Validation of a real-time PCR for the quantitative estimation of a G143A mutation in the cytochrome bc1 gene of Pyrenophora teres

A single nucleotide polymorphism (SNP) in the cytochrome b gene confers resistance to strobilurin fungicides for several fungal pathogens. Therefore, on the basis of a change at amino acid position 143 from glycine to alanine, a real-time PCR assay was established for the quantitative detection of the analogous SNP in the cytochrome b sequence of Pyrenophora teres Drechsler, which causes barley net blotch. Allelic discrimination was achieved by using allele specific primers with artificially mismatched nucleic acid bases and minor groove binding probes. Validation parameters for the lower limits of the working range, namely limits of detection (LOD) and limits of quantification (LOQ), were statistically determined by the variance of calibration data, as well as by the variance of the 100% non-strobilurin-resistant allele DNA sample (blank values). It was found that the detection was limited by the variance of blank values (five in 801 458 copies; 0.0006%), whereas the quantification was limited by the variance of calibration data (37 in 801 458 copies; 0.0046%). The real-time PCR assay was finally used to monitor strobilurin-resistant cytochrome b alleles in barley net blotch field samples, which were already classified in in vivo biotests to be fully sensitive to strobilurins. All signals for strobilurin-resistant cytochrome b alleles were below the LOD, and therefore the results are in total agreement with the phenotypes revealed by biotests.     

Different reactions of central and marginal provenances of Fagus sylvatica to experimental drought

Climate extremes are expected to increase in frequency and magnitude as a consequence of global warming, threatening the functioning, services and goods of forest ecosystems. Across Europe, the ecologically and economically important tree species Fagus sylvatica is expected to suffer particularly under such conditions. The regional introduction of provenances from drier and warmer climates is one option to adapt beech forest ecosystems to these adverse effects of climate change. Marginal populations from the drought-prone southern and north-eastern edges of the species’ distribution come into focus in search of suitable candidates for Central European deciduous forests. Here, we test three marginal provenances (Spain, Bulgaria and Poland) and three provenances from the centre of the distribution range (Germany) for their response to drought in two different soil types (sand, loam) in a full factorial common garden experiment in Landau, Germany. Drought impacted all growth parameters negatively (leaf damage +22 % (percentage points), height ?40 % and diameter increment ?41 %), and the sandy substrate exacerbated this effect. However, provenances differed in their response to drought and soil type. Evidence for a local adaptation to summer drought was detected, especially in terms of mortality rates. The Bulgarian and Spanish provenance showed a stable performance under drought conditions (BG ?27 % in diameter increment; ES ?32 %), compared to the Polish (?48 %) or the most sensitive German provenances (?57 %), yet for Bulgaria on a low level of total increment. This may indicate a trade-off between drought tolerance and growth. Therefore, a sole focus on drought-resistant marginal provenances seems to not be conducive, as they might be less adapted to other climatic factors, e.g. frost, as well. However, intermixed with local Central European provenances, these may act as functional insurance in future drought-prone forest stands.     

Household and farm attributes affecting adoption of smallholder timber management practices by tree growers in Gunungkidul region,Indonesia

Farm household characteristics determine the success of programs promoting agroforestry systems and practices. This paper reports household and farm factors affecting the adoption of timber management practices by smallholders in the Gunungkidul region, Central Java, Indonesia. The research used three logistic regression analysis models—based on each household and farm characteristic, and a composite of both together—to identify the key factors influencing farmers’ adoption and management decisions, and their relative importance. A sample of 152 farmers who managed their trees primarily for timber production was compared to a sample of 115 farmers with similar socio-economic characteristics who did not. The household condition and composite models identified both on-farm and off-farm gross incomes as significant factors affecting farmers’ decisions to manage timber trees. The models confirmed that farmers with larger farms, and with higher on- and off-farm incomes, were more likely to manage their trees for timber production. These results have implications for extension programs that promote adoption of commercial timber management by smallholders in the case study and similar regions.     

