Mitochondrial DNA Variability in Bosnians and Slovenians

Summary Mitochondrial DNA variability in two Slavonic-speaking populations of the northwestern Balkan peninsula, Bosnians (N = 144) and Slovenians (N = 104), was studied by hypervariable segments I and II (HVS I and II) sequencing and restriction fragment-length polymorphism (RFLP) analysis of the mtDNA coding region

QTL mapping in autotetraploids using SNP dosage information

Dense linkage maps derived by analysing SNP dosage in autotetraploids provide detailed information about the location of, and genetic model at, quantitative trait loci. Recent developments in sequencing and genotyping technologies enable researchers to generate high-density single nucleotide polymorphism (SNP) genotype data for mapping studies. For polyploid species, the SNP genotypes are informative about allele dosage, and Hackett et al. (PLoS ONE 8:e63939, 2013) presented theory about how dosage information can be used in linkage map construction and quantitative trait locus (QTL) mapping for an F1 population in an autotetraploid species. Here, QTL mapping using dosage information is explored for simulated phenotypic traits of moderate heritability and possibly non-additive effects. Different mapping strategies are compared, looking at additive and more complicated models, and model fitting as a single step or by iteratively re-weighted modelling. We recommend fitting an additive model without iterative re-weighting, and then exploring non-additive models for the genotype means estimated at the most likely position. We apply this strategy to re-analyse traits of high heritability from a potato population of 190 F1 individuals: flower colour, maturity, height and resistance to late blight (Phytophthora infestans (Mont.) de Bary) and potato cyst nematode (Globodera pallida), using a map of 3839 SNPs. The approximate confidence intervals for QTL locations have been improved by the detailed linkage map, and more information about the genetic model at each QTL has been revealed. For several of the reported QTLs, candidate SNPs can be identified, and used to propose candidate trait genes. We conclude that the high marker density is informative about the genetic model at loci of large effects, but that larger populations are needed to detect smaller QTLs

The novel gene Ny-1 on potato chromosome IX confers hypersensitive resistance to Potato virus Y and is an alternative to Ry genes in potato breeding for PVY resistance

Hypersensitive resistance (HR) is an efficient defense strategy in plants that restricts pathogen growth and can be activated during host as well as non-host interactions. HR involves programmed cell death and manifests itself in tissue collapse at the site of pathogen attack. A novel hypersensitivity gene, Ny-1, for resistance to Potato virus Y (PVY) was revealed in potato cultivar Rywal. This is the first gene that confers HR in potato plants both to common and necrotic strains of PVY. The locus Ny-1 mapped on the short arm of potato chromosome IX, where various resistance genes are clustered in Solanaceous genomes. Expression of HR was temperature-dependent in cv. Rywal. Strains PVYO and PVYN, including subgroups PVYNW and PVYNTN, were effectively localized when plants were grown at 20°C. At 28°C, plants were systemically infected but no symptoms were observed. In field trials, PVY was restricted to the inoculated leaves and PVY-free tubers were produced. Therefore, the gene Ny-1 can be useful for potato breeding as an alternative donor of PVY resistance, because it is efficacious in practice-like resistance conferred by Ry genes

Genic SNP markers and legume synteny reveal candidate genes underlying QTL for Macrophomina phaseolina resistance and maturity in cowpea [Vigna unguiculata (L) Walp.]

