The Dimensionality of Genomic Information and Its Effect on Genomic Prediction

The genomic relationship matrix (GRM) can be inverted by the algorithm for proven and young (APY) based on recursion on a random subset of animals. While a regular inverse has a cubic cost, the cost of the APY inverse can be close to linear. Theory for the APY assumes that the optimal size of the subset (maximizing accuracy of genomic predictions) is due to a limited dimensionality of the GRM, which is a function of the effective population size (N(e)). The objective of this study was to evaluate these assumptions by simulation. Six populations were simulated with approximate effective population size (N(e)) from 20 to 200. Each population consisted of 10 nonoverlapping generations, with 25,000 animals per generation and phenotypes available for generations 1–9. The last 3 generations were fully genotyped assuming genome length L = 30. The GRM was constructed for each population and analyzed for distribution of eigenvalues. Genomic estimated breeding values (GEBV) were computed by single-step GBLUP, using either a direct or an APY inverse of GRM. The sizes of the subset in APY were set to the number of the largest eigenvalues explaining x% of variation (EIGx, x = 90, 95, 98, 99) in GRM. Accuracies of GEBV for the last generation with the APY inverse peaked at EIG98 and were slightly lower with EIG95, EIG99, or the direct inverse. Most information in the GRM is contained in ∼N(e)L largest eigenvalues, with no information beyond 4N(e)L. Genomic predictions with the APY inverse of the GRM are more accurate than by the regular inverse

J/\Psi production, χ\chi polarization and Color Fluctuations

The hard contributions to the heavy quarkonium-nucleon cross sections are calculated based on the QCD factorization theorem and the nonrelativistic quarkonium model. We evaluate the nonperturbative part of these cross sections which dominates at $\sqrt{s_{NN}}\approx 20$ GeV at the Cern Super Proton Synchrotron (SPS) and becomes a correction at $\sqrt{s_{NN}}\approx 6$ TeV at the CERN Large Hadron Collider (LHC). \J production at the CERN SPS is well described by hard QCD, when the larger absorption cross sections of the $\chi$ states predicted by QCD are taken into account. We predict an $A$-dependent polarization of the $\chi$ states. The expansion of small wave packets is discussed.Comment: 13 pages REVTEX, 1 table, 2 PostScript, corrected some typo

Diversidade florística em quintais agroflorestais de quatro localidades, Parintins - Amazonas.

O objetivo deste trabalho foi verificar a diversidade das espécies em pomares caseiros no assentamento de Vila Amazônia

Deep electronic states in ion-implanted Si

In this paper we present an overview of the deep states present after ion-implantation by various species into n-type silicon, measured by Deep Level Transient Spectroscopy (DLTS) and high resolution Laplace DLTS (LDLTS). Both point and small extended defects are found, prior to any anneal, which can therefore be the precursors to more detrimental defects such as end of range loops. We show that the ion mass is linked to the concentrations of defects that are observed, and the presence of small interstitial clusters directly after ion implantation is established by comparing their behaviour with that of electrically active stacking faults. Finally, future applications of the LDLTS technique to ion-implanted regions in Si-based devices are outlined.</p

Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations

International audienceAbstractBackgroundColumnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US. The objectives of this study were to: (1) identify common genomic regions that explain a large proportion of the additive genetic variance for resistance to CD in two rainbow trout (Oncorhynchus mykiss) populations; and (2) estimate the gains in prediction accuracy when genomic information is used to evaluate the genetic potential of survival to columnaris infection in each population.MethodsTwo aquaculture populations were investigated: the National Center for Cool and Cold Water Aquaculture (NCCCWA) odd-year line and the Troutlodge, Inc., May odd-year (TLUM) nucleus breeding population. Fish that survived to 21 days post-immersion challenge were recorded as resistant. Single nucleotide polymorphism (SNP) genotypes were available for 1185 and 1137 fish from NCCCWA and TLUM, respectively. SNP effects and variances were estimated using the weighted single-step genomic best linear unbiased prediction (BLUP) for genome-wide association. Genomic regions that explained more than 1% of the additive genetic variance were considered to be associated with resistance to CD. Predictive ability was calculated in a fivefold cross-validation scheme and using a linear regression method.ResultsValidation on adjusted phenotypes provided a prediction accuracy close to zero, due to the binary nature of the trait. Using breeding values computed from the complete data as benchmark improved prediction accuracy of genomic models by about 40% compared to the pedigree-based BLUP. Fourteen windows located on six chromosomes were associated with resistance to CD in the NCCCWA population, of which two windows on chromosome Omy 17 jointly explained more than 10% of the additive genetic variance. Twenty-six windows located on 13 chromosomes were associated with resistance to CD in the TLUM population. Only four associated genomic regions overlapped with quantitative trait loci (QTL) between both populations.ConclusionsOur results suggest that genome-wide selection for resistance to CD in rainbow trout has greater potential than selection for a few target genomic regions that were found to be associated to resistance to CD due to the polygenic architecture of this trait, and because the QTL associated with resistance to CD are not sufficiently informative for selection decisions across populations

