The First High-Density Genetic Map Construction in Tree Peony (Paeonia Sect. Moutan) using Genotyping by Specific-Locus Amplified Fragment Sequencing.
The First High-Density Genetic Map Construction in Tree Peony (Paeonia Sect. Moutan) using Genotyping by Specific-Locus Amplified Fragment Sequencing.
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首次利用特异性位点扩增片段测序基因分型构建牡丹高密度遗传图谱
DOI：
10.1371/journal.pone.0128584
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Liu G
中科院分区：
文献类型：
--
作者：
Cai C;Cheng FY;Wu J;Zhong Y;Liu G
遗传连锁图谱有助于阐明基因组结构，是加速分子标记辅助育种的最有力的基因组工具之一。然而，由于缺乏足够的用户友好的分子标记，还没有开发出牡丹的遗传连锁图谱(牡丹组。牡丹)，是世界范围内的一组重要的园艺植物。特定基因座扩增片段测序技术(SLAF-SEQ)是近年来发展起来的一种分子标记技术，能够在全基因组范围内大规模发现基于序列的标记并进行基因分型。本研究以牡丹粉丹白×牡丹红桥杂交F1群体为材料，进行了SLAF测序，为牡丹高密度遗传连锁图谱的构建提供了足够的高质量标记。在SLAF测序后，总共产生了78 GB的测序数据和285,403,225对末端读取。我们从这些数据中检测到309,198个高质量的SLAF，其中85,124个(27.5%)是多态的。随后，将编码成功的符合优质标记标准的3518个多态标记确定为有效标记，并用于遗传连锁作图。最后构建了一个完整的遗传图谱，该图谱由5个连锁群上的1 189个标记组成，跨度为920.699 cM，平均标记间距离为0.774 cM。图谱上共有1115个SNP标记、18个Indel标记和56个SNP&Indel标记。在这些标记中，450个标记(37.85%)表现出显著的分离扭曲(P<；0.05)。综上所述，本研究首次报道了牡丹的大规模标记开发和高密度连锁图谱构建。本研究结果不仅为牡丹分子标记辅助育种奠定了基础，也为牡丹基因组序列拼接奠定了基础。
Genetic linkage maps, permitting the elucidation of genome structure, are one of most powerful genomic tools to accelerate marker-assisted breeding. However, due to a lack of sufficient user-friendly molecular markers, no genetic linkage map has been developed for tree peonies (Paeonia Sect. Moutan), a group of important horticultural plants worldwide. Specific-locus amplified fragment sequencing (SLAF-seq) is a recent molecular marker development technology that enable the large-scale discovery and genotyping of sequence-based marker in genome-wide. In this study, we performed SLAF sequencing of an F1 population, derived from the cross P. ostti ‘FenDanBai’ × P. × suffruticosa ‘HongQiao’, to identify sufficient high-quality markers for the construction of high-density genetic linkage map in tree peonies. After SLAF sequencing, a total of 78 Gb sequencing data and 285,403,225 pair-end reads were generated. We detected 309,198 high-quality SLAFs from these data, of which 85,124 (27.5%) were polymorphic. Subsequently, 3518 of the polymorphic markers, which were successfully encoded in to Mendelian segregation types, and were in conformity with the criteria of high-quality markers, were defined as effective markers and used for genetic linkage mapping. Finally, we constructed an integrated genetic map, which comprised 1189 markers on the five linkage groups, and spanned 920.699 centiMorgans (cM) with an average inter-marker distance of 0.774 cM. There were 1115 ‘SNP-only’ markers, 18 ‘InDel-only’ markers, and 56 ‘SNP&InDel’ markers on the map. Among these markers, 450 (37.85%) showed significant segregation distortion (P < 0.05). In conclusion, this investigation reported the first large-scale marker development and high-density linkage map construction for tree peony. The results of this study will serve as a solid foundation not only for marker-assisted breeding, but also for genome sequence assembly for tree peony.
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