Trees progress through various growth stages,each marked by specific responses and adaptation strate-gies to environmental conditions.Despite the importance of age-related growth responses on overall forest health and...Trees progress through various growth stages,each marked by specific responses and adaptation strate-gies to environmental conditions.Despite the importance of age-related growth responses on overall forest health and management policies,limited knowledge exists regarding age-related effects on dendroclimatic relationships in key subtropical tree species.In this study,we employed a den-drochronological method to examine the impact of rapid warming on growth dynamics and climatic sensitivity of young(40–60 years)and old(100–180 years)Pinus mas-soniana forests across six sites in central-southern China.The normalized log basal area increment of trees in both age groups increased significantly following rapid warming in 1984.Trees in young forests further showed a distinct growth decline during a prolonged severe drought(2004–2013),whereas those in old forests maintained growth increases.Tree growth was more strongly influenced by temperature than by moisture,particularly in old forests.Spring tem-peratures strongly and positively impacted the growth of old trees but had a weaker effect on young ones.Old forests had a significantly lower resistance to extreme drought but faster recovery compared to young forests.The“divergence problem”was more pronounced in younger forests due to their heightened sensitivity to warming-induced drought and heat stress.With ongoing warming,young forests also may initially experience a growth decline due to their heightened sensitivity to winter drought.Our findings underscore the importance of considering age-dependent changes in forest/tree growth response to warming in subtropical forest man-agement,particularly in the context of achieving“Carbon Peak&Carbon Neutrality”goals in China.展开更多
Understanding the relationship between forest management and water use efficiency(WUE)is important for evaluating forest adaptability to climate change.However,the effects of thinning and understory removal on WUE and...Understanding the relationship between forest management and water use efficiency(WUE)is important for evaluating forest adaptability to climate change.However,the effects of thinning and understory removal on WUE and its key controlling processes are not well understood,which limits our comprehension of the physiological mechanisms of various management practices.In this study,four forest management measures(no thinning:NT;understory removal:UR;light thinning:LT;and heavy thinning:HT)were carried out in Pinus massoniana plantations in a subtropical region of China.Photosynthetic capacity and needle stable carbon isotope composition(δ^(13)C)were measured to assess instantaneous water use efficiency(WUE_(inst))and long-term water use efficiency(WUE_(i)).Multiple regression models and structural equation modelling(SEM)identified the effects of soil properties and physiological performances on WUE_(inst)and WUE_(i).The results show that WUE_(inst)values among the four treatments were insignificant.However,compared with the NT stand(35.8μmol·mol^(-1)),WUE_(i)values significantly increased to 41.7μmol·mol^(-1)in the UR,50.1μmol·mol^(-1)in the LT and 46.6μmol·mol^(-1)in HT treatments,largely explained by photosynthetic capacity and soil water content.Understory removal did not change physiological performance(needle water potential and photosynthetic capacity).Thinning increased the net photosynthetic rate(A_n)but not stomatal conductance(g_s)or predawn needle water potential(ψ_(pd)),implying that the improvement in water use efficiency for thinned stands was largely driven by radiation interception than by soil water availability.In general,thinning may be an appropriate management measure to promote P.massoniana WUE to cope with seasonal droughts under future extreme climates.展开更多
Accurate cropland information is critical for agricultural planning and production,especially in foodstressed countries like China.Although widely used medium-to-high-resolution satellite-based cropland maps have been...Accurate cropland information is critical for agricultural planning and production,especially in foodstressed countries like China.Although widely used medium-to-high-resolution satellite-based cropland maps have been developed from various remotely sensed data sources over the past few decades,considerable discrepancies exist among these products both in total area and in spatial distribution of croplands,impeding further applications of these datasets.The factors influencing their inconsistency are also unknown.In this study,we evaluated the consistency and accuracy of six cropland maps widely used in China in circa 2020,including three state-of-the-art 10-m products(i.e.,Google Dynamic World,ESRI Land Cover,and ESA WorldCover)and three 30-m ones(i.e.,GLC_FCS30,GlobeLand 30,and CLCD).We also investigated the effects of landscape fragmentation,climate,and agricultural management.Validation using a ground-truth sample revealed that the 10-m-resolution WorldCover provided the highest accuracy(92.3%).These maps collectively overestimated Chinese cropland area by up to 56%.Up to 37%of the land showed spatial inconsistency among the maps,concentrated mainly in mountainous regions and attributed to the varying accuracy of cropland maps,cropland fragmentation and management practices such as irrigation.Our work shed light on the promotion of future cropland mapping efforts,especially in highly inconsistent regions.展开更多
