Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato.

KEY MESSAGE: De novo genotyping in potato using methylation-sensitive GBS discovers SNPs largely confined to genic or gene-associated regions and displays enhanced effectiveness in estimating LD decay rates, population structure and detecting GWAS associations over 'fixed' SNP genotyping platform. Study also reports the genetic architectures including robust sequence-tagged marker-trait associations for sixteen important potato traits potentially carrying higher transferability across a wider range of germplasm. This study deploys recent advancements in polyploid analytical approaches to perform complex trait analyses in cultivated tetraploid potato. The study employs a 'fixed' SNP Infinium array platform and a 'flexible and open' genome complexity reduction-based sequencing method (GBS, genotyping-by-sequencing) to perform genome-wide association studies (GWAS) for several key potato traits including the assessment of population structure and linkage disequilibrium (LD) in the studied population. GBS SNPs discovered here were largely confined (~ 90%) to genic or gene-associated regions of the genome demonstrating the utility of using a methylation-sensitive restriction enzyme (PstI) for library construction. As compared to Infinium array SNPs, GBS SNPs displayed enhanced effectiveness in estimating LD decay rates and discriminating population subgroups. GWAS using a combined set of 30,363 SNPs identified 189 unique QTL marker-trait associations (QTL-MTAs) covering all studied traits. The majority of the QTL-MTAs were from GBS SNPs potentially illustrating the effectiveness of marker-dense de novo genotyping platforms in overcoming ascertainment bias and providing a more accurate correction for different levels of relatedness in GWAS models. GWAS also detected QTL 'hotspots' for several traits at previously known as well as newly identified genomic locations. Due to the current study exploiting genome-wide genotyping and de novo SNP discovery simultaneously on a large tetraploid panel representing a greater diversity of the cultivated potato gene pool, the reported sequence-tagged MTAs are likely to have higher transferability across a wider range of potato germplasm and increased utility for expediting genomics-assisted breeding for the several complex traits studied.

Pollen metabarcoding reveals the origin and multigenerational migratory pathway of an intercontinental-scale butterfly outbreak.

Migratory insects may move in large numbers, even surpassing migratory vertebrates in biomass. Long-distance migratory insects complete annual cycles through multiple generations, with each generation's reproductive success linked to the resources available at different breeding grounds. Climatic anomalies in these grounds are presumed to trigger rapid population outbreaks. Here, we infer the origin and track the multigenerational path of a remarkable outbreak of painted lady (Vanessa cardui) butterflies that took place at an intercontinental scale in Europe, the Middle East, and Africa from March 2019 to November 2019. Using metabarcoding, we identified pollen transported by 264 butterflies captured in 10 countries over 7 months and modeled the distribution of the 398 plants detected. The analysis showed that swarms collected in Eastern Europe in early spring originated in Arabia and the Middle East, coinciding with a positive anomaly in vegetation growth in the region from November 2018 to April 2019. From there, the swarms advanced to Northern Europe during late spring, followed by an early reversal toward southwestern Europe in summer. The pollen-based evidence matched spatiotemporal abundance peaks revealed by citizen science, which also suggested an echo effect of the outbreak in West Africa during September-November. Our results show that population outbreaks in a part of species' migratory ranges may disseminate demographic effects across multiple generations in a wide geographic area. This study represents an unprecedented effort to track a continuous multigenerational insect migration on an intercontinental scale.

Post-Contrast 3D Inversion Recovery Magnetic Resonance Neurography for Evaluation of Branch Nerves of the Brachial Plexus.

PURPOSE: To compare 3.0 Tesla brachial plexus three-dimensional (3D) T2-weighted short tau inversion recovery fast spin echo (STIR-FSE) MRI sequences before (pre-contrast STIR) and after (post-contrast STIR) administration of gadolinium intravenous contrast. METHOD: Eighteen patients were included. Each patient was imaged before and after intravenous contrast administration during the same session. 3D STIR-FSE sequences were obtained at 3.0 Tesla using two 16-channel flexible coils positioned over the lower neck and chest wall region. Three musculoskeletal radiologists qualitatively assessed degree of vascular signal suppression, visualization of the axillary, musculocutaneous, and suprascapular nerves, diagnostic confidence in nerve evaluation, and lesion conspicuity. Marginal ordinal logistic regression models were used to compare subjective ratings between sequences. Pre- and post-STIR lesion conspicuity was compared using Wilcoxon signed-rank test. Inter- and intra-observer agreements were assessed using Gwet's agreement coefficient. RESULTS: Vascular signal suppression significantly improved following contrast administration (odds ratio, OR = 209.9, 95% confidence interval, CI: 21.0-2094.6, p < .001). The post-contrast STIR technique significantly improved nerve visualization (OR = 8.4, 95% CI: 3.6-19.9, p < .001) and diagnostic confidence in evaluation (OR = 13.2, 95% CI: 4.8-36.0, p < .001) across all nerve segments. Post-contrast STIR improved lesion conspicuity by 1 point, but statistical significance was not reached (Reader 1: p = 0.5, Reader 2: p = 0.063). Post-contrast STIR imaging demonstrated substantial to near-perfect inter- and intra-rater agreement coefficients for both nerve visualization (inter-rater: 0.74-1.0, intra-rater: 0.94-1.0) and diagnostic confidence (inter-rater: 0.79-1.0, intra-rater: 0.94-1.0). Quantitatively, post-contrast STIR demonstrated a 24% increase in mean C6 nerve-to-muscle signal intensity ratio (p = 0.017). CONCLUSIONS: Post-contrast STIR improved nerve-to-muscle contrast ratio, allowing for enhanced visualization and diagnostic confidence in evaluation of branch nerves of the brachial plexus.

