Lara Giongo

Molecular genetics and genomics of the Rosoideae: state of the art and future perspectives

The Rosoideae is a subfamily of the Rosaceae that contains a number of species of economic importance, including the soft fruit species strawberry (Fragaria ×ananassa), red (Rubus idaeus) and black (Rubus occidentalis) raspberries, blackberries (Rubus spp.) and one of the most economically important cut flower genera, the roses (Rosa spp.). Molecular genetics and genomics resources for the Rosoideae have developed rapidly over the past two decades, beginning with the development and application of a number of molecular marker types including restriction fragment length polymorphisms, amplified fragment length polymorphisms and microsatellites, and culminating in the recent publication of the genome sequence of the woodland strawberry, Fragaria vesca, and the development of high throughput single nucleotide polymorphism (SNP)-genotyping resources for Fragaria, Rosa and Rubus. These tools have been used to identify genes and other functional elements that control traits of economic importance, to study the evolution of plant genome structure within the subfamily, and are beginning to facilitate genomic-assisted breeding through the development and deployment of markers linked to traits such as aspects of fruit quality, disease resistance and the timing of flowering. In this review, we report on the developments that have been made over the last 20 years in the field of molecular genetics and structural genomics within the Rosoideae, comment on how the knowledge gained will improve the efficiency of cultivar development and discuss how these advances will enhance our understanding of the biological processes determining agronomically important traits in all Rosoideae species.

Characterization of 14 raspberry cultivars by solid-phase microextraction and relationship with gray mold susceptibility.

Fourteen raspberry varieties were evaluated over two cropping seasons by solid-phase microextraction (SPME) followed by gas chromatography-mass spectrometry. Thirty-six compounds were fully identified, and 10 more compounds were tentatively identified. Despite interannual variability, raspberry varieties can be divided in two main groups on the basis of terpenes and C-13 norisoprenoids. Susceptibility toward Botrytis cinerea , one of the most relevant pathogenic fungi for soft fruits during storage, was also evaluated. On the basis of volatile profiles, it was possible to highlight the relationship between different volatile compounds and resistance to B. cinerea. Volatile profiles and Botrytis susceptibility of the different raspberry varieties evaluated should assist future breeding programs.

Monochromatic light increases anthocyanin content during fruit development in bilberry.

BackgroundLight is one of the most significant environmental factors affecting to the accumulation of flavonoids in fruits. The composition of the light spectrum has been shown to affect the production of phenolic compounds during fruit ripening. However, specific information on the biosynthesis of flavonoids in fruits in response to different wavelengths of light is still scarce. In the present study bilberry (Vaccinium myrtillus L.) fruits, which are known to be rich with anthocyanin compounds, were illuminated with blue, red, far-red or white light during the berry ripening process. Following the illumination, the composition of anthocyanins and other phenolic compounds was analysed at the mature ripening stage of fruits.ResultsAll the three monochromatic light treatments had significant positive effect on the accumulation of total anthocyanins in ripe fruits compared to treatment with white light or plants kept in darkness. The elevated levels of anthocyanins were mainly due to a significant increase in the accumulation of delphinidin glycosides. A total of 33 anthocyanin compounds were detected in ripe bilberry fruits, of which six are novel in bilberry (cyanidin acetyl-3-O-galactose, malvidin acetyl-3-O-galactose, malvidin coumaroyl-3-O-galactose, malvidin coumaroyl-3-O-glucose, delphinidin coumaroyl-3-O-galactose, delphinidin coumaroyl-3-O-glucose).ConclusionsOur results indicate that the spectral composition of light during berry development has significant effect on the flavonoid composition of ripe bilberry fruits.

Anthocyanin Profile in Berries of Wild and Cultivated Vaccinium spp. along Altitudinal Gradients in the Alps.

Vaccinium spp. berries provide some of the best natural sources of anthocyanins. In the wild bilberry (Vaccinium myrtillus L.), a clear increasing trend in anthocyanin biosynthesis has been reported toward northern latitudes of Europe, but studies related to altitude have given contradictory results. The present study focused on the anthocyanin composition in wild bilberries and highbush blueberry (Vaccinium corymbosum L. cv. Brigitta Blue) growing along altitudinal gradients in the Alps of northern Italy. Our results indicate an increasing accumulation of anthocyanins in bilberries along an altitudinal gradient of about 650 m. The accumulation was due to a significant increase in delphinidin and malvidin glycosides, whereas the accumulation of cyanidin and peonidin glycosides was not affected by altitude. Seasonal differences, especially temperature, had a major influence on the accumulation of anthocyanins in blueberries.

Soft Fruit Traceability in Food Matrices using Real-Time PCR

Food product authentication provides a means of monitoring and identifying products for consumer protection and regulatory compliance. There is a scarcity of analytical methods for confirming the identity of fruit pulp in products containing Soft Fruit. In the present work we have developed a very sensible qualitative and quantitative method to determine the presence of berry DNAs in different food matrices. To our knowledge, this is the first study that shows the applicability, to Soft Fruit traceability, of melting curve analysis and multiplexed fluorescent probes, in a Real-Time PCR platform. This methodology aims to protect the consumer from label misrepresentation.

