Istituto Sperimentale per la Frutticoltura

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

The International Peach Genome Initiative reports the high quality draft genome sequence of peach (Prunus persica). They also resequenced ten additional P. persica accessions, as well as those of Prunus ferganensis, Prunus kansuensis, Prunus davidiana and Prunus mira. Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.

The emergence of agriculture in the Near East also involved the domestication of einkorn wheat. Phylogenetic analysis that was based on the allelic frequency at 288 amplified fragment length polymorphism molecular marker loci indicates that a wild group of Triticum monococcum boeoticum lines from the Karacadağ mountains (southeast Turkey) is the likely progenitor of cultivated einkorn varieties. Evidence from archeological excavations of early agricultural settlements nearby supports the conclusion that domestication of einkorn wheat began near the Karacadağmountains.

BACKGROUND: The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. RESULTS: Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. CONCLUSIONS: The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes.

The effects of salinity on growth, stomatal conductance, photosynthetic capacity, and carbon isotope discrimination (Delta) of Gossypium hirsutum L. and Phaseolus vulgaris L. were evaluated. Plants were grown at different NaCl concentrations from 10 days old until mature reproductive structures were formed. Plant growth and leaf area development were strongly reduced by salinity, in both cotton and bean. Stomatal conductance also was reduced by salinity. The Delta always declined with increasing external salinity concentration, indicating that stomatal limitation of photosynthesis was increased. In cotton plant dry matter, Delta correlated with the ratio of intercellular to atmospheric CO(2) partial pressures (p(l)/p(a)) calculated by gas exchange. This correlation was not clear in bean plants, although Delta showed a more pronounced salt induced decline in bean than in cotton. Possible effects of heterogeneity of stomatal aperture and consequent overestimation of p(l) as determined from gas exchange could explain these results. Significant differences of Delta between leaf and seed material were observed in cotton and bean. This suggests different patterns of carbon allocation between leaves and seeds. The photon yield of O(2) evolution determined at rate-limiting photosynthetic photon flux density was insensitive to salinity in both species analyzed. The light- and CO(2)-saturated rate of CO(2) uptake and O(2) evolution showed a salt induced decline in both species. Possible explanations of this observation are discussed. O(2) hypersensitivity was observed in salt stressed cotton plants. These results clearly demonstrate that the effect of salinity on assimilation rate was mostly due to the reduction of stomatal conductance, and that calculation of p(l) may be overestimated in salt stressed plants, because of heterogeneity of stomatal aperture over the leaf surface.

In all, 4379 isolates from 35 products, including 24 artisanal cheeses, were surveyed with a view to identifying strains that could be used as starters in commercial dairy fermentations. Of the isolates, 38% were classified as Lactococcus , 17% as Enterococcus , 14% as Streptococcus thermophilus , 12% as mesophilic Lactobacillus , 10% as Leuconostoc and 9% as thermophilic Lactobacillus . Acid production by the isolates varied considerably. Of the 1582 isolates of Lactococcus and 482 isolates of mesophilic Lactobacillus tested, only 8 and 2% respectively produced sufficient acid to lower the pH of milk to <5·3 in 6 h at 30°C. In contrast, 53, 32 and 13% of Str. thermophilus , thermophilic Lactobacillus and Enterococcus isolates respectively reduced the pH to 5·3. These isolates were found only in some French, Italian and Greek cheeses. Bacteriocins were produced by 11% of the 2257 isolates tested and 26 of them produced broad-spectrum bacteriocins which inhibited at least eight of the ten target strains used, which included lactic acid bacteria, clostridia and Listeria innocua . The most proteolytic of the 2469 isolates tested were Str. thermophilus from Fontina cheese followed by Enterococcus from Fiore Sardo and Toma cheese and thermophilic Lactobacillus from all sources. Exopolysaccharides were produced by 5·3% of the 2224 isolates tested.

