Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials.

BackgroundMutations often accompany DNA replication. Since there may be fewer cell cycles per year in the germlines of long-lived than short-lived angiosperms, the genomes of long-lived angiosperms may be diverging more slowly than those of short-lived angiosperms. Here we test this hypothesis.ResultsWe first constructed a genetic map for walnut, a woody perennial. All linkage groups were short, and recombination rates were greatly reduced in the centromeric regions. We then used the genetic map to construct a walnut bacterial artificial chromosome (BAC) clone-based physical map, which contained 15,203 exonic BAC-end sequences, and quantified with it synteny between the walnut genome and genomes of three long-lived woody perennials, Vitis vinifera, Populus trichocarpa, and Malus domestica, and three short-lived herbs, Cucumis sativus, Medicago truncatula, and Fragaria vesca. Each measure of synteny we used showed that the genomes of woody perennials were less diverged from the walnut genome than those of herbs. We also estimated the nucleotide substitution rate at silent codon positions in the walnut lineage. It was one-fifth and one-sixth of published nucleotide substitution rates in the Medicago and Arabidopsis lineages, respectively. We uncovered a whole-genome duplication in the walnut lineage, dated it to the neighborhood of the Cretaceous-Tertiary boundary, and allocated the 16 walnut chromosomes into eight homoeologous pairs. We pointed out that during polyploidy-dysploidy cycles, the dominant tendency is to reduce the chromosome number.ConclusionSlow rates of nucleotide substitution are accompanied by slow rates of synteny erosion during genome divergence in woody perennials

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

Improved Dielectric Properties of Epoxy Nano Composites

Epoxy-based nanodielectrics with 2, 5 and 7 wt.% of organically modified montmorillonite clay (oMMT) were prepared using high shear melt mixing technique. The interface of oMMT and epoxy of the nanodielectrics play a very important role in improving electrical, mechanical, thermal and wear properties. Therefore detailed study on the interfacial effects of filler-matrix has been investigated for understanding the chemical bonding using Fourier transform infrared spectroscopy (FTIR) and the cross linking between polymer and filler was studied using glass transition temperature (Tg) through differential scanning calorimetry (DSC). Further, positron annihilation lifetime spectroscopy (PALS) was used to determine precise and accurate value of free volume of the nanodielectrics. The interaction between the nanoparticles and polymer chains has a direct bearing on dielectric strength characteristics of the epoxy-oMMT nanocomposite system and accordingly, the ac dielectric strength of the nanodielectrics increases with the addition of oMMT into epoxy up to 5 wt.% and further increase in filler loading (7 wt.%) causes decrease in ac dielectric strength

Mechanical and Tribological Properties of Epoxy Nano Composites for High Voltage Applications

The tribological and mechanical properties of organomodified montmorillonite (oMMT)-incorporated Epoxy (Epoxy-oMMT), vinyl ester (vinyl ester-oMMT) and titanium dioxide (TiO2)-filled Epoxy (Epoxy-TiO2) nanocomposites are discussed below. Implications of introducing oMMT and TiO2 nanoparticles on mechanical and dry sliding wear properties are presented using micrographs of cast samples and through observations of wear affected surface of nanocomposites. Distribution of nanoparticles and their influence on properties are being emphasized for understanding the wear properties. The data on mechanical and tribological properties determined experimentally are compared with published literature. The main focus is to highlight the importance of nanofillers in the design of wear-resistant thermoset polymer composites. A detailed study of strength and moduli of Epoxy-oMMT, Epoxy-TiO2 and vinyl ester-oMMT nanocomposites was taken up as a part of the investigation. A discussion on density, hardness, tensile, flexural test data, and friction and wear of nanocomposites and analysis of results by comparison with prevalent theoretical models and published results of experiments are presented

The cognitive development from childhood to adolescence of low birthweight children born after medically assisted reproduction-a UK longitudinal cohort study.

BACKGROUND: Previous research has documented that children conceived through medically assisted reproduction (MAR) are at increased risk of poor birth outcomes, such as low birthweight (LBW), which are risk factors for stunted longer-term cognitive development. However, parents who undergo MAR to conceive have, on average, advantaged socioeconomic backgrounds which could compensate for the negative effects of being born LBW. Previous studies have not analysed whether the negative effects of LBW are attenuated among MAR conceived children. METHODS: We draw on the UK Millennium Cohort Study (sweeps 1-6) which contains a sub-sample of (N = 396) MAR-conceived children. The dependent variable measures cognitive ability at around ages 3, 5, 7, 11 and 14. We examine the cognitive development of four groups of children: MAR-conceived low birthweight (MAR LBW); MAR-conceived non-low birthweight (MAR NLBW); naturally conceived low birthweight (NC LBW); naturally conceived non-low birthweight (NC NLBW). We estimate the two following linear regression models for each sweep: (i) a baseline model to examine the unadjusted association between cognitive development and low birthweight by mode of conception; and (ii) a model adjusted by socio-demographic family characteristics. RESULTS: In baseline models, MAR LBW children [age 3: β  =  0.021, 95% confidence interval (CI): -0.198, 0.241; age 5: β  =  0.21, 95% CI: 0.009, 0.418; age 7: β  =  0.163, 95% CI: -0.148, 0.474; age 11: β  =  0.003, 95% CI: -0.318, 0.325; age 14: β  =  0.156, 95% CI: -0.205, 0.517], on average perform similarly in cognitive ability relative to NC NLBW at all ages, and display higher cognitive scores than NC LBW children until age 7. When we account for family characteristics, differences are largely attenuated and become close to zero at age 14. CONCLUSIONS: Despite the higher incidence of LBW among MAR compared with NC children, they do not seem to experience any disadvantage in their cognitive development compared with naturally conceived children. This finding is likely explained by the fact that, on average, MAR children are born to socioeconomically advantaged parents

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

Editorial: Breeding Innovations in Underutilized Temperate Fruit Trees

The recent growing interest in minor species (i.e., fig, pomegranate, feijoa, etc.) has recently driven new research on breeding and genetics to address producer and consumer traits. Since these species have received little attention from the scientific community, they were less improved via conventional breeding, and lacked detailed genomic information on important traits. This lack of data, together with a general poor genetic knowledge of these species, has limited a wider cultivation of varieties with improved characteristics