An accurate assessment of host and pathogen gene expression during infection is critical for understanding the molecular aspects of host-pathogen interactions.Often,pathogen-derived transcripts are difficult to ascert...An accurate assessment of host and pathogen gene expression during infection is critical for understanding the molecular aspects of host-pathogen interactions.Often,pathogen-derived transcripts are difficult to ascertain at early infection stages owing to the unfavourable transcript representation compared to the host genes.In this study,we compare two sequencing techniques,RNAseq and enrichment sequencing(RenSeq and PenSeq)of cDNA,to investigate gene expression patterns in the doubled monoploid potato(DM)infected with the late blight pathogen Phytophthora infestans.Our results reveal distinct advantages of cDNA RenSeq and PenSeq over traditional RNAseq in terms of target gene representation and transcriptional quantification at early infection stages.Throughout the infection time course,cDNA enrichment sequencing enables transcriptomic analyses for more targeted host and pathogen genes.For highly expressed genes that were sampled in parallel by both cDNA enrichment and RNAseq,a high level of concordance in expression profiles is observed,indicative of at least semi-quantitative gene expression representation following enrichment.展开更多
Soil biota mediates key ecological processes and delivers a range of societally important ecosystem services.However,the impacts of atmospheric changes on soil metazoans have been understudied.To address this knowledg...Soil biota mediates key ecological processes and delivers a range of societally important ecosystem services.However,the impacts of atmospheric changes on soil metazoans have been understudied.To address this knowledge gap,we evaluated the short-term responses of soil metazoans to elevated carbon dioxide(CO_(2))and ozone(O_(3))with two commonly grown rice varieties(Nanjing 5055 and Wuyujing 3)in a paddy soil.A simultaneous increase of CO_(2)and O_(3)concentrations had a negligible effect on the diversity of Annelida,Mollusca,Porifera,and total soil metazoans,suggesting that soil metazoan taxa had an inherent resilience to atmospheric changes.However,elevated CO_(2)alone significantly enhanced the diversity and relative abundances of Craniata and Platyhelminthes for Wuyujing 3 under ambient O_(3)conditions.However,elevated O_(3)decreased the diversity and relative abundance of Craniata by 42.7%and 47.7%,respectively,especially under elevated CO_(2)conditions for Wuyujing 3,demonstrating significant interactive effects.Furthermore,soil NO_(3)^(-)-N and NH_(4)^(+)-N contents mostly shaped the changes in the diversity and composition of soil metazoan communities.These results highlight the crucial role of rice variety regulating soil metazoan communities under the complex interaction between short-term elevated CO_(2)and O3.Thus,to better understand the mechanisms and processes within soil food webs,future studies should include the combined effects of various climate change factors and different crop varieties on soil metazoan communities.展开更多
Potato is the thirdmost important food crop in theworld.Diverse pathogens threaten sustainable crop production but can be controlled,in many cases,through the deployment of disease resistance genes belonging to the fa...Potato is the thirdmost important food crop in theworld.Diverse pathogens threaten sustainable crop production but can be controlled,in many cases,through the deployment of disease resistance genes belonging to the family of nucleotide-binding,leucine-rich-repeat(NLR)genes.To identify effective disease resistance genes in established varieties,we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR-AgRenSeq-d.The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score.Using a SMRT-RenSeq-based sequence representation of the NLRome from the cultivar Innovator,SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1,Rpi-R2-like,Rpi-R3a,and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations.All benchmark genes were identified with an F1 score of 1,which indicates absolute linkage in the panel.This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode(PCN)species Globodera pallida(pathotypes Pa2/3).Assuming that NLRs are involved in controlling many types of resistances,SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems.展开更多
Rubus fruits are high-value crops that are sought after by consumers for their flavor,visual appeal,and health benefits.To meet this demand,production of red and black raspberries(R.idaeus L.and R.occidentalis L.),bla...Rubus fruits are high-value crops that are sought after by consumers for their flavor,visual appeal,and health benefits.To meet this demand,production of red and black raspberries(R.idaeus L.and R.occidentalis L.),blackberries(R.subgenus Rubus),and hybrids,such as Boysenberry and marionberry,is growing worldwide.Rubus breeding programmes are continually striving to improve flavor,texture,machine harvestability,and yield,provide pest and disease resistance,improve storage and processing properties,and optimize fruits and plants for different production and harvest systems.Breeders face numerous challenges,such as polyploidy,the lack of genetic diversity in many of the elite cultivars,and until recently,the relative shortage of genetic and genomic resources available for Rubus.This review will highlight the development of continually improving genetic maps,the identification of Quantitative Trait Loci(QTL)s controlling key traits,draft genomes for red and black raspberry,and efforts to improve gene models.The development of genetic maps and markers,the molecular characterization of wild species and germplasm,and highthroughput genotyping platforms will expedite breeding of improved cultivars.Fully sequenced genomes and accurate gene models facilitate identification of genes underlying traits of interest and enable gene editing technologies such as CRISPR/Cas9.展开更多