<p>Abstract</p> <p>Background</p> <p><it>Macrophomina phaseolina </it>is an emerging and devastating fungal pathogen that causes significant losses in crop production under high temperatures and drought stress. An increasing number of disease incidence reports highlight the wide prevalence of the pathogen around the world and its contribution toward crop yield suppression. In cowpea [<it>Vigna unguiculata </it>(L) Walp.], limited sources of low-level host resistance have been identified, the genetic basis of which is unknown. In this study we report on the identification of strong sources of host resistance to <it>M. phaseolina </it>and the genetic mapping of putative resistance loci on a cowpea genetic map comprised of gene-derived single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs).</p> <p>Results</p> <p>Nine quantitative trait loci (QTLs), accounting for between 6.1 and 40.0% of the phenotypic variance (R²), were identified using plant mortality data taken over three years in field experiments and disease severity scores taken from two greenhouse experiments. Based on annotated genic SNPs as well as synteny with soybean (<it>Glycine max</it>) and <it>Medicago truncatula</it>, candidate resistance genes were found within mapped QTL intervals. QTL <it>Mac-2 </it>explained the largest percent R²and was identified in three field and one greenhouse experiments where the QTL peak co-located with a SNP marker derived from a pectin esterase inhibitor encoding gene. Maturity effects on the expression of resistance were indicated by the co-location of <it>Mac-6 </it>and <it>Mac-7 </it>QTLs with maturity-related senescence QTLs <it>Mat-2 </it>and <it>Mat-1</it>, respectively. Homologs of the <it>ELF4 </it>and <it>FLK </it>flowering genes were found in corresponding syntenic soybean regions. Only three <it>Macrophomina </it>resistance QTLs co-located with delayed drought-induced premature senescence QTLs previously mapped in the same population, suggesting that largely different genetic mechanisms mediate cowpea response to drought stress and <it>Macrophomina </it>infection.</p> <p>Conclusion</p> <p>Effective sources of host resistance were identified in this study. QTL mapping and synteny analysis identified genomic loci harboring resistance factors and revealed candidate genes with potential for further functional genomics analysis.</p

High density SNP and DArT-based genetic linkage maps of two closely related oil palm populations

Oil palm (Elaeis guineensis Jacq.) is an outbreeding perennial tree crop with long breeding cycles, typically 12 years. Molecular marker technologies can greatly improve the breeding efficiency of oil palm. This study reports the first use of the DArTseq platform to genotype two closely related self-pollinated oil palm populations, namely AA0768 and AA0769 with 48 and 58 progeny respectively. Genetic maps were constructed using the DArT and SNP markers generated in combination with anchor SSR markers. Both maps consisted of 16 major independent linkage groups (2n = 2× = 32) with 1399 and 1466 mapped markers for the AA0768 and AA0769 populations, respectively, including the morphological trait “shell-thickness” (Sh). The map lengths were 1873.7 and 1720.6 cM with an average marker density of 1.34 and 1.17 cM, respectively. The integrated map was 1803.1 cM long with 2066 mapped markers and average marker density of 0.87 cM. A total of 82% of the DArTseq marker sequence tags identified a single site in the published genome sequence, suggesting preferential targeting of gene-rich regions by DArTseq markers. Map integration of higher density focused around the Sh region identified closely linked markers to the Sh, with D.15322 marker 0.24 cM away from the morphological trait and 5071 bp from the transcriptional start of the published SHELL gene. Identification of the Sh marker demonstrates the robustness of using the DArTseq platform to generate high density genetic maps of oil palm with good genome coverage. Both genetic maps and integrated maps will be useful for quantitative trait loci analysis of important yield traits as well as potentially assisting the anchoring of genetic maps to genomic sequences

Comparative analysis of underfloor wheel lathes with monolithic and bolted structure in terms of static and dynamic properties based on the results of FEM analyzes

The subject of the research was Underfloor Wheel Lathes de-signed to regenerate the profiles of the running wheels and brake discs of heavy rail vehicles without removing the wheelsets. These machines can also be used to regenerate wheel sets in trolleys dismantled from vehicles or the wheel sets themselves. The machine tools operate in a pass-through system. Two machine tools differing in the structure of the supporting sys-tem were tested: monolithic and folding. Conclusions are based on the re-sults of the FEA simulation. They concerned the influence of the type of supporting structure and connection between the bodies on the static stiff-ness, forms of vibrations and dynamic stiffness of machine tools

Application of 1H NMR spectroscopy in assessment of the course of hydrocarbon contaminant biodegradation