We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate(Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis(WGCNA) to...We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate(Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis(WGCNA) to describe the functionality and complexity of the physiological and morphogenetic processes as well as gene expression and metabolic differences during seed germination stages. In total, 489 metabolites were detected, including 40 differentially accumulated metabolites. The transcriptomic analysis showed the expression of 6 984 genes changed significantly throughout the whole germination process. Using WGCNA, we identified modules related to the various seed germination stages and hub genes. In the initial imbibition stage(stage 1), the pivotal genes involved in RNA transduction and the glycolytic pathway were most active, while in the sprouting stage(stage 4), the pivotal genes were involved in multiple metabolic pathways. In terms of secondary metabolic pathways, we found flavonoid 4-reductase genes of anthocyanin biosynthesis pathway are most significantly affected during pomegranate seed germination, while the flavonol synthase gene was mainly involved in the regulation of isoflavonoid biosynthesis.展开更多
Expert opinions have been used in a variety of fields to identify relevant issues and courses of action. This study surveys experts in forestry and climate change from the Asia–Pacific region to gauge their perspecti...Expert opinions have been used in a variety of fields to identify relevant issues and courses of action. This study surveys experts in forestry and climate change from the Asia–Pacific region to gauge their perspectives on the impacts of climate change and on the challenges faced by forest adaptation in the region, and explores recommendations and initiatives for adapting forests to climate change. There was consensus regarding the impacts of climate change on forest ecosystems and on economic sectors such as agriculture and forestry. Respondents also indicated a lack of public awareness and policy and legislation as challenges to addressing climate change. However, the results indicate differences in opinion between regions on the negative impacts of climate change and in satisfaction with actions taken to address climate change,highlighting the need for locally specific policies and research. The study presents specific recommendations to address issues of most concern, based on subregion and professional affiliation throughout the Asia–Pacific region.The results can be used to improve policy and forest management throughout the region. This research will also provide valuable suggestions on how to apply research findings and management recommendations outside of the AP region. The conclusions should be communicated relative to the level of the research and the target audience,ensuring that scientific findings and management recommendations are effectively communicated to ensure successful implementation of forest adaptation strategies.展开更多
The genus Rhododendron(Ericaceae),with more than 1000 species highly diverse in f lower color,is providing distinct ornamental values and a model system for f lower color studies.Here,we investigated the divergence be...The genus Rhododendron(Ericaceae),with more than 1000 species highly diverse in f lower color,is providing distinct ornamental values and a model system for f lower color studies.Here,we investigated the divergence between two parental species with different f lower color widely used for azalea breeding.Gapless genome assembly was generated for the yellow-f lowered azalea,Rhododendron molle.Comparative genomics found recent proliferation of long terminal repeat retrotransposons(LTR-RTs),especially Gypsy,has resulted in a 125 Mb(19%)genome size increase in species-specific regions,and a significant amount of dispersed gene duplicates(13402)and pseudogenes(17437).Metabolomic assessment revealed that yellow f lower coloration is attributed to the dynamic changes of carotenoids/f lavonols biosynthesis and chlorophyll degradation.Time-ordered gene co-expression networks(TO-GCNs)and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct f lower pigmentation.B3 and ERF TFs were found dominating the gene regulation of carotenoids/f lavonols characterized pigmentation in R.molle,while WRKY,ERF,WD40,C2H2,and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-f lowered R simsii.This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.展开更多
Polyploidization plays a key role in plant evolution,but the forces driving the fate of homoeologs in polyploid genomes,i.e.,paralogs resulting from a whole-genome duplication(WGD)event,remain to be elucidated.Here,we...Polyploidization plays a key role in plant evolution,but the forces driving the fate of homoeologs in polyploid genomes,i.e.,paralogs resulting from a whole-genome duplication(WGD)event,remain to be elucidated.Here,we present a chromosome-scale genome assembly of tetraploid scarlet sage(Salvia splendens),one of the most diverse ornamental plants.We found evidence for three WGD events following an older WGD event shared by most eudicots(theγevent).A comprehensive,spatiotemporal,genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries,which could be associated with genomic rearrangements,transposable element proximity discrepancies,coding sequence variation,selection pressure,and transcription factor binding site differences.The observed differences between homoeologs may reflect the first step toward sub-and/or neofunctionalization.This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.展开更多
In angiosperms, low red (R)/far-red (FR) ratio light increases gibberellin (GA) levels. GA signaling in conifer seedlings requires FR to promote shoot elongation and reduce the inhibition of shoot elongation induced b...In angiosperms, low red (R)/far-red (FR) ratio light increases gibberellin (GA) levels. GA signaling in conifer seedlings requires FR to promote shoot elongation and reduce the inhibition of shoot elongation induced by paclobutrazol (PAC), yet the effects of far-red light in inducing shoot elongation in the presence or absence of PAC is poorly understood. In this study, transcriptomic and proteomic analyses was used to examine the molecular mechanism of FR regulation of shoot elongation in Chinese pine (Pinus tabuliformis Carr.) seedlings in the presence of PAC. Four treatments were compared: white light + water (WW), FR + water (RW), white light + PAC (WP), and FR + PAC (RP), and 1436 differentially expressed genes (DEGs) and 450 differentially expressed proteins (DEPs) were identified in RW_WW (RW contrast WW), and 1862 DEGs and 481 DEPs in RP_WP (RP contrast WP). Metabolic and signal transduction pathway analyses of DEGs and DEPs in RW_WW and RP_WP, indicated that the former required more energy than the latter. Moreover, gibberellic acid, auxin, and brassinolide are equally important in RW_WW and RP_WP for shoot elongation, except for the ethylene pathway. Amino acid metabolism and cell wall organization were significantly enriched in RW_WW and RP_WP, respectively. In summary, RW_WW and RP_WP had different effects in secondary metabolism, energy metabolism, amino acid metabolism, cell wall organization, and hormone response. These results provide an important theoretical and reference basis for studying the regulatory effect of low R/FR and PAC in conifer shoot elongation.展开更多
