Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing.
Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing.
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基于特定长度扩增片段（SLAF）测序大规模标记开发的芝麻高密度遗传图谱构建
DOI：
10.1186/1471-2229-13-141
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发表时间：
2013-09-24
影响因子：
5.3
通讯作者：
Zhang X
中科院分区：
文献类型：
--
作者：
Zhang Y;Wang L;Xin H;Li D;Ma C;Ding X;Hong W;Zhang X
背景芝麻是一种重要的油料作物，但对芝麻的遗传学和分子生物学的研究才刚刚开始。由于缺乏足够的分子标记，芝麻的高密度遗传图谱尚未公布。特定长度扩增片段测序(SLAF-SEQ)是近年来发展起来的一种用于大规模新SNP发现和基因分型的高分辨率策略。结果测序后共获得28.21 GB的数据，包含201,488,285个双端阅读片段。每个SLAF标记的平均覆盖率在父本是23.48倍，在母本是23.38倍，在F2代平均是14.46倍。总共检测到71,793个高质量的SLAF，其中3,673个SLAF是多态的，其中1,272个多态标记符合构建遗传图谱的要求。最终的图谱包括15个连锁群上的1233个标记，长度为1474.87万cM，相邻标记之间的平均距离为1.20cM。据我们所知，该图谱是迄今为止芝麻密度最高的遗传连锁图谱。‘SNP_Only’标记占图谱标记总数的87.51%。共有2 0 5个标记在该图谱上表现出显著的分离扭曲(P<； 0.0 5)。该图谱是使用F2群体和SLAF-SEQ方法构建的，这使得在短时间内有效地开发出大量的多态标记。本研究结果不仅将为芝麻基因/QTL精细定位、基于图谱的基因分离和分子育种提供平台，而且还将为在物理图谱上定位序列支架提供参考，辅助芝麻基因组序列的组装过程。
BackgroundThe genetics and molecular biology of sesame has only recently begun to be studied even though sesame is an important oil seed crop. A high-density genetic map for sesame has not been published yet due to a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for large-scalede novoSNP discovery and genotyping. SLAF-seq was employed in this study to obtain sufficient markers to construct a high-density genetic map for sesame.ResultsIn total, 28.21 Gb of data containing 201,488,285 pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 23.48-fold in the male parent, 23.38-fold in the female parent, and 14.46-fold average in each F2individual. In total, 71,793 high-quality SLAFs were detected of which 3,673 SLAFs were polymorphic and 1,272 of the polymorphic markers met the requirements for use in the construction of a genetic map. The final map included 1,233 markers on the 15 linkage groups (LGs) and was 1,474.87 cM in length with an average distance of 1.20 cM between adjacent markers. To our knowledge, this map is the densest genetic linkage map to date for sesame. 'SNP_only’ markers accounted for 87.51% of the markers on the map. A total of 205 markers on the map showed significant (P< 0.05) segregation distortion.ConclusionsWe report here the first high-density genetic map for sesame. The map was constructed using an F2population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time. Results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for sesame, but will also serve as a reference for positioning sequence scaffolds on a physical map, to assist in the process of assembling the sesame genome sequence.
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影响因子：
5.4
作者：
Bindler, Gregor;Plieske, Joerg;Bakaher, Nicolas;Gunduz, Irfan;Ivanov, Nikolai;Van der Hoeven, Rutger;Ganal, Martin;Donini, Paolo
通讯作者：
Donini, Paolo
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：
3.7
作者：
Baxter SW;Davey JW;Johnston JS;Shelton AM;Heckel DG;Jiggins CD;Blaxter ML
通讯作者：
Blaxter ML
影响因子：
4.4
作者：
Chutimanitsakun Y;Nipper RW;Cuesta-Marcos A;Cistué L;Corey A;Filichkina T;Johnson EA;Hayes PM
通讯作者：
Hayes PM
DOI：
10.1111/j.1471-8286.2005.01048.x
发表时间：
2005-12-01
期刊：
MOLECULAR ECOLOGY NOTES
影响因子：
--
作者：
Dixit, A;Jin, MH;Cho, EG
通讯作者：
Cho, EG