Rapid genomic characterization of the genus vitis.
Rapid genomic characterization of the genus vitis.
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DOI：
10.1371/journal.pone.0008219
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发表时间：
2010-01-13
期刊：
影响因子：
3.7
通讯作者：
Ware D
中科院分区：
文献类型：
--
作者：
Myles S;Chia JM;Hurwitz B;Simon C;Zhong GY;Buckler E;Ware D
下一代测序技术有望通过促进农业重要表型的遗传图谱，大大加快遗传信息用于作物改良的使用。优化遗传作图研究设计的第一步涉及大规模多态性发现和随后的全基因组群体结构和连锁不平衡（LD）模式的评估。在本研究中，我们提供了这样的评估葡萄藤（属葡萄属），世界上最重要的经济水果作物。利用合成测序技术对17个葡萄样品（10个栽培种和7个野生葡萄属种）的简化代表文库（RRL）进行了测序。我们开发了SNP调用的启发式方法，鉴定了数十万个SNP，并在9K基因分型阵列上验证了这些SNP的子集。我们证明，9K SNP阵列提供了足够的分辨率来区分葡萄品种，葡萄和野生葡萄属物种，甚至不同的野生葡萄属物种。我们发现，有大量的共享之间的多态性的葡萄和野生葡萄属物种，并发现之间的遗传关系的葡萄品种同意，以及其拟议的地理起源使用主成分分析（PCA）。在驯化的葡萄藤LD的水平是低的，即使在短距离，但LD持续高于背景水平至3 kb。虽然基因分型阵列是有用的，用于评估人口结构和大量样本的LD衰减，我们建议，全基因组测序将成为高多样性植物物种的全基因组遗传图谱研究的基因分型方法的选择。这项研究表明，我们可以使用下一代测序技术快速进行作物物种的全基因组研究。我们的研究为其他高多样性作物物种的未来工作奠定了基础，并为葡萄藤遗传社区提供了现有遗传资源的显着增强。
Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvement by facilitating the genetic mapping of agriculturally important phenotypes. The first step in optimizing the design of genetic mapping studies involves large-scale polymorphism discovery and a subsequent genome-wide assessment of the population structure and pattern of linkage disequilibrium (LD) in the species of interest. In the present study, we provide such an assessment for the grapevine (genus Vitis), the world's most economically important fruit crop. Reduced representation libraries (RRLs) from 17 grape DNA samples (10 cultivated V. vinifera and 7 wild Vitis species) were sequenced with sequencing-by-synthesis technology. We developed heuristic approaches for SNP calling, identified hundreds of thousands of SNPs and validated a subset of these SNPs on a 9K genotyping array. We demonstrate that the 9K SNP array provides sufficient resolution to distinguish among V. vinifera cultivars, between V. vinifera and wild Vitis species, and even among diverse wild Vitis species. We show that there is substantial sharing of polymorphism between V. vinifera and wild Vitis species and find that genetic relationships among V. vinifera cultivars agree well with their proposed geographic origins using principal components analysis (PCA). Levels of LD in the domesticated grapevine are low even at short ranges, but LD persists above background levels to 3 kb. While genotyping arrays are useful for assessing population structure and the decay of LD across large numbers of samples, we suggest that whole-genome sequencing will become the genotyping method of choice for genome-wide genetic mapping studies in high-diversity plant species. This study demonstrates that we can move quickly towards genome-wide studies of crop species using next-generation sequencing. Our study sets the stage for future work in other high diversity crop species, and provides a significant enhancement to current genetic resources available to the grapevine genetic community.
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DOI：
10.1093/bioinformatics/btn565
发表时间：
2009-01-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Malhis N;Butterfield YS;Ester M;Jones SJ
通讯作者：
Jones SJ
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick
DOI：
10.1017/s0016672303006177
发表时间：
2003-06-01
期刊：
GENETICAL RESEARCH
影响因子：
--
作者：
Aradhya, MK;Dangl, GS;Simon, CJ
通讯作者：
Simon, CJ
SNP使用SNPLEX基因分型系统在葡萄藤中进行高通量筛选。
影响因子：
5.3
作者：
Pindo, Massimo;Vezzulli, Silvia;Coppola, Giuseppina;Cartwright, Dustin A.;Zharkikh, Andrey;Velasco, Riccardo;Troggio, Michela
通讯作者：
Troggio, Michela
通过454转录组测序发现SNP。
影响因子：
7.2
作者：
Barbazuk, W Brad;Emrich, Scott J;Chen, Hsin D;Li, Li;Schnable, Patrick S
通讯作者：
Schnable, Patrick S