Sunflower(Helianthus annuus L.)is an important oilseed crop in China and is grown in rotation with potato in the northern parts of China,including Inner Mongolia,Hebei,Shaanxi,Shanxi,Gansu,Jilin,Liaoning and Heilongji...Sunflower(Helianthus annuus L.)is an important oilseed crop in China and is grown in rotation with potato in the northern parts of China,including Inner Mongolia,Hebei,Shaanxi,Shanxi,Gansu,Jilin,Liaoning and Heilongjiang provinces.In 2014,diseased samples of sunflower(variety 3638C)with black sunken lesions on bracts and stems of sunflower were collected in Wuchuan,Hohhot(41°50′N,111°27′E)and Chahaeryouyihouqi,Wulanchabu(41°52′N,113°0′E),Inner Mongolia,China.We used morphological and molecular techniques to identify the causal agent of Alternaria leaf blight.Phylogenetic analysis based on a combined phylogenetic dataset using the glyceraldehyde-3-phosphate dehydrogenase(gpd)and Alternaria major allergen gene(Alt a1)was done to support the morphological identification.In addition,PCR was performed with specific primers targeted on Alt a1 and calmodulin genes of A.solani and A.tomatophila.The results showed that HaAs7 gave an amplicon of the expected size(164 bp)with A.solani-specific primers,however,no band was observed with the A.tomatophilaspecific primers.The opposite pattern of PCR result(483 bp)was obtained with DNA of HaAt4 as template,indicating that HaAs7 is A.solani and HaAt4 is A.tomatophila.Furthermore,evaluation the pathogenicity of the recovered Alternaria isolates and their potential as causal agents of Alternaria leaf blight of sunflower was done.Pathogenicity tests showed that A.solani and A.tomatophila tested could be capable of causing Alternaria leaf blight of sunflower.Till now,nine species of Alternaria have been reported causing Alternaria leaf blight of sunflower,this is the first report that A.solani and A.tomatophila as causal pathogens for Alternaria leaf blight on sunflower.展开更多
Biomass production and nutrient （N, P, K, Ca and Mg） accumulation, distribution and cycling were quantified in young, mature and over-mature （10-, 22-, and 34-year old） Chinese fir [Cunninghamia lanceolate （Lamb....Biomass production and nutrient （N, P, K, Ca and Mg） accumulation, distribution and cycling were quantified in young, mature and over-mature （10-, 22-, and 34-year old） Chinese fir [Cunninghamia lanceolate （Lamb.） Hook] plantations in southern China. Total stand biomass of young, mature and over-mature stands was 38, 104 and 138 t ha-1 respectively. Biomass production increased significantly with age. Stem wood represented the highest percentage of stand biomass, accounting for 41, 55 and 63 % in the young, mature and over-mature plan- tations respectively. Nutrients concentration was highest in live needles and branches, and lowest in stem wood. The plantations accumulated more N, followed by K, Ca, Mg, and P. Nutrient return amount, nutrient utilization effi- ciency, nutrient turnover time, the ratio of nutrient return and uptake increased with stand age, which implies that young Chinese fir deplete soil nutrients to maintain growth, and efficiently utilize nutrients to decrease dependence on soil nutrients as they age. Harvesting young Chinese fir plantations would therefore lead to high nutrient loss, but prolonging the rotation length could improve soil recovery, and help sustain productivity in the long-term. Improved nutrient return through litterfall as stands get older may also be beneficial to nutrient pool recovery.展开更多
Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a hap...Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.展开更多
Anoplophora glabripennis(Asian longhorn beetle,ALB)and Anoplophora chinensis(Citrus longhorn beetle,CLB)are native forest pests in China;they have become important international quarantine pests.They are found using t...Anoplophora glabripennis(Asian longhorn beetle,ALB)and Anoplophora chinensis(Citrus longhorn beetle,CLB)are native forest pests in China;they have become important international quarantine pests.They are found using the same Salix aureopendula host tree of Cixi,Zhejiang province,China.On this host tree,we collected additional beetles that appeared to be morphologically intermediate between ALB and CLB.By using a stereoscope,we observed that there were several bumps on the base of the elytra,which was inconsistent with ALB,which typically has a smooth elytral base,but was more like CLB,which has numerous short tubercles on the elytral base.Given their sympatry and intermediate morphology,we hypothesized that these may represent ALB×CLB hybrids.We studied the genomic profiles for 46 samples(ALB,CLB,and putative hybrids)using genotyping-by-sequencing(GBS)providing a reduced representation of the entire genome.Employing principal component analyses on the 163 GBS-derived single nucleotide polymorphism data,we found putative hybrids tightly clustered with ALB,but genetically distinct from the CLB individuals.Therefore,our initial hybrid hypothesis was not supported by genomic data.Further,while mating experiments between adult ALB and CLB were successful in 4 separate years(2017,2018,2020,and 2021),and oviposition behavior was observed,no progeny was produced.Having employed population genomic analysis and biological hybridization experiments,we conclude that the putative hybrids represent newly discovered morphological variants within ALB.Our approach further confirmed the advantage of genome-wide information for Anoplophora species assignment in certain ambiguous classification cases.展开更多
