Patterns of genomic and phenomic diversity in wine and table grapes.

Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes

Exact Solutions of Augmented GP Equation: Solitons, Droplets and Supersolid

The augmented nonlinear Schr\"odinger equation (ANLSE), describing BEC, with the Lee-Huang-Yang (LHY) correction has exhibited a quantum droplet state, which has found experimental verification. In addition to the droplet, exact kink-antikink and supersolid phases have been recently obtained in different parameter domains. Interestingly, these solutions are associated with a constant background, unlike the form of BEC in quasi-one dimension, where dark, bright, and grey solitons have been experimentally obtained. Here, we connect a wide class of solutions of the ANLSE with the Jacobi elliptic functions using a fractional transformation method in a general scenario. The conserved energy and momentum are obtained in this general setting which differentiates and characterizes the different phases of the solution space. We then concentrate on the Jacobi-elliptic $dn(x, m^2)$ function, as the same is characterized by a non-vanishing background as compared to the other $cn$ and $sn$ functions.Comment: 10 pages, two figure

Probabilistic Neural Network based Approach for Handwritten Character Recognition

In this paper, recognition system for totally unconstrained handwritten characters for south Indian language of Kannada is proposed. The proposed feature extraction technique is based on Fourier Transform and well known Principal Component Analysis (PCA). The system trains the appropriate frequency band images followed by PCA feature extraction scheme. For subsequent classification technique, Probabilistic Neural Network (PNN) is used. The proposed system is tested on large database containing Kannada characters and also tested on standard COIL-20 object database and the results were found to be better compared to standard techniques

Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Indexación: Web of Science; PubMedBackground Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6–8 mm berries (B68) phenological stages. Results A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0789-

Genetic structure and domestication history of the grape

The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germ-plasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity

Genetic structure and differentiation in cultivated fig (Ficus carica L.)

Abstract One hundred ninety-four germplasm accessions of fig representing the four fig types, Common, Smyrna, San Pedro, and Caprifig were analyzed for genetic diversity, structure, and differentiation using genetic polymorphism at 15 microsatellite loci. The collection showed considerable polymorphism with observed number of alleles per locus ranging from four for five different loci, MFC4, LMFC14, LMFC22, LMFC31 and LMFC35 to nine for LMFC30 with an average of 4.9 alleles per locus. Seven of the 15 loci included in the genetic structure analyses exhibited significant deviation from panmixia, of which two showed excess and five showed deficiency of heterozygote. The cluster analysis (CA) revealed ten groups with 32 instances of synonymy among cultivars and groups differed significantly for frequency and composition of alleles for different loci. The principal components analysis (PCA) confirmed the results of CA with some groups more differentiated than the others. Further, the model based Bayesian approach clustering suggested a subtle population structure with mixed ancestry for most figs. The gene diversity analysis indicated that much of the total variation is found within groups (H G /H T = 0.853; 85.3%) and the among groups within total component (G GT = 0.147) accounted for the remaining 14.7%, of which *64% accounted for among groups within clusters (G GC = 0.094) and *36% among clusters (G CT = 0.053). The analysis of molecular variance (AMOVA) showed approximately similar results with nearly 87% of variation within groups and *10% among groups within clusters, and *3% among clusters. Overall, the gene pool o

Teleportation of quantum coherence

We investigate whether it is possible to teleport the coherence of an unknown quantum state from Alice to Bob by communicating a smaller number of classical bits in comparison to what is required for teleporting an unknown quantum state. We find that we cannot achieve perfect teleportation of coherence with one bit of classical communication for an arbitrary qubit. However, we find that if the qubit is partially known, i.e., chosen from the equatorial and polar circles of the Bloch sphere, then teleportation of coherence is possible with the transfer of one cbit of information when we have maximally entangled states as a shared resource. In the case of the resource being a nonmaximally entangled state, we can teleport the coherence with a certain probability of success. In a general teleportation protocol for coherence, we derive a compact formula for the final state at Bob's laboratory in terms of the composition of the completely positive maps corresponding to the shared resource state and a joint positive operator-valued measure (POVM) performed by Alice on her qubit and the unknown state. Using this formula, we show that teleportation of the coherence of a partially known state with real matrix elements is perfectly possible with the help of a maximally entangled state as a resource. Furthermore, we explore the teleportation of coherence with Werner states and show that even when Werner states become separable, the amount of teleported coherence is nonzero, implying the possibility of teleportation of coherence without entanglement

Nanooptics of molecular-shunted plasmonic nanojunctions.

Gold nanoparticles are separated above a planar gold film by 1.1 nm thick self-assembled molecular monolayers of different conductivities. Incremental replacement of the nonconductive molecules with a chemically equivalent conductive version differing by only one atom produces a strong 50 nm blue-shift of the coupled plasmon. With modeling this gives a conductance of 0.17G(0) per biphenyl-4,4'-dithiol molecule and a total conductance across the plasmonic junction of 30G(0). Our approach provides a reliable tool quantifying the number of molecules in each plasmonic hotspot, here <200.We acknowledge financial support from EPSRC grant EP/ G060649/1, EP/I012060/1, EP/L027151/1, EP/K028510/1, ERC grant LINASS 320503. F.B. acknowledges support from the Winton Programme for the Physics of Sustainability. C.T. and J.A. acknowledge financial support from Project FIS2013- 41184-P from MINECO, ETORTEK 2014-15 of the Basque Department of Industry and IT756-13 from the Basque consolidated groups.This paper was originally published in Nano Letters under a CC-BY licence (F Benz, C Tserkezis, LO Herrmann, B de Nijs, A Sanders, DO Sigle, L Pukenas, SD Evans, J Aizpurua, JJ Baumberg, Nano Letters 2015, 15, 669−674