The red fox is one of the most adaptable carnivores inhabiting cities. The aim of our study was to describe the process of Warsaw colonization by the red fox. We focused on: (1) the fox distribution ...in Warsaw on the basis of presence-absence data (2005-2012) over a grid of 1 × 1 km
, (2) the process of settlement in 29 green areas (study periods 1976-1978, 2004-2012, and 2016-2019) in relation to habitat type, and (3) temporal and spatial patterns of the red fox incidents (1998-2015) reported by Warsaw citizens. We found out that: (1) the red fox penetrated the whole city (i.e. its presence was confirmed in all squares of the grid), (2) 21% of the green areas were colonized in 1976-1978 but 93% in 2016-2019. Forests and riparian habitats were occupied more frequently than parks and cemeteries in 1976-1978 with no difference in the further years; (3) the probability of the fox incidents increased over years, was higher in June-October, on working days, and around noon, and with the share of discontinuous urban fabric in the buffers around incident locations. Nevertheless, the incidents only partially reflect population abundance trends and activity patterns of the species, so should be treated cautiously.
Loss of genetic variation negatively impacts breeding efforts and food security. Genebanks house over 7 million accessions representing vast allelic diversity that is a resource for sustainable ...breeding. Discovery of DNA variations is an important step in the efficient use of these resources. While technologies have improved and costs dropped, it remains impractical to consider resequencing millions of accessions. Candidate genes are known for most agronomic traits, providing a list of high priority targets. Heterogeneity in seed stocks means that multiple samples from an accession need to be evaluated to recover available alleles. To address this we developed a pooled amplicon sequencing approach and applied it to the out-crossing cereal rye (Secale cereale L.).
Using the amplicon sequencing approach 95 rye accessions of different improvement status and worldwide origin, each represented by a pooled sample comprising DNA of 96 individual plants, were evaluated for sequence variation in six candidate genes with significant functions on biotic and abiotic stress resistance, and seed quality. Seventy-four predicted deleterious variants were identified using multiple algorithms. Rare variants were recovered including those found only in a low percentage of seed.
We conclude that this approach provides a rapid and flexible method for evaluating stock heterogeneity, probing allele diversity, and recovering previously hidden variation. A large extent of within-population heterogeneity revealed in the study provides an important point for consideration during rye germplasm conservation and utilization efforts.
During domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future ...targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection.
Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production.
Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.
Artificial canopy gaps (forest openings) are frequently used as an element of regeneration cutting. The development of regeneration in gaps can be controlled by selecting a relevant size and shape ...for the gap, which will regulate the radiation microclimate inside it. Based on the size and shape of a gap computer models can assess where solar radiation is decreased or eliminated by the surrounding canopy. The accuracy of such models to a large extent depends on how the modeled shape of a gap matches the actual shape of the gap. The aim of this study was to compare the results of modeling solar radiation availability by applying Solar Radiation Tools (SRT) that use a different digital surface model (DSM) for a description of the shape of a studied gap, with the results of the analysis of 27 hemispherical photographs. The three-dimensional gap shape was approximated with the use of simple geometrical prisms or airborne laser scanning (LiDAR) data. The impact of two variations of exposure (automatic and manual underexposure) and two variations of automatic thresholding on the congruence of SRT and Gap Light Analyzer (GLA) results were studied. Taking into account information on differences in height between trees surrounding the gap enhanced the results of modeling. The best results were obtained when the boundary of the gap base estimated from LiDAR was expanded in all directions by a value close to a mean radius of the crowns of surrounding trees. Modeling of radiation conditions on the gap floor based on LiDAR data by an SRT program is efficient and more time effective than taking hemispherical photographs. The proposed solution can be successfully applied as a trustworthy source of information about light conditions in gaps, which is needed for management decision-making in silviculture.