Bifurcaria bifurcata is a seaweed of the Order Fucales(Ochrophyta,Phaeophyceae)that can be found all year round along the Portuguese Atlantic shore.Although it is considered edible in some countries,its biotechnologic...Bifurcaria bifurcata is a seaweed of the Order Fucales(Ochrophyta,Phaeophyceae)that can be found all year round along the Portuguese Atlantic shore.Although it is considered edible in some countries,its biotechnological potential has not yet been assessed in detail and here we report its antimicrobial potential against human dermatophyte fungi.Three samples were harvested from Baleal Island(Peniche,Portugal)harvested in winter(BbPe);from Aguda Beach(Arcozelo,Vila Nova de Gaia,Portugal),harvested in autumn(BbAg)and a sample obtained by culturing the Aguda sample under laboratory conditions(BbLC).A broth macrodilution assay was applied to determine the MIC(minimum inhibitory concentration)and MLC(minimum lethal concentration)of the B.bifurcata extracts.Results show that the BbPe MeOH extracts were the most effective and had higher antifungal activity against all the tested dermatophyte strains than the BbLC and BaAg extracts[Epidermophyton floccosum FF9(100–200μg/mL MIC;200μg/mL MLC),Microsporum canis FF1(400μg/mL MIC;≥400μg/mL MLC),Trichophyton mentagrophytes FF7(100μg/mL MIC;>800μg/mL MLC),M.gypseum CECT 2908(800μg/mL MIC;≥800μg/mL MLC),T.mentagrophytes var.interdigitale CECT 2958(800μg/mL MIC;≥800μg/mL MLC),T.rubrum CECT 2794(200μg/mL MIC;≥400μg/mL MLC)].In fact,only E.floccosum FF9 was sensitive to BbAg and BbLC MeOH extracts.To our knowledge,this is the first report of antifungal activity of B.bifurcata against human dermatophyte fungi.展开更多
More than 170 years after causing the potato famine in Ireland,late blight is still considered one of the most devastating crop diseases.Commercial potato breeding efforts depend on natural sources of resistance to pr...More than 170 years after causing the potato famine in Ireland,late blight is still considered one of the most devastating crop diseases.Commercial potato breeding efforts depend on natural sources of resistance to protect crops from the rapidly evolving late blight pathogen,Phytophthora infestans.We have identified and mapped a novel broad-spectrum disease resistance gene effective against P.infestans from the wild,diploid potato species Solanum bulbocastanum.Diagnostic resistance gene enrichment sequencing(dRenSeq)was used to confirm the uniqueness of the identified resistance.RenSeq and GenSeq-based mapping of the resistance,referred to as Rpi-blb4,alongside recombinant screening,positioned the locus responsible for the resistance to potato chromosome 5.The interval spans approximately 2.3 Mb and corresponds to the DM reference genome positions of 11.25 and 13.56 Mb.展开更多
Three field trials were set up to measure the effect of previous crops or soil amendments on the yields of subsequent crops of cereals under a cool temperate maritime climate in arable crop land in the east of Scotlan...Three field trials were set up to measure the effect of previous crops or soil amendments on the yields of subsequent crops of cereals under a cool temperate maritime climate in arable crop land in the east of Scotland. Winter wheat and winter barley direct drilled into legume and cereal + legume stubble (pre-crop) gave substantial yield boost compared with other pre-crop cereals, but pre-crop effects of oats were similarly great. Restored rotation after continuous barley gave expected yield enhancement to subsequent winter and spring barley but not to subsequent wheat. Some diseases were reduced on restored rotation crops. Slurry effects on yield were generally small but beneficial and compost effects were greater. However, compost had effects on plant developmental speed and was difficult to compare directly with other treatments. NDRE measurements in the restored rotation and soil amendment trials indicated that yield gains were associated with improved crop health as indicated by leaf chlorophyll content. There were no clear cultivar interactions within crop type with treatments effects in any of these trials.展开更多
Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant's response to these environmental signa...Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant's response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka ×Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL colocating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley.展开更多
Dear Editor, Phosphorus (P) deficiency is the most limiting factor in tropical agriculture since most soils in this region are predominantly acids with high-energy P-binding compounds. Therefore, up to 90% of the P ap...Dear Editor, Phosphorus (P) deficiency is the most limiting factor in tropical agriculture since most soils in this region are predominantly acids with high-energy P-binding compounds. Therefore, up to 90% of the P applied becomes fixed in soils, which raises environmental concerns and production costs (Syers et al., 2008). Thus, developing strategies to imptove P use efficiency (PUE) is essential to mitigate environmental problems and improve profits. These strategies should consider the soil-root-rhizosphere system because it is the most biochemical active site where nutrient uptake occurs (Hinsinger, 2011).展开更多
Over the past two decades,it has become increasingly apparent that early Mars may once have been warmer,wetter and more habitable for microbial life than it is today,which has spurred discussions about potential biosi...Over the past two decades,it has become increasingly apparent that early Mars may once have been warmer,wetter and more habitable for microbial life than it is today,which has spurred discussions about potential biosignatures that may be preserved in Martian sediments.An impediment to this line of research is the pervasive oxidation of Mars’surface due to photochemical oxidants that have likely destroyed remnants of organic matter.Here,we investigate whether nitrogen(N)transferred from biomass to phyllosilicate minerals during diagenesis can be preserved in oxidized mudrocks.We investigate two sequences of terrestrial Proterozoic red beds,namely the Sibley Group(1.4 Ga)in Canada and the Stoer Group(1.2 Ga)in Scotland,and we find enrichments in authigenic N in the range of several tens of ppm in both units.The highest concentrations(ca.100 ppm on average)are found in the most desiccated red beds of the Stoer Group,concurrent with enrichments in potassium(K).We discuss similarities and differences between the two sets of rocks with regards to salinity,pH,biological productivity and K-metasomatism,and we conclude that the ideal mechanism for the preservation of biogenic N in red beds may be in-situ release of ammonium from microbial mats into the clay substrate,possibly facilitated by early diagenetic,biologically induced illitization.Illite and smectite have been observed on Mars,and experiments suggest that Martian waters contained moderate amounts of dissolved K.Hence,it is conceivable that a similar K and N enrichment process could have occurred as to what we document for the Proterozoic,preserving evidence of life that may have survived to the modern day.展开更多
