Identification of PCR-amplified genetically modified organisms (GMOs) DNA by peptide nucleic acid (PNA) probes in anion-exchange chromatographic analysis

PCR products obtained by selective amplification of transgenic DNA derived from food samples containing Roundup Ready soybean or Bt-176 maize have been analyzed by anion-exchange HPLC. Peptide nucleic acids (PNAs), oligonucleotide analogues known to bind to complementary single-stranded DNA with high affinity and specificity, have been used as specific probes in order to assess the identity of the peaks observed. Two different protocols were adopted in order to obtain single-stranded DNA: amplification with an excess of one primer or digestion of one DNA strand. The single-stranded DNA was mixed with the PNA probe, and the presence of a specific sequence was revealed through detection of the corresponding PNA:DNA peak with significantly different retention time. Advantages and limits of this approach are discussed. The method was tested with reference materials and subsequently applied to commercial samples.     

Landscape evaluation of female black bear habitat effectiveness and capability in the North Cascades, Washington

We used logistic regression to derive scaled resource selection functions (RSFs) for female black bears at two study areas in the North Cascades Mountains. We tested the hypothesis that the influence of roads would result in potential habitat effectiveness (RSFs without the influence of roads) being greater than realized habitat effectiveness (RSFs with roads). Roads consistently had a negative influence on black bear RSFs across seasons and study areas. Roads reduced habitat effectiveness during all seasons at both study areas and changes in the potential habitat values ranged from 1.7% to 16.9%. The greatest reduction in habitat values occurred during the early-season on the west-side study area due to high open road densities. These results support the hypothesis that roads reduce habitat effectiveness for black bears. The influence of roads could be reduced through road closures to reduce open road densities and limit traffic volumes. We then used the scaled RSFs in a habitat-based population model to assess the influences of timber harvest and roads on potential black bear population sizes. On the west-side study area the potential black bear population size was most influenced by moderate use roads and timber harvest during the early-season (41% reduction). On the east-side study area, low use roads had the greatest effect on potential black bear population during the early-season (10% reduction). During the late-season, in both study areas, roads had less influence on the potential population sizes as bears were able to access habitats away from roads. The habitat-population model provided reasonable estimates of bear densities compared to other study areas with similar habitats and could be extrapolated to estimate potential black bear populations in other areas with similar habitats. This approach may provide a useful link between the landscape ecology and population biology of black bears, and could eventually be useful in the development of habitat-based population viability analyses.     

Durum wheat varieties in N‐deficient environments and organic farming: a comparison of yield,quality and stability performances

Stability and reliability of yield and quality for 15 durum wheat genotypes (old and modern) were evaluated in a 5‐year experiment (southern Italy) in organic farming. Genotypes were grown at two N levels (0 and 80 kg/ha), with the aim of evaluating ‘genotype × environment’ (GE) interactions and their role on genotype selection in N‐limited environments. Several approaches to stability were used, within the frame of mixed models and additive main effects and multiplicative interaction analysis, and their validity in stressful conditions and organic farming was discussed. Especially for protein and gluten content, results indicate high environmental variability and the presence of crossover ‘N × environment’ interactions, which supports the need for specific breeding programmes in N‐deficient environments. The average response was strongly affected by N availability (on average, yield was 2.95 and 3.42 t/ha, protein content was 11.6% and 12.85%, gluten content was 8.55% and 9.92%, respectively, at 0 and 80 kg N/ha), and few genotypes gave high yield and quality at both fertilization levels. Only ‘Gargano’ and ‘Fortore’ showed a good inter‐year stability at both N levels. The old cultivars gave minimal responsiveness to increased N input, but gave good results in limiting conditions, indicating that they may play a role in organic farming.     

