Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement

Background: 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.Results: 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.Conclusions: 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

Modelo bioético para el análisis de la habitabilidad en la vivienda

La habitabilidad se refiere a estas configuraciones del espacio edificado, y se expresa en las diferentes escalas y entornos que el ser humano ha creado para su desarrollo como especie.La habitabilidad, en palabras de Macías, es “la capacidad de los espacios construidos para satisfacer las necesidades objetivas y subjetivas de los individuos, en estrecha relación con los ambientes socioculturales y naturales hacia la mejora de la calidad de vida”. (De Hoyos Martínez, et al., 2014)El ser humano ha modificado la configuración del espacio que lo rodea a lo largo de la historia, con el fin de hacer del mundo un lugar habitable, adaptándolo para proveerse de sitios para vivir, descansar, transitar, en fin, para realizar todas sus actividades cotidianas. Dichas modificaciones tienen lugar en las diversas escalas del espacio construido, entre los que se encuentran la vivienda, el barrio y la ciudad, y que, según Paola Coppola (2004), varían de acuerdo con las características socio-territoriales dentro de las que son creadas

Assessment of sea buckthorn (Hippophaë rhamnoides L.) long distance dispersal on the internal waste heap of the Bełchatów lignite mine

Long distance dispersal is a key process occurring in plant communities and is particularly important for pioneer species like sea-buckthorn (Hippophaë rhamnoides L.) which survival strongly depends on colonizing newly created post-disturbance habitats. Sea-buckthorn, a cluster-forming shrub, is commonly used in Poland in the reclamation of soil-less areas devastated the by mining industry and for these areas a generative expansion of planted populations is usually observed. The main objective of this study was to assess the long-distance dispersal of this species in areas previously disturbed by industrial activity. Our observations were made on a 223.75 ha large section of the internal waste heap of the Bełchatów lignite mine, Central Poland. The area was colonized by sea-buckthorn specimens originating from a population planted on the nearby external waste heap. During the search for newly established sea-buckthorn clusters, their position and size were recorded and the preferences for specific site conditions were assessed using the Ivlev’s electivity index. New specimen were observed at distances between 600 m and 3600 m from their potential seed source. The mean cluster density was 1.37 ha−1. The observed pattern of long distance dispersal is linked with to behavior of frugivorous birds. The largest cluster densities were observed along ditches (9.83 ha−1) and on open areas with less developed plant cover, while the lowest cluster density occurred in afforested areas (0.51 ha−1). Poor sandy substrate reduced the probability of plant establishment compared to richer loamy sands. There appeared to be no influence of slope aspect on the probability of sea-buckthorn establishment

Modeling light conditions on the forest floor

Contemporary models of light conditions on the forest floor can be divided into two categories: undercanopy models that allow the light conditions in a stand under the canopy to be simulated, and models that take into account shielding from the side. Under-canopy models precisely estimate the availability of wavelengths of light spatially distributed under the canopy of stands: however these models require a large amount of data on the spatial structure of forest stands. The other class of models describes the light conditions on a particular open surface. These incorporate shielding from the side and are easier to use as they require less data than under-canopy models. In practice, in forest conditions, such models require data on the size, shape, and geographical location of surveyed surfaces (e.g. gaps, and cut areas) and on the height of the surrounding stand. Often, these data are available in databases, such as the State Forest Information System (SILP), can otherwise be obtained relatively easily (and inexpensively). Compared to under-canopy models, these models provide a cheap way to obtain useful information on variation in the light environment that affects the microclimate for regenerating plants on clearcuts and canopy gaps

Scots pine Pinus sylvestris mortality after surface fire in oligotrophic pine forest Peucedano-Pinetum in Kampinos National Park

Pines are generally fire-resistant trees. There is a shortage of research on the behaviour of Scots pine after surface fire in older stands. The aim of the work was to describe the effect of the surface fire intensity on the mortality of pines of various diameter at breast height (DBH), including older trees. The research was conducted in Peucedano-Pinetum oligotrophic Scots-pine forest in Kampinos National Park (KPN, central Poland) on the area of two adjacent surface fire sites originated in spring 2015 in 60- to 200-year-old stands (site area: 10,92 ha). There were 45 (28 burned and 17 control) permanent plots established after the fire. The share of not burned, superficially burned and completely burnout organic horizon of the soil was determined within all of them. DBH and location of pine trees were measured within all of the plots on the area of 200 m2. For all of the trees for which full information about soil organic horizon damage was mapped, the prevailing type of disturbance in their close neighbourhoods with radii of 1 and 2 m was assessed. The mortality of trees was assessed after each vegetation period up to 2017, basing on the presence of green needles on the trees. The influence of fire intensity on the survival of trees was examined on whole permanent plot level as well as on individual tree level. Strong linear correlation was observed between Scots pine mortality and the share of plots area with damaged organic layer, especially at the end of the third vegetation period after fire. Logistic regression models constructed for individual trees suggest that bigger tree diameter (hence, thicker bark) diminished the odds of mortality only after two vegetation periods from the fire. After the third vegetation period, only the intensity of surface fire in the close neighbourhood of trees influenced (negatively) the chance on survival. The size of trees did no matter in this case. Nearly all of the trees that were located within burnout organic matter areas died. The results did not support the commonly known mechanism of enhancement of bigger Scots pine tree survival after surface fire because of thicker bark responsible for heat protection. Probably, the main cause of observed mortality was not overheating of cambium but it was rather connected to massive fine root loses. Scots pines growing on oligotrophic arid sites modify their root system to explore topsoil layers with higher proportion of shallow roots, growing even in organic litter layer. This corresponds with massive (regardless of size) pine mortality within sites characterised by complete burnout of organic matter layer and very high survival in those ones with only surfacely burned litter layer. The results can improve the assessment of surface fires consequences in managed Scots pine stands growing in oligotrophic conditions

