Generation and analysis of ESTs from strawberry (Fragaria xananassa) fruits and evaluation of their utility in genetic and molecular studies

Abstract

BackgroundCultivated 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.ResultsWe 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.ConclusionsThe 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.

An R2R3-MYB Transcription Factor Regulates Eugenol Production in Ripe Strawberry Fruit Receptacles

“…We compared the cDNA sequences contained in Kevin Folta's libraries (Shulaev et al, 2011) with our own previously obtained cDNA libraries (Bombarely et al, 2010). The percentage identity between the cDNA sequences from F. ananassa and those from F. vesca was always over 98.6% and similar to that found previously (Bombarely et al, 2010).…”

“…The percentage identity between the cDNA sequences from F. ananassa and those from F. vesca was always over 98.6% and similar to that found previously (Bombarely et al, 2010). Therefore, we decided to generate a custom-made oligonucleotide-based (60-mer length) microarray platform containing a total of 34,187 singletons corresponding to those sequences published in the Strawberry Genome Project (https://strawberry.…”

Effect of ethylene treatment on phytochemical and ethylene-related gene expression during ripening in strawberry fruit Fragaria x ananassa cv. Camino Real

“…Gene-specific primer sequences were as follows: FaERF2 (Bombarely et al, 2010), FaACO1 (forward: 5'-TGCTTTTGTTGCGAAATCAG-3'; reverse: 5'-ACCAAGTCCACTTCCAC CAG-3'). Primers specific for actin (Chai et al, 2011;Sun et al, 2013) and the intergenic region 26S-18S (Cumplido-Laso et al, 2012) were used as internal standards.…”

“…ETR and ERS encode the first subfamily of ethylene receptor proteins (ETR), which are located in the membrane of endoplasmic reticulum (Shakeel et al, 2013). ERF encodes an ethylene response transcription factor, which is located in the nucleus, and ACC oxidase, coded by ACO, is a cytosolic enzyme that converts 1-aminocyclopropane-1-carboxylic acid (ACC) to yield ethylene and CO 2 (Trainotti et al, 2005;Bombarely et al, 2010;Zhao and Guo, 2011).…”

Gene mining a marama bean expressed sequence tags (ESTs) database: Embryonic seed development genes and microsatellite marker identification

“…Takundwa et al (2010) stated that it is desirable to isolate and characterize more DNA markers in the plant for more productive genetic studies such as genetic mapping, marker associated selection and gene discovery. In a study by Bombarely et al (2010), ESTs were generated and analyzed in the evaluation of Fragaria xananassa at a genetic and molecular level. The analysis of the transcription analysis generated knowledge and molecular tools that would be essential in ongoing breeding programs and had also allowed the development of molecular markers that have been applied to germplasm characterization.…”