While low-to-moderate resolution gridded climate data are suitable for climate-impact modeling at global and ecosystems levels, spatial analyses conducted at local scales require climate data with increased spatial ac...While low-to-moderate resolution gridded climate data are suitable for climate-impact modeling at global and ecosystems levels, spatial analyses conducted at local scales require climate data with increased spatial accuracy. This is particularly true for research focused on the evaluation of adaptive forest management strategies. In this study, we developed an application, Climate AP, to generate scale-free(i.e., specific to point locations) climate data for historical(1901–2015) and future(2011–2100)years and periods. Climate AP uses the best available interpolated climate data for the reference period 1961–1990 as baseline data. It downscales the baseline data from a moderate spatial resolution to scale-free point data through dynamic local elevation adjustments. It also integrates and downscales the historical and future climate data using a delta approach. In the case of future climate data, two greenhouse gas representative concentration pathways(RCP 4.5 and 8.5) and 15 general circulation models are included to allow for the assessment of alternative climate scenarios. In addition, Climate AP generates a large number of biologically relevant climate variables derived from primary monthly variables. The effectiveness of the local downscaling was determined based on the strength of the local linear regression for the estimate of lapse rate. The accuracy of the Climate AP output was evaluated through comparisons of Climate AP output against observations from 1805 weather stations in the Asia Pacific region. The local linear regression explained 70%–80% and 0%–50% of the total variation in monthly temperatures and precipitation, respectively, in most cases. Climate AP reduced prediction error by up to27% and 60% for monthly temperature and precipitation,respectively, relative to the original baselines data. The improvements for baseline portions of historical and futurewere more substantial. Applications and limitations of the software are discussed.展开更多
Background:Inbreeding in seed orchards is expected to increase with the advancement of breeding cycles,which results in the delivery of crops with suboptimal genetic gain,reduced genetic diversity,and lower seed set.H...Background:Inbreeding in seed orchards is expected to increase with the advancement of breeding cycles,which results in the delivery of crops with suboptimal genetic gain,reduced genetic diversity,and lower seed set.Here,a genetic distance-dependent method for clonal spatial deployment in seed orchards was developed and demonstrated,which reduced the inbreeding levels.The method’s main evaluation parameter of inbreeding is the genetic distance among individuals and the deployment method used an improved adaptive parallel genetic algorithm(IAPGA)based on Python language.Using inbreeding-prone Chinese Mongolian pine breeding population material originating from a single natural population,the proposed method was compared to a traditional orchard design and a distance-based design;namely,complete randomized block(RCB)and optimum neighborhood(ONA)designs,respectively.Results:With the advancement of selective breeding cycles,group separation among orchard related individuals is expected to increase.Based on the genetic distance among individuals,the IAPGA design was superior in significantly reducing the inbreeding level as compared to the two existing designs,confirming its suitability to advanced-generation orchards where relatedness among parents is common.In the 1st,2nd,and mixed generations clonal deployment schemes,the IAPGA design produced lower inbreeding with 87.22%,81.49%,and 87.23%of RCB,and 92.78%,91.30%,and 91.67%of ONA designs,respectively.Conclusions:The IAPGA clonal deployment proposed in this study has the obvious advantage of controlling inbreeding,and it is expected to be used in clonal deployment in seed orchards on a large-scale.Further studies are needed to focus on the actual states of pollen dispersal and mating in seed orchards,and more assumptions should be taken into account for the optimized deployment method.展开更多
The analysis of molecular variance(AMOVA)is a widely used statistical method in population genetics and molec-ular ecology.The classic framework of AMOVA only supports haploid and diploid data,in which the number of h...The analysis of molecular variance(AMOVA)is a widely used statistical method in population genetics and molec-ular ecology.The classic framework of AMOVA only supports haploid and diploid data,in which the number of hierarchies ranges from two to four.In practice,natural populations can be classified into more hierarchies,and polyploidy is frequently observed in extant species.The ploidy level may even vary within the same species,and/or within the same individual.We generalized the framework of AMOVA such that it can be used for any number of hierarchies and any level of ploidy.Based on this framework,we present four methods to account for data that are multilocus genotypic and allelic phenotypic(with unknown allele dosage).We use simulated datasets and an empirical dataset to evaluate the performance of our framework.We make freely available our methods in a new software package,polygene,which is freely available at https://github.com/huangkang1987/polygene.展开更多
基金funded by the National Natural Science Foundation of China(42107476,31901241)the China Postdoctoral Science Foundation(2020M682600)+1 种基金the China Postdoctoral International Exchange Fellowship Program(PC2021099)the Natural Science Foundation of Hunan Province(2021JJ41075).