Scots pine Pinus sylvestris mortality after surface fire in oligotrophic pine forest Peucedano-Pinetum in Kampinos National Park

Pines are generally fire-resistant trees. There is a shortage of research on the behaviour of Scots pine after surface fire in older stands. The aim of the work was to describe the effect of the surface fire intensity on the mortality of pines of various diameter at breast height (DBH), including older trees. The research was conducted in Peucedano-Pinetum oligotrophic Scots-pine forest in Kampinos National Park (KPN, central Poland) on the area of two adjacent surface fire sites originated in spring 2015 in 60- to 200-year-old stands (site area: 10,92 ha). There were 45 (28 burned and 17 control) permanent plots established after the fire. The share of not burned, superficially burned and completely burnout organic horizon of the soil was determined within all of them. DBH and location of pine trees were measured within all of the plots on the area of 200 m2. For all of the trees for which full information about soil organic horizon damage was mapped, the prevailing type of disturbance in their close neighbourhoods with radii of 1 and 2 m was assessed. The mortality of trees was assessed after each vegetation period up to 2017, basing on the presence of green needles on the trees. The influence of fire intensity on the survival of trees was examined on whole permanent plot level as well as on individual tree level. Strong linear correlation was observed between Scots pine mortality and the share of plots area with damaged organic layer, especially at the end of the third vegetation period after fire. Logistic regression models constructed for individual trees suggest that bigger tree diameter (hence, thicker bark) diminished the odds of mortality only after two vegetation periods from the fire. After the third vegetation period, only the intensity of surface fire in the close neighbourhood of trees influenced (negatively) the chance on survival. The size of trees did no matter in this case. Nearly all of the trees that were located within burnout organic matter areas died. The results did not support the commonly known mechanism of enhancement of bigger Scots pine tree survival after surface fire because of thicker bark responsible for heat protection. Probably, the main cause of observed mortality was not overheating of cambium but it was rather connected to massive fine root loses. Scots pines growing on oligotrophic arid sites modify their root system to explore topsoil layers with higher proportion of shallow roots, growing even in organic litter layer. This corresponds with massive (regardless of size) pine mortality within sites characterised by complete burnout of organic matter layer and very high survival in those ones with only surfacely burned litter layer. The results can improve the assessment of surface fires consequences in managed Scots pine stands growing in oligotrophic conditions

Scots pine Pinus sylvestris

Pines are generally fire-resistant trees. There is a shortage of research on the behaviour of Scots pine after surface fire in older stands. The aim of the work was to describe the effect of the surface fire intensity on the mortality of pines of various diameter at breast height (DBH), including older trees. The research was conducted in Peucedano-Pinetum oligotrophic Scots-pine forest in Kampinos National Park (KPN, central Poland) on the area of two adjacent surface fire sites originated in spring 2015 in 60- to 200-year-old stands (site area: 10,92 ha). There were 45 (28 burned and 17 control) permanent plots established after the fire. The share of not burned, superficially burned and completely burnout organic horizon of the soil was determined within all of them. DBH and location of pine trees were measured within all of the plots on the area of 200 m2. For all of the trees for which full information about soil organic horizon damage was mapped, the prevailing type of disturbance in their close neighbourhoods with radii of 1 and 2 m was assessed. The mortality of trees was assessed after each vegetation period up to 2017, basing on the presence of green needles on the trees. The influence of fire intensity on the survival of trees was examined on whole permanent plot level as well as on individual tree level. Strong linear correlation was observed between Scots pine mortality and the share of plots area with damaged organic layer, especially at the end of the third vegetation period after fire. Logistic regression models constructed for individual trees suggest that bigger tree diameter (hence, thicker bark) diminished the odds of mortality only after two vegetation periods from the fire. After the third vegetation period, only the intensity of surface fire in the close neighbourhood of trees influenced (negatively) the chance on survival. The size of trees did no matter in this case. Nearly all of the trees that were located within burnout organic matter areas died. The results did not support the commonly known mechanism of enhancement of bigger Scots pine tree survival after surface fire because of thicker bark responsible for heat protection. Probably, the main cause of observed mortality was not overheating of cambium but it was rather connected to massive fine root loses. Scots pines growing on oligotrophic arid sites modify their root system to explore topsoil layers with higher proportion of shallow roots, growing even in organic litter layer. This corresponds with massive (regardless of size) pine mortality within sites characterised by complete burnout of organic matter layer and very high survival in those ones with only surfacely burned litter layer. The results can improve the assessment of surface fires consequences in managed Scots pine stands growing in oligotrophic conditions

Supplementary data

This data file contains tree quantities and basal area sums in 50mm-wide classes of diameter at breast height (dbh), given separately for (a) all live, ingrowth and outgrowth trees, (b) 8 major woodland community types, (c) 5 research plots, (d) 57 separate community patches, (e) 7 subsequent measurement censuses, and (f) 11 tree species. Additionally, community patch areas are given