Oceniono przydatność techniki spektroskopii 1H NMR do charakterystyki zmian w strukturze chemicznej substancji naftowych (olej napędowy i ropa naftowa) oraz odpadowej smoły gazowniczej zachodzących w procesie ich biodegradacji. Proces biodegradacji prowadzono przez 14 dób, wykorzystując szczepy bakterii wyizolowane z gleby skażonej produktami naftowymi. Skuteczność biodegradacji była zróżnicowana i w przypadku oleju napędowego wynosiła 89%, ropy naftowej – 45% i smoły gazowniczej – 26%. Analiza widm 1H NMR substratów wykazała duże różnice w rozkładzie protonów alifatycznych i aromatycznych między próbkami naftowymi i smołą gazowniczą. Substraty naftowe charakteryzowały się około 3-krotnie mniejszym współczynnikiem aromatyczności (fA=0,12 i 0,14) oraz wzrostem wartości tego parametru w produktach biodegradacji. Potwierdza to obecność w substancjach naftowych składników alifatycznych, łatwo ulegających biodegradacji. Duże różnice wartości parametru fA wskazują, że może być on wykorzystany do różnicowania źródeł zanieczyszczeń węglowodorowych w próbkach środowiskowych. Dodatkową zaletą techniki 1H NMR jest mała ilość analitów potrzebna do analizy oraz fakt, że należy do grupy badań nieniszczących.Suitability of 1H NMR spectroscopy for evaluation of changes in chemical structure of petroleum substances (diesel and crude oils) and coal tar waste upon their biodegradation was assessed. Biodegradation was carried out for 14 days using bacterial strains isolated from petroleum-contaminated soil. Biodegradation effectiveness varied, amounting to 89% for diesel oil, 45% for crude oil and 26% for coal tar. 1H NMR spectra analysis demonstrated major differences in the distribution of aliphatic and aromatic protons between petroleum samples and coal tar. The aromaticity factor of petroleum substrates was about 3 times lower (fA=0.12 and 0.14) and it increased in the biodegradation products. This confirms presence of aliphatic components, readily biodegradable, in petroleum substances. Major differences in the fA parameter values indicate that it can be used to differentiate between the sources of hydrocarbon contamination in environmental samples. An additional advantage of the 1H NMR technique is a small amount of analyte required for analysis and the non-destructive character of the technique

Strategic research project of The National Centre for Research and Development ‘Technologies supporting the development of safe nuclear power’ Research task No. 6 „Development of nuclear safety and radiological protection methods for the nuclear power engineering’s current and future needs” Objective 1: General concept and methodology for baseline environmental research and public health investigation in the foreseen location of NPP

Zasadniczym celem studiów eksperckich CELU 1 było opracowanie szczegółowych procedur pozwalających na stworzenie sieci monitoringu w otoczeniu obiektu jądrowego, ze zróżnicowaniem na monitoring na terenie EJ (w strefie kontrolowanej) oraz otoczenia elektrowni jądrowej rozumianego jako obszar ograniczanego użytkowania, jak również sieci monitoringu na obszarze całego kraju. Opracowania adresowane są do szerokiego kręgu użytkowników, jak np: służby pomiarów skażeń promieniotwórczych środowiska, kierowników projektów badawczych ukierunkowanych na prowadzenie badań środowiskowych, operatorów i personelu przyszłej polskiej elektrowni jądrowej, ekspertów w zakresie ochrony środowiska. Podstawą tych opracowań były ostatnie zalecenia i poradniki Międzynarodowej Agencji Energii Atomowej (MAEA) oraz Dyrektywy UE jak również metodyka wdrożona przez Komisję do spraw Energii Atomowej USA (NRC). W szczególności opracowana w ramach CELU 1 metodyka pozwala na profesjonalne planowanie badań środowiskowych oraz na przestrzenną analizę uzyskanych danych pomiarowych metodami geostatystycznymi.The main goal of Objective 1 was development of detailed procedures that could provide guidance how design and construct the monitoring networks around nuclear facility both inside the object i.e. for controlled zone and outside the object i.e. in restricted area as well as network for whole country. Presented techniques are addressed to large groups of users as: radiation monitoring service of environmental contamination, leaders of environmental research projects, operators and staff of planned polish NPP, specialists of environmental protection etc. The Objective 1 documentation was elaborated base on last IAEA recommendations, Directives of European Commission and USA Nuclear Regulatory Commission procedures. Particularly, developed methodology can be used for professional planning of environmental research and special analysis of measurement data by advanced geostatistics models