Background
A challenge in current forestry is adaptation of managed forests to climate change, which is likely to alter the main processes of forest dynamics, i.e. natural regeneration. Scots pine ...will probably lose some parts of its distribution area in Europe. However, two native oaks, pedunculate and sessile may maintain or expand the area of their occurrence in central Europe. The utilization of spontaneous (not initialized by foresters) oak regeneration in Scots pine stands for the creation of next generation stands is one of the adaptation methods to climate change. Many factors influencing pedunculate oak regeneration are well known, but there is a lack of knowledge on the relation between soil enzyme activity and the establishment and development of the species. The aim of the study was to identify the relationships among stand characteristics, herb species composition, soil enzyme activity and the establishment or recruitment of oak regeneration in Scots pine-dominated stands.
Results
The one of the most influential factors shaping the oak seedling count was dehydrogenase activity in the humus horizon. We found that plots without litter and fern cover had higher seedling density. The raspberry ground cover and birch crown projection area had a positive influence on oak seedling number. The factor indicating good conditions for high density of oak saplings was phosphatase activity in the organic horizon. The same enzyme activity but in humus horizon described conditions in which more numerous recruits were observed.
Conclusions
The activity of soil enzymes can be used as the predictor of the establishment and advancement of oak regeneration but also could be seen as a new dimension of oak regeneration. The general density of spontaneous oak regeneration was not sufficient for the creation of new generation forest stands dominated by oak, but it is possible to use them as admixtures in new generation stands.
Benzoxazinoids (BXs) are secondary metabolites with diverse functions, but are primarily involved in protecting plants, mainly from the family Poaceae, against insects and fungal pathogens. Rye is a ...cereal crop that is highly resistant to biotic stresses. However, its susceptibility to brown rust caused by Puccinia recondita f. sp. secalis (Prs) is still a major problem affecting its commercial production. Additionally, the genetic and metabolic factors related to this disease remain poorly characterized. In this study, we investigated whether and to what extent the brown rust infection and the inoculation procedure affect the contents of specific BXs (HBOA, GDIBOA, DIBOA, GDIMBOA, DIMBOA, and MBOA) and the expression of genes related to BX (ScBx1-5, ScIgl, and Scglu). We revealed that treatments with water and a urediniospore suspension usually downregulate gene expression levels. Moreover, HBOA and DIBOA contents decreased, whereas the contents of the remaining metabolites increased. Specifically, the MBOA content increased more after the mock treatment than after the Prs treatment, whereas the increase in GDIBOA and GDIMBOA levels was usually due to the Prs infection, especially at two of the most critical time-points, 17 and 24 h post-treatment. Therefore, GDIBOA and GDIMBOA are glucosides that are important components of rye defence responses to brown rust. Furthermore, along with MBOA, they protect rye against the stress associated with the inoculation procedure used in this study.
Benzoxazinoids (BXs) are specialized metabolites with protective properties that are synthesized predominantly by Poaceae species, including rye (Secale cereale). Among factors known to influence BXs ...production, prolonged low temperature has not been studied previously. In this study, the influence of cultivation at 4 °C, which is essential for vernalization, on the concentration of BXs (HBOA, DIBOA, GDIBOA, DIMBOA, GDIMBOA, and MBOA) and the expression level of genes involved in the BX biosynthesis pathway (ScBx1–ScBx5 and ScIgl) in three rye inbred lines was investigated. After cultivation for seven weeks at 4 °C, the expression level of all analyzed genes and BX concentrations had decreased compared with those at the initiation of treatment (21 days after germination) in control and cold-treated plants. At this time point, the decrease in BX concentrations and gene expression was lower in cold-treated plants than in untreated plants. In contrast, at 77 days after germination, the gene expression levels and BX concentrations in untreated plants had generally increased. Investigation of the vernalization impact on rye BXs accumulation, as well as on Bx gene expression, may aid with determination of the most suitable winter lines and cultivars of rye for cultivation and breeding purposes.
•The advancement of silver fir to high sapling stage is worse outside its range.•Climate factors were important at the beginning of the regeneration.•The advancement to higher classes depends on ...stand composition and stand structure.•Mono-layered structure of planted stands hamper advancement of fir regeneration.•Improper silviculture limits success of fir regeneration outside the natural range.