Short-term blueberry intake enhances biological antioxidant potential and modulates inflammation markers in overweight and obese children

Oxidative stress and inflammation together play a crucial role in the obesogenic process, and imbalances in reactive oxygen species, free radicals and antioxidants have been reported as being major mechanisms underlying obesity-related co- morbidities. Obesity and oxidative stress may be present even within the first two decades of life, and chronic exposure to systemic inflammation may contribute to the onset and progression of cardiovascular disease and diabetes. Bioactive compounds present in blueberry have been shown to have many positive effects on human health. The present study was carried out in northern Italy on a population of 24 overweight and obese children (8-13 years), divided into three groups: the first consumed fresh blueberries, the second blueberry puree, while a third control group did not consume any blueberries. The childrens anthropometric measures were taken and serum markers related to inflammation, CRP, ceruloplasmin, and complements C3 and C4 were measured during the eight weeks they ate either fresh blueberries or blueberry puree. BAP test (Biological Antioxidant Potential) values of the three groups were monitored throughout the entire study and correlated with inflammatory, metabolic and anthropometric markers. The results showed a higher increase in antioxidant levels in the group that ate fresh berries than in the group that ate puree, while the control groups BAP values decreased over the eight weeks of the study. Our results show that increased consumption of blueberries, hence antioxidant intake, may also have a positive effect on markers of inflammation and oxidative stress in overweight and obese patients during childhood.

Modification of Sunlight Radiation through Colored Photo-Selective Nets Affects Anthocyanin Profile in Vaccinium spp. Berries

Objectives In recent years, the interest on the effects of the specific wavelengths of the light spectrum on growth and metabolism of plants has been increasing markedly. The present study covers the effect of modified sunlight conditions on the accumulation of anthocyanin pigments in two Vaccinium species: the European wild bilberry (V. myrtillus L.) and the cultivated highbush blueberry (V. corymbosum L.). Methods The two Vaccinium species were grown in the same test field in the Alps of Trentino (Northern Italy) under modified light environment. The modification of sunlight radiation was carried out in field, through the use of colored photo-selective nets throughout the berry ripening during two consecutive growing seasons. The anthocyanin profile was then assessed in berries at ripeness. Results The results indicated that the light responses of the two Vaccinium species studied were different. Although both studied species are shade-adapted plants, 90% shading of sunlight radiation was beneficial only for bilberry plants, which accumulated the highest content of anthocyanins in both seasons. The same condition, instead, was not favorable for blueberries, whose maturation was delayed for at least two weeks, and anthocyanin accumulation was significantly decreased compared to berries grown under sunlight conditions. Moreover, the growing season had strong influence on the anthocyanin accumulation in both species, in relation to temperature flow and sunlight spectra composition during the berry ripening period. Conclusions Our results suggest that the use of colored photo-selective nets may be a complementary agricultural practice for cultivation of Vaccinium species. However, further studies are needed to analyze the effect of the light spectra modifications to other nutritional properties, and to elucidate the molecular mechanisms behind the detected differences between the two relative Vaccinium species.

Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin

High throughput arrays for the simultaneous genotyping of thousands of single-nucleotide polymorphisms (SNPs) have made the rapid genetic characterisation of plant genomes and the development of saturated linkage maps a realistic prospect for many plant species of agronomic importance. However, the correct calling of SNP genotypes in divergent polyploid genomes using array technology can be problematic due to paralogy, and to divergence in probe sequences causing changes in probe binding efficiencies. An Illumina Infinium II whole-genome genotyping array was recently developed for the cultivated apple and used to develop a molecular linkage map for an apple rootstock progeny (M432), but a large proportion of segregating SNPs were not mapped in the progeny, due to unexpected genotype clustering patterns. To investigate the causes of this unexpected clustering we performed BLAST analysis of all probe sequences against the ‘Golden Delicious’ genome sequence and discovered evidence for paralogous annealing sites and probe sequence divergence for a high proportion of probes contained on the array. Following visual re-evaluation of the genotyping data generated for 8,788 SNPs for the M432 progeny using the array, we manually re-scored genotypes at 818 loci and mapped a further 797 markers to the M432 linkage map. The newly mapped markers included the majority of those that could not be mapped previously, as well as loci that were previously scored as monomorphic, but which segregated due to divergence leading to heterozygosity in probe annealing sites. An evaluation of the 8,788 probes in a diverse collection of Malus germplasm showed that more than half the probes returned genotype clustering patterns that were difficult or impossible to interpret reliably, highlighting implications for the use of the array in genome-wide association studies.

The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)

Abstract Background The genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. Potentilla micrantha is a species that does not develop berries but shares numerous morphological and ecological characteristics with Fragaria vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca. Findings In this study, the P. micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed. The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the micro-syntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of bench-marking universal single-copy orthologous genes were complete within the presented sequence. Thus, we argue that the majority of the gene-rich regions of the genome have been sequenced. Conclusions Comparisons of RNA-Seq data from the stages of floral and fruit development revealed genes differentially expressed between P. micrantha and F. vesca.The data presented are a valuable resource for future studies of berry development in Fragaria and the Rosaceae and they also shed light on the evolution of genome size and organization in this family.