Genetic analysis of Barley (Hordeum vulgare L.) grain (1,3;1,4)-β-glucan concentration and fine structure.

(1,3;1,4)-β-glucan accumulated in barley (Hordeum vulgare L.) cell walls is an important determinant for grain end-use as food, malt, feed or fuel. As a trait affected by multiple genes and the environment, grain (1,3;1,4)-β-glucan concentration qualifies as a quantitative trait. A major QTL on chromosome 7H contains a cellulose synthase like gene HvCslF6, coding for an enzyme associated with (1,3;1,4)-β-glucan biosynthesis. To develop gene based perfect markers, HvCslF6 was analyzed to determine allelic variation between CDC Bold, a low (1,3;1,4)-β-glucan (~ 3.3 %) cultivar and TR251, a high (1,3;1,4)-β-glucan (~ 5.2 %) genotype. Comparison of the CDC Bold and TR251 nucleotide sequences downstream of the ATG start codon in HvCslF6 alleles revealed 16 single nucleotide polymorphisms (SNPs) and two indels. The two indels added 16 nucleotides to the first intron of HvCslF6 of CDC Bold and a single SNP in the third exon changed alanine 590 codon in the CDC Bold sequence to a threonine codon in TR251 allele. Five polymorphic sites were converted into genetic markers and confirmed to select low and high (1,3;1,4)-β-glucan lines in a previously characterized CDC Bold / TR251 doubled haploid genetic mapping population and a novel F5 recombinant inbred line (RIL) population derived from a Merit / H93174006 (4.8 and 5.3 % (1,3;1,4)-β-glucan) cross. An analysis of parental lines of six populations segregating for (1,3;1,4)-β-glucan concentration validated the association between the TR251 HvCslF6 haplotype and high (1,3;1,4)-β-glucan concentration in populations showing a (1,3;1,4)-β-glucan quantitative trait locus (QTL) on chromosome 7H. To further investigate the role of HvCslF6 alleles, 91 lines of the Merit / H93174006 RIL grown in two environments were phenotyped for (1,3;1,4)-β-glucan grain concentration, cellotriose content (DP3), cellotetraose content (DP4) and cellotriose:cellotetraose (DP3:DP4) ratio. DP3, DP4, (1,3;1,4)-β-glucan and total DP3+DP4 were strongly positively correlated (r>0.9) to each other, suggesting no preference for DP3 or DP4 subunit production in high or low (1,3;1,4)-β-glucan lines. DP3:DP4 ratio showed no strong correlation with any other measured trait. Significant effects arising from genotype and environment were associated with grain (1,3;1,4)-β-glucan concentration, DP3, DP4 and DP3:DP4 ratio. Only DP3:DP4 ratio showed a significant GxE (genotype by environment) interaction. Hereditability of grain (1,3;1,4)-β-glucan concentration was moderate (~ 30 %), DP3 and DP4 had low heritability (> 21 %) and DP3:DP4 ratio had moderate heritability (~ 43 %). Single marker analysis showed an association between marker CSLF6_4105 and (1,3;1,4)-β-glucan fine structure in Vegreville but not in Castor, supporting significant GxE interaction in (1,3;1,4)-β-glucan fine structure. Association mapping of candidate markers in 119 barley genotypes of diverse origin grown in greenhouses showed that on chromosome 7H, marker CSLF6_4105 was associated only with (1,3;1,4)-β-glucan concentration, while Bmac273e was associated with both (1,3;1,4)-β-glucan concentration and DP3:DP4 ratio. In addition on chromosome 1H, markers Bmac504 and Bmac211 were associated only with DP3:DP4 ratio. This study suggests that DP3:DP4 ratio is strongly affected by genotype and environment. To identify new markers with (1,3;1,4)-β-glucan concentration, ninety-four two-row spring varieties were genotyped using double digestion Restriction-site Associated DNA (ddRAD) sequencing on an Illumina sequencer. Two bioinformatics pipelines were used to discover and call SNPs for association linkage analysis. SAMtools bioinformatics pipeline identified 9,062 markers and UNEAK identified 3,060 markers, 2,311 of which were identical between both bioinformatics pipelines. Both sets of markers showed excellent coverage of the genome and distinguished the ninety-four varieties into the same subgroups based on geographical region of origin. Association mapping was performed using TASSEL 3.0 and grain (1,3;1,4)-β-glucan concentration was associated with a region on the 5HS telomere by markers generated using both UNEAK and SAMtools. Some putative candidate genes were identified, including a UDP-glucosyltransferase, two phosphorylation signaling proteins and two transcription factors. The markers developed and tested in this study can be used in marker assisted selection to develop barley genotypes with desired (1,3;1,4)-β-glucan concentration

Purified pre-sertoli cells express genes involved in cell proliferation and cell signalling during a critical window in male sex determination

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal

Graphene growth on h-BN by Molecular Beam Epitaxy

The growth of single layer graphene nanometer size domains by solid carbon source molecular beam epitaxy on hexagonal boron nitride (h-BN) flakes is demonstrated. Formation of single-layer graphene is clearly apparent in Raman spectra which display sharp optical phonon bands. Atomic-force microscope images and Raman maps reveal that the graphene grown depends on the surface morphology of the h-BN substrates. The growth is governed by the high mobility of the carbon atoms on the h-BN surface, in a manner that is consistent with van der Waals epitaxy. The successful growth of graphene layers depends on the substrate temperature, but is independent of the incident flux of carbon atoms.Comment: Solid State Communications, 201

