Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa.

BackgroundPopulus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation.ResultsWe identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value < 6.1479E-8) in association with diameter, height, leaf carbon and nitrogen contents, and δ15N. The number of significant SNPs ranged from 2 to 220 per trait. Additionally, multiple-marker analyses by sliding-windows tests detected between 6 and 192 significant windows for the analyzed traits. The significant SNPs resided within genes that encode proteins belonging to different functional classes as such protein synthesis, energy/metabolism and DNA/RNA metabolism, among others.ConclusionsSNP-markers within genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture of P. trichocarpa biomass required to support the development and application of marker breeding technologies

Estudo de Antoniniani de um tesouro de localização incerta pelo método de fluorescência de raios X

O conjunto de antoniniani estudados não permite conclusões de muito interesse numismático, visto ser grande o f'raccionamento previsível que sofreu o conjunto inicial, a par do desconhecimento da sua proveniência segura.info:eu-repo/semantics/publishedVersio

Diversidad, abundancia relativa y patrones de actividad de los mamíferos medianos y grandes, asociados a los bosques riparios del río Bita, Vichada, Colombia

La diversidad de mamíferos en la cuenca del Orinoco es derivada de la mezcla de especies de diferentes regiones biogeográficas y es poco conocida. Por lo tanto se emplearon técnicas de fototrampeo para el registro de los mamíferos medianos y grandes asociados al bosque ribereño en la cuenca alta y media del río Bita, Vichada, Colombia. Se estimó la diversidad, el índice de abundancia relativa y los patrones de actividad. Se instalaron 77 cámaras trampa a lo largo de 200 km del río en dos periodos hidroclimáticos (baja y alta precipitación). Se obtuvieron en total 16439 imágenes, con un esfuerzo muestreo de 7700 días-trampa. Se registraron 24 especies de mamíferos, agrupados en 17 familias y 9 órdenes. El índice de diversidad de Shannon-Wiener obtenido a través de este método fue H´= 1,995, las especies mejor representadas a través del índice de abundancia relativa fueron Tayassu pecari (IAR = 0,176, n = 1360), Cuniculus paca (IAR = 0,174, n = 1346), Tapirus terrestris (IAR = 0,144, n = 1114) y Dasyprocta fuliginosa (IAR = 0,116, n=900). En términos de patrones de actividad Dasyprocta fuliginosa presentó patrones de actividad diurnos, Leopardus pardalis catemeral, Tayassu pecari crepuscular matutino, Cuniculus paca y Didelphis marsupialis nocturna y Tapirus terrestris crepuscular vespertino. Esta información puede ser de utilidad para la generación de programas para el manejo y conservación de la mastofauna en la cuenca del río Bita

Diversidad, abundancia relativa y patrones de actividad de los mamíferos medianos y grandes, asociados a los bosques riparios del río Bita, Vichada, Colombia

The diversity of mammals in the Orinoco River basin is derived from the mixture of species from different biogeographic regions and remains poorly known. Therefore, we used camera trapping techniques for the registration of the large and medium mammals associated to the riparian forest in the upper and middle basins of the Bita River, Vichada, Colombia. Diversity, relative abundance index and activity patterns were estimated. Seventy-seven camera traps were installed along 200 km of the river in two hydroclimatic periods (low and high precipitation). A total of 16439 images were obtained with a sampling effort of 7700 traps-days. Twenty-four species of mammals were recorded, corresponding to 17 families and 9 orders. The Shannon-Wiener diversity index obtained through this method was H ́=1.995, the best-represented species through the relative abundance index were Tayassu pecari (IAR= 0.176, n = 1360), Cuniculus paca (IAR = 0.174, n = 1346), Tapirus terrestris (IAR = 0.144, n = 1114) and Dasyprocta fuliginosa (IAR = 0.116, n = 900). In terms of activity patterns, Dasyprocta fuliginosa showed a pattern of diurnal activity, Leopardus pardalis catemeral, Tayassu pecari morning twilight, Cuniculus paca and Didelphis marsupialis nocturnal and Tapirus terrestris twilight evening. This information may be useful to plan conservation and management actions for the mast ofauna of the Bita River basin.La diversidad de mamíferos en la cuenca del Orinoco es derivada de la mezcla de especies de diferentes regiones biogeográficas y es poco conocida. Por lo tanto se emplearon técnicas de fototrampeo para el registro de los mamíferos medianos y grandes asociados al bosque ribereño en la cuenca alta y media del río Bita, Vichada, Colombia. Se estimó la diversidad, el índice de abundancia relativa y los patrones de actividad. Se instalaron 77 cámaras trampa a lo largo de 200 km del río en dos periodos hidroclimáticos (baja y alta precipitación). Se obtuvieron en total 16439 imágenes, con un esfuerzo muestreo de 7700 días-trampa. Se registraron 24 especies de mamíferos, agrupados en 17 familias y 9 órdenes. El índice de diversidad de Shannon-Wiener obtenido a través de este método fue H´= 1,995, las especies mejor representadas a través del índice de abundancia relativa fueron Tayassu pecari (IAR = 0,176, n = 1360), Cuniculus paca (IAR = 0,174, n = 1346), Tapirus terrestris (IAR = 0,144, n = 1114) y Dasyprocta fuliginosa (IAR = 0,116, n=900). En términos de patrones de actividad Dasyprocta fuliginosa presentó patrones de actividad diurnos, Leopardus pardalis catemeral, Tayassu pecari crepuscular matutino, Cuniculus paca y Didelphis marsupialis nocturna y Tapirus terrestris crepuscular vespertino. Esta información puede ser de utilidad para la generación de programas para el manejo y conservación de la mastofauna en la cuenca del río Bita

