Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing.
Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing.
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利用下一代限制性位点相关 DNA 测序构建葡萄高密度遗传图谱
DOI：
10.1186/1471-2229-12-148
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发表时间：
2012-08-21
影响因子：
5.3
通讯作者：
Li S
中科院分区：
文献类型：
--
作者：
Wang N;Fang L;Xin H;Wang L;Li S
遗传定位和QTL检测是植物改良育种的有力手段。构建一个高密度、高质量的遗传图谱，将有利于生产优质葡萄，满足人类的需求。新一代测序技术的高通量和低成本使其在基因组研究中得到了广泛的应用。测序限制性位点相关DNA （RAD）可能是一种简化基因分型的有效策略。NGS与RAD的结合已被证明是开发单核苷酸多态性（SNP）标记的有力手段。结果培育出100株单株的1代群体。利用计算机消化位点预测选择合适的限制性内切酶构建RAD测序文库。应用下一代RAD测序对F1群体及其亲本进行基因分型。应用SNP调控聚类策略，共开发了1814个高质量SNP标记：其中1121个定位于女性遗传图谱，759个定位于男性遗传图谱，1646个定位于综合遗传图谱。将遗传图谱与已发表的葡萄基因组进行比较，揭示了葡萄的保守性和变异性。结论下一代RAD测序技术在葡萄F1群体基因分型中的适用性得到了验证，利用我们设计的SNP标记成功构建了高密度、高质量的遗传图谱。详细分析表明，该遗传图谱可用于QTL检测、序列组装和基因组比较等多种基因组研究。
BackgroundGenetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development.ResultsAn F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the publishedVitis viniferagenome revealed both conservation and variations.ConclusionsThe applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.
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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：
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
影响因子：
7
作者：
Huang, Xuehui;Feng, Qi;Han, Bin
通讯作者：
Han, Bin
影响因子：
2.2
作者：
Divne, AM;Allen, M
通讯作者：
Allen, M
影响因子：
5.4
作者：
Doligez, A.;Adam-Blondon, A. F.;Di Gaspero, G.
通讯作者：
Di Gaspero, G.