Characterization of resistance to the wheat stem sawfly in spring wheat landrace accessions from targeted geographic regions of the world

Plant landraces have long been recognized as potential gene pools for biotic and abiotic stress-related genes. This research used spring wheat landrace accessions to identify new sources of resistance to the wheat stem sawfly (WSS) (Cephus cinctus Norton), an important insect pest of wheat in the northern Great Plains of North America. Screening efforts targeted 1409 accessions from six geographical areas of the world where other species of grain sawflies are endemic or where a high frequency of accessions possesses the resistance characteristic of solid stems. Resistance was observed in approximately 14% of accessions. Half of the lines displayed both antixenosis and antibiosis types of resistance. Among the resistant accessions, 41% had solid or semi-solid stems. Molecular genetic screening for haplotypes at the solid stem QTL, Qss.msub.3BL, showed that 15% of lines shared the haplotype derived from ‘S-615’, the original donor of the solid stem trait to North American germplasm. Other haplotypes associated with solid stems were also observed. Haplotype diversity was greater in the center of origin of wheat. Evaluation of a representative set of resistant landrace accessions in replicated field trials at four locations over a three year period identified accessions with potential genes for reduced WSS infestation, increased WSS mortality, and increased indirect defense via parasitoids. Exploitation of distinct types of plant defense will expand the genetic diversity for WSS resistance currently present in elite breeding lines.     

Association mapping reveals loci associated with multiple traits that affect grain yield and adaptation in soft winter wheat

Genome-wide association studies (GWAS) are useful to facilitate crop improvement via enhanced knowledge of marker-trait associations (MTA). A GWAS for grain yield (GY), yield components, and agronomic traits was conducted using a diverse panel of 239 soft red winter wheat (Triticum aestivum) genotypes evaluated across two growing seasons and eight site-years. Analysis of variance showed significant environment, genotype, and genotype-by-environment effects for GY and yield components. Narrow sense heritability of GY (h ²  = 0.48) was moderate compared to other traits including plant height (h ²  = 0.81) and kernel weight (h ²  = 0.77). There were 112 significant MTA (p < 0.0005) detected for eight measured traits using compressed mixed linear models and 5715 single nucleotide polymorphism markers. MTA for GY and agronomic traits coincided with previously reported QTL for winter and spring wheat. Highly significant MTA for GY showed an overall negative allelic effect for the minor allele, indicating selection against these alleles by breeders. Markers associated with multiple traits observed on chromosomes 1A, 2D, 3B, and 4B with positive minor effects serve as potential targets for marker assisted breeding to select for improvement of GY and related traits. Following marker validation, these multi-trait loci have the potential to be utilized for MAS to improve GY and adaptation of soft red winter wheat.     

QTL mapping of volatile compounds in ripe apples detected by proton transfer reaction-mass spectrometry

The availability of genetic linkage maps enables the detection and analysis of QTLs contributing to quality traits of the genotype. Proton Transfer Reaction Mass Spectrometry (PTR-MS), a relatively novel spectrometric technique, has been applied to measure the headspace composition of the Volatile Organic Compounds (VOCs) emitted by apple fruit genotypes of the progeny ‘Fiesta’ × ‘Discovery’. Fruit samples were characterised by their PTR-MS spectra normalised to total area. QTL analysis for all PTR-MS peaks was carried out and 10 genomic regions associated with the peaks at m/z = 28, 43, 57, 61, 103, 115 and 145 were identified (LOD > 2.5). We show that it is possible to find quantitative trait loci (QTLs) related to PTR-MS characterisation of the headspace composition of single whole apple fruits indicating the presence of a link between molecular characterisation and PTR-MS data. We provide tentative information on the metabolites related to the detected QTLs based on available chemical information. A relation between apple skin colour and peaks related to carbonyl compounds was established. The two authors contributed equally to this work.     

Phosphorus and iron erosion from non-vegetated sites in a post-mining landscape,Lusatia, Germany: Impact on aborning mining lakes

