Seedling development traits in Brassica napus examined by gene expression analysis and association mapping

BACKGROUND: An optimal seedling development of Brassica napus plants leads to a higher yield stability even under suboptimal growing conditions and has therefore a high importance for plant breeders. The objectives of our study were to (i) examine the expression levels of candidate genes in seedling leaves of B. napus and correlate these with seedling development as well as (ii) detect genome regions associated with gene expression levels and seedling development traits in B. napus by genome-wide association mapping. RESULTS: The expression levels of the 15 candidate genes examined in the 509 B. napus inbreds showed an averaged standard deviation of 5.6 across all inbreds and ranged from 3.2 to 8.8. The gene expression differences between the 509 B. napus inbreds were more than adequate for the correlation with phenotypic variation of seedling development. The average of the absolute value correlations of the correlation coefficients of 0.11 were observed with a range from 0.00 to 0.39. The candidate genes GER1, AILP1, PECT, and FBP were strongly correlated with the seedling development traits. In a genome-wide association study, we detected a total of 63 associations between single nucleotide polymorphisms (SNPs) and the seedling development traits and 31 SNP-gene associations for the candidate genes with a P-value < 0.0001. For the projected leaf area traits we identified five different association hot spots on the chromosomes A2, A7, C3, C6, and C7. CONCLUSION: A total of 99.4% of the adjacent SNPs on the A genome and 93.0% of the adjacent SNPs on the C genome had a distance smaller than the average range of linkage disequilibrium. Therefore, this genome-wide association study is expected to result on average in 14.7% of the possible power. Compared to previous studies in B. napus, the SNP marker density of our study is expected to provide a higher power to detect SNP-trait/-gene associations in the B. napus diversity set. The large number of associations detected for the examined 14 seedling development traits indicated that these are genetically complex inherited. The results of our analyses suggested that the studied genes ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit (RBC) on the chromosomes A4 and C4 and fructose-1,6-bisphosphatase precursor (FBP) on the chromosomes A9 and C8 are cis-regulated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-015-0496-3) contains supplementary material, which is available to authorized users

Transparent Conducting Oxides for Photovoltaics: Manipulation of Fermi Level, Work Function and Energy Band Alignment

Doping limits, band gaps, work functions and energy band alignments of undoped and donor-doped transparent conducting oxides Zn₀, In₂O₃, and SnO₂ as accessed by X-ray and ultraviolet photoelectron spectroscopy (XPS/UPS) are summarized and compared. The presented collection provides an extensive data set of technologically relevant electronic properties of photovoltaic transparent electrode materials and illustrates how these relate to the underlying defect chemistry, the dependence of surface dipoles on crystallographic orientation and/or surface termination, and Fermi level pinning

Quasiparticle spin susceptibility in heavy-fermion superconductors : An NMR study compared with specific heat results

Quasi-particle spin susceptibility ($\chi^{qp}$) for various heavy-fermion (HF) superconductors are discussed on the basis of the experimental results of electronic specific heat ($\gamma_{el}$), NMR Knight shift ($K$) and NMR relaxation rate ($1/T_1$) within the framework of the Fermi liquid model for a Kramers doublet crystal electric field (CEF) ground state. $\chi^{qp}_{\gamma}$ is calculated from the enhanced Sommerfeld coefficient $\gamma_{el}$ and $\chi^{qp}_{T_1}$ from the quasi-particle Korringa relation $T_1T(K^{qp}_{T_1})^2=const.$ via the relation of $\chi^{qp}_{T_1}=(N_A\mu_B/A_{hf})K^{qp}_{T_1}$ where $A_{hf}$ is the hyperfine coupling constant, $N_A$ the Abogadoro's number and $\mu_B$ the Bohr magneton. For the even-parity (spin-singlet) superconductors CeCu$_2$Si$_2$, CeCoIn$_5$ and UPd$_2$Al$_3$, the fractional decrease in the Knight shift, $\delta K^{obs}$, below the superconducting transition temperature ($T_c$) is due to the decrease of the spin susceptibility of heavy quasi-particle estimated consistently from $\chi^{qp}_{\gamma}$ and $\chi^{qp}_{T_1}$. This result allows us to conclude that the heavy quasi-particles form the spin-singlet Cooper pairs in CeCu$_2$Si$_2$, CeCoIn$_5$ and UPd$_2$Al$_3$. On the other hand, no reduction in the Knight shift is observed in UPt$_3$ and UNi$_2$Al$_3$, nevertheless the estimated values of $\chi^{qp}_{\gamma}$ and $\chi^{qp}_{T_1}$ are large enough to be probed experimentally. The odd-parity superconductivity is therefore concluded in these compounds. The NMR result provides a convincing way to classify the HF superconductors into either even- or odd- parity paring together with the identification for the gap structure, as long as the system has Kramers degeneracy.Comment: 11 pages, 3 tables, 5 figures, RevTex4(LaTex2e

Seasonal methane accumulation and release from a gas emission site in the central North Sea