Numerous volatile organic compounds (VOCs) exist in Earth's atmosphere, most of which originate from biogenic emissions. Despite VOCs' critical role in tropospheric chemistry, studies for evaluating their atmosphere-ecosystem exchange (emission and deposition) have been limited to a few dominant compounds owing to a lack of appropriate measurement techniques. Using a high-mass resolution proton transfer reaction-time of flight-mass spectrometer and an absolute value eddy-covariance method, we directly measured 186 organic ions with net deposition, and 494 that have bidirectional flux. This observation of active atmosphere-ecosystem exchange of the vast majority of detected VOCs poses a challenge to current emission, air quality, and global climate models, which do not account for this extremely large range of compounds. This observation also provides new insight for understanding the atmospheric VOC budget.

The effectiveness of chitosan fruit coating to delay the qualitative and nutraceutical traits of three strawberry cultivars, namely "Candonga", "Jonica" and "Sabrina", as well as the effects of chitosan on antioxidant enzymes were evaluated. The fruits were coated with 1% and 2% chitosan solution and stored at 2 °C for nine days. Samples were taken every three days. Physico-chemical (weight loss, soluble solid content and titratable acidity) and nutraceutical (total polyphenol, anthocyanin, flavonoid, ascorbic acid content and antioxidant capacity) properties along with the enzymatic activity (catalase (CAT), ascorbate peroxidase (APX), polyphenol oxidase (PPO), guaiacol peroxidase (GPX) and lipoxygenase (LOX)) were evaluated. Chitosan treatment significantly reduced water loss and delayed the qualitative changes in color, titratable acidity and ascorbic acid content in dose- and cultivar-dependent manners. Additionally, changes in the total polyphenol, anthocyanin and flavonoid contents and the antioxidant capacity of chitosan-coated strawberry fruits were delayed. Chitosan coating enhanced the activity of some antioxidant enzymes, preventing flesh browning and reducing membrane damage. A global view of the responses of the three strawberry cultivars to chitosan coating and storage temperature was obtained using principal component analysis. Chitosan-coated fruit exhibited a slower rate of deterioration, compared to uncoated fruit in all tested cultivars.

The endoplasmic reticulum (ER) is an important site for protein folding and becomes "stressed" when its capacity to fold proteins is overwhelmed. In response, "unfolded protein response" (UPR) genes are induced, increasing the capacity to fold proteins; if the response is insufficient, then apoptosis ensues. For investigation of whether proteinuria and hyperglycemia induce ER stress in renal epithelial cells, microarray data from biopsies of established diabetic nephropathy (DN) were analyzed. Expression of UPR genes was significantly different in these biopsies than in control kidneys or biopsies of patients with mild DN, suggesting an association between the degree of DN and UPR gene expression. Expression of the transcription factor XBP1 and the ER chaperones HSPA5 and HYOU1 were increased, but the proapoptotic gene DDIT3 was unchanged. These findings were replicated in an independent cohort of patients with established DN by real-time reverse transcriptase-PCR. Immunofluorescence of renal biopsies from patients with DN confirmed the upregulation for HSPA5 and HYOU1 proteins in tubular epithelia. In biopsies of minimal-change disease, the mRNA levels of some ER stress molecules were also induced, but protein expression of HSPA5 and HYOU1 remained significantly lower than that observed in DN. Exposure of renal tubular epithelial cells to albumin and high glucose in vitro enhanced expression of genes involved in ER stress. These observations suggest that in proteinuric diseases, tubular epithelial cells undergo ER stress, which induces an adaptive, protective UPR. Although this may protect the cells from ER stress, persistence of hyperglycemia and proteinuria may eventually lead to apoptosis.