Association of Blood Pressure Level With Left Ventricular Mass in Adolescents.

Hypertension is associated with left ventricular hypertrophy (LVH), a risk factor for cardiovascular events. Since cardiovascular events in youth are rare, hypertension has historically been defined by the 95th percentile of the normal blood pressure (BP) distribution in healthy children. The optimal BP percentile associated with LVH in youth is unknown. We aimed to determine the association of systolic BP (SBP) percentile, independent of obesity, on left ventricular mass index (LVMI), and to estimate which SBP percentile best predicts LVH in youth. We evaluated SBP, anthropometrics, and echocardiogram in 303 adolescents (mean age 15.6 years, 63% white, 55% male) classified by SBP as low-risk (L=141, <80th percentile), mid-risk (M=71, 80-<90th percentile), or high-risk (H=91, ≥90th percentile) using the mean of 6 measurements at 2 visits according to the 2017 guidelines. Logistic regression was used to determine the sensitivity and specificity of various SBP percentiles associated with LVH. Results: BP groups did not differ by age or demographics but differed slightly by body mass index. Mean BP, LVMI, and prevalence of LVH increased across groups (BP: L=111/75, M=125/82, and H=133/92 mm Hg; LVMI: L=31.2, M=34.2, and H=34.9 g/m2.7; LVH: L=13%, M=21%, H=27%, all P<0.03). SBP percentile remained a significant determinant of LVMI after adjusting for covariates. The 90th percentile for SBP resulted in the best balance between sensitivity and specificity for predicting LVH (LVMI≥38.6 g/m2.7). Abnormalities in cardiac structure in youth can be found at BP levels below those used to define hypertension.

Linkage Disequilibrium and Evaluation of Genome-Wide Association Mapping Models in Tetraploid Potato.

Genome-wide association studies (GWAS) have become a powerful tool for analyzing complex traits in crop plants. The current study evaluates the efficacy of various GWAS models and methods for elucidating population structure in potato. The presence of significant population structure can lead to detection of spurious marker-trait associations, as well as mask true ones. While appropriate statistical models are needed to detect true marker-trait associations, in most published potato GWAS, a 'one model fits all traits' approach has been adopted. We have examined various GWAS models on a large association panel comprising diverse tetraploid potato cultivars and breeding lines, genotyped with single nucleotide polymorphism (SNP) markers. Phenotypic data were generated for 20 quantitative traits assessed in different environments. Best Linear Unbiased Estimates (BLUEs) for these traits were obtained for use in assessing GWAS models. Goodness of fit of GWAS models, derived using different combinations of kinship and population structure for all traits, was evaluated using Quantile-Quantile (Q-Q) plots and genomic control inflation factors (λGC). Kinship was found to play a major role in correcting population confounding effects and results advocate a 'trait-specific' fit of different GWAS models. A survey of genome-wide linkage disequilibrium (LD), one of the critical factors affecting GWAS, is also presented and our findings are compared to other recent studies in potato. The genetic material used here, and the outputs of this study represent a novel resource for genetic analysis in potato.

Blood pressure differences by ethnic group among United States children and adolescents.

Large differences in blood pressure (BP) by ethnic group are apparent among adults. There is uncertainty as to whether similar differences by ethnic group exist among children and, if so, the age of onset. BP measurements were obtained from 58 698 children at 78 556 visits using Pediatric Task Force data, a collection of 11 studies with BP data from children and adolescents age 1 to 17 years. Generalized estimating equation methods were used to identify sex-specific differences in body mass index (BMI)-adjusted rates of BP elevation and prehypertension by ethnic group. Significant BMI-adjusted differences in rates of BP elevation were found between Hispanic boys versus white boys (odds ratio: 1.21; 95% CI: 1.07 to 1.37; P=0.002). No overall significant differences were found between black boys versus white boys (odds ratio: 1.03; 95% CI: 0.95 to 1.12; P=0.49); however, there was significant effect modification (P=0.01) with significant differences found for normal-weight boys (BMI: <85th percentile; OR black versus white: 1.14; 95% CI: 1.03 to 1.27; P=0.01) but not for overweight boys (BMI: > or =85th percentile; OR black versus white: 0.90; 95% CI: 0.78 to 1.05; P=0.20). No overall ethnic group differences in BMI-adjusted rates of hypertension were found for girls. Ethnic differences in prevalence rates of pediatric BP elevation that are not explained by obesity are present, primarily in boys. Whether these differences are attributable to genetic or environmental factors is unknown.

