Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation.
Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation.
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DOI：
10.1186/1471-2229-12-46
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发表时间：
2012-04-02
影响因子：
5.3
通讯作者：
Main D
中科院分区：
文献类型：
--
作者：
Rowland LJ;Alkharouf N;Darwish O;Ogden EL;Polashock JJ;Bassil NV;Main D
近年来，人们对蓝莓的消费有所增加，部分原因是它们的许多公认的健康益处。蓝莓果实含有很高的花青素，它与改善夜视、预防黄斑变性、抗癌活性和降低心脏病风险有关。然而，蓝莓的基因组资源非常少。进一步开发表达序列标签(EST)、分子标记和遗传连锁图谱等基因组资源可能会导致更快的遗传改良。分子标记辅助选择可用于将气候适应性状与果实和营养品质性状相结合。本文介绍了商业高丛蓝莓品种Bluecrop的转录组测序工作，并利用这些序列鉴定与冷驯化和果实发育相关的基因，以及开发用于定位研究的SSR标记。通过下一代罗氏454测序，从蓝莓不同发育阶段的果实、不同冷驯化阶段的花蕾和叶片中获得了转录组序列。超过600,000个读数被组装成大约15,000个重叠群和124,000个单体。组装的序列被注释并功能映射到基因本体论(GO)术语。每个文库中最丰富的序列的频率在所有文库中进行了比较，以确定在冷驯化和果实发育过程中潜在差异表达的基因。实时荧光定量聚合酶链式反应(Real-Time-PCR)验证它们的差异表达模式。总体而言，在被检查的17个基因中，有14个基因的差异表达模式与仅从它们的读数预测的相似。组装的序列也被挖掘出来寻找SSR。从这些序列中鉴定出15,886个蓝莓EST-SSR基因座。从7,705个含有足够侧翼序列的SSR序列中设计了引物。对目前用于构建遗传连锁图谱的两个蓝莓群体的亲本进行了100对引物的扩增和多态性检测。四倍体作图群体是基于高灌木品种Draper和Jewel之间的杂交(V.darrowii也在‘Jewel’的背景中)。二倍体作图群体是以达罗维葡萄与二倍体伞房葡萄的F1杂种与另一株二倍体伞房葡萄杂交为基础建立的。SSR总扩增率为68%，多态率为43%。这些结果表明，这454个EST集合将是一个有价值的资源，可以用来鉴定在蓝莓及其近缘物种的花芽发育、低温驯化、冷藏单位积累和果实发育中发挥重要作用的潜在差异表达基因。此外，EST已被证明可用于SSR和EST-PCR标记的开发，目前正被用于构建蓝莓的遗传连锁图谱。
There has been increased consumption of blueberries in recent years fueled in part because of their many recognized health benefits. Blueberry fruit is very high in anthocyanins, which have been linked to improved night vision, prevention of macular degeneration, anti-cancer activity, and reduced risk of heart disease. Very few genomic resources have been available for blueberry, however. Further development of genomic resources like expressed sequence tags (ESTs), molecular markers, and genetic linkage maps could lead to more rapid genetic improvement. Marker-assisted selection could be used to combine traits for climatic adaptation with fruit and nutritional quality traits. Efforts to sequence the transcriptome of the commercial highbush blueberry (Vaccinium corymbosum) cultivar Bluecrop and use the sequences to identify genes associated with cold acclimation and fruit development and develop SSR markers for mapping studies are presented here. Transcriptome sequences were generated from blueberry fruit at different stages of development, flower buds at different stages of cold acclimation, and leaves by next-generation Roche 454 sequencing. Over 600,000 reads were assembled into approximately 15,000 contigs and 124,000 singletons. The assembled sequences were annotated and functionally mapped to Gene Ontology (GO) terms. Frequency of the most abundant sequences in each of the libraries was compared across all libraries to identify genes that are potentially differentially expressed during cold acclimation and fruit development. Real-time PCR was performed to confirm their differential expression patterns. Overall, 14 out of 17 of the genes examined had differential expression patterns similar to what was predicted from their reads alone. The assembled sequences were also mined for SSRs. From these sequences, 15,886 blueberry EST-SSR loci were identified. Primers were designed from 7,705 of the SSR-containing sequences with adequate flanking sequence. One hundred primer pairs were tested for amplification and polymorphism among parents of two blueberry populations currently being used for genetic linkage map construction. The tetraploid mapping population was based on a cross between the highbush cultivars Draper and Jewel (V. darrowii is also in the background of 'Jewel'). The diploid mapping population was based on a cross between an F1 hybrid of V. darrowii and diploid V. corymbosum and another diploid V. corymbosum. The overall amplification rate of the SSR primers was 68% and the polymorphism rate was 43%. These results indicate that this large collection of 454 ESTs will be a valuable resource for identifying genes that are potentially differentially expressed and play important roles in flower bud development, cold acclimation, chilling unit accumulation, and fruit development in blueberry and related species. In addition, the ESTs have already proved useful for the development of SSR and EST-PCR markers, and are currently being used for construction of genetic linkage maps in blueberry.
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影响因子：
6.9
作者：
Marín-Rodríguez, MC;Orchard, J;Seymour, GB
通讯作者：
Seymour, GB
影响因子：
5.2
作者：
Dhanaraj, AL;Slovin, JP;Rowland, LJ
通讯作者：
Rowland, LJ
影响因子：
4.3
作者：
Jimenez, A;Creissen, G;Mullineaux, P
通讯作者：
Mullineaux, P
影响因子：
56.9
作者：
Poinar, HN;Schwarz, C;Schuster, SC
通讯作者：
Schuster, SC
DOI：
10.1111/j.1471-8286.2005.01025.x
发表时间：
2005-09-01
期刊：
MOLECULAR ECOLOGY NOTES
影响因子：
--
作者：
Boches, PS;Bassil, NV;Rowland, LJ
通讯作者：
Rowland, LJ