文摘Trees progress through various growth stages,each marked by specific responses and adaptation strate-gies to environmental conditions.Despite the importance of age-related growth responses on overall forest health and management policies,limited knowledge exists regarding age-related effects on dendroclimatic relationships in key subtropical tree species.In this study,we employed a den-drochronological method to examine the impact of rapid warming on growth dynamics and climatic sensitivity of young(40–60 years)and old(100–180 years)Pinus mas-soniana forests across six sites in central-southern China.The normalized log basal area increment of trees in both age groups increased significantly following rapid warming in 1984.Trees in young forests further showed a distinct growth decline during a prolonged severe drought(2004–2013),whereas those in old forests maintained growth increases.Tree growth was more strongly influenced by temperature than by moisture,particularly in old forests.Spring tem-peratures strongly and positively impacted the growth of old trees but had a weaker effect on young ones.Old forests had a significantly lower resistance to extreme drought but faster recovery compared to young forests.The“divergence problem”was more pronounced in younger forests due to their heightened sensitivity to warming-induced drought and heat stress.With ongoing warming,young forests also may initially experience a growth decline due to their heightened sensitivity to winter drought.Our findings underscore the importance of considering age-dependent changes in forest/tree growth response to warming in subtropical forest man-agement,particularly in the context of achieving“Carbon Peak&Carbon Neutrality”goals in China.
基金supported by the National Key Research and Development Program of China(2016YFD0600201)the National Nonprofit Institute Research Grant of CAF(CAFYBB2017ZB003)+1 种基金the National Natural Science Foundation of China(3187071631670720)。
文摘Understanding the relationship between forest management and water use efficiency(WUE)is important for evaluating forest adaptability to climate change.However,the effects of thinning and understory removal on WUE and its key controlling processes are not well understood,which limits our comprehension of the physiological mechanisms of various management practices.In this study,four forest management measures(no thinning:NT;understory removal:UR;light thinning:LT;and heavy thinning:HT)were carried out in Pinus massoniana plantations in a subtropical region of China.Photosynthetic capacity and needle stable carbon isotope composition(δ^(13)C)were measured to assess instantaneous water use efficiency(WUE_(inst))and long-term water use efficiency(WUE_(i)).Multiple regression models and structural equation modelling(SEM)identified the effects of soil properties and physiological performances on WUE_(inst)and WUE_(i).The results show that WUE_(inst)values among the four treatments were insignificant.However,compared with the NT stand(35.8μmol·mol^(-1)),WUE_(i)values significantly increased to 41.7μmol·mol^(-1)in the UR,50.1μmol·mol^(-1)in the LT and 46.6μmol·mol^(-1)in HT treatments,largely explained by photosynthetic capacity and soil water content.Understory removal did not change physiological performance(needle water potential and photosynthetic capacity).Thinning increased the net photosynthetic rate(A_n)but not stomatal conductance(g_s)or predawn needle water potential(ψ_(pd)),implying that the improvement in water use efficiency for thinned stands was largely driven by radiation interception than by soil water availability.In general,thinning may be an appropriate management measure to promote P.massoniana WUE to cope with seasonal droughts under future extreme climates.
基金This work was supported by the National Natural Science Foundation of China(72221002,42271375)the Strategic Priority Research Program(XDA28060100)the Informatization Plan Project(CAS-WX2021PY-0109)of the Chinese Academy of Sciences.
文摘Accurate cropland information is critical for agricultural planning and production,especially in foodstressed countries like China.Although widely used medium-to-high-resolution satellite-based cropland maps have been developed from various remotely sensed data sources over the past few decades,considerable discrepancies exist among these products both in total area and in spatial distribution of croplands,impeding further applications of these datasets.The factors influencing their inconsistency are also unknown.In this study,we evaluated the consistency and accuracy of six cropland maps widely used in China in circa 2020,including three state-of-the-art 10-m products(i.e.,Google Dynamic World,ESRI Land Cover,and ESA WorldCover)and three 30-m ones(i.e.,GLC_FCS30,GlobeLand 30,and CLCD).We also investigated the effects of landscape fragmentation,climate,and agricultural management.Validation using a ground-truth sample revealed that the 10-m-resolution WorldCover provided the highest accuracy(92.3%).These maps collectively overestimated Chinese cropland area by up to 56%.Up to 37%of the land showed spatial inconsistency among the maps,concentrated mainly in mountainous regions and attributed to the varying accuracy of cropland maps,cropland fragmentation and management practices such as irrigation.Our work shed light on the promotion of future cropland mapping efforts,especially in highly inconsistent regions.
基金supported by the Doctorate Fellowship Foundation of Nanjing Forestry University, China (163010550)the Priority Academic Program Development of Jiangsu High Education Institutions, China (PAPD)。
文摘We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate(Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis(WGCNA) to describe the functionality and complexity of the physiological and morphogenetic processes as well as gene expression and metabolic differences during seed germination stages. In total, 489 metabolites were detected, including 40 differentially accumulated metabolites. The transcriptomic analysis showed the expression of 6 984 genes changed significantly throughout the whole germination process. Using WGCNA, we identified modules related to the various seed germination stages and hub genes. In the initial imbibition stage(stage 1), the pivotal genes involved in RNA transduction and the glycolytic pathway were most active, while in the sprouting stage(stage 4), the pivotal genes were involved in multiple metabolic pathways. In terms of secondary metabolic pathways, we found flavonoid 4-reductase genes of anthocyanin biosynthesis pathway are most significantly affected during pomegranate seed germination, while the flavonol synthase gene was mainly involved in the regulation of isoflavonoid biosynthesis.
