Detection and genotyping of restriction fragment associated polymorphisms in polyploid crops with a pseudo-reference sequence: a case study in allotetraploid Brassica napus.
Detection and genotyping of restriction fragment associated polymorphisms in polyploid crops with a pseudo-reference sequence: a case study in allotetraploid Brassica napus.
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具有伪参考序列的多倍体作物中限制性片段相关多态性的检测和基因分型：异源四倍体甘蓝型油菜的案例研究
DOI：
10.1186/1471-2164-14-346
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发表时间：
2013-05-24
期刊：
影响因子：
4.4
通讯作者：
Liu K
中科院分区：
文献类型：
--
作者：
Chen X;Li X;Zhang B;Xu J;Wu Z;Wang B;Li H;Younas M;Huang L;Luo Y;Wu J;Hu S;Liu K
同源序列的存在和参考基因组序列的缺失使得多倍体作物中单核苷酸多态性（snp）的发现和基因分型更具挑战性。结果利用改进的ddRADseq技术，构建了2个甘蓝型油菜自交系及其91个双单倍体（DH）后代的简化表示文库（RRLs）。开发了一种称为RFAPtools的生物信息学管道，用于发现snp和存在/缺失变异（pav）并进行基因分型。利用该管道，构建了包含180,991个序列标签的伪参考序列（PRF）。通过将序列reads与伪参考序列比对，利用RFAPtools对等位基因snp和pav进行鉴定和分型。构建了两个平行连锁图谱，一个SNP bin图谱包含8780个SNP位点，一个PAV连锁图谱包含12423个显性位点。通过将标记序列对齐到b。我们将44个包含8.15 Mb的未组装序列支架分配到b上。rapachromosomal，还鉴定出14个错误组装的实例和8个错误排序的支架实例。结论改进的ddRADseq方法是一种经济、简便的方法，可对多倍体植物进行数万个snp和PAV标记的基因分型。结果还表明，本研究开发的RFAPtools能够有效地从多倍体同源序列中挖掘等位snp，因此该工具一般适用于具有或不具有参考基因组序列的二倍体或多倍体物种。
BackgroundThe presence of homoeologous sequences and absence of a reference genome sequence make discovery and genotyping of single nucleotide polymorphisms (SNPs) more challenging in polyploid crops.ResultsTo address this challenge, we constructed reduced representation libraries (RRLs) for twoBrassica napusinbred lines and their 91 doubled haploid (DH) progenies using a modified ddRADseq technique. A bioinformatics pipeline termed RFAPtools was developed to discover and genotype SNPs and presence/absence variations (PAVs). Using this pipeline, a pseudo-reference sequence (PRF) containing 180,991 sequence tags was constructed. By aligning sequence reads to the pseudo-reference sequence, allelic SNPs as well as PAVs were identified and genotyped with RFAPtools. Two parallel linkage maps, one SNP bin map containing 8,780 SNP loci and one PAV linkage map containing 12,423 dominant loci, were constructed. By aligning marker sequences toB.rapasequence scaffolds, whose genome is available, we assigned 44 unassembled sequence scaffolds comprising 8.15 Mb onto theB.rapachromosomes, and also identified 14 instances of misassembly and eight instances of mis-ordering sequence scaffolds.ConclusionsThese results indicate that the modified ddRADseq approach is a cost-effective and simple method to genotype tens of thousands SNPs and PAV markers in a polyploidy plant species. The results also demonstrated that RFAPtools developed in this study are powerful to mine allelic SNPs from homoeologous sequences in polyploids, therefore they are generally applicable in either diploid or polyploid species with or without a reference genome sequence.
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影响因子：
48
作者：
Craig, David W.;Pearson, John V.;Szelinger, Szabolcs;Sekar, Aswin;Redman, Margot;Corneveaux, Jason J.;Pawlowski, Traci L.;Laub, Trisha;Nunn, Gary;Stephan, Dietrich A.;Homer, Nils;Huentelman, Matthew J.
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作者：
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影响因子：
3.7
作者：
Weng J;Xie C;Hao Z;Wang J;Liu C;Li M;Zhang D;Bai L;Zhang S;Li X
通讯作者：
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