A diet rich in phytonutrients from fruit and vegetables has been acknowledged to afford protection against a range of human diseases,but many of the most popular vegetables are low in phytonutrients.Wild relatives of ...A diet rich in phytonutrients from fruit and vegetables has been acknowledged to afford protection against a range of human diseases,but many of the most popular vegetables are low in phytonutrients.Wild relatives of crops may contain allelic variation for genes determining the concentrations of these beneficial phytonutrients,and therefore understanding the genetic basis of this variation is important for breeding efforts to enhance nutritional quality.In this study,lettuce recombinant inbred lines,generated from a cross between wild and cultivated lettuce(Lactuca serriola and Lactuca sativa,respectively),were analysed for antioxidant(AO)potential and important phytonutrients including carotenoids,chlorophyll and phenolic compounds.When grown in two environments,96 quantitative trait loci(QTL)were identified for these nutritional traits:4 for AO potential,2 for carotenoid content,3 for total chlorophyll content and 87 for individual phenolic compounds(two per compound on average).Most often,the L.serriola alleles conferred an increase in total AOs and metabolites.Candidate genes underlying these QTL were identified by BLASTn searches;in several cases,these had functions suggesting involvement in phytonutrient biosynthetic pathways.Analysis of a QTL on linkage group 3,which accounted for>30%of the variation in AO potential,revealed several candidate genes encoding multiple MYB transcription factors which regulate flavonoid biosynthesis and flavanone 3-hydroxylase,an enzyme involved in the biosynthesis of the flavonoids quercetin and kaempferol,which are known to have powerful AO activity.Follow-up quantitative RT-PCR of these candidates revealed that 5 out of 10 genes investigated were significantly differentially expressed between the wild and cultivated parents,providing further evidence of their potential involvement in determining the contrasting phenotypes.These results offer exciting opportunities to improve the nutritional content and health benefits of lettuce through marker-assisted breeding.展开更多
The Valab project (Integrated Ecosystemic value-enhancement of the Guadeloupean Forest Agrobiodiversity) is a participatory action research that aims to explore the feasibility of diversification activities within the...The Valab project (Integrated Ecosystemic value-enhancement of the Guadeloupean Forest Agrobiodiversity) is a participatory action research that aims to explore the feasibility of diversification activities within the forest understorey. In the exploratory phase of the project, we studied stakeholders’ opinions on the positive and negative impacts of introducing livestock activities within a forest environment, as well as breeders’ constraints or motivations for setting up livestock units within agroforestry systems in the private forests of Guadeloupe. To establish a diagnosis of the current situation, 51 stakeholders (St) and 49 farmers (Fr) were interviewed on their perceptions, opinions, motivations and preferences. Forty-one percent of the St has had a generally positive appreciation of livestock activities, while on the opposite 31% have had a resolutely negative posture depending on their area of expertise. Their views on the possible positive effects or negative interactions between livestock and agroforestry activities were analysed in order to suggest possible approaches for the authorities or associations. Unanimously, the farmers replied that their motivations followed economic strategies: for self-consumption or sale. But their decision-making processes were also non-economic. Many of them (36% Fr) gave importance to their activity in the construction of their identity, whether it was through a desire to perpetuate traditions or to maintain family activities. The main constraints identified were natural constraints (61% Fr), including topography, climate and predators. While 28% of Fr notified their motivations for environmental protection. Another constraint was of a technical nature (44% Fr) since farmers asked for more technical references or support services. Further researches are required to study the interactions between animals and the undergrowth by describing their respective ecosystem services in order to enhance their positive interactions.展开更多
Micro-tubers are important propagules in potato breeding and potato production, and they are also dormant and easily transported and therefore good targets for mutation induction in potato mutation breeding. A prerequ...Micro-tubers are important propagules in potato breeding and potato production, and they are also dormant and easily transported and therefore good targets for mutation induction in potato mutation breeding. A prerequisite for mutation breeding is to determine optimal mutation treatments. Therefore, radio-sensitivity tests of a tetraploid and a diploid potato to gamma irradiation were undertaken. Effects of different gamma sources on radio-activity were also studied. In vitro potato cuttings were gamma irradiated using a wide dose range (0, 3, 6, 9, 12, 15 and 20 Gy). The irradiated cuttings were then cultured to induce micro-tubers directly in vitro. Micro-tuber morphotypes were assessed after irradiation of cuttings using three gamma sources with emission activities of 1.8, 7.07 and 139 Gy/min. The diploid species (Solanum verrucosum) was more radio-sensitive than the tetraploid cultivar Desirée (Solanum tuberosum). Gamma dose rates had significant influences on subsequent micro-tuber production at various mutant generations. Effects included reductions in the number, size and weight of micro-tubers produced. Gamma dose was more lethal for the diploid potato genotype and micro-tubers produced were small compared to those produced by the tetraploid genotype after irradiation. Different treatments are recommended for diploid and tetraploid potato irradiation in producing large mutant micro-tuber populations. The mutant micro-tuber populations may then be screened for interesting mutations/trait for both genetics and plant breeding purposes.展开更多