基金supported by the Asia Pacific Network for Sustainable Forest Management and Rehabilitation(APFNet)under the project ‘‘Adaption of Asia Pacific Forests to Climate Change’’
文摘Expert opinions have been used in a variety of fields to identify relevant issues and courses of action. This study surveys experts in forestry and climate change from the Asia–Pacific region to gauge their perspectives on the impacts of climate change and on the challenges faced by forest adaptation in the region, and explores recommendations and initiatives for adapting forests to climate change. There was consensus regarding the impacts of climate change on forest ecosystems and on economic sectors such as agriculture and forestry. Respondents also indicated a lack of public awareness and policy and legislation as challenges to addressing climate change. However, the results indicate differences in opinion between regions on the negative impacts of climate change and in satisfaction with actions taken to address climate change,highlighting the need for locally specific policies and research. The study presents specific recommendations to address issues of most concern, based on subregion and professional affiliation throughout the Asia–Pacific region.The results can be used to improve policy and forest management throughout the region. This research will also provide valuable suggestions on how to apply research findings and management recommendations outside of the AP region. The conclusions should be communicated relative to the level of the research and the target audience,ensuring that scientific findings and management recommendations are effectively communicated to ensure successful implementation of forest adaptation strategies.
基金This work was supported by grants from the Strategic Prior-ity Research Program,Chinese Academy of Sciences(Grant No.XDA23080000)Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0502).
文摘The genus Rhododendron(Ericaceae),with more than 1000 species highly diverse in f lower color,is providing distinct ornamental values and a model system for f lower color studies.Here,we investigated the divergence between two parental species with different f lower color widely used for azalea breeding.Gapless genome assembly was generated for the yellow-f lowered azalea,Rhododendron molle.Comparative genomics found recent proliferation of long terminal repeat retrotransposons(LTR-RTs),especially Gypsy,has resulted in a 125 Mb(19%)genome size increase in species-specific regions,and a significant amount of dispersed gene duplicates(13402)and pseudogenes(17437).Metabolomic assessment revealed that yellow f lower coloration is attributed to the dynamic changes of carotenoids/f lavonols biosynthesis and chlorophyll degradation.Time-ordered gene co-expression networks(TO-GCNs)and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct f lower pigmentation.B3 and ERF TFs were found dominating the gene regulation of carotenoids/f lavonols characterized pigmentation in R.molle,while WRKY,ERF,WD40,C2H2,and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-f lowered R simsii.This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.
基金This study was supported by the National Natural Science Foundation(31600527)The Fundamental Research Funds for the Central Universities in Beijing Forestry University(2018BLCB08)+2 种基金the Project of Construction of World Class Universities in Beijing Forestry University(2019XKJS0308)Y.V.d.P.acknowledges funding from the European Research Council(ERC)under the European Union’s Horizon 2020 research and innovation program(grant agreement no.833522)from Ghent University(Methusalem funding,BOF.MET.2021.0005.01).
文摘Polyploidization plays a key role in plant evolution,but the forces driving the fate of homoeologs in polyploid genomes,i.e.,paralogs resulting from a whole-genome duplication(WGD)event,remain to be elucidated.Here,we present a chromosome-scale genome assembly of tetraploid scarlet sage(Salvia splendens),one of the most diverse ornamental plants.We found evidence for three WGD events following an older WGD event shared by most eudicots(theγevent).A comprehensive,spatiotemporal,genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries,which could be associated with genomic rearrangements,transposable element proximity discrepancies,coding sequence variation,selection pressure,and transcription factor binding site differences.The observed differences between homoeologs may reflect the first step toward sub-and/or neofunctionalization.This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
基金This work was supported by the National Natural Science Foundation of China(31770713)Biosafety and Genetic Resources Management Project of State Forestry and Grassland Administration(KJZXSA202030).
文摘In angiosperms, low red (R)/far-red (FR) ratio light increases gibberellin (GA) levels. GA signaling in conifer seedlings requires FR to promote shoot elongation and reduce the inhibition of shoot elongation induced by paclobutrazol (PAC), yet the effects of far-red light in inducing shoot elongation in the presence or absence of PAC is poorly understood. In this study, transcriptomic and proteomic analyses was used to examine the molecular mechanism of FR regulation of shoot elongation in Chinese pine (Pinus tabuliformis Carr.) seedlings in the presence of PAC. Four treatments were compared: white light + water (WW), FR + water (RW), white light + PAC (WP), and FR + PAC (RP), and 1436 differentially expressed genes (DEGs) and 450 differentially expressed proteins (DEPs) were identified in RW_WW (RW contrast WW), and 1862 DEGs and 481 DEPs in RP_WP (RP contrast WP). Metabolic and signal transduction pathway analyses of DEGs and DEPs in RW_WW and RP_WP, indicated that the former required more energy than the latter. Moreover, gibberellic acid, auxin, and brassinolide are equally important in RW_WW and RP_WP for shoot elongation, except for the ethylene pathway. Amino acid metabolism and cell wall organization were significantly enriched in RW_WW and RP_WP, respectively. In summary, RW_WW and RP_WP had different effects in secondary metabolism, energy metabolism, amino acid metabolism, cell wall organization, and hormone response. These results provide an important theoretical and reference basis for studying the regulatory effect of low R/FR and PAC in conifer shoot elongation.
