Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae).
Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae).
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DOI：
10.1186/1471-2164-12-104
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发表时间：
2011-02-10
期刊：
影响因子：
4.4
通讯作者：
Picó B
中科院分区：
文献类型：
--
作者：
Blanca J;Cañizares J;Roig C;Ziarsolo P;Nuez F;Picó B
西葫芦属于葫芦科。 “西葫芦”类型是世界上价值最高的蔬菜之一，而其他西葫芦和相关的西葫芦属植物则是主食以及丰富的脂肪和维生素来源。如今，有多种基因组工具可用于其他葫芦科植物，这些葫芦科植物已成为研究不同代谢过程的模型。然而，葫芦属仍然缺乏这些工具，从而限制了基因发现和育种过程。我们报告使用 454 GS FLX Titanium 技术生成了总共 512,751 个 C. pepo EST 序列。 EST 是从标准化 cDNA 文库（根、叶和花组织）中获得的，该文库使用两个具有植物、开花和果实性状对比表型的品种制备，代表了两个 C. pepo 亚种：亚种。佩波河西葫芦及其亚种。 ovifera cv 扇贝。进行从头组装以生成 49,610 个 Cucurbita unigenes（平均长度为 626 bp）的集合，代表该物种的第一个转录组。超过 60% 的 unigene 进行了功能注释并分配给一个或多个基因本体术语。葫芦科 Unigenes 的分布遵循与拟南芥或甜瓜报道相似的趋势，表明该数据集可能代表整个葫芦转录组。大约 34% 的 unigenes 被发现具有拟南芥或甜瓜的已知直系同源物，包括可能与抗病性、开花和果实品质相关的基因。此外，还鉴定了西葫芦和扇贝之间的一组 1,882 个具有 SSR 基序的 unigenes 和 9,043 个高置信度 SNP，其中 3,538 个 SNP 符合高通量基因分型平台的使用标准，144 个可以被检测为 CAPS。验证了一组标记，其中 80% 在一组可变的 C. pepo 和 C. moschata 种质中具有多态性。我们首次对 C. pepo 的基因序列和等位基因变异进行了广泛的调查，其中先前的基因组信息有限。转录组为生物学研究提供了宝贵的新工具。开发的分子标记是未来遗传连锁和数量性状位点分析的基础，对于加快培育新的、适应性更强的南瓜品种的进程至关重要。
Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding. We report the generation of a total of 512,751 C. pepo EST sequences, using 454 GS FLX Titanium technology. ESTs were obtained from normalized cDNA libraries (root, leaves, and flower tissue) prepared using two varieties with contrasting phenotypes for plant, flowering and fruit traits, representing the two C. pepo subspecies: subsp. pepo cv. Zucchini and subsp. ovifera cv Scallop. De novo assembling was performed to generate a collection of 49,610 Cucurbita unigenes (average length of 626 bp) that represent the first transcriptome of the species. Over 60% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The distributions of Cucurbita unigenes followed similar tendencies than that reported for Arabidopsis or melon, suggesting that the dataset may represent the whole Cucurbita transcriptome. About 34% unigenes were detected to have known orthologs of Arabidopsis or melon, including genes potentially involved in disease resistance, flowering and fruit quality. Furthermore, a set of 1,882 unigenes with SSR motifs and 9,043 high confidence SNPs between Zucchini and Scallop were identified, of which 3,538 SNPs met criteria for use with high throughput genotyping platforms, and 144 could be detected as CAPS. A set of markers were validated, being 80% of them polymorphic in a set of variable C. pepo and C. moschata accessions. We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed. The transcriptome provides an invaluable new tool for biological research. The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties.
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影响因子：
56.9
作者：
Boualem, Adnane;Fergany, Mohamed;Bendahmane, Abdelhafid
通讯作者：
Bendahmane, Abdelhafid
影响因子：
5.1
作者：
Ellard-Ivey, M;Hopkins, RB;Lomax, TL
通讯作者：
Lomax, TL
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
影响因子：
5.3
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
通讯作者：
Garcia-Mas J
测序的Medicago truncatula使用454个生命科学技术表达了测序标签。
影响因子：
4.4
作者：
Cheung, Foo;Haas, Brian J;Goldberg, Susanne M D;May, Gregory D;Xiao, Yongli;Town, Christopher D
通讯作者：
Town, Christopher D