Particulate phosphorus (P) can be transported via soil erosion in overland flow to waters, where it provides a long-term source of P for aquatic biota, and can accelerate freshwater eutrophication. Hence, knowledge of P sources is important for good environmental management. However, data on P, and related Fe, losses from various structures of a post-mining landscape are lacking. A year-long monitoring, and ten short rainfall simulations on plot scale, at ridges and rills and a combination of them, revealed high erosion from bare lignite mining dumps at Schlabendorf-North, Lusatia, Germany. The mean annual soil erosion rate from the year-long monitoring site was 18 × 10⁶ kg km^− 2 yr^− 1, corresponding to 0.034 g m^− 2 min^− 1. The erosion rates were lowest at rill plots (1.9–4.4 g m^− 2 min^− 1), intermediate at ridge plots (14.3–37.1 g m^− 2 min^− 1), and highest at a combined rill and ridge plot (48.7–63.4 g m^− 2 min^− 1). These differences in extent were due to small scale differences in morphology and extreme water repellency. The hydrophobicity leads to very low infiltration, thus generating surface runoff even at low rainfall intensities. Loss rates of P and Fe, as deduced from the year-long erosion rate, were 470–650 kg km^− 2 yr^− 1, and 37.9 × 10³–71 × 10³ kg km^− 2 yr^− 1 respectively. However, these P inputs from lignite mining dump erosion, consisting of P-poor (17–90 μg g^− 1) tertiary spoil materials, into aborning mining lakes, are negligible since they are accompanied by high Fe inputs, which favour an efficient P co-precipitation in the water column.     

Validation of two models for self‐incompatibility in autotetraploid perennial ryegrass using high resolution melting‐based markers

Perennial ryegrass (Lolium perenne L.) displays a two‐locus gametophytic self‐incompatibility (SI) system that remains intact at the tetraploid level. Two models are plausible for SI in autotetraploids. In Model I: both alleles at the S locus and both at the Z locus in diploid pollen matching the female genotype results in incompatibility. In Model II: only one allele at S and one at Z locus in diploid pollen matching the female results in incompatibility. The goals were to determine which of the models best explains SI in our autotetraploid ryegrass population and to evaluate the efficiency of high‐resolution melting (HRM) genotyping for discriminating different iso‐allelic genotypes. The progeny of a cross between two autotetraploids was characterized with three HRM‐based markers co‐segregating with Z. Segregation ratios were used to make inferences about the mode of action of the SI system. The observed segregation differed significantly (P < 0.001) from the expected under Model I, but not from the expected under Model II (P = 0.463). Thus, Model II explains SI in this population, and HRM is an efficient tool to distinguish different iso‐allelic genotypic classes.     

Modelling local-scale determinants and the probability of microarthropod species occurrence in Antarctic soils

Soil fauna in the extreme conditions of Antarctica consists of a few microinvertebrate species patchily distributed at different spatial scales. Populations of the prostigmatic mite Stereotydeus belli and the collembolan Gressittacantha terranova from northern Victoria Land (Antarctica) were used as models to study the effect of soil properties on microarthropod distributions. In agreement with the general assumption that the development and distribution of life in these ecosystems is mainly controlled by abiotic factors, we found that the probability of occurrence of S. belli depends on soil moisture and texture and on the sampling period (which affects the general availability of water); surprisingly, none of the analysed variables were significantly related to the G. terranova distribution. Based on our results and literature data, we propose a theoretical model that introduces biotic interactions among the major factors driving the local distribution of collembolans in Antarctic terrestrial ecosystems.     

Multi-attribute responses of maize inbred lines across managed environments

In maize (Zea mays L.) breeding programs, selection among and within segregating progenies is based mainly on indirect selection criteria. A better understanding of the environment influence on physiological attributes of maize inbred lines is important to the identification and selection of superior inbred lines as well as to successful hybrid seed production. In this study, the size and form of genotype (G) and genotype × environment (G × E) interaction effects for plant grain yield (PGY) and several physiological attributes were examined for 12 maize inbred lines grown in four managed environments, represented by two seasons (Y) and two nitrogen levels. Mixed model analysis revealed that the G effect was relatively high for attributes related to light capture, phenology, early biomass production, and numerical components of PGY. The G × E interaction effect explained most of the variability for PGY, harvest index (HI), and biomass production at maturity. Three-mode principal component analysis allowed us to: (1) describe the associations among multiple attributes across environments, (2) reveal the form of the main patterns of G × E interaction, (3) establish the importance of the genotype × year (G × Y) interaction for kernel number, HI, and biomass at maturity in determining PGY, (4) identify promising genotypes of high-PGY across environments, and (5) detect genotypes of similar response patterns for PGY but with a contrasting relative behavior for other attributes, which may permit the simultaneous selection for grain yield and desired secondary traits. Such selection results would contribute greatly in the identification of superior inbreds than selecting for grain yield alone.