Fundamental parameters related to selenium kα and kβ emission x-ray spectra

This research was funded in part by FCT (Portugal) under research center grants UID/FIS/04559/2020 (LIBPhys) and UID/MULTI/04046/2020 (BioISI). This work was also funded through the project PTDC/FIS-AQM/31969/2017, "Ultra-high-accuracy x-ray spectroscopy of transition metal oxides and rare earths." J.M. and J.P.S acknowledge the support of EMPIR, under Contract No. 17FUN02MetroMMC. The EMPIR initiative is co-funded by the European Union's Horizon 2020 research and innovation programme and the EMPIR participating States.We present relativistic ab initio calculations of fundamental parameters for atomic selenium, based on the Multiconfiguration Dirac-Fock method. In detail, fluorescence yields and subshell linewidths, both of K shell, as well as Kβ to Kα intensity ratio are provided, showing overall agreement with previous theoretical calculations and experimental values. Relative intensities were evaluated assuming the same ionization cross-section for the K-shell hole states, leading to a statistical distribution of these initial states. A method for estimating theoretical linewidths of X-ray lines, where the lines are composed by a multiplet of fine-structure levels that are spread in energy, is proposed. This method provides results that are closer to Kα1,2 experimental width values than the usual method, although slightly higher discrepancies occur for the Kβ1,3 lines. This indicates some inaccuracies in the calculation of Auger rates that have a higher contribution for partial linewidths of the subshells involved in the Kβ1,3 profile. Apart from this, the calculated value of Kβ to Kα intensity ratio, which is less sensitive to Auger rates issues, is in excellent agreement with recommended values.publishersversionpublishe

Ampliación de la distribución geográfica de cacomixtle tropical, bassariscus sumichrasti (carnivora: procyonidae) en méxico

El cacaomixtle tropical (Bassariscus sumichrasti: Saussure, 1860: Carnivora: Procyonidae) se distribuye desde el sureste de México hasta Panamá (COATESESTRADA y ESTRADA, 1986; EMMONS, 1999). Su hábitat son las selvas altas y medianas perennifolias, el bosque mesófilo de montaña y las áreas húmedas y densas de bosques de encino-pino, desde el nivel del mar hasta los 2.900 m. de altitud. La especie es simpátrica con el cacomixtle común (Bassariscus astutus: Lichtenstein, 1830) en algunas zonas de los estados de Guerrero, Veracruz y Oaxaca; se ha registrado en el sureste de México y en la Península de Yucatán (NAVA, 2005). La especie está incluida en el Apéndice III de CITES (Convention on International Trade in Endangered Species), en México está considerada como sujeta a protección especial por el Instituto Nacional de Ecología, en la norma oficial mexicana NOM-059-ECOL (DIARIO OFICIAL DE LA FEDERACIÓN, 2001

