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Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change

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Plant Communications 2024年第10期5卷 59-81页

作者： Jiajun Feng Xuming Dan Yangkai Cui Yi Gong Minyue Peng Yupeng Sang Par K.Ingvarsson Jing Wang Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengduChina Department of Plant Biology Linnean Centre for Plant BiologySwedish University of Agricultural SciencesUppsalaSweden

Global climate change is leading to rapid and drastic shifts in environmental conditions,posing threats to biodiversity and nearly all life forms *** trees serve as foundational components of terrestrial ecosystems and play a crucial and leading role in combating and mitigating the adverse effects of extreme climate events,despite their own vulnerability to these ***,understanding and monitoring how natural forests respond to rapid climate change is a key priority for biodiversity conserva*** progress in evolutionary genomics,driven primarily by cutting-edge multi-omics technologies,offers powerful new tools to address several key *** include precise delineation of species and evolutionary units,inference of past evolutionary histories and demographic fluctuations,identification of environmentally adaptive variants,and measurement of genetic load *** the urgency to deal with more extreme environmental stresses grows,understanding the genomics of evolutionary history,local adaptation,future responses to climate change,and conservation and restoration of natural forest trees will be critical for research at the nexus of global change,population genomics,and conservation *** this review,we explore the application of evolutionary genomics to assess the effects of global climate change using multi-omics approaches and discuss the outlook for breeding of climate-adapted trees.

关键词： forest trees climate change multi-omics evolutionary genomics breeding

Influence of upstream solar wind on magnetic field distribution in the Martian nightside ionosphere

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Earth and Planetary Physics 2024年第5期8卷 728-741页

作者： JiaWei Gao ZhaoJin Rong Qi Zhang Anna Mittelholz Chi Zhang Yong Wei Key Laboratory of Earth and Planetary Physics Institute of Geology and Geophysics Chinese Academy of Sciences College of Earth and Planetary sciences University of Chinese Academy of Sciences swedish Institute of Space Physics Department of Earth sciences Center for Space Physics and Department of Astronomy Boston University

Using over eight years of Mars Atmosphere and Volatile Evolutio N （MAVEN） data,from November 2014 to May 2023,we have investigated the Martian nightside ionospheric magnetic field distribution under the influence of upstream solar wind drivers,including the interplanetary magnetic field intensity (∣BIMF∣),solar wind dynamic pressure （PSW）,solar extreme ultraviolet flux （EUV）,and Martian seasons （Ls）.Our analysis reveals pronounced correlations between magnetic field residuals and both∣BIMF∣and *** observed with EUV flux and Lswere weaker—notably,magnetic field residuals increased during periods of high EUV flux and at Mars *** find that the IMF penetrates to an altitude of 200 km under a wide range of upstream conditions,penetrating notably deeper under high∣BIMF∣*** analysis also indicates that EUV flux and IMF cone angle have minimal impact on IMF penetration *** findings provide useful constraints on the dynamic nature of Martian atmospheric escape processes and their evolution,suggesting that historical solar wind conditions may have facilitated deeper IMF penetration and higher rates of ionospheric escape than are observed ***,by establishing criteria for magnetic‘quiet’conditions,this study offers new insights into the planet’s magnetic environment under varying solar wind influences,knowledge that should help refine models of the Martian crustal magnetic field.

关键词： Martian magnetic field external magnetic field upstream solar wind drivers IMF penetration altitude magnetic field activity indices

Why ecosystem characteristics predicted from remotely sensed data are unbiased and biased at the same time-and how this affects applications

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Forest Ecosystems 2024年第1期11卷 24-31页

作者： Goran Ståhl Terje Gobakken Svetlana Saarela Henrik J.Persson Magnus Ekstrom Sean P.Healey Zhiqiang Yang Johan Holmgren Eva Lindberg Kenneth Nystrom Emanuele Papucci Patrik Ulvdal Hans OleØrka Erik Næsset Zhengyang Hou Håkan Olsson Ronald E.McRoberts Department of Forest Resource Management Swedish University of Agricultural Sciences90183UmeåSweden Faculty of Environmental sciences and Natural Resource Management Norwegian University of Life SciencesÅsNorway USDA Forest Service Rocky Mountain Research StationOgdenUTUSA The Key Laboratory for Silviculture and Conservation of Ministry of Education Beijing Forestry UniversityBeijing100083China Department of Forest Resources University of MinnesotaSt.PaulMNUSA

