Genetic relationships and introgression events between wild and cultivated grapevines (Vitis vinifera L.): focus on Italian Lambruscos.

Research efforts on genomic structure and ecology of wild populations of Vitis vinifera L. offer insights on grape domestication processes and on the assortment evolution of the cultivated forms. Attention is also paid to the origin of traditional, long-cultivated varieties, often producing renowned and valuable wines. The genetic relationships between 283 Vitis vinifera cultivated varieties (subsp. sativa) and 65 individuals from 9 populations of the sylvestris subspecies mainly from northern Italy were explored by means of molecular markers (27 nuclear and 4 chloroplastic microsatellites). Several episodes of contamination of the wild germplasm by the pollen of specific grape cultivars were detected, implying concern for maintaining the purity of the wild form. At the same time, events of introgression from the wild subspecies resulted playing a crucial role in the emergence of several cultivated varieties with a clear admixed genome ancestry sativa-sylvestris. These included Lambruscos originated from the flat areas crossed by the Po and Adige rivers in northern Italy, while other cultivars still called Lambrusco but typical of hilly areas did not show the same admixed genome. Historical and ecological evidences suggesting an adaptative recent post-domestication process in the origin of several Italian Lambruscos are discussed.

Application of the split-gradient method to 3D image deconvolution in fluorescence microscopy.

The methods of image deconvolution are important for improving the quality of the detected images in the different modalities of fluorescence microscopy such as wide-field, confocal, two-photon excitation and 4Pi. Because deconvolution is an ill-posed problem, it is, in general, reformulated in a statistical framework such as maximum likelihood or Bayes and reduced to the minimization of a suitable functional, more precisely, to a constrained minimization, because non-negativity of the solution is an important requirement. Next, iterative methods are designed for approximating such a solution. In this paper, we consider the Bayesian approach based on the assumption that the noise is dominated by photon counting, so the likelihood is of the Poisson-type, and that the prior is edge-preserving, as derived from a simple Markov random field model. By considering the negative logarithm of the a posteriori probability distribution, the computation of the maximum a posteriori (MAP) estimate is reduced to the constrained minimization of a functional that is the sum of the Csiszár I-divergence and a regularization term. For the solution of this problem, we propose an iterative algorithm derived from a general approach known as split-gradient method (SGM) and based on a suitable decomposition of the gradient of the functional into a negative and positive part. The result is a simple modification of the standard Richardson-Lucy algorithm, very easily implementable and assuring automatically the non-negativity of the iterates. Next, we apply this method to the particular case of confocal microscopy for investigating the effect of several edge-preserving priors proposed in the literature using both synthetic and real confocal images. The quality of the restoration is estimated both by computation of the Kullback-Leibler divergence of the restored image from the detected one and by visual inspection. It is observed that the noise artefacts are considerably reduced and desired characteristics (edges and minute features as islets) are retained in the restored images. The algorithm is stable, robust and tolerant at various noise (Poisson) levels. Finally, by remarking that the proposed method is essentially a scaled gradient method, a possible modification of the algorithm is briefly discussed in view of obtaining fast convergence and reduction in computational time.

Experimental validation of a linear model for data reduction in chirp-pulse microwave CT.

Chirp-pulse microwave computerized tomography (CP-MCT) is an imaging modality developed at the Department of Biocybernetics, University of Niigata (Niigata, Japan), which intends to reduce the microwave-tomography problem to an X-ray-like situation. We have recently shown that data acquisition in CP-MCT can be described in terms of a linear model derived from scattering theory. In this paper, we validate this model by showing that the theoretically computed response function is in good agreement with the one obtained from a regularized multiple deconvolution of three data sets measured with the prototype of CP-MCT. Furthermore, the reliability of the model as far as image restoration in concerned, is tested in the case of space-invariant conditions by considering the reconstruction of simple on-axis cylindrical phantoms.

Image restoration in chirp-pulse microwave CT (CP-MCT).

Chirp-pulse microwave computed tomography (CP-MCT) is a technique for imaging the distribution of temperature variations inside biological tissues. Even if resolution and contrast are adequate to this purpose, a further improvement of image quality is desirable. In this paper, we discuss the blur of CP-MCT images and we propose a method for estimating the corresponding point spread function (PSF). To this purpose we use both a measured and a computed projection of a cylindrical phantom. We find a good agreement between the two cases. Finally the estimated PSF is used for deconvolving data corresponding to various kinds of cylindrical phantoms. We use an iterative nonlinear deconvolution method which assures nonnegative solutions and we demonstrate the improvement of image quality which can be obtained in such a way.

Super-resolution in computational imaging.

Super-resolution is a word used in different contexts but mainly in the case of methods aimed at improving the resolution of an optical instrument beyond the diffraction limit. Such a result may be achieved by means of specific instrumental techniques (such as, for instance, interferometry) or by means of a suitable processing of a digital image; in the latter case we will use the expression computational super-resolution (CSR). In this paper we describe the basic concepts underlying CSR without using the mathematics required for establishing its theoretical validity. The aim is to introduce a wide audience to this topic, to specify the situations where CSR is feasible and to emphasize the point that unlimited CSR is not possible.