A conservation roadmap for the subterranean biome

The 15th UN Convention on Biological Diversity (CBD) (COP15) will be held in Kunming, China in October 2021. Historically, CBDs and other multilateral treaties have either alluded to or entirely overlooked the subterranean biome. A multilateral effort to robustly examine, monitor, and incorporate the subterranean biome into future conservation targets will enable the CBD to further improve the ecological effectiveness of protected areas by including groundwater resources, subterranean ecosystem services, and the profoundly endemic subsurface biodiversity. To this end, we proffer a conservation roadmap that embodies five conceptual areas: (1) science gaps and data management needs; (2) anthropogenic stressors; (3) socioeconomic analysis and conflict resolution; (4) environmental education; and (5) national policies and multilateral agreements.Peer reviewe

Differential cross section measurements for the production of a W boson in association with jets in proton–proton collisions at √s = 7 TeV

Measurements are reported of differential cross sections for the production of a W boson, which decays into a muon and a neutrino, in association with jets, as a function of several variables, including the transverse momenta (pT) and pseudorapidities of the four leading jets, the scalar sum of jet transverse momenta (HT), and the difference in azimuthal angle between the directions of each jet and the muon. The data sample of pp collisions at a centre-of-mass energy of 7 TeV was collected with the CMS detector at the LHC and corresponds to an integrated luminosity of 5.0 fb[superscript −1]. The measured cross sections are compared to predictions from Monte Carlo generators, MadGraph + pythia and sherpa, and to next-to-leading-order calculations from BlackHat + sherpa. The differential cross sections are found to be in agreement with the predictions, apart from the pT distributions of the leading jets at high pT values, the distributions of the HT at high-HT and low jet multiplicity, and the distribution of the difference in azimuthal angle between the leading jet and the muon at low values.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

Impacts of the Tropical Pacific/Indian Oceans on the Seasonal Cycle of the West African Monsoon

The current consensus is that drought has developed in the Sahel during the second half of the twentieth century as a result of remote effects of oceanic anomalies amplified by local land–atmosphere interactions. This paper focuses on the impacts of oceanic anomalies upon West African climate and specifically aims to identify those from SST anomalies in the Pacific/Indian Oceans during spring and summer seasons, when they were significant. Idealized sensitivity experiments are performed with four atmospheric general circulation models (AGCMs). The prescribed SST patterns used in the AGCMs are based on the leading mode of covariability between SST anomalies over the Pacific/Indian Oceans and summer rainfall over West Africa. The results show that such oceanic anomalies in the Pacific/Indian Ocean lead to a northward shift of an anomalous dry belt from the Gulf of Guinea to the Sahel as the season advances. In the Sahel, the magnitude of rainfall anomalies is comparable to that obtained by other authors using SST anomalies confined to the proximity of the Atlantic Ocean. The mechanism connecting the Pacific/Indian SST anomalies with West African rainfall has a strong seasonal cycle. In spring (May and June), anomalous subsidence develops over both the Maritime Continent and the equatorial Atlantic in response to the enhanced equatorial heating. Precipitation increases over continental West Africa in association with stronger zonal convergence of moisture. In addition, precipitation decreases over the Gulf of Guinea. During the monsoon peak (July and August), the SST anomalies move westward over the equatorial Pacific and the two regions where subsidence occurred earlier in the seasons merge over West Africa. The monsoon weakens and rainfall decreases over the Sahel, especially in August.Peer reviewe

Search for anomalous production of events with three or more leptons in pp collisions at √s = 8TeV

Published by the American Physical Society under the terms of the Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published articles title, journal citation, and DOI.A search for physics beyond the standard model in events with at least three leptons is presented. The data sample, corresponding to an integrated luminosity of 19.5fb-1 of proton-proton collisions with center-of-mass energy s=8TeV, was collected by the CMS experiment at the LHC during 2012. The data are divided into exclusive categories based on the number of leptons and their flavor, the presence or absence of an opposite-sign, same-flavor lepton pair (OSSF), the invariant mass of the OSSF pair, the presence or absence of a tagged bottom-quark jet, the number of identified hadronically decaying τ leptons, and the magnitude of the missing transverse energy and of the scalar sum of jet transverse momenta. The numbers of observed events are found to be consistent with the expected numbers from standard model processes, and limits are placed on new-physics scenarios that yield multilepton final states. In particular, scenarios that predict Higgs boson production in the context of supersymmetric decay chains are examined. We also place a 95% confidence level upper limit of 1.3% on the branching fraction for the decay of a top quark to a charm quark and a Higgs boson (t→cH), which translates to a bound on the left- and right-handed top-charm flavor-violating Higgs Yukawa couplings, λtcH and λctH, respectively, of |λtcH|2+|λctH|2<0.21

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Correction: Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map.

[This corrects the article DOI: 10.1371/journal.pone.0170941.]