ABSTRACT Static magnetic fields with intensities starting from 6 gauss (6×10 −4 tesla, T) were found to decrease in an intensity‐dependent fashion, reaching a plateau at 6 × 10 −3 T, the extent of cell death by apoptosis induced by several agents in different human cell systems. This is not due to a change in the mode of cell death (i.e., to necrosis) or to a delay of the process itself; rather, the presence of magnetic fields allows the indefinite survival and replication of the cells hit by apoptogenic agents. The protective effect was found to be mediated by the ability of the fields to enhance Ca 2+ influx from the extracellular medium; accordingly, it was limited to those cell systems where Ca 2+ influx was shown to have an antiapoptotic effect. Magnetic fields thus might interfere with human health by altering/restoring the equilibrium between cell death and proliferation; indeed, the rescue of damaged cells may be the mechanism explaining why magnetic fields that are not mutagenic per se are often able to increase mutation and tumor frequencies.—Fanelli, C., Coppola, S., Barone, R., Colussi, C., Gualandi, G., Volpe, P., Ghibelli, L. Magnetic fields increase cell survival by inhibiting apoptosis via modulation of Ca 2+ influx. FASEB J. 13, 95–102 (1999)

BACKGROUND: Apparent Amylose Content (AAC), regulated by the Waxy gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited. RESULTS: In this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125 japonica ssp. and 2 indica ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the Waxy gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers. CONCLUSIONS: The addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the waxy locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the Wxa and Wxb alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection.

The origin of modern wheats involved alloploidization among related genomes. To determine if Aegilops speltoides was the donor of the B and G genomes in AABB and AAGG tetraploids, we used a 3-tiered approach. Using 70 amplified fragment length polymorphism (AFLP) loci, we sampled molecular diversity among 480 wheat lines from their natural habitats encompassing all S genome Aegilops, the putative progenitors of wheat B and G genomes. Fifty-nine Aegilops representatives for S genome diversity were compared at 375 AFLP loci with diploid, tetraploid, and 11 nulli-tetrasomic Triticum aestivum wheat lines. B genome-specific markers allowed pinning the origin of the B genome to S chromosomes of A. speltoides, while excluding other lineages. The outbreeding nature of A. speltoides influences its molecular diversity and bears upon inferences of B and G genome origins. Haplotypes at nuclear and chloroplast loci ACC1, G6PDH, GPT, PGK1, Q, VRN1, and ndhF for approximately 70 Aegilops and Triticum lines (0.73 Mb sequenced) reveal both B and G genomes of polyploid wheats as unique samples of A. speltoides haplotype diversity. These have been sequestered by the AABB Triticum dicoccoides and AAGG Triticum araraticum lineages during their independent origins.

BACKGROUND: Carotenoids are plant metabolites which are not only essential in photosynthesis but also important quality factors in determining the pigmentation and aroma of flowers and fruits. To investigate the regulation of carotenoid metabolism, as related to norisoprenoids and other volatile compounds in peach (Prunus persica L. Batsch.), and the role of carotenoid dioxygenases in determining differences in flesh color phenotype and volatile composition, the expression patterns of relevant carotenoid genes and metabolites were studied during fruit development along with volatile compound content. Two contrasted cultivars, the yellow-fleshed 'Redhaven' (RH) and its white-fleshed mutant 'Redhaven Bianca' (RHB) were examined. RESULTS: The two genotypes displayed marked differences in the accumulation of carotenoid pigments in mesocarp tissues. Lower carotenoid levels and higher levels of norisoprenoid volatiles were observed in RHB, which might be explained by differential activity of carotenoid cleavage dioxygenase (CCD) enzymes. In fact, the ccd4 transcript levels were dramatically higher at late ripening stages in RHB with respect to RH. The two genotypes also showed differences in the expression patterns of several carotenoid and isoprenoid transcripts, compatible with a feed-back regulation of these transcripts. Abamine SG - an inhibitor of CCD enzymes - decreased the levels of both isoprenoid and non-isoprenoid volatiles in RHB fruits, indicating a complex regulation of volatile production. CONCLUSIONS: Differential expression of ccd4 is likely to be the major determinant in the accumulation of carotenoids and carotenoid-derived volatiles in peach fruit flesh. More in general, dioxygenases appear to be key factors controlling volatile composition in peach fruit, since abamine SG-treated 'Redhaven Bianca' fruits had strongly reduced levels of norisoprenoids and other volatile classes. Comparative functional studies of peach carotenoid cleavage enzymes are required to fully elucidate their role in peach fruit pigmentation and aroma.