Physiological and physical traits are excellent indicators of many crop characteristics,but precise phenotyping of these traits is time consuming and,therefore,limits progress in crop breeding and the speed of crop mo...Physiological and physical traits are excellent indicators of many crop characteristics,but precise phenotyping of these traits is time consuming and,therefore,limits progress in crop breeding and the speed of crop monitoring.Hyperspectral imaging offers an opportunity to overcome these barriers as a technique for high throughput field measurements.Using a recently developed hyperspectral imaging platform devised for plantations of the perennial crop raspberry,this study aimed to further develop the tool and test its capacity as an innovative approach for high throughput field phenotyping,data collection and analysis.Hyperspectral imaging and visual crop assessments were carried out over two growing seasons in a field-grown raspberry mapping population,and data were subject to Quantitative Trait Loci(QTL)analysis.The findings show that reflectance intensity at multiple wavelengths can be linked to known genetic markers in raspberry,and many of these‘spectral traits'are expressed consistently through the growing season and between years,for example spectral ratio 719 nm/691 nm shows up consistently as a QTL on LG4.Spectral traits were identified that co-located with previously mapped physical traits,such as 719 nm/691 nm and cane density.The study indicates that hyperspectral imaging can be used as an innovative approach for high throughput field phenotyping of raspberry and could be transferred readily to other perennial crops.Our approach provides a pipeline for automated field data collection and analysis that can be used for rapid QTL detection of spectral traits.展开更多
To efficiently obtain P from soil,most terrestrial plants form symbiosis with arbuscular mycorrhizal(AM)fungi and thus have two P uptake pathways,i.e.,the direct pathway(DP)via roots,particularly root hairs,and the my...To efficiently obtain P from soil,most terrestrial plants form symbiosis with arbuscular mycorrhizal(AM)fungi and thus have two P uptake pathways,i.e.,the direct pathway(DP)via roots,particularly root hairs,and the mycorrhizal pathway(MP)via AM fungal hyphae.AM fungi form an extraradical hyphal network to expand their contact area with soil and release carbon-rich compounds,which provide a high-energy habitat for soil bacteria.The bacteria affected by AM fungi support P nutrition of AM fungi by secreting extracellular phosphatases.During the P acquisition process,both DP and MP function and require C fixed by plant photosynthesis to maintain P transport.Plants make trade-offs between DP and MP based on C inputs and P benefits.This review first systematically explores the potential trade-offs between plant C inputs and P gains of DP and MP as well as the factors that influence such trade-offs.Then the response of AM fungi to soil nutrient heterogeneity and the mechanisms by which AM fungi select bacteria to mineralize organic P and increase the P contribution of MP were analyzed.Future studies need to apply emerging methods and technologies to accurately quantify the contribution of DP and MP to plant P absorption under different conditions and provide the theoretical basis for optimizing sustainable agricultural production systems.展开更多
Tetracycline(TC),which is widely employed in agriculture,constitutes a serious source of environmental pollution.In this study,mechanical ball-milling(B)treated iron/manganese-nitrogen(Fe/Mn-N)doped hydrochars(Fe/Mn-B...Tetracycline(TC),which is widely employed in agriculture,constitutes a serious source of environmental pollution.In this study,mechanical ball-milling(B)treated iron/manganese-nitrogen(Fe/Mn-N)doped hydrochars(Fe/Mn-BNHT)synthesized using saponin-containing seed meal(T)as a carbon source,showed excellent removal ability of tetracycline with a removal efficiency 95%.The Fe/Mn-BNHT showed superior performance in batch experiments with solution pH(3-9),coexisting ions,and after 5 cycles of application.Further analysis showed that Fe/Mn-BNHT mediated the degradation of adsorbed tetracycline with a degradation efficiency 87%.Surface complexation,electrostatic interactions,and hydrogen bonding facilitated the adsorption of tetracycline.・OH induced by oxygen vacancy(O_(V))was identified as the main reactive oxidation species in tetracycline degradation.Fe(III)-tetracycline complexes gained electrons through graphitic N,leading to tetracycline degradation and Fe(III)reduction.The degradation pathways for tetracycline are shown through density functional theory calculation and intermediate identification,and the ecological toxicity risk of 10 degradation intermediates is evaluated.This research provides a new perspective on the development of environmentally friendly materials that can simultaneously adsorb and degrade pollutants.展开更多
Host-pathogen co-evolution shapes resistance(R)proteins and their recognition of pathogen avirulence factors.However,little attention has been paid to naturally occurring genetic diversity in R genes.In this study,12 ...Host-pathogen co-evolution shapes resistance(R)proteins and their recognition of pathogen avirulence factors.However,little attention has been paid to naturally occurring genetic diversity in R genes.In this study,12 Solanum bulbocastanum accessions from the Commonwealth Potato Collection were screened for resistance to Phytophthora infestans,identifying 11 resistant and one susceptible accession.Targeted enrichment sequencing of nucleotide-binding leucine-rich repeat(NLR)genes using RenSeq,followed by diagnostic RenSeq(dRenSeq)analysis,revealed that all accessions except 7650 contained Rpi-blb1/RB variants.Variants in accessions 7641 and 7648 were non-functional,while three novel functional variants were identified.Cloning and functional analysis of Rpi-blb1/RB variants assessed their recognition of the avirulence factor IPI-O1.Three variants were functional,conferring resistance to P.infestans.Variants in accessions 7644 and 7647 also recognized IPI-O4,confirmed in transgenic potatoes.Analysis of a non-functional variant in S.bulbocastanum accession 7648 identified amino acid Ser347 in the nucleotide-binding(NB-ARC)domain as critical for cell-death initiation following IPI-O1 recognition.Predictions from the FunFOLD2 protein-ligand interaction model suggested that Ser347 is essential for ATP binding,suggesting potential inhibition on pentameric resistosome assembly.Western blot analysis revealed that the mutation of Ser347 to Asn markedly compromises the Rpi-blb1/RB protein stability,and co-immunoprecipitation assay further confirmed that this mutation severely disrupts the self-association of CCNB,thereby preventing Rpi-blb1/RB activation.Consistently,substituting Asn347 with serine restored function,underscoring its key role in Rpi-blb1/RB activity.Cell biology experiments demonstrated that Rpi-blb1/RB relocalize to the plasma membrane in response to IPI-O1.This relocalization depends on Ser347,further supporting the idea that its mutation affects resistosome formation,impairing resistance.This study provides an in-depth functional analysis of natural Rpi-blb1/RB diversity,offering insights into NLR protein evolution and resistance mechanisms in potatoes.展开更多