Towards real-time image deconvolution: application to confocal and STED microscopy.

Although deconvolution can improve the quality of any type of microscope, the high computational time required has so far limited its massive spreading. Here we demonstrate the ability of the scaled-gradient-projection (SGP) method to provide accelerated versions of the most used algorithms in microscopy. To achieve further increases in efficiency, we also consider implementations on graphic processing units (GPUs). We test the proposed algorithms both on synthetic and real data of confocal and STED microscopy. Combining the SGP method with the GPU implementation we achieve a speed-up factor from about a factor 25 to 690 (with respect the conventional algorithm). The excellent results obtained on STED microscopy images demonstrate the synergy between super-resolution techniques and image-deconvolution. Further, the real-time processing allows conserving one of the most important property of STED microscopy, i.e the ability to provide fast sub-diffraction resolution recordings.

Bayesian denoising in digital radiography: a comparison in the dental field.

We compared two Bayesian denoising algorithms for digital radiographs, based on Total Variation regularization and wavelet decomposition. The comparison was performed on simulated radiographs with different photon counts and frequency content and on real dental radiographs. Four different quality indices were considered to quantify the quality of the filtered radiographs. The experimental results suggested that Total Variation is more suited to preserve fine anatomical details, whereas wavelets produce images of higher quality at global scale; they also highlighted the need for more reliable image quality indices.

'Cardinal' grape parentage: a case of a breeding mistake.

The grapevine (Vitis vinifera L.) is one of the most widely grown fruit plants, with table grapes accounting for at least 20% of the total world production. A few traditional table grape cultivars have achieved great international prominence. Among the most important cultivars is 'Cardinal', a historical Californian grapevine obtained by E. Snyder and F. Harmon in 1939 by crossing 'Flame Tokay' (syn. 'Ahmer Bou Amer') with 'Ribier' (syn. 'Alphonse Lavallée') at the Horticultural Field Station of Fresno, Calif.. In the course of DNA typing grapevine varieties collected in Algeria and other Mediterranean countries, we found, surprisingly, that 'Cardinal'could not result from this cross. Here, we present molecular genetic evidence that 'Cardinal' has no parentage relationship with 'Flame Tokay'. We also show, for the first time, that 'Flame Tokay' is a mutant version, at the VVS5 microsatellite locus, of the table grape 'Ahmer Bou Amer', which is considered its synonym.

DNA typing and genetic relations among European hazelnut (Corylus avellana L.) cultivars using microsatellite markers.

In this work, 78 hazelnut (Corylus avellana L.) cultivars from various germplasm repositories were studied at 16 simple sequence repeat (SSR) loci in order to identify the genotypes and investigate their genetic relations. Polymorphism at SSR loci was evaluated on the basis of number of alleles (mean: 9.4), expected heterozygosity (mean: 0.78), and power of discrimination (mean: 0.91). Several synonyms reported in the literature were confirmed, and new cases of synonymy were identified. The parentage of North American cultivars 'Butler', 'Ennis', and 'Royal', the French selection 'Fercoril-Corabel', and 'Impératrice Eugenie' was investigated on the basis of the alleles present at 16 loci and analysis at 8 additional loci. A dendrogram generated from cluster analysis using the unweighted pair group method with arithmetic mean grouped cultivars according to their pedigrees or geographical origins. There was an evident differentiation of the northern European cultivars from the southern European ones and from the Turkish cultivars. The latter clustered close to but separate from the Italian and Spanish clusters. It is very likely that exchanges of cultivars occurred between the central and western Mediterranean basin as a result of human migration and trade. A database containing the SSR profiles of the most important hazelnut cultivars will be useful for identification of cultivars and synonyms, legal protection, and parentage analysis.

Development of a standard set of microsatellite reference alleles for identification of grape cultivars.

In order to investigate the comparability of microsatellite profiles obtained in different laboratories, ten partners in seven countries analyzed 46 grape cultivars at six loci (VVMD5, VVMD7, VVMD27, VVS2, VrZAG62, and VrZAG79). No effort was made to standardize equipment or protocols. Although some partners obtained very similar results, in other cases different absolute allele sizes and, sometimes, different relative allele sizes were obtained. A strategy for data comparison by means of reference to the alleles detected in well-known cultivars was proposed. For each marker, each allele was designated by a code based on the name of the reference cultivar carrying that allele. Thirty-three cultivars, representing from 13 to 23 alleles per marker, were chosen as references. After the raw data obtained by the different partners were coded, more than 97% of the data were in agreement. Minor discrepancies were attributed to errors, suboptimal amplification and visualization, and misscoring of heterozygous versus homozygous allele pairs. We have shown that coded microsatellite data produced in different laboratories with different protocols and conditions can be compared, and that it is suitable for the identification and SSR allele characterization of cultivars. It is proposed that the six markers employed here, already widely used, be adopted as a minimal standard marker set for future grapevine cultivar analyses, and that additional cultivars be characterized by means of the coded reference alleles presented here. The complete database is available at http://www.genres.de/eccdb/vitis/ Cuttings of the 33 reference cultivars are available on request from the Institut National de la Recherche Agronomique Vassal collection (didier.vares@ensam.inra.fr).