Abstract I. Introduction 218 II. Quality Improvement 219 III. Grape and Wine Polyphenols 220 IV. Mass Spectrometry in the Study of Polyphenols and Procyanidins 222 V. Mass Spectrometry in the Study of Anthocyanins and their Derivatives 229 VI. Mass Spectrometry in the Study of Structures Formed by Polymerization of Anthocyanins and Flavan‐3‐ols 234 VII. Mass Spectrometry and Grape and Wine Resveratrol 240 VIII. Application of MALDI in the Study of Polyphenols 243 IX. Mass Spectrometry Applied to the Study of Wine Polyphenols from Cork Bottle Stoppers and Oak Barrels 245 X. Conclusions 246 References 247 Mass spectrometry, had and still has, a very important role for research and quality control in the viticulture and enology field, and its analytical power is relevant for structural studies on aroma and polyphenolic compounds. Polyphenols are responsible for the taste and color of wine, and confer astringency and structure to the beverage. The knowledge of the anthocyanic structure is very important to predict the aging attitude of wine, and to attempt to resolve problems about color stability. Moreover, polyphenols are the main compounds related to the benefits of wine consumption in the diet, because of their properties in the treatment of circulatory disorders such as capillary fragility, peripheral chronic venous insufficiency, and microangiopathy of the retina. Liquid Chromatography‐Mass Spectrometry (LC‐MS) techniques are nowadays the best analytical approach to study polyphenols in grape extracts and wine, and are the most effective tool in the study of the structure of anthocyanins. The MS/MS approach is a very powerful tool that permits anthocyanin aglycone and sugar moiety characterization. LC‐MS allows the characterization of complex structures of grape polyphenols, such as procyanidins, proanthocyanidins, prodelphinidins, and tannins, and provides experimental evidence for structures that were previously only hypothesized. The matrix‐assisted‐laser‐desorption‐ionization‐time‐of‐flight (MALDI‐TOF) technique is suitable to determine the presence of molecules of higher molecular weight with high accuracy, and it has been applied with success to study procyanidin oligomers up to heptamers in the reflectron mode, and up to nonamers in the linear mode. The levels of resveratrol in wine, an important polyphenol well‐known for its beneficial effects, have been determined by SPME and LC‐MS, and the former approach led to the best results in terms of sensitivity. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 22:218–250, 2003; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/mas.10052

International audience

A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.

In autumn 2013, the presence of Xylella fastidiosa, a xylem-limited Gram-negative bacterium, was detected in olive stands of an area of the Ionian coast of the Salento peninsula (Apulia, southern Italy), that were severely affected by a disease denoted olive quick decline syndrome (OQDS). Studies were carried out for determining the involvement of this bacterium in the genesis of OQDS and of the leaf scorching shown by a number of naturally infected plants other than olive. Isolation in axenic culture was attempted and assays were carried out for determining its pathogenicity to olive, oleander and myrtle-leaf milkwort. The bacterium was readily detected by quantitative polymerase chain reaction (qPCR) in all diseased olive trees sampled in different and geographically separated infection foci, and culturing of 51 isolates, each from a distinct OQDS focus, was accomplished. Needle-inoculation experiments under different environmental conditions proved that the Salentinian isolate De Donno belonging to the subspecies pauca is able to multiply and systemically invade artificially inoculated hosts, reproducing symptoms observed in the field. Bacterial colonization occurred in prick-inoculated olives of all tested cultivars. However, the severity of and timing of symptoms appearance differed with the cultivar, confirming their differential reaction.