Hybrid potato breeding based on diploid inbred lines is transforming the way of genetic improvement of this staple food crop,which requires a deep understanding of potato domestication and differentiation.In the prese...Hybrid potato breeding based on diploid inbred lines is transforming the way of genetic improvement of this staple food crop,which requires a deep understanding of potato domestication and differentiation.In the present study,we resequenced 314 diploid wild and landrace accessions to generate a variome map of 47,203,407 variants.Using the variome map,we discovered the reshaping of tuber transcriptome during potato domestication,characterized genome-wide differentiation between landrace groups Stenotomum and Phureja.We identified a jasmonic acid biosynthetic gene possibly affecting the tuber dormancy period.Genome-wide association studies revealed a UDP-glycosyltransferase gene for the biosynthesis of anti-nutritional steroidal glycoalkaloids(SGAs),and a Dehydration Responsive Element Binding(DREB)transcription factor conferring increased average tuber weight.In addition,genome similarity and group-specific SNP analyses indicated that tetraploid potatoes originated from the diploid Solanum tuberosum group Stenotomum.These findings shed light on the evolutionary trajectory of potato domestication and improvement,providing a solid foundation for advancing hybrid potato-breeding practices.展开更多
While global efforts to operationalize soil spectroscopy are progressing,cooperation is needed to fully leverage its potential for generating digital soil information to support sustainable soil management worldwide.T...While global efforts to operationalize soil spectroscopy are progressing,cooperation is needed to fully leverage its potential for generating digital soil information to support sustainable soil management worldwide.The Global Soil Laboratory Network’s soil spectroscopy initiative(GLOSOLANSpec),led by the Food and Agriculture Organization of the United Nations(FAO)through its Global Soil Partnership(GSP),is dedicated to the further development and adoption of soil spectroscopy by fostering international collaboration via a scientific community of practice to produce accurate and reliable soil information for sustainable soil management and decision-making.To support this effort,we,a global consortium of soil scientists under the auspices of the International Union of Soil Sciences(IUSS)and GLOSOLAN-Spec,aim to address seven key challenges hindering the adoption of soil spectroscopy worldwide.Here,we offer perspectives on what is needed to advance soil spectroscopy as a routine soil analysis method,emphasizing its potential to generate new and reliable spatial and temporal soil data.展开更多
基金supported by the Rural & Environment Science & Analytical Services (RESAS) Division of the Scottish Government through project JHI-B1-1the Biotechnology and Biological Sciences Research Council (BBSRC) through awards BB/ S015663/1+2 种基金BB/X009068/1Research Leaders 2025 fellowship funded by European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement no. 754380the Research/Scientific Computing teams at The James Hutton Institute and NIAB for providing computational resources and technical support for the “UK’s Crop Diversity Bioinformatics HPC” (BBSRC grant BB/ S019669/1)。
文摘An accurate assessment of host and pathogen gene expression during infection is critical for understanding the molecular aspects of host-pathogen interactions.Often,pathogen-derived transcripts are difficult to ascertain at early infection stages owing to the unfavourable transcript representation compared to the host genes.In this study,we compare two sequencing techniques,RNAseq and enrichment sequencing(RenSeq and PenSeq)of cDNA,to investigate gene expression patterns in the doubled monoploid potato(DM)infected with the late blight pathogen Phytophthora infestans.Our results reveal distinct advantages of cDNA RenSeq and PenSeq over traditional RNAseq in terms of target gene representation and transcriptional quantification at early infection stages.Throughout the infection time course,cDNA enrichment sequencing enables transcriptomic analyses for more targeted host and pathogen genes.For highly expressed genes that were sampled in parallel by both cDNA enrichment and RNAseq,a high level of concordance in expression profiles is observed,indicative of at least semi-quantitative gene expression representation following enrichment.
基金financially supported by the National Natural Science Foundation of China(Nos.42077209,32271679,and 32071631)the Natural Science Foundation of Fujian Province of China(Nos.2023R1002004 and 2023J06024)The James Hutton Institute of UK received funding from the Scottish Government Rural and Environment Science and Analytical Services(RESAS)under Healthy Soils for a Green Recovery,as part of the 2022-2027 Strategic Research Programme。
文摘Soil biota mediates key ecological processes and delivers a range of societally important ecosystem services.However,the impacts of atmospheric changes on soil metazoans have been understudied.To address this knowledge gap,we evaluated the short-term responses of soil metazoans to elevated carbon dioxide(CO_(2))and ozone(O_(3))with two commonly grown rice varieties(Nanjing 5055 and Wuyujing 3)in a paddy soil.A simultaneous increase of CO_(2)and O_(3)concentrations had a negligible effect on the diversity of Annelida,Mollusca,Porifera,and total soil metazoans,suggesting that soil metazoan taxa had an inherent resilience to atmospheric changes.However,elevated CO_(2)alone significantly enhanced the diversity and relative abundances of Craniata and Platyhelminthes for Wuyujing 3 under ambient O_(3)conditions.However,elevated O_(3)decreased the diversity and relative abundance of Craniata by 42.7%and 47.7%,respectively,especially under elevated CO_(2)conditions for Wuyujing 3,demonstrating significant interactive effects.Furthermore,soil NO_(3)^(-)-N and NH_(4)^(+)-N contents mostly shaped the changes in the diversity and composition of soil metazoan communities.These results highlight the crucial role of rice variety regulating soil metazoan communities under the complex interaction between short-term elevated CO_(2)and O3.Thus,to better understand the mechanisms and processes within soil food webs,future studies should include the combined effects of various climate change factors and different crop varieties on soil metazoan communities.
