：
FOMINAYA, A;VEGA, C;FERRER, E
通讯作者：
FERRER, E
影响因子：
4.8
作者：
DICE, LR
通讯作者：
DICE, LR