基金This work was funded by the China Agricultural Research System(CARS-14)Special Fund for Agro-scientific Research in the Public Interest No.201503109the Science and Technology Application Projects(201803048).
文摘Sunflower(Helianthus annuus L.)is an important oilseed crop in China and is grown in rotation with potato in the northern parts of China,including Inner Mongolia,Hebei,Shaanxi,Shanxi,Gansu,Jilin,Liaoning and Heilongjiang provinces.In 2014,diseased samples of sunflower(variety 3638C)with black sunken lesions on bracts and stems of sunflower were collected in Wuchuan,Hohhot(41°50′N,111°27′E)and Chahaeryouyihouqi,Wulanchabu(41°52′N,113°0′E),Inner Mongolia,China.We used morphological and molecular techniques to identify the causal agent of Alternaria leaf blight.Phylogenetic analysis based on a combined phylogenetic dataset using the glyceraldehyde-3-phosphate dehydrogenase(gpd)and Alternaria major allergen gene(Alt a1)was done to support the morphological identification.In addition,PCR was performed with specific primers targeted on Alt a1 and calmodulin genes of A.solani and A.tomatophila.The results showed that HaAs7 gave an amplicon of the expected size(164 bp)with A.solani-specific primers,however,no band was observed with the A.tomatophilaspecific primers.The opposite pattern of PCR result(483 bp)was obtained with DNA of HaAt4 as template,indicating that HaAs7 is A.solani and HaAt4 is A.tomatophila.Furthermore,evaluation the pathogenicity of the recovered Alternaria isolates and their potential as causal agents of Alternaria leaf blight of sunflower was done.Pathogenicity tests showed that A.solani and A.tomatophila tested could be capable of causing Alternaria leaf blight of sunflower.Till now,nine species of Alternaria have been reported causing Alternaria leaf blight of sunflower,this is the first report that A.solani and A.tomatophila as causal pathogens for Alternaria leaf blight on sunflower.
基金supported by the Forestry Public Benefit Research Projects of National Forestry Administration under Grant No.201304303National Natural Science Foundation of China under Grant No.31370619+1 种基金Science and Technology Project of the Fujian Province under Grant No.2014N0002China Postdoctoral Science Foundation under Grant No.132300148
文摘Biomass production and nutrient （N, P, K, Ca and Mg） accumulation, distribution and cycling were quantified in young, mature and over-mature （10-, 22-, and 34-year old） Chinese fir [Cunninghamia lanceolate （Lamb.） Hook] plantations in southern China. Total stand biomass of young, mature and over-mature stands was 38, 104 and 138 t ha-1 respectively. Biomass production increased significantly with age. Stem wood represented the highest percentage of stand biomass, accounting for 41, 55 and 63 % in the young, mature and over-mature plan- tations respectively. Nutrients concentration was highest in live needles and branches, and lowest in stem wood. The plantations accumulated more N, followed by K, Ca, Mg, and P. Nutrient return amount, nutrient utilization effi- ciency, nutrient turnover time, the ratio of nutrient return and uptake increased with stand age, which implies that young Chinese fir deplete soil nutrients to maintain growth, and efficiently utilize nutrients to decrease dependence on soil nutrients as they age. Harvesting young Chinese fir plantations would therefore lead to high nutrient loss, but prolonging the rotation length could improve soil recovery, and help sustain productivity in the long-term. Improved nutrient return through litterfall as stands get older may also be beneficial to nutrient pool recovery.
基金This study was supported by the Foundation for the Introduction of Talent of Pingdingshan University(PXY-BSQD2016009)the Key Research Project of Colleges and Universities of Henan Province(182102110132,172102110111)+6 种基金the National Natural Science Foundation(31600527)the Fundamental Research Funds for the Central Universities of Beijing Forestry University(2018BLCB08)the Project for the Construction of World Class Universities of Beijing Forestry University(2019XKJS0308)the Scientific Research Foundation for National Natural Science Fund(31600527)Z.L.is funded by a postdoctoral fellowship from the Special Research Fund of Ghent University(BOFPDO2018001701)Y.V.P.acknowledges fundings from the European Research Council(ERC)under the European Union’s Horizon 2020 research and innovation program(grant agreement No 833522)from Ghent University(Methusalem funding,BOF.MET.2021.0005.01).
文摘Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.
基金supported by the Fundamental Research Funds for the Central Universities(No.QNTD202304)National Natural Science Foundation ofChina(No.32171794).
文摘Anoplophora glabripennis(Asian longhorn beetle,ALB)and Anoplophora chinensis(Citrus longhorn beetle,CLB)are native forest pests in China;they have become important international quarantine pests.They are found using the same Salix aureopendula host tree of Cixi,Zhejiang province,China.On this host tree,we collected additional beetles that appeared to be morphologically intermediate between ALB and CLB.By using a stereoscope,we observed that there were several bumps on the base of the elytra,which was inconsistent with ALB,which typically has a smooth elytral base,but was more like CLB,which has numerous short tubercles on the elytral base.Given their sympatry and intermediate morphology,we hypothesized that these may represent ALB×CLB hybrids.We studied the genomic profiles for 46 samples(ALB,CLB,and putative hybrids)using genotyping-by-sequencing(GBS)providing a reduced representation of the entire genome.Employing principal component analyses on the 163 GBS-derived single nucleotide polymorphism data,we found putative hybrids tightly clustered with ALB,but genetically distinct from the CLB individuals.Therefore,our initial hybrid hypothesis was not supported by genomic data.Further,while mating experiments between adult ALB and CLB were successful in 4 separate years(2017,2018,2020,and 2021),and oviposition behavior was observed,no progeny was produced.Having employed population genomic analysis and biological hybridization experiments,we conclude that the putative hybrids represent newly discovered morphological variants within ALB.Our approach further confirmed the advantage of genome-wide information for Anoplophora species assignment in certain ambiguous classification cases.