基金supported by the Rural&Environment Science&Analytical Services(RESAS)Division of the Scottish Government through project JHI-B1-1,the Biotechnology and Biological Sciences Research Council(BBSRC)through award BB/S015663/1 and the Royal Society through award NAF\R1\201061YW was supported through the CSC scholarship program,China.LB was supported through the East of Scotland Bioscience Doctoral Training Partnership(EASTBIO DTP)funded by the BBSRC award BB/T00875X/1.AK was supported through a Research Leaders 2025 fellowship funded by European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement no.754380.
文摘Potato is the thirdmost important food crop in theworld.Diverse pathogens threaten sustainable crop production but can be controlled,in many cases,through the deployment of disease resistance genes belonging to the family of nucleotide-binding,leucine-rich-repeat(NLR)genes.To identify effective disease resistance genes in established varieties,we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR-AgRenSeq-d.The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score.Using a SMRT-RenSeq-based sequence representation of the NLRome from the cultivar Innovator,SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1,Rpi-R2-like,Rpi-R3a,and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations.All benchmark genes were identified with an F1 score of 1,which indicates absolute linkage in the panel.This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode(PCN)species Globodera pallida(pathotypes Pa2/3).Assuming that NLRs are involved in controlling many types of resistances,SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems.
文摘Rubus fruits are high-value crops that are sought after by consumers for their flavor,visual appeal,and health benefits.To meet this demand,production of red and black raspberries(R.idaeus L.and R.occidentalis L.),blackberries(R.subgenus Rubus),and hybrids,such as Boysenberry and marionberry,is growing worldwide.Rubus breeding programmes are continually striving to improve flavor,texture,machine harvestability,and yield,provide pest and disease resistance,improve storage and processing properties,and optimize fruits and plants for different production and harvest systems.Breeders face numerous challenges,such as polyploidy,the lack of genetic diversity in many of the elite cultivars,and until recently,the relative shortage of genetic and genomic resources available for Rubus.This review will highlight the development of continually improving genetic maps,the identification of Quantitative Trait Loci(QTL)s controlling key traits,draft genomes for red and black raspberry,and efforts to improve gene models.The development of genetic maps and markers,the molecular characterization of wild species and germplasm,and highthroughput genotyping platforms will expedite breeding of improved cultivars.Fully sequenced genomes and accurate gene models facilitate identification of genes underlying traits of interest and enable gene editing technologies such as CRISPR/Cas9.
基金the support of Fundacao para a Ciência e Tecnologia(FCT),through the strategic project UID/MAR/04292/2013 granted to MAREthe support from the European Union through EASME Blue Labs project AMALIA-Algae-to-MArket Lab IdeAs(EASME/EMFF/2016/1.2.1.4/03/SI2.750419)+2 种基金funding from European Structural&Investment Funds through the COMPETE ProgrammeNational Funds through FCT-Fundacao para a Ciência e a Tecnologia under the Programme grant SAICTPAC/0019/2015the support of ALGAplus for giving the opportunity of culturing the B.bifurcata sample
文摘Bifurcaria bifurcata is a seaweed of the Order Fucales(Ochrophyta,Phaeophyceae)that can be found all year round along the Portuguese Atlantic shore.Although it is considered edible in some countries,its biotechnological potential has not yet been assessed in detail and here we report its antimicrobial potential against human dermatophyte fungi.Three samples were harvested from Baleal Island(Peniche,Portugal)harvested in winter(BbPe);from Aguda Beach(Arcozelo,Vila Nova de Gaia,Portugal),harvested in autumn(BbAg)and a sample obtained by culturing the Aguda sample under laboratory conditions(BbLC).A broth macrodilution assay was applied to determine the MIC(minimum inhibitory concentration)and MLC(minimum lethal concentration)of the B.bifurcata extracts.Results show that the BbPe MeOH extracts were the most effective and had higher antifungal activity against all the tested dermatophyte strains than the BbLC and BaAg extracts[Epidermophyton floccosum FF9(100–200μg/mL MIC;200μg/mL MLC),Microsporum canis FF1(400μg/mL MIC;≥400μg/mL MLC),Trichophyton mentagrophytes FF7(100μg/mL MIC;>800μg/mL MLC),M.gypseum CECT 2908(800μg/mL MIC;≥800μg/mL MLC),T.mentagrophytes var.interdigitale CECT 2958(800μg/mL MIC;≥800μg/mL MLC),T.rubrum CECT 2794(200μg/mL MIC;≥400μg/mL MLC)].In fact,only E.floccosum FF9 was sensitive to BbAg and BbLC MeOH extracts.To our knowledge,this is the first report of antifungal activity of B.bifurcata against human dermatophyte fungi.
基金the Rural&Environment Science&Analytical Services(RESAS)Division of the Scottish Government(JHI-B1-1)the Biotechnology and Biological Sciences Research Council(BBSRC,BB/S015663/1)+3 种基金the Royal Society(NAF\R1\201061)the National Natural Science Foundation of China(32061130211,32372558)AK was supported through a Research Leaders 2025 fellowship funded by European Union’s Horizon 2020 Research and Innovation Programme under Marie Sklodowska-Curie Grant Agreement(754380)The authors acknowledge the Research/Scientific Computing teams at The James Hutton Institute and NIAB for providing computational resources and technical support for the‘‘UK’s Crop Diversity Bioinformatics HPC”(BBSRC Grant BB/S019669/1),use of which has contributed to the results reported within this paper.
文摘More than 170 years after causing the potato famine in Ireland,late blight is still considered one of the most devastating crop diseases.Commercial potato breeding efforts depend on natural sources of resistance to protect crops from the rapidly evolving late blight pathogen,Phytophthora infestans.We have identified and mapped a novel broad-spectrum disease resistance gene effective against P.infestans from the wild,diploid potato species Solanum bulbocastanum.Diagnostic resistance gene enrichment sequencing(dRenSeq)was used to confirm the uniqueness of the identified resistance.RenSeq and GenSeq-based mapping of the resistance,referred to as Rpi-blb4,alongside recombinant screening,positioned the locus responsible for the resistance to potato chromosome 5.The interval spans approximately 2.3 Mb and corresponds to the DM reference genome positions of 11.25 and 13.56 Mb.
