A set of EST-SNPs for map saturation and cultivar identification in melon.
A set of EST-SNPs for map saturation and cultivar identification in melon.
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DOI：
10.1186/1471-2229-9-90
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发表时间：
2009-07-15
影响因子：
5.3
通讯作者：
Garcia-Mas J
中科院分区：
文献类型：
--
作者：
Deleu W;Esteras C;Roig C;González-To M;Fernández-Silva I;Gonzalez-Ibeas D;Blanca J;Aranda MA;Arús P;Nuez F;Monforte AJ;Picó MB;Garcia-Mas J
甜瓜(Cucumis Melo L.)是葫芦科(Cucurbitaceae)的一员，尽管它是一种重要的作物，但几乎没有基因组工具可用。在这些工具中，构建遗传图谱的方法主要有简单序列重复序列(SSR)、限制性片段长度多态(RFLP)和扩增片段长度多态(AFLP)等标记类型。人们越来越需要用单核苷酸多态(SNP)来饱和遗传图谱，以便更好地进行高通量分析，特别是如果这些标记位于基因编码区，则提供功能标记。来自甜瓜的表达序列标签(EST)在公共数据库中可用，重新测序EST或验证在电子计算机中检测到的SNPs是发现SNPs的极好方法。对Pi 161375(SC)בPiel de Sapo’(PS)遗传图谱的亲本之间的EST进行重新测序或利用EST数据库中的SNP信息，发现了基于EST的SNP。利用二元组作图策略在甜瓜遗传图谱上定位了200个基于EST的SNPs，使图谱密度提高到2.35 cM/标记。45个SNPs的子集被用来研究48个甜瓜材料的变异，涵盖了该物种的广泛遗传多样性。与其他标记体系相比，SNP分析能较好地反映材料间的亲缘关系，能够区分所有的材料和品种。这是葫芦科物种遗传图谱的第一个例子，其中包括使用EST发现的一组主要SNP标记。Pi 161375בPiel de Sapo’甜瓜遗传图谱有约700个标记，其中500多个是基于基因的标记(SNP、RFLP和SSR)。这张遗传图谱将是构建甜瓜物理图谱的核心工具，这是对完整基因组进行测序之前的一步。利用这组SNP标记，可以像使用SSR标记一样有效地确定48份甜瓜材料的遗传关系，这些标记也可能用于西方甜瓜品种的品种鉴定。
There are few genomic tools available in melon (Cucumis melo L.), a member of the Cucurbitaceae, despite its importance as a crop. Among these tools, genetic maps have been constructed mainly using marker types such as simple sequence repeats (SSR), restriction fragment length polymorphisms (RFLP) and amplified fragment length polymorphisms (AFLP) in different mapping populations. There is a growing need for saturating the genetic map with single nucleotide polymorphisms (SNP), more amenable for high throughput analysis, especially if these markers are located in gene coding regions, to provide functional markers. Expressed sequence tags (ESTs) from melon are available in public databases, and resequencing ESTs or validating SNPs detected in silico are excellent ways to discover SNPs. EST-based SNPs were discovered after resequencing ESTs between the parental lines of the PI 161375 (SC) × 'Piel de sapo' (PS) genetic map or using in silico SNP information from EST databases. In total 200 EST-based SNPs were mapped in the melon genetic map using a bin-mapping strategy, increasing the map density to 2.35 cM/marker. A subset of 45 SNPs was used to study variation in a panel of 48 melon accessions covering a wide range of the genetic diversity of the species. SNP analysis correctly reflected the genetic relationships compared with other marker systems, being able to distinguish all the accessions and cultivars. This is the first example of a genetic map in a cucurbit species that includes a major set of SNP markers discovered using ESTs. The PI 161375 × 'Piel de sapo' melon genetic map has around 700 markers, of which more than 500 are gene-based markers (SNP, RFLP and SSR). This genetic map will be a central tool for the construction of the melon physical map, the step prior to sequencing the complete genome. Using the set of SNP markers, it was possible to define the genetic relationships within a collection of forty-eight melon accessions as efficiently as with SSR markers, and these markers may also be useful for cultivar identification in Occidental melon varieties.
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影响因子：
3.9
作者：
NEI, M;TAJIMA, F;TATENO, Y
通讯作者：
TATENO, Y
影响因子：
5.4
作者：
Moreno, Eduard;Obando, Javier M.;Garcia-Mas, Jordi
通讯作者：
Garcia-Mas, Jordi
影响因子：
5.4
作者：
Eduardo, I;Arús, P;Monforte, AJ
通讯作者：
Monforte, AJ
影响因子：
5.4
作者：
NEUHAUSEN, SL
通讯作者：
NEUHAUSEN, SL
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