Ecological and genetic measurements of dispersal in a threatened dragonfly

Leucorrhinia caudalis is a rare dragonfly, threatened throughout its European distribution. The species was formerly widespread in the Swiss lowlands, but only a single population remained in the 1980s. However, a spread has recently been observed, with additional ponds being colonised, sometimes at considerable distance. Despite this evidence of recent long-distance dispersal, it is unknown whether L. caudalis regularly moves among ponds or whether this is a rather rare event. A combination of an ecological mark-resight and a population genetic study was applied to investigate contemporary dispersal and the genetic footprint of the recent population history of L. caudalis in Switzerland. DNA for genetic microsatellite analysis was extracted from exuviae. The mark-resight study and the genetic analysis gave congruent results. They showed that L. caudalis is mostly a sedentary species, with only a few contemporary dispersal events over distances up to 5 km being observed. The genetic analysis was in agreement with the recent population history of the Swiss populations. The oldest and largest population showed large genetic diversity and acted as source population for the recent spread of L. caudalis in Switzerland. Recurrent gene flow among this source population and close populations caused substantial local genetic variation in the latter, as well as low population differentiation. The two recently founded distant populations (?30 km distance) were genetically less diverse and highly differentiated. These distant populations and another recently colonised population also expressed signatures of genetic bottlenecks.     

Mikrosondenuntersuchungen an unterschiedlich stark mit Schwermetallen belasteten Böden. 2. Gehalte an Schwermetallen und anderen Elementen in Huminstoffaggregationen,Streustoffen und Holzkohlepartikeln

Electron microprobe studies on soil samples with varying heavy metal contamination. 2. Contents of heavy metals and other elements in aggregations of humic substances, litter residues and charcoal particles EMA point analysis show that the organic matter constituents of heavy metal contaminated soils are highly enriched with heavy metals. The maximal trace element accumulation were for Cu up to 13,000 mg/kg, for Zn up to 48,000 mg/kg, for Cd up to 2,100 mg/kg and for Pb up to 193,000 mg/kg. The affinity for the accumulation of the different heavy metals in aggregations of humic substances can be described by the sequence Cu > Pb ? Cd > Zn ? Ni > Co. In very strongly acidified humic top soil horizons the Pb and Cd accumulation in the organic matter constituents is in competition with the accumulation in Fe and Mn oxides. The heavy metal contents (especially of Cu) of the organic matter are often correlated with the content of organically bound calcium. The EMA results also show that high heavy metal amounts occur in combination with Ca-accumulations in the epidermis and the outer bark parenchym of decayed roots. EMA point analysis of the interior of fungus sclerotias show that sclerotias can contain high amounts of heavy metals, in particular lead (up to 49,700 mg Pb/kg). From statistical results of EMA point analysis follows that lead and other heavy metals attached to humic substances are not only bound as metal organic complexes but also as organic metal phosphate complexes. Also charcoal particles of polluted soils contain high amounts of heay metals. The accumulation affinity is quite similar to that of humic substances.     

Recultivation of Agricultural Land Impaired by Construction of a Hydropower Plant on the Sava River,Slovenia

Hydropower plants on the lower river Sava, Slovenia, were developed without sealing the underground upstream. As a consequence, without the countermeasures of elevating and recultivating, the agricultural land on the river banks would be inundated because of the water‐table increase of the river. To remedy this, the fields were elevated and recultivated. The goal of this study was to assess soil quality and production potential after land raising and recultivation and to answer the question whether it is possible to recover soil quality and crop yield after large‐scale mass manipulation, such as land raising. After recultivation and after the second year of land reuse for the two cultures grass–clover mixture and corn on two sites, Middle Pijavsko and Lower Pijavsko, soil physical and chemical characteristics and crop yields were evaluated. Mixing of topsoil with the second horizon during removal and during backfill with filling material resulted in uneven soil fertility, plant growth and decreased yield. Driving on the refilled second layer with heavy machinery caused soil compaction in the Middle Pijavsko in spite of favourable soil texture (loam, 38·7% sand). On the areas with very high sand content (over 55%) and low clay content (10%), soil compaction was not as severe or persistent. Recultivation measures restored the agricultural land almost to the production potential prior to powerplant construction. Immediate intensive land use (corn) showed less favourable effect on soil characteristics. Copyright © 2015 John Wiley & Sons, Ltd.     