Remotely sensed data are frequently used for predicting and mapping ecosystem characteristics,and spatially explicit wall-to-wall information is sometimes proposed as the best possible source of information for ***,wall-to-wall information typically relies on model-based prediction,and several features of model-based prediction should be understood before extensively relying on this type of *** such feature is that model-based predictors can be considered both unbiased and biased at the same time,which has important implications in several areas of *** this discussion paper,we first describe the conventional model-unbiasedness paradigm that underpins most prediction techniques using remotely sensed(or other)auxiliary *** this point of view,model-based predictors are typically ***,we show that for specific domains,identified based on their true values,the same model-based predictors can be considered biased,and sometimes severely *** suggest distinguishing between conventional model-bias,defined in the statistical literature as the difference between the expected value of a predictor and the expected value of the quantity being predicted,and design-bias of model-based estimators,defined as the difference between the expected value of a model-based estimator and the true value of the quantity being *** show that model-based estimators(or predictors)are typically design-biased,and that there is a trend in the design-bias from overestimating small true values to underestimating large true ***,we give examples of applications where this is important to acknowledge and to potentially make adjustments to correct for the design-bias *** argue that relying entirely on conventional model-unbiasedness may lead to mistakes in several areas of application that use predictions from remotely sensed data.

关键词： Bias Model-based inference Design-based inference

Inbreeding and genetic load in a pair of sibling grouse species:Tetrastes sewersowi and ***

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Avian Research 2024年第2期15卷 265-270页

作者： Kai Song Tom van der Valk Bin Gao Peter Halvarsson Yun Fang Wendong Xie Siegfried Klaus Zhiming Han Yue-Hua Sun Jacob Hoglund Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing100101China Animal Ecology Department of Ecology and GeneticsUppsala UniversityNorbyvagen 18DUppsala75236Sweden Department of Cell and Molecular Biology Uppsala75273Sweden Unit of Parasitology Department of Biomedicine and Veterinary Public HealthSwedish University of Agricultural SciencesPO Box 7036Uppsala75007Sweden Lindenhohe 5 JenaD-07749Germany The State Key Laboratory of Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing100101China

Genetic load and inbreeding are recognized as important factors to be considered in conservation *** levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals,including humans(inbreeding depression).Genomic tech-niques are increasingly used in measuring and understanding genetic load and inbreeding and their importance in evolution and *** used whole genome resequencing data from two sibling grouse species in subarctic Eurasia to quantify *** found a large range of inbreeding measured as FROH(fraction of runs of homozygosity)in individuals from different populations of Chinese Grouse(Tetrastes sewerzowi)and Hazel Grouse(***).FROH estimated from genome-wide runs of homozygosity(ROH)ranged from 0.02 to 0.24 among Chinese Grouse populations and from 0.01 to 0.44 in Hazel *** from a population of Chinese Grouse residing in the Qilian mountains and from the European populations of Hazel Grouse(including samples from Sweden,Germany and Northeast Poland)were the most inbred(FROH ranged from 0.10 to 0.23 and 0.11 to 0.44,respectively).These levels are comparable to other highly inbred populations of *** Grouse from northern China and Chinese Grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding *** of the ratio between deleterious missense mutations and synonymous mutations revealed higher levels in Chinese Grouse as compared to Hazel *** results are possibly explained by higher fixation rates,mutational melt down,in the range-restricted Chinese Grouse compared to the wide-ranging Hazel ***,when we compared the relatively more severe class of loss-of-function muta-tions,Hazel Grouse had slightly higher levels than Chinese Grouse,a result which may indicate that purifying selection(purging)has been more efficient in Chinese Grouse on this class of mutations.

关键词： Genetic load Inbreeding Purifying selection Qinghai-Tibetan Plateau ROH Tetrastes

Relating estimates of wood properties of birch to stem form, age and species

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Journal of Forestry Research 2024年第3期35卷 1-11页

作者： Grace Jones Maria Ulan Mateusz Liziniewicz Johan Lindeberg Stergios Adamopoulos Teagasc Forestry Development Department Ashtown Research CentreDublin 15 D15DY05Ireland Research Institutes of Sweden(RISE) GoteborgSweden The Forest Research Institute of Sweden(Skogforsk) Ekebo 225026890SvalovSweden Department of Forestry and Wood Technology Linnaeus University35195VaxjoSweden Department of Forest Biomaterials and Technology Swedish University of Agricultural SciencesBox 700875007 UppsalaSweden