Comportamento produtivo de búfalos do tipo Baio para produção de leite e carne em pastagem nativa de terra inundável.

bitstream/item/57847/1/CPATU-PA29.pd

Rapidity Distributions of Dileptons from a Hadronizing Quark-Gluon Plasma

It has been predicted that dilepton production may be used as a quark-gluon plasma probe. We calculate the rapidity distributions of thermal dileptons produced by an evolving quark-gluon plasma assuming a longitudinal scaling expansion with initial conditions locally determined from the hadronic rapidity density. These distributions are compared with Drell-Yan production and semileptonic charm decays at invariant mass $M = 2$, 4, and 6 GeV.Comment: 17 pages (standard LaTeX), 6 figures (available as topdraw files or printed versions upon request), GSI-93-6

Hybrid Stars in a Strong Magnetic Field

We study the effects of high magnetic fields on the particle population and equation of state of hybrid stars using an extended hadronic and quark SU(3) non-linear realization of the sigma model. In this model the degrees of freedom change naturally from hadrons to quarks as the density and/or temperature increases. The effects of high magnetic fields and anomalous magnetic moment are visible in the macroscopic properties of the star, such as mass, adiabatic index, moment of inertia, and cooling curves. Moreover, at the same time that the magnetic fields become high enough to modify those properties, they make the star anisotropic.Comment: Revised version with updated reference

Genome-wide association study provides insights into genes related with horn development in Nelore beef cattle.

Abstract The causal mutation for polledness in Nelore (Bos taurus indicus) breed seems to have appeared first in Brazil in 1957. The expression of the polled trait is known to be ruled by a few groups of alleles in taurine breeds; however, the genetic basis of this trait in indicine cattle is still unclear. The aim of this study was to identify genomic regions associated with the hornless trait in a commercial Nelore population. A total of 107,294 animals had phenotypes recorded and 2,238 were genotyped/imputed for 777k SNP. The weighted single-step approach for genome-wide association study (WssGWAS) was used to estimate the SNP effects and variances accounted for by 1 Mb sliding SNP windows. A centromeric region of chromosome 1 with 3.11 Mb size (BTA1: 878,631?3,987,104 bp) was found to be associated with hornless in the studied population. A total of 28 protein-coding genes are mapped in this region, including the taurine Polled locus and the IFNAR1, IFNAR2, IFNGR2, KRTAP11-1, MIS18A, OLIG1, OLIG2, and SOD1 genes, which expression can be related to the horn formation as described in literature. The functional enrichment analysis by DAVID tool revealed cytokine-cytokine receptor interaction, JAK-STAT signaling, natural killer cell mediated cytotoxicity, and osteoclast differentiation pathways as significant (P < 0.05). In addition, a runs of homozygosity (ROH) analysis identified a ROH island in polled animals with 2.47 Mb inside the region identified by WssGWAS. Polledness in Nelore cattle is associated with one region in the genome with 3.1 Mb size in chromosome 1. Several genes are harbored in this region, and they may act together in the determination of the polled/horned phenotype. Fine mapping the locus responsible for polled trait in Nelore breed and the identification of the molecular mechanisms regulating the horn growth deserve further investigation