文摘Three field trials were set up to measure the effect of previous crops or soil amendments on the yields of subsequent crops of cereals under a cool temperate maritime climate in arable crop land in the east of Scotland. Winter wheat and winter barley direct drilled into legume and cereal + legume stubble (pre-crop) gave substantial yield boost compared with other pre-crop cereals, but pre-crop effects of oats were similarly great. Restored rotation after continuous barley gave expected yield enhancement to subsequent winter and spring barley but not to subsequent wheat. Some diseases were reduced on restored rotation crops. Slurry effects on yield were generally small but beneficial and compost effects were greater. However, compost had effects on plant developmental speed and was difficult to compare directly with other treatments. NDRE measurements in the restored rotation and soil amendment trials indicated that yield gains were associated with improved crop health as indicated by leaf chlorophyll content. There were no clear cultivar interactions within crop type with treatments effects in any of these trials.
基金supported by the Spanish Ministry of Economy and Competitiveness(grant numbers AGL2010-21929 and AGL2013-48756-R)the Spanish Ministry of Economy and Competitiveness,the Agencia Estatal de Investigación,and the European Regional Development Fund(grant number AGL2016–80967-R)Government of Aragon(Research Group A08_20R)。
文摘Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant's response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka ×Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL colocating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley.
基金The Sao Paulo Research Foundation(FAPESP)of Brazil funded the first authorprovided financial support for this research through the processes Nos.2013/18870-1 and 2015/12399-0
文摘Dear Editor, Phosphorus (P) deficiency is the most limiting factor in tropical agriculture since most soils in this region are predominantly acids with high-energy P-binding compounds. Therefore, up to 90% of the P applied becomes fixed in soils, which raises environmental concerns and production costs (Syers et al., 2008). Thus, developing strategies to imptove P use efficiency (PUE) is essential to mitigate environmental problems and improve profits. These strategies should consider the soil-root-rhizosphere system because it is the most biochemical active site where nutrient uptake occurs (Hinsinger, 2011).
基金EES acknowledges funding from a NERC Frontiers grant(NE/V010824/1)Leverhulme Trust research grant(RPG-2022-313).
文摘Over the past two decades,it has become increasingly apparent that early Mars may once have been warmer,wetter and more habitable for microbial life than it is today,which has spurred discussions about potential biosignatures that may be preserved in Martian sediments.An impediment to this line of research is the pervasive oxidation of Mars’surface due to photochemical oxidants that have likely destroyed remnants of organic matter.Here,we investigate whether nitrogen(N)transferred from biomass to phyllosilicate minerals during diagenesis can be preserved in oxidized mudrocks.We investigate two sequences of terrestrial Proterozoic red beds,namely the Sibley Group(1.4 Ga)in Canada and the Stoer Group(1.2 Ga)in Scotland,and we find enrichments in authigenic N in the range of several tens of ppm in both units.The highest concentrations(ca.100 ppm on average)are found in the most desiccated red beds of the Stoer Group,concurrent with enrichments in potassium(K).We discuss similarities and differences between the two sets of rocks with regards to salinity,pH,biological productivity and K-metasomatism,and we conclude that the ideal mechanism for the preservation of biogenic N in red beds may be in-situ release of ammonium from microbial mats into the clay substrate,possibly facilitated by early diagenetic,biologically induced illitization.Illite and smectite have been observed on Mars,and experiments suggest that Martian waters contained moderate amounts of dissolved K.Hence,it is conceivable that a similar K and N enrichment process could have occurred as to what we document for the Proterozoic,preserving evidence of life that may have survived to the modern day.
基金Research was funded by a BBSRC studentship to GFB and funding from Vitacress LtdSainsbury’s Supermarkets Ltd and Shamrock Seeds Ltd in the laboratory of Gail TaylorThe contributions of MJT and RWM were supported by a grant from USDA NIFA SCRI No.2010-51181-21631 as well as funding from the California Leafy Greens Research Board.
文摘A diet rich in phytonutrients from fruit and vegetables has been acknowledged to afford protection against a range of human diseases,but many of the most popular vegetables are low in phytonutrients.Wild relatives of crops may contain allelic variation for genes determining the concentrations of these beneficial phytonutrients,and therefore understanding the genetic basis of this variation is important for breeding efforts to enhance nutritional quality.In this study,lettuce recombinant inbred lines,generated from a cross between wild and cultivated lettuce(Lactuca serriola and Lactuca sativa,respectively),were analysed for antioxidant(AO)potential and important phytonutrients including carotenoids,chlorophyll and phenolic compounds.When grown in two environments,96 quantitative trait loci(QTL)were identified for these nutritional traits:4 for AO potential,2 for carotenoid content,3 for total chlorophyll content and 87 for individual phenolic compounds(two per compound on average).Most often,the L.serriola alleles conferred an increase in total AOs and metabolites.Candidate genes underlying these QTL were identified by BLASTn searches;in several cases,these had functions suggesting involvement in phytonutrient biosynthetic pathways.Analysis of a QTL on linkage group 3,which accounted for>30%of the variation in AO potential,revealed several candidate genes encoding multiple MYB transcription factors which regulate flavonoid biosynthesis and flavanone 3-hydroxylase,an enzyme involved in the biosynthesis of the flavonoids quercetin and kaempferol,which are known to have powerful AO activity.Follow-up quantitative RT-PCR of these candidates revealed that 5 out of 10 genes investigated were significantly differentially expressed between the wild and cultivated parents,providing further evidence of their potential involvement in determining the contrasting phenotypes.These results offer exciting opportunities to improve the nutritional content and health benefits of lettuce through marker-assisted breeding.