Implications on Mineral Elements, Sugars and Fatty Acids Accumulation in Tissues

Funding Information: This work received funding from PDR2020-101-030734 and Fundação para a Ciência e a Tecnologia, I.P. (FCT), Portugal, through the research units UIDB/04035/2020 (GeoBioTec), UIDB/00239/2020 (CEF) and UID/FIS/04559/2020 (LIBPhys) from the FCT/MCTES/PIDDAC. This work was further supported by the grant of Fundação para a Ciência e Tecnologia (FCT) UI/BD/150718/2020. Publisher Copyright: © 2022 by the authors.Following an agronomic approach for the Ca enrichment of Rocha pears, this study aimed to assess the interactions between mineral nutrients in fruit tissues at harvest and after storage for 5 months and to characterize the implications on the profile of sugars and fatty acids (FA). A total of seven foliar sprays (with concentrations of 0.1–0.6 kg·ha−1 Ca(NO3)2 and 0.8–8 kg·ha−1 CaCl2) were applied to pear trees. After harvest, the fruits were stored for 5 months, in environmentally controlled chambers, and the mineral contents in five regions (on the equatorial section) of the fruits were assessed, while the sugar and FA content were quantified. For both dates, all foliar sprayed treatments, at different extends, increased Ca content in the center and near the epidermis of Rocha pear fruits and the levels of K, Mn, Fe, Zn and Cu also varied. At harvest, the Ca treatments did not affect the levels of sucrose, glucose, fructose and sorbitol and, after storage, their concentrations remained higher in Ca-treated fruits. Additionally, the tendency of the relative proportions of FA was C18:2 > C18:1 > C16:0 > C18:3 > C18:0 > chains inferior to 16 C ( C16:0 > C18:3 > C18:0 > C18:1 > chains inferior to 16 C (<16:0). It is concluded that the heterogeneous distribution of Ca in the tissues of Rocha pear fruits results from its absorption in the peel after Ca(NO3)2 and CaCl2 sprays and from the xylemic flux in the core prior to maturity. Additionally, the hydrolysis of complex polysaccharides affects the contents of simpler sugars during maturation, ripening and senescence, while storage decreases the amount of total fatty acids (TFA), but the double bond index (DBI) indicate that cell membrane fluidity remains unaffected.publishersversionpublishe

K- and L-shell theoretical fluorescence yields for the Fe isonuclear sequence

Funding Information: This research was funded in part by FCT (Portugal) under research center grant UID/FIS/04559/2020 (LIBPhys). This work was also funded through the project PTDC/FIS-AQM/31969/2017, “Ultra-high-accuracy X-ray spectroscopy of transition metal oxides and rare earths”. F.G. acknowledges support from FCT, Portugal through contract UI/BD/151000/2021 . J. M and J.P.S acknowledge the support of EMPIR, Germany , under Contract No. 20FUN04 PrimA-LTD. The EMPIR initiative is co-funded by the European Union’s Horizon 2020 research and innovation programme and the EMPIR, Germany participating States. Part of this work has been carried out under the High Performance Computing Chair - a R&D infrastructure (based at the University of Évora; PI: M. Avillez), endorsed by Hewlett Packard Enterprise (HPE), and involving a consortium of higher education institutions (University of Algarve, University of Évora, NOVA University Lisbon, and University of Porto), research centres (CIAC, CIDEHUS, CHRC), enterprises (HPE, ANIET, ASSIMAGRA, Cluster Portugal Mineral Resources, DECSIS, FastCompChem, GeoSense, GEOtek, Health Tech, Starkdata), and public/private organizations (Alentejo Tourism-ERT, KIPT Colab). Funding Information: This research was funded in part by FCT (Portugal) under research center grant UID/FIS/04559/2020 (LIBPhys). This work was also funded through the project PTDC/FIS-AQM/31969/2017, “Ultra-high-accuracy X-ray spectroscopy of transition metal oxides and rare earths”. F.G. acknowledges support from FCT, Portugal through contract UI/BD/151000/2021. J. M and J.P.S acknowledge the support of EMPIR, Germany, under Contract No. 20FUN04 PrimA-LTD. The EMPIR initiative is co-funded by the European Union's Horizon 2020 research and innovation programme and the EMPIR, Germany participating States. Part of this work has been carried out under the High Performance Computing Chair - a R&D infrastructure (based at the University of Évora; PI: M. Avillez), endorsed by Hewlett Packard Enterprise (HPE), and involving a consortium of higher education institutions (University of Algarve, University of Évora, NOVA University Lisbon, and University of Porto), research centres (CIAC, CIDEHUS, CHRC), enterprises (HPE, ANIET, ASSIMAGRA, Cluster Portugal Mineral Resources, DECSIS, FastCompChem, GeoSense, GEOtek, Health Tech, Starkdata), and public/private organizations (Alentejo Tourism-ERT, KIPT Colab). Publisher Copyright: © 2022 The Author(s)In this work, we present K- and L- shell fluorescence yield values of the full isonuclear sequence of Fe ions, using a state-of-the-art multiconfiguration Dirac–Fock approach. These results may be of importance for spectral fitting and plasma modeling, both in laboratory and astrophysical studies, where Fe is an important benchmark element. The K-shell fluorescence yields were found to be very similar up to the removal of 14 electrons.publishersversionpublishe

