Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley.
Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley.
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DOI：
10.1186/1471-2164-12-4
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发表时间：
2011-01-04
期刊：
影响因子：
4.4
通讯作者：
Hayes PM
中科院分区：
文献类型：
--
作者：
Chutimanitsakun Y;Nipper RW;Cuesta-Marcos A;Cistué L;Corey A;Filichkina T;Johnson EA;Hayes PM
连锁图谱是分析动植物物种复杂遗传性状的重要资源。典型的图谱构建遵循一个完善的工作流程：最初的发现阶段，从一小群个体中挖掘遗传标记，然后使用标记组对选定的作图群体进行基因分型。新开发的基于序列的标记技术--限制性位点相关DNA（RAD），能够使用大规模平行测序进行同步单核苷酸多态性（SNP）标记发现和基因分型。本研究的目的是以大麦为模型系统，评估RAD标记在构建连锁图谱中的实用性。以已发表的俄勒冈州Wolfe Barley（OWB）作图群体的高密度EST SNP图谱为参考，利用有限的先验标记构建RAD图谱，整合RAD和先验数据，并利用两张图谱进行QTL检测。使用RAD方案与Illumina测序合成平台串联，从OWB亲本近交系的初始扫描中鉴定总共530个SNP标记-"显性"和"隐性"标记原种-并在93个成员的双单倍体（DH）作图群体中评分。将来自结构化群体的RAD序列数据转换成等位基因基因型，由此构建遗传图谱。组装的仅RAD地图由445个标记组成，平均间隔长度为5厘米，而综合地图包括463个RAD位点和2383个先前标记。测序RAD标记分布在所有七条染色体上，多态位点来自大麦基因组的编码区和非编码区。总图谱长度相当，两个图谱中共同标记的顺序相同。两个图谱均检测到相同的生殖适合度QTL，其中大部分QTL与决定大麦二棱和六棱种质群的矮秆基因（ZEO）和VRS 1基因一致。我们演示了如何利用测序的RAD标记来产生高质量的连锁图，用于检测单基因位点和QTL。通过将SNP发现和基因分型结合到并行测序事件中，RAD标记应该是一系列作物物种的有用分子育种工具。第二代和第三代测序技术在成本和通量方面的预期改进将使测序的RAD标记系统的应用更加强大，包括从头基因组组装的改进、超高密度遗传图谱和关联图谱的开发。
Linkage maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage map construction, employing barley as a model system. Using the published high density EST-based SNP map in the Oregon Wolfe Barley (OWB) mapping population as a reference, we created a RAD map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both maps for detection of quantitative trait loci (QTL). Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines - the "dominant" and "recessive" marker stocks - and scored in a 93 member doubled haploid (DH) mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic map was constructed. The assembled RAD-only map consists of 445 markers with an average interval length of 5 cM, while an integrated map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the Hordeum genome. Total map lengths are comparable and the order of common markers is identical in both maps. The same large-effect QTL for reproductive fitness traits were detected with both maps and the majority of these QTL were coincident with a dwarfing gene (ZEO) and the VRS1 gene, which determines the two-row and six-row germplasm groups of barley. We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in de novo genome assembly, development of ultra-high density genetic maps and association mapping.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
7
作者：
Miller, Michael R.;Dunham, Joseph P.;Johnson, Eric A.
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Johnson, Eric A.
影响因子：
5.4
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影响因子：
7.4
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通讯作者：
Denyer, K
影响因子：
7
作者：
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通讯作者：
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