Development and application of functional markers in maize

Summary Functional markers (FMs) are derived from polymorphic sites within genes causally involved in phenotypic trait variation (Andersen, J.R. & T. Lübberstedt, 2003. Trends Plant Sci 8: 554–560). FM development requires allele sequences of functionally characterized genes from which polymorphic, functional motifs affecting plant phenotype can be identified. In maize and other species with low levels of linkage disequilibrium, association studies have the potential to identify sequence motifs, such as a few nucleotides or insertions/deletions, affecting trait expression. In one of the pioneering studies, nine sequence motifs in the dwarf8 gene of maize were shown to be associated with variation for flowering time (Thornsberry, J.M., M.M. Goodman, J. Doebley, S. Kresovich, D. Nielsen & E.S. Buckler, 2001. Nat Genet 28: 286–289). Proof of sequence motif function can be obtained by comparing isogenic genotypes differing in single sequence motifs. At current, the most appropriate approach for this purpose in crops is targeting induced local lesions in genomes (TILLING) (McCallum, C.M., L. Comai, E.A. Greene & S. Henikoff, 2000. Nat Biotechnol 18: 455–457). In central Europe, maize is mainly grown as forage crop, with forage quality as major trait, which can be determined as proportion of digestible neutral detergent fiber (DNDF). Brown midrib gene knock out mutations have been shown to be beneficial for forage quality but disadvantageous for overall agronomic performance. Two brown midrib genes (bm1 and bm3) have been shown to be involved in monolignol biosynthesis. These two and additional lignin biosynthesis genes have been isolated based on sequence homology. Additional candidate genes putatively affecting forage quality have been identified by expression profiling using, e.g., isogenic bm lines. Furthermore, we identified an association between a polymorphism at the COMT locus and DNDF in a collection of European elite inbred lines.     

Chromosomal location of genes for resistance to powdery mildew in common wheat (Triticum aestivum L. em Thell.). 9. Gene MlZec1 from the Triticum dicoccoides-derived wheat line Zecoi-1

The Triticum dicoccoides-derived wheat line Zecoi-1 provides effective protection against powdery mildew. F₃ segregation analysis of Chinese Spring × Zecoi-1 hybrids showed that resistance in line Zecoi-1 is controlled by a single dominant gene. Amplified fragment length polymorphism (AFLP) analysis of bulked segregants from F₃s showing the homozygous resistant and susceptible phenotypes identified eight markers, of which four were associated with the resistance allele in repulsion phase. Following the assignment of these four repulsion phase AFLP markers to wheat chromosome 2B with the aid of Chinese Spring nulli-tetrasomic lines, they were physically mapped in the terminal breakpoint interval 0.89 (2BL-6)–1.00 (telomere) of chromosome 2BL. Genetic and physical mapping of simple sequence repeat markers from the distal half of chromosome 2BL located the wild emmer-derived powdery mildew resistance gene distal of breakpoint 0.89 in deletion line 2BL-6. Based on disease response patterns, genomic origin and chromosomal location the resistance gene in Zecoi-1 is temporarily designated MlZec1.     

Adsorption—desorption and/or precipitation—dissolution processes of zinc in soils

The concentrations of trace and toxic metals in soil solutions are explained by several authors either in terms of adsorption—desorption or precipitation—dissolution reactions in soils. Data have been given for zinc to test the applicability of both concepts. The results show that the concentrations of zinc in equilibrium solutions with soil clay fractions and whole soil samples at pH values below 7 are determined exclusively by adsorption—desorption reactions for various pH's, contents of bound zinc and compositions of soils. At neutral to alkaline pH values precipitation—dissolution reactions of zinc may take place. There is some evidence that formation of zinc silicates may control the zinc concentration in solution provided natural complexing agents are absent, the affinity of the soil for zinc is low and the content of reaching zinc is high (> ～ 100 ppm). Even at pH values above 7, the formation of other zinc compounds is unlikely in most soils because additions of large amounts of zinc are required to ensure saturation of the adsorption sites of different soil components before the zinc concentration in the soil solution can increase sufficiently to bring about the precipitation of definite compounds. Model experiments in CaCO₃-buffered systems showed that the adsorption capacity for specifically adsorbed zinc (in μmole/g) by the following components increased in the order CaCO₃ (0.44), bentonite (44), humic acid (842), amorphous Fe- and Al-oxides (1190, 1310) and δ -MnO₂ (1540) and demonstrated the importance of Mn-, Fe-, and Al-oxides and humic substances for the binding of zinc in soils containing carbonates, and thus indicate the special role of these components in limiting precipitation reactions.