Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Spain.
BMC Genomics. 2010 Sep 17;11:503. doi: 10.1186/1471-2164-11-503.
Cultivated strawberry is a hybrid octoploid species (Fragaria xananassa Duchesne ex. Rozier) whose fruit is highly appreciated due to its organoleptic properties and health benefits. Despite recent studies on the control of its growth and ripening processes, information about the role played by different hormones on these processes remains elusive. Further advancement of this knowledge is hampered by the limited sequence information on genes from this species, despite the abundant information available on genes from the wild diploid relative Fragaria vesca. However, the diploid species, or one ancestor, only partially contributes to the genome of the cultivated octoploid. We have produced a collection of expressed sequence tags (ESTs) from different cDNA libraries prepared from different fruit parts and developmental stages. The collection has been analysed and the sequence information used to explore the involvement of different hormones in fruit developmental processes, and for the comparison of transcripts in the receptacle of ripe fruits of diploid and octoploid species. The study is particularly important since the commercial fruit is indeed an enlarged flower receptacle with the true fruits, the achenes, on the surface and connected through a network of vascular vessels to the central pith.
We have sequenced over 4,500 ESTs from Fragaria xananassa, thus doubling the number of ESTs available in the GenBank of this species. We then assembled this information together with that available from F. xananassa resulting a total of 7,096 unigenes. The identification of SSRs and SNPs in many of the ESTs allowed their conversion into functional molecular markers. The availability of libraries prepared from green growing fruits has allowed the cloning of cDNAs encoding for genes of auxin, ethylene and brassinosteroid signalling processes, followed by expression studies in selected fruit parts and developmental stages. In addition, the sequence information generated in the project, jointly with previous information on sequences from both F. xananassa and F. vesca, has allowed designing an oligo-based microarray that has been used to compare the transcriptome of the ripe receptacle of the diploid and octoploid species. Comparison of the transcriptomes, grouping the genes by biological processes, points to differences being quantitative rather than qualitative.
The present study generates essential knowledge and molecular tools that will be useful in improving investigations at the molecular level in cultivated strawberry (F. xananassa). This knowledge is likely to provide useful resources in the ongoing breeding programs. The sequence information has already allowed the development of molecular markers that have been applied to germplasm characterization and could be eventually used in QTL analysis. Massive transcription analysis can be of utility to target specific genes to be further studied, by their involvement in the different plant developmental processes.
培育的草莓是一种八倍体杂交种（Fragaria xananassa Duchesne ex. Rozier），因其具有感官特性和健康益处而备受推崇。尽管最近对其生长和成熟过程的控制进行了研究，但关于不同激素在这些过程中所起作用的信息仍然难以捉摸。尽管有关其野生二倍体亲缘种 Fragaria vesca 的基因信息丰富，但由于该物种的基因序列信息有限，因此进一步推进这方面的知识仍受到阻碍。然而，二倍体种或其一个祖先仅部分贡献于栽培八倍体的基因组。我们从不同果实部位和发育阶段制备的不同 cDNA 文库中生成了一批表达序列标签 (EST)。对该文库进行了分析，并利用序列信息来探讨不同激素在果实发育过程中的作用，以及比较二倍体和八倍体种果实成熟时花托中的转录本。该研究非常重要，因为商业果实实际上是一个扩大的花托，其上表面有真正的果实——瘦果，通过维管束网络与中央髓质相连。
我们从 Fragaria xananassa 中测序了超过 4500 个 EST，使该物种在 GenBank 中可用的 EST 数量增加了一倍。然后，我们将这些信息与 Fragaria xananassa 中的信息一起组装，总共得到了 7096 个单基因。许多 EST 中 SSR 和 SNP 的鉴定允许将其转换为功能性分子标记。从绿色生长果实中制备文库的可用性使得可以克隆编码生长素、乙烯和油菜素甾体信号转导过程的基因的 cDNA，然后在选定的果实部位和发育阶段进行表达研究。此外，该项目生成的序列信息，加上以前来自 Fragaria xananassa 和 Fragaria vesca 的序列信息，使得可以设计基于寡核苷酸的微阵列，该微阵列已用于比较二倍体和八倍体种成熟花托的转录组。通过按生物过程对基因进行分组来比较转录组表明，差异是数量上的而不是质量上的。
本研究产生了重要的知识和分子工具，这将有助于提高对栽培草莓（F. xananassa）的分子水平的研究。这些知识可能为正在进行的育种计划提供有用的资源。该序列信息已经允许开发分子标记，这些标记已应用于种质特性描述，并最终可用于 QTL 分析。大规模转录分析可以通过涉及不同植物发育过程来靶向特定基因进行进一步研究。