基金funded by a research grant"Adaptation of Asia-Pacific Forests to Climate Change"(APFNet/2010/PPF/001)funded by the Asia-Pacific Network for Sustainable Forest Management and Rehabilitation
文摘While low-to-moderate resolution gridded climate data are suitable for climate-impact modeling at global and ecosystems levels, spatial analyses conducted at local scales require climate data with increased spatial accuracy. This is particularly true for research focused on the evaluation of adaptive forest management strategies. In this study, we developed an application, Climate AP, to generate scale-free(i.e., specific to point locations) climate data for historical(1901–2015) and future(2011–2100)years and periods. Climate AP uses the best available interpolated climate data for the reference period 1961–1990 as baseline data. It downscales the baseline data from a moderate spatial resolution to scale-free point data through dynamic local elevation adjustments. It also integrates and downscales the historical and future climate data using a delta approach. In the case of future climate data, two greenhouse gas representative concentration pathways(RCP 4.5 and 8.5) and 15 general circulation models are included to allow for the assessment of alternative climate scenarios. In addition, Climate AP generates a large number of biologically relevant climate variables derived from primary monthly variables. The effectiveness of the local downscaling was determined based on the strength of the local linear regression for the estimate of lapse rate. The accuracy of the Climate AP output was evaluated through comparisons of Climate AP output against observations from 1805 weather stations in the Asia Pacific region. The local linear regression explained 70%–80% and 0%–50% of the total variation in monthly temperatures and precipitation, respectively, in most cases. Climate AP reduced prediction error by up to27% and 60% for monthly temperature and precipitation,respectively, relative to the original baselines data. The improvements for baseline portions of historical and futurewere more substantial. Applications and limitations of the software are discussed.
基金grants from The Fundamental Research Funds for the Central Universities(2015-02)the National Natural Science Foundation of China(Nos.31770713,31860221).
文摘Background:Inbreeding in seed orchards is expected to increase with the advancement of breeding cycles,which results in the delivery of crops with suboptimal genetic gain,reduced genetic diversity,and lower seed set.Here,a genetic distance-dependent method for clonal spatial deployment in seed orchards was developed and demonstrated,which reduced the inbreeding levels.The method’s main evaluation parameter of inbreeding is the genetic distance among individuals and the deployment method used an improved adaptive parallel genetic algorithm(IAPGA)based on Python language.Using inbreeding-prone Chinese Mongolian pine breeding population material originating from a single natural population,the proposed method was compared to a traditional orchard design and a distance-based design;namely,complete randomized block(RCB)and optimum neighborhood(ONA)designs,respectively.Results:With the advancement of selective breeding cycles,group separation among orchard related individuals is expected to increase.Based on the genetic distance among individuals,the IAPGA design was superior in significantly reducing the inbreeding level as compared to the two existing designs,confirming its suitability to advanced-generation orchards where relatedness among parents is common.In the 1st,2nd,and mixed generations clonal deployment schemes,the IAPGA design produced lower inbreeding with 87.22%,81.49%,and 87.23%of RCB,and 92.78%,91.30%,and 91.67%of ONA designs,respectively.Conclusions:The IAPGA clonal deployment proposed in this study has the obvious advantage of controlling inbreeding,and it is expected to be used in clonal deployment in seed orchards on a large-scale.Further studies are needed to focus on the actual states of pollen dispersal and mating in seed orchards,and more assumptions should be taken into account for the optimized deployment method.
基金funded by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31020302)the National Natural Science Foundation of China(31770411,31730104,31572278,31770425)+2 种基金the Young Elite Scientists Sponsorship Program by CAST(2017QNRC001)the National Key Programme of Research and Development,Ministry of Science and Technology(2016YFC0503200)the Shaanxi Science and Technology Innovation Team(2019TD-012).
文摘The analysis of molecular variance(AMOVA)is a widely used statistical method in population genetics and molec-ular ecology.The classic framework of AMOVA only supports haploid and diploid data,in which the number of hierarchies ranges from two to four.In practice,natural populations can be classified into more hierarchies,and polyploidy is frequently observed in extant species.The ploidy level may even vary within the same species,and/or within the same individual.We generalized the framework of AMOVA such that it can be used for any number of hierarchies and any level of ploidy.Based on this framework,we present four methods to account for data that are multilocus genotypic and allelic phenotypic(with unknown allele dosage).We use simulated datasets and an empirical dataset to evaluate the performance of our framework.We make freely available our methods in a new software package,polygene,which is freely available at https://github.com/huangkang1987/polygene.
