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

<p>Abstract</p> <p>Background</p> <p>Cultivated strawberry is a hybrid octoploid species (<it>Fragaria xananassa </it>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 <it>Fragaria vesca</it>. 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.</p> <p>Results</p> <p>We have sequenced over 4,500 ESTs from <it>Fragaria xananassa</it>, thus doubling the number of ESTs available in the GenBank of this species. We then assembled this information together with that available from <it>F. xananassa </it>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 <it>F. xananassa </it>and <it>F. vesca</it>, 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.</p> <p>Conclusions</p> <p>The present study generates essential knowledge and molecular tools that will be useful in improving investigations at the molecular level in cultivated strawberry (<it>F. xananassa</it>). 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.</p

Regulation of L-ascorbic acid content in strawberry fruits

Plants have several L-ascorbic acid (AsA) biosynthetic pathways, but the contribution of each one to the synthesis of AsA varyies between different species, organs, and developmental stages. Strawberry (Fragaria×ananassa) fruits are rich in AsA. The pathway that uses D-galacturonate as the initial substrate is functional in ripe fruits, but the contribution of other pathways to AsA biosynthesis has not been studied. The transcription of genes encoding biosynthetic enzymes such as D-galacturonate reductase (FaGalUR) and myo-inositol oxygenase (FaMIOX), and the AsA recycling enzyme monodehydroascorbate reductase (FaMDHAR) were positively correlated with the increase in AsA during fruit ripening. Fruit storage for 72 h in a cold room reduced the AsA content by 30%. Under an ozone atmosphere, this reduction was 15%. Ozone treatment increased the expression of the FaGalUR, FaMIOX, and L-galactose-1-phosphate phosphatase (FaGIPP) genes, and transcription of the L-galactono-1,4-lactone dehydrogenase (FaGLDH) and FAMDHAR genes was higher in the ozone-stored than in the air-stored fruits. Analysis of AsA content in a segregating population from two strawberry cultivars showed high variability, which did not correlate with the transcription of any of the genes studied. Study of GalUR protein in diverse cultivars of strawberry and different Fragaria species showed that a correlation between GalUR and AsA content was apparent in most cases, but it was not general. Three alleles were identified in strawberry, but any sequence effect on the AsA variability was eliminated by analysis of the allele-specific expression. Taken together, these results indicate that FaGalUR shares the control of AsA levels with other enzymes and regulatory elements in strawberry fruit

DNA test for predicting mesifurane and gamma-decalactone in strawberry fruits

En este documento se describe la metodolog&iacute;a a seguir para la identificaci&oacute;n de dos compuestos aromaticos (mesifurano y gama -decalactona) directamente&nbsp;implicados en el sabor de los frutos de fresa.</p

Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses

Abstract Background Understanding the basis for volatile organic compound (VOC) biosynthesis and regulation is of great importance for the genetic improvement of fruit flavor. Lactones constitute an essential group of fatty acid-derived VOCs conferring peach-like aroma to a number of fruits including peach, plum, pineapple and strawberry. Early studies on lactone biosynthesis suggest that several enzymatic pathways could be responsible for the diversity of lactones, but detailed information on them remained elusive. In this study, we have integrated genetic mapping and genome-wide transcriptome analysis to investigate the molecular basis of natural variation in γ-decalactone content in strawberry fruit. Results As a result, the fatty acid desaturase FaFAD1 was identified as the gene underlying the locus at LGIII-2 that controls γ-decalactone production in ripening fruit. The FaFAD1 gene is specifically expressed in ripe fruits and its expression fully correlates with the presence of γ-decalactone in all 95 individuals of the mapping population. In addition, we show that the level of expression of FaFAH1, with similarity to cytochrome p450 hydroxylases, significantly correlates with the content of γ-decalactone in the mapping population. The analysis of expression quantitative trait loci (eQTL) suggests that the product of this gene also has a regulatory role in the biosynthetic pathway of lactones. Conclusions Altogether, this study provides mechanistic information of how the production of γ-decalactone is naturally controlled in strawberry, and proposes enzymatic activities necessary for the formation of this VOC in plants.This work was supported by the Spanish Ministry of Economy and Competitivity and FEDER (grant numbers AGL2012-40066, BIO2010-15630), the EUBerry Project (EU FP7 KBBE–2010-4 Grant Agreement number 265942) and by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme to I.A (IOF Flavor 328052).Peer Reviewe

Identification of quantitative trait loci and candidate genes for primary metabolite content in strawberry fruit

Selective breeding: The genetic basis of better strawberries Investigations have yielded early insights into the genetic basis of strawberry taste and nutrition. Such information informs efforts to selectively breed the fruit to maximize these qualities. A team of researchers from Spain and Germany, led by the University of Malaga’s Sonia Osorio and the IFAPA´s Iraida Amaya, found 133 locations within strawberry DNA that correlated to variation in metabolic pathways and desirable traits including acidity, sugar content, and the concentration of l-ascorbic acid (vitamin C). Only a small number of associations persisted over the 2 years of investigations, suggesting that environmental factors also wield a significant influence over the strawberry fruit’s molecular makeup. The team then used their data to identify a series of candidate genes that may be functionally linked to strawberry qualities; however, further research is needed to validate those connections