Birch has long suffered from a lack of active forest management,leading many researchers to use mate-rial without a detailed management *** collected from three birch(Betula pendula Roth,*** Ehrh.)sites in southern Sweden were analyzed using regression analysis to detect any trends or differences in wood proper-ties that could be explained by stand history,tree age and stem *** sites were genetics trials established in the same *** of acoustic velocity(AV)from non-destructive testing(NDT)and predicted AV had a higher correlation if data was pooled across sites and other stem form factors were considered.A subsample of stems had radial profiles of X-ray wood density and ring width by year created,and wood density was related to ring number from the pith and ring *** seemed likely that wood density was negatively related to ring width for both birch *** models had slight improvements if site and species were included,but only the youngest site with trees at age 15 had both birch *** paper indicated that NDT values need to be considered separately,and any predictive models will likely be improved if they are specific to the site and birch species measured.

关键词： Acoustic velocity Non-destructive testing Predictive models Regression analysis Wood density

The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

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Molecular Plant 2024年第5期17卷 725-746页

作者： Tingting Shi Xinxin Zhang Yukang Hou Changfu Jia Xuming Dan Yulin Zhang Yuanzhong Jiang Qiang Lai Jiajun Feng Jianju Feng Tao Ma Jiali Wu Shuyu Liu Lei Zhang Zhiqin Long Liyang Chen Nathaniel R.Street Par K.Ingvarsson Jianquan Liu Tongming Yin Jing Wang Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengduSichuanChina College of Horticulture and Forestry Tarim UniversityAlar 843300China Umea Plant Science Centre Department of Plant PhysiologyUmea UniversityUmeaVasterbottenSweden Linnean Centre for Plant Biology Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural SciencesUppsalaSweden The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China Nanjing Forestry UniversityNanjingJiangsuChina

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary ***,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental *** this study,we present a genus-level super-pangenome comprising 19 Populus genomes,revealing the likely pivotal role of private genes in facilitating local environmental and climate *** the integration of pangenomes with transcriptomes,methylomes,and chromatin accessibility mapping,we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures,notably CG methylation in gene-body *** comparative genomic analyses have enabled the identification of 142202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive *** have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration ***,we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome(http://***).Together,the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

关键词： Populus pangenomes whole-genome duplication structural variation genome evolution

Adsorption of yttrium(Y^(3+)) and concentration of rare earth elements from phosphogypsum using chitin and chitin aerogel

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Journal of Rare Earths 2024年第4期42卷 775-782页

作者： Glaydson S.dos Reis Diana Pinto Sabrina F.Lütke Eder C.Lima Luis F.O.Silva Irineu A.S.De Brum Guilherme L.Dotto Department of Forest Biomaterials and Technology Biomass Technology Centre Swedish University of Agricultural SciencesUmeaE13Swedn univ.rsidad De La Costa Calle 58#55-66080002BarranquillaAtlanticoColombia Research Group on Adsorptive and Catalytic Process Engineering(ENGEPAC) Federal University of Santa MariaAv.Roraima100079705900Santa MariaRSBrazil Institute of Chemistry Federal University of Rio Grande do Sul90040060Porto AlegreBrazil

Chitin powder and chitin-aerogel were prepared from shrimp wastes and used to uptake Y^(3+)from aqueous solutions and concentrate this rare earth element from phosphogypsum(PG).Chitin aerogel displays a specific surface area of 945 m^(2)/g,while chitin powder is 3.6 m^(2)/g,which largely influences its adsorption *** the adsorption in synthetic solutions,the effect of pH on Y^(3+)removal is strong for chitin powder *** contrast,no big pH influence was detected for chitin *** interactions and chelation can highlight the proposed mechanism of Y^(3+)on chitin adsorbents for the powder and ***,in addition to these interactions,pore filling/pore diffusion is the main mechanism of Y^(3+)removal in the chitin *** aerogel is efficient in concentrating 8 times the Y^(3+)from PG,a very complex *** complex chitin aerogel-Y^(3+)can be a secondary source of rare earth elements for other applications.