We studied the effect of salinity on amino acid, proline and glycine betaine accumulation in leaves of different stages of development in durum wheat under high and low nitrogen supply. Our results suggest that protective compounds against salt stress are accumulated in all leaves. The major metabolites are glycine betaine, which preferentially accumulates in younger tissues, and proline, which is found predominantly in older tissues. Proline tended to accumulate early, at the onset of the stress, while glycine betaine accumulation was observed during prolonged stress. Nitrate reductase (NR) and glutamate synthase (GOGAT) are positively correlated with these compatible solutes: proline is associated with NR in the oldest leaves of high-nitrate plants and glycine betaine is associated with GOGAT in the youngest leaves of both low- and high-nitrate plants. In high-nitrate conditions proline accounts for more than 39% of the osmotic adjustment in the cytoplasmic compartments of old leaves. Its nitrogen-dependent accumulation may offer an important advantage in that it can be metabolised to allow reallocation of energy, carbon and nitrogen from the older leaves to the younger tissues. The contribution of glycine betaine is higher in young leaves and is independent of nitrogen nutrition.

Abstract Predicting sediment yield at the catchment scale is one of the main challenges in geomorphologic research. The application of both physics‐based models and regression models has until now not provided very satisfying results for prediction of sediment yield for medium to large sized catchments ( c . >50 km 2 ). The explanation for this lies in a combination of the large data requirements of most models and a lack of knowledge to describe all processes and process interactions at the catchment scale. In particular, point sources of sediment (e.g. gullies, mass movements), connectivity and sediment transport remain difficult to describe in most models. From reservoir sedimentation data of 44 Italian catchments, it appeared that there was a (non‐significant) positive relation between catchment area and sediment yield. This is in contrast to what is generally expected from the theory of decreasing sediment delivery rates with increasing catchment area. Furthermore, this positive relation suggests that processes other than upland erosion are responsible for catchment sediment yield. Here we explore the potential of the Factorial Scoring Model (FSM) and the Pacific Southwest Interagency Committee (PSIAC) model to predict sediment yield, and indicate the most important sediment sources. In these models different factors are used to characterize a drainage basin in terms of sensitivity to erosion and connectivity. In both models an index is calculated that is related to sediment yield. The FSM explained between 36 and 61 per cent of the variation in sediment yield, and the PSIAC model between 57 and 62 per cent, depending on the factors used to characterize the catchments. The FSM model performed best based on a factor to describe gullies , lithology , landslides , catchment shape and vegetation . Topography and catchment area did not explain additional variance. In particular, the addition of the landslide factor resulted in a significantly increased model performance. The FSM and PSIAC model both performed better than a spatially distributed model describing water erosion and sediment transport, which was applied to the same catchments but explained only between 20 and 51 per cent of the variation in sediment yield. Model results confirmed the hypothesis that processes other than upland erosion are probably responsible for sediment yield in the Italian catchments. A promising future development of the models is by the use of detailed spatially distributed data to determine the scores, decrease model subjectivity and provide spatially distributed output. Copyright © 2006 John Wiley & Sons, Ltd.

Pigments are essential to the life of all living organisms. Animals and plants have been the subjects of basic and applied research with the aim of determining the basis of the accumulation and physiological roles of pigments. In crop species, the edible organs show large variations in colour. In durum wheat grain, which is a staple food for humans, the colour is mainly due to two natural classes of pigment: carotenoids and anthocyanins. The carotenoids provide the yellow pigmentation of the durum wheat endosperm, and consequently of the semolina, which has important implications for the marketing of end products based on durum wheat. Anthocyanins accumulate in the aleurone or pericarp of durum wheat and provide the blue, purple and red colours of the grain. Both the carotenoids and the anthocyanins are known to provide benefits for human health, in terms of decreased risks of certain diseases. Therefore, accumulation of these pigments in the grain represents an important trait in breeding programs aimed at improving the nutritional value of durum wheat grain and its end products. This review focuses on the biochemical and genetic bases of pigment accumulation in durum wheat grain, and on the breeding strategies aimed at modifying grain colour.