Macaronesia Acts as a Museum of Genetic Diversity of Relict Ferns: The Case of Diplazium caudatum (Athyriaceae)

Macaronesia has been considered a refuge region of the formerly widespread subtropical lauroid flora that lived in Southern Europe during the Tertiary. The study of relict angiosperms has shown that Macaronesian relict taxa preserve genetic variation and revealed general patterns of colonization and dispersal. However, information on the conservation of genetic diversity and range dynamics rapidly diminishes when referring to pteridophytes, despite their dominance of the herbaceous stratum in the European tropical palaeoflora. Here we aim to elucidate the pattern of genetic diversity and phylogeography of Diplazium caudatum, a hypothesized species of the Tertiary Palaeotropical flora and currently with its populations restricted across Macaronesia and disjunctly in the Sierras de Algeciras (Andalusia, southern Iberian Peninsula). We analysed 12 populations across the species range using eight microsatellite loci, sequences of a region of plastid DNA, and carry out species-distribution modelling analyses. Our dating results confirm the Tertiary origin of this species. The Macaronesian archipelagos served as a refuge during at least the Quaternary glacial cycles, where populations of D. caudatum preserved higher levels of genetic variation than mainland populations. Our data suggest the disappearance of the species in the continent and the subsequent recolonization from Macaronesia. The results of the AMOVA analysis and the indices of clonal diversity and linkage disequilibrium suggest that D. caudatum is a species in which inter-gametophytic outcrossing predominates, and that in the Andalusian populations there was a shift in mating system toward increased inbreeding and/or clonality. The model that best explains the genetic diversity distribution pattern observed in Macaronesia is, the initial and recurrent colonization between islands and archipelagos and the relatively recent diversification of restricted area lineages, probably due to the decrease of favorable habitats and competition with lineages previously established. This study extends to ferns the concept of Macaronesia archipelagos as refugia for genetic variation

Can foliar pulverization with CaCl2 and Ca(NO3)2 trigger Ca enrichment in solanum tuberosum L. tubers?

project PDR2020-101-030719 IDB/00239/2020 UIDP/04035/2020This study aimed to assess the efficiency of Ca enrichment in tubers of three genotypes of Solanum tuberosum L., through foliar spraying with CaCl2 and Ca(NO3)2 solutions. In this context, soil heterogeneity of three potato-growing fields, as well as the implications of Ca accumulation among tissues and some quality parameters were assessed. Three potato varieties (Agria, Picasso and Rossi) were grown in three production fields and during the life cycle, four pulverizations with calcium chloride (3 and 6 kg ha−1) or calcium nitrate (0.5, 2 and 4 kg ha−1) were applied. For screening the potential phytotoxicity, using Agria as a test system, the potential synthesis of photoassimilates was determined, and it was found that after the 3rd Ca application, leaf gas exchanges were moderately (net photosynthesis), to strongly (stomatal conductance) affected, although without impact on Ca accumulation in tubers. At harvest, the average Ca biofortification index varied between 5–40%, 40–35% and 4.3–13% in Agria, Picasso and Rossi, respectively. Moreover, the equatorial region of the tubers in general showed that Ca accumulation prevailed in the epidermis and, in some cases, in inner areas of the potato tubers. Biofortified tubers with Ca also showed some significant changes in total soluble solids and colorimetric parameters. It is concluded that Ca enrichment of potato tubers through foliar spraying complemented the xylem mass flow of Ca from roots, through phloem redistribution. Both fertilizers showed similar efficiency, but Rossi revealed a lower index of Ca accumulation, eventually due to different metabolic characteristics. Although affected by Ca enrichment, potato tubers maintained a high quality for industrial processing.publishersversionpublishe