关键词： Rare earths Sustainable material Chitin powder Chitin porous aerogel Yttrium adsorption and recovery

Mshpy23:a user-friendly,parameterized model of magnetosheath conditions

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Earth and Planetary Physics 2024年第1期8卷 89-104页

作者： Jaewoong Jung Hyunju Connor Andrew Dimmock Steve Sembay Andrew Read Jan Soucek NASA Goddard Space Flight Center GreenbeltMDUSA Department of Astronomy University of MarylandCollege ParkMDUSA swedish Institude of Space Physics UppsalaSweden univ.rsity of Leicester LeicesterUK Institute of Atmospheric Physics Academy of Sciences of the Czech Republic

Lunar Environment heliospheric X-ray Imager(LEXI)and Solar wind−Magnetosphere−Ionosphere Link Explorer(SMILE)will observe magnetosheath and its boundary motion in soft X-rays for understanding magnetopause reconnection modes under various solar wind conditions after their respective launches in 2024 and *** conditions,namely,plasma density,velocity,and temperature,are key parameters for predicting and analyzing soft X-ray images from the LEXI and SMILE *** developed a userfriendly model of magnetosheath that parameterizes number density,velocity,temperature,and magnetic field by utilizing the global Magnetohydrodynamics(MHD)model as well as the pre-existing gas-dynamic and analytic *** this parameterized magnetosheath model,scientists can easily reconstruct expected soft X-ray images and utilize them for analysis of observed images of LEXI and SMILE without simulating the complicated global magnetosphere ***,we created an MHD-based magnetosheath model by running a total of 14 OpenGGCM global MHD simulations under 7 solar wind densities(1,5,10,15,20,25,and 30 cm)and 2 interplanetary magnetic field Bz components(±4 nT),and then parameterizing the results in new magnetosheath *** compared the magnetosheath model result with THEMIS statistical data and it showed good agreement with a weighted Pearson correlation coefficient greater than 0.77,especially for plasma density and plasma ***,we compiled a suite of magnetosheath models incorporating previous magnetosheath models(gas-dynamic,analytic),and did two case studies to test the *** MHD-based model was comparable to or better than the previous models while providing self-consistency among the magnetosheath ***,we constructed a tool to calculate a soft X-ray image from any given vantage point,which can support the planning and data analysis of the aforementioned LEXI and SMILE missions.A release of the code has been uploaded to a Git

关键词： magnetosheath python modeling

Genomic selection in plant breeding:Key factors shaping two decades of progress

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Molecular Plant 2024年第4期17卷 552-578页

作者： Admas Alemu Johanna Astrand Osval A.Montesinos-López Julio Isidro y Sanchez Javier Fernandez-Gónzalez Wuletaw Tadesse Ramesh R.Vetukuri Anders S.Carlsson Alf Ceplitis JoséCrossa Rodomiro Ortiz Aakash Chawade Department of Plant Breeding Swedish University of Agricultural SciencesAlnarpSweden Lantmannen Lantbruk SvalövSweden Facultad de Telematica University de ColimaColimaColima 28040Mexico Centro de Biotecnología y Genómica de Plantas(CBGP UPM-INIA)Universidad Politécnica de Madrid(UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria(INIA)Campus de Montegancedo-UPM28223 MadridSpain International Center for agricultural Research in the Dry Areas(ICARDA) RabatMorocco International Maize and Wheat Improvement Center(CIMMYT) Km 45Carretera México-VeracruzTexcocoMéxico 52640Mexico

Genomic selection,the application of genomic prediction(GP)models to select candidate individuals,has significantly advanced in the past two decades,effectively accelerating genetic gains in plant *** article provides a holistic overview of key factors that have influenced GP in plant breeding during this *** delved into the pivotal roles of training population size and genetic diversity,and their relationship with the breeding population,in determining GP *** emphasis was placed on optimizing training population *** explored its benefits and the associated diminishing returns beyond an optimum *** was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization *** density and distribution of single-nucleotide polymorphisms,level of linkage disequilibrium,genetic complexity,trait heritability,statistical machine-learning methods,and non-additive effects are the other vital *** wheat,maize,and potato as examples,we summarize the effect of these factors on the accuracy of GP for various *** search for high accuracy in GP—theoretically reaching one when using the Pearson’s correlation as a metric—is an active research area as yet far from optimal for various *** hypothesize that with ultra-high sizes of genotypic and phenotypic datasets,effective training population optimization methods and support from other omics approaches(transcriptomics,metabolomics and proteomics)coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy,making genomic selection an effective tool in plant breeding.

关键词： genomic selection genetic gain genomic prediction optimization deep learning training population optimization