文摘The Valab project (Integrated Ecosystemic value-enhancement of the Guadeloupean Forest Agrobiodiversity) is a participatory action research that aims to explore the feasibility of diversification activities within the forest understorey. In the exploratory phase of the project, we studied stakeholders’ opinions on the positive and negative impacts of introducing livestock activities within a forest environment, as well as breeders’ constraints or motivations for setting up livestock units within agroforestry systems in the private forests of Guadeloupe. To establish a diagnosis of the current situation, 51 stakeholders (St) and 49 farmers (Fr) were interviewed on their perceptions, opinions, motivations and preferences. Forty-one percent of the St has had a generally positive appreciation of livestock activities, while on the opposite 31% have had a resolutely negative posture depending on their area of expertise. Their views on the possible positive effects or negative interactions between livestock and agroforestry activities were analysed in order to suggest possible approaches for the authorities or associations. Unanimously, the farmers replied that their motivations followed economic strategies: for self-consumption or sale. But their decision-making processes were also non-economic. Many of them (36% Fr) gave importance to their activity in the construction of their identity, whether it was through a desire to perpetuate traditions or to maintain family activities. The main constraints identified were natural constraints (61% Fr), including topography, climate and predators. While 28% of Fr notified their motivations for environmental protection. Another constraint was of a technical nature (44% Fr) since farmers asked for more technical references or support services. Further researches are required to study the interactions between animals and the undergrowth by describing their respective ecosystem services in order to enhance their positive interactions.
文摘Micro-tubers are important propagules in potato breeding and potato production, and they are also dormant and easily transported and therefore good targets for mutation induction in potato mutation breeding. A prerequisite for mutation breeding is to determine optimal mutation treatments. Therefore, radio-sensitivity tests of a tetraploid and a diploid potato to gamma irradiation were undertaken. Effects of different gamma sources on radio-activity were also studied. In vitro potato cuttings were gamma irradiated using a wide dose range (0, 3, 6, 9, 12, 15 and 20 Gy). The irradiated cuttings were then cultured to induce micro-tubers directly in vitro. Micro-tuber morphotypes were assessed after irradiation of cuttings using three gamma sources with emission activities of 1.8, 7.07 and 139 Gy/min. The diploid species (Solanum verrucosum) was more radio-sensitive than the tetraploid cultivar Desirée (Solanum tuberosum). Gamma dose rates had significant influences on subsequent micro-tuber production at various mutant generations. Effects included reductions in the number, size and weight of micro-tubers produced. Gamma dose was more lethal for the diploid potato genotype and micro-tubers produced were small compared to those produced by the tetraploid genotype after irradiation. Different treatments are recommended for diploid and tetraploid potato irradiation in producing large mutant micro-tuber populations. The mutant micro-tuber populations may then be screened for interesting mutations/trait for both genetics and plant breeding purposes.
基金supported by Innovate UK(grant No.102130)the Scottish Government Rural and Environment Science and Analytical Services Division(RESAS)through the strategic research program and the Underpinning Capacity project‘Maintenance of Insect Pest Collections'.
文摘Physiological and physical traits are excellent indicators of many crop characteristics,but precise phenotyping of these traits is time consuming and,therefore,limits progress in crop breeding and the speed of crop monitoring.Hyperspectral imaging offers an opportunity to overcome these barriers as a technique for high throughput field measurements.Using a recently developed hyperspectral imaging platform devised for plantations of the perennial crop raspberry,this study aimed to further develop the tool and test its capacity as an innovative approach for high throughput field phenotyping,data collection and analysis.Hyperspectral imaging and visual crop assessments were carried out over two growing seasons in a field-grown raspberry mapping population,and data were subject to Quantitative Trait Loci(QTL)analysis.The findings show that reflectance intensity at multiple wavelengths can be linked to known genetic markers in raspberry,and many of these‘spectral traits'are expressed consistently through the growing season and between years,for example spectral ratio 719 nm/691 nm shows up consistently as a QTL on LG4.Spectral traits were identified that co-located with previously mapped physical traits,such as 719 nm/691 nm and cane density.The study indicates that hyperspectral imaging can be used as an innovative approach for high throughput field phenotyping of raspberry and could be transferred readily to other perennial crops.Our approach provides a pipeline for automated field data collection and analysis that can be used for rapid QTL detection of spectral traits.
基金funded by the National Key R&D Program of China(2022YFD1901304)China Scholarship Council(202206350052)。
文摘To efficiently obtain P from soil,most terrestrial plants form symbiosis with arbuscular mycorrhizal(AM)fungi and thus have two P uptake pathways,i.e.,the direct pathway(DP)via roots,particularly root hairs,and the mycorrhizal pathway(MP)via AM fungal hyphae.AM fungi form an extraradical hyphal network to expand their contact area with soil and release carbon-rich compounds,which provide a high-energy habitat for soil bacteria.The bacteria affected by AM fungi support P nutrition of AM fungi by secreting extracellular phosphatases.During the P acquisition process,both DP and MP function and require C fixed by plant photosynthesis to maintain P transport.Plants make trade-offs between DP and MP based on C inputs and P benefits.This review first systematically explores the potential trade-offs between plant C inputs and P gains of DP and MP as well as the factors that influence such trade-offs.Then the response of AM fungi to soil nutrient heterogeneity and the mechanisms by which AM fungi select bacteria to mineralize organic P and increase the P contribution of MP were analyzed.Future studies need to apply emerging methods and technologies to accurately quantify the contribution of DP and MP to plant P absorption under different conditions and provide the theoretical basis for optimizing sustainable agricultural production systems.
基金supported by the National Key Research