Silver fir (Abies alba Mill.) is one of the most important forest tree species in Europe potentially prone to climate changes. The northern limit of its distribution is in central Poland but fir stands were planted also in northern part of the country. It gives opportunity to investigate the potential for silver fir to expand into northern (cooler) Europe which could be an important issue in the face of changing climate. The aim of this research was to identify factors influencing the establishment and advancement of silver fir regeneration within and outside its natural range. Using data collected on sample plots in 48 stands, we examined influences of climatic and stand factors on establishment and development of silver fir regeneration. The Boruta algorithm was used to identify variables relevant for particular stages of fir regeneration (short and tall seedlings and saplings). The variable location (indicating that the analysed plot was located inside or outside the natural range of silver fir) was not the most important variable for any size classes of silver fir regeneration (Boruta algorithm). We found that the mean values of diameter of breast height (DBH) and height of the dominant firs were larger for northerly plantations than for stands within the natural range. The density of seedlings was similar within and outside the natural range but density of saplings was lower, especially tall saplings. Climatic variables (continentality index and summer heat: moisture ratio) were significant in the models predicting the probability of establishing tall seedlings and short saplings. Stand composition was an important factor for all the regeneration stages. For short seedlings, local (sample plot) stand composition was important. The establishment of short seedlings was negatively influenced by shade-tolerant species (sum of the heights of the shade-tolerant trees per plot). Species composition at the forest stand spatial scale was more important for tall seedlings and saplings. The proportion of Scots pine in forest stand volume positively influenced the establishment of tall seedlings. We found that with the growth of regeneration, the role of free space availability increased. The occurrence of tall seedlings and saplings was negatively influenced by increased space filling. Introducing silver fir outside of its natural range requires adjustment to management practices such as creation of vertically diversified mixed stands, decreasing stand stocking, regulation of stand species composition. A lack of experience with silver fir silviculture in northern Poland is one of important factors limiting the advancement of regeneration to the stage of high saplings outside the natural range.
The wild population of fallow deer in Central Europe has grown considerably over the last decade. However, information on feeding habits of this alien species in relation to the indigenous red deer ...or roe deer, in areas of their co-occurrence, is scarce. A prevailing view maintains that their food-niches are distinct, although direct comparative studies have not been carried out. Therefore, the aim of the research was to compare the diets of fallow, red, and roe deer feeding in the same habitat. Research was based on the rumen contents of 242 animals hunted in the autumn-winter season in the forests of Southern Poland. The analyses demonstrated that fallow deer are moderate grazers in such conditions and eat more graminoids in comparison to red or roe deer (36.4% vs. 16.1% or 5.5%, respectively). On the other hand, it feeds on less browse (17.2% vs. 41.4%) or dwarf shrubs (8.4% vs. 19.0%) than red deer, and on less bramble (10.9% vs. 34.6%) or forbs (4.0% vs. 7.6%) in comparison to roe deer (P=0.05). Although the diets of the three deer species differ in terms of the proportion of each food type in their diet, overlapping of their food-niches is high (52.6%).
Two genes,
and
, both encoding indole-3-glycerol phosphate lyase (IGL), are believed to control the conversion of indole-3-glycerol phosphate (IGP) to indole. The first of these has generally been ...supposed to be regulated developmentally, being expressed at early stages of plant development with the indole being used in the benzoxazinoid (BX) biosynthesis pathway. In contrast, it has been proposed that the second one is regulated by stresses and that the associated free indole is secreted as a volatile. However, our previous results contradicted this. In the present study, we show that the
gene takes over the role of
at later developmental stages, between the 42nd and 70th days after germination. In the majority of plants with silenced
expression,
was either expressed at a significantly higher level than
or it was the only gene with detectable expression. Therefore, we postulate that the synthesis of indole used in BX biosynthesis in rye is controlled by both
and
, which are both regulated developmentally and by stresses. In silico and in vivo analyses of the promoter sequences further confirmed our hypothesis that the roles and modes of regulation of the
and
genes are similar.
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