Investigation of the internal heterostructure of highly luminescent quantum dot-quantum well nanocrystals.

In this paper, we report on the growth and characterization of quantum dot-quantum well nanostructures with photoluminescence (PL) that is tunable over the visible range. The material exhibits a PL efficiency as high as approximately 60% and is prepared by reacting ZnS nanocrystals in turn with precursors for CdSe and ZnS in an attempt to form a simple "ZnS/CdSe/ZnS quantum-well structure". Through the use of synchrotron radiation-based photoelectron spectroscopy in conjunction with detailed overall compositional analysis and correlation with the size of the final composite nanostructure, the internal structure of the composite nanocrystals is shown to consist of a graded alloy core whose composition gradually changes from ZnS at the very center to CdSe at the onset of a CdSe layer. The outer shell is ZnS with a sharp interface, probably reflecting the relative thermodynamic stabilities of the parent binary phases. These contrasting aspects of the internal structure are discussed in terms of the various reactivities and are shown to be crucial for understanding the optical properties of such complex heterostructured nanomaterials.

A highly luminescent ZnS/CdSe/ZnS nanocrystals-tetrapeptide biolabeling agent.

Stable colloidal ZnS/CdSe/ZnS nanocrystals capped with hexadecylamine were transferred into water by encapsulation in a protective shell of an amphiphilic polymer. The properties of the products have been investigated by dynamic lighting scattering, absorption, and photoluminescence spectroscopy. These nanocrystals, when conjugated with tuftsin in aqueous suspension, formed an effective labeling reagent for macrophages or lymphocytes. The labeling of cells was demonstrated by confocal microscopy. Hybrid bio-inorganic nanoconjugates are potentially powerful fluorescent tracking tools in biological systems.

Photorefractive performance of a CdSe/ZnS core/shell nanoparticle-sensitized polymer.

We report the photorefractive performance of a polymer composite sensitized by CdSe/ZnS core/shell nanoparticles, and also comprising poly(N-vinylcarbazole) and an electro-optic chromophore. The nanoparticles are characterized by absorption and photoluminescence spectroscopy, elemental analysis, transmission electron microscopy, and powder x-ray diffraction. The electro-optic response of the composite is measured independently of the photorefractive effect by transmission ellipsometry. An asymmetric two-beam coupling gain of 30.6+/-0.4 cm(-1) is obtained, confirming photorefractivity. Degenerate four-wave mixing is used to assess photorefractive performance and, at a poling field of 70 V microm(-1), yields a diffraction efficiency of 4.21%+/-0.03%, a holographic contrast of 3.05 x 10(-4)+/-1 x 10(-6), a space-charge rise time of 25+/-2 s, and a sensitivity of 4.7 x 10(-5)+/-4 x 10(-6) cm3 J(-1). These results constitute a significant improvement on the performance of previous nanoparticle-sensitized photorefractive polymer composites.

Arabidopsis is susceptible to the cereal ear blight fungal pathogens Fusarium graminearum and Fusarium culmorum.

The fungal pathogens Fusarium graminearum and F. culmorum cause ear blight disease on cereal crops worldwide. The disease lowers both grain quality and grain safety. Disease prevalence is increasing due to changes in cropping practices and the difficulties encountered by plant breeders when trying to introgress the polygene-based resistance. The molecular basis of resistance to Fusarium ear blight in cereal species is poorly understood. This is primarily due to the large size of cereal genomes and the expensive resources required to undertake gene function studies in cereals. We therefore explored the possibility of developing various model floral infection systems that would be more amenable to experimental manipulation and high-throughput gene function studies. The floral tissues of tobacco, tomato, soybean and Arabidopsis were inoculated with Fusarium conidia and this resulted in disease symptoms on anthers, anther filaments and petals in each plant species. However, only in Arabidopsis did this initial infection then spread into the developing siliques and seeds. A survey of 236 Arabidopsis ecotypes failed to identify a single genotype that was extremely resistant or susceptible to Fusarium floral infections. Three Arabidopsis floral mutants that failed to develop anthers and/or functional pollen (i.e. agamous-1, apetala1-3 and dad1) were significantly less susceptible to Fusarium floral infection than wild type. Deoxynivalenol (DON) mycotoxin production was also detected in Fusarium-infected flowers at >1 ppm. This novel floral pathosystem for Arabidopsis appears to be highly representative of a serious cereal crop disease.