We investigated dissolved methane distributions along a 6 km transect crossing active seep sites at 40 m water depth in the central North Sea. These investigations were done under conditions of thermal stratification in summer (July 2013) and homogenous water column in winter (January 2014). Dissolved methane accumulated below the seasonal thermocline in summer with a median concentration of 390 nM, whereas during winter, methane concentrations were typically much lower (median concentration of 22 nM). High-resolution methane analysis using an underwater mass-spectrometer confirmed our summer results and was used to document prevailing stratification over the tidal cycle. We contrast estimates of methane oxidation rates (from 0.1 to 4.0 nM day⁻¹) using the traditional approach scaled to methane concentrations with microbial turnover time values and suggest that the scaling to concentration may obscure the ecosystem microbial activity when comparing systems with different methane concentrations. Our measured and averaged rate constants (k') were on the order of 0.01 day−1, equivalent to a turnover time of 100 days, even when summer stratification led to enhanced methane concentrations in the bottom water. Consistent with these observations, we could not detect known methanotrophs and pmoA genes in water samples collected during both seasons. Estimated methane fluxes indicate that horizontal transport is the dominant process dispersing the methane plume. During periods of high wind speed (winter), more methane is lost to the atmosphere than oxidized in the water. Microbial oxidation seems of minor importance throughout the year.This work is part of the DFG project “Limitations of Marine Methane Oxidation” (MA 3961/2-1). This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Copernicus Publications on behalf of the European Geosciences Union. The published article can be found at: http://www.biogeosciences.net/ For a previous discussion paper please see: http://hdl.handle.net/1957/5749

Seasonal methane accumulation and release from a gas emission site in the central North Sea

Hydroacoustic data document the occurrence of 5 flare clusters and several single flares from which bubbles rise through the entire water column from an active seep site at 40 m water depth in the central North Sea. We investigated the difference in dissolved methane distributions along a 6 km transect crossing this seep site during a period of seasonal summer stratification (July 2013) and a period of well mixed winter water column (January 2014). Dissolved methane accumulated below the seasonal thermocline in summer with a median concentration of 390 nM, whereas during winter, methane concentrations were much lower (median concentration of 22 nM) and punctually elevated due to bubble transport. High resolution methane analysis by an underwater mass-spectrometer confirmed our summer results and were used to document prevailing stratification over the tidal cycle. Although sufficient methane was available, microbial methane oxidation was limited during both seasons. Measured and averaged rate constants (k') using Michaelis Menten kinetics were on the order of 0.01 days⁻¹, equivalent to a turnover time of 100 days. Time series measurements indicated an uptake of only 5–6% of the gas after 4 days, and no known methanotrophs and pmoA-genes were detected. Estimated methane fluxes indicate that horizontal eddy transport rapidly disperses dissolved methane, vertical transport becomes dominant during phases of high wind speeds, and relative to these processes, microbial methane oxidation appears to be comparably low. To bridge the discrete field data we developed a 1-D seasonal model using available year-long records of wind speed, surface temperature and thermocline depth. The model simulations show a peak release of methane at the beginning of fall when the water column becomes mixed. Consistent with our field data, inclusion of microbial methane oxidation does not change the model results significantly, thus microbial oxidation appears to be not sufficient to notably reduce methane during summer stratification before the peak release in fall.This work is part of the DFG project “Limitations of Marine Methane Oxidation” (MA 3961/2-1). This discussion paper has been under review for the journal Biogeosciences (BG). Please refer to the corresponding final paper in BG. The published article is copyrighted by the author(s) and published by Copernicus Publications on behalf of the European Geosciences Union. The published article can be found at: http://www.biogeosciences.net/ The final revised paper is available at: http://hdl.handle.net/1957/5749

Genetic and antigenic characterization of complete genomes of Type 1 Porcine Reproductive and Respiratory Syndrome viruses (PRRSV) isolated in Denmark over a period of 10 years

AbstractPorcine Reproductive and Respiratory Syndrome (PRRS) caused by the PRRS virus (PRRSV) is considered one of the most devastating swine diseases worldwide. PRRS viruses are divided into two major genotypes, Type 1 and Type 2, with pronounced diversity between and within the genotypes. In Denmark more than 50% of the herds are infected with Type 1 and/or Type 2 PRRSV. The main objective of this study was to examine the genetic diversity and drift of Type 1 viruses in a population with limited introduction of new animals and semen. A total of 43 ORF5 and 42 ORF7 nucleotide sequences were obtained from viruses collected from 2003 to February 2013. Phylogenetic analysis of ORF5 nucleotide sequences showed that the Danish isolates formed two major clusters within the subtype 1. The nucleotide identity to the subtype 1 protogenotype Lelystad virus (LV) spanned 84.9–98.8% for ORF5 and 90.7–100% for ORF7. Among the Danish viruses the pairwise nucleotide identities in ORF5 and ORF7 were 81.2–100% and 88.9–100%, respectively. Sequencing of the complete genomes, including the 5′- and 3′-end nucleotides, of 8 Danish PRRSV Type 1 showed that the genome lengths differed from 14,876 to 15,098 nucleotides and the pairwise nucleotide identity among the Danish viruses was 86.5–97.3% and the identity to LV was 88.7–97.9%. The study strongly indicated that there have been at least two independent introductions of Type 1 PRRSV in Denmark and analysis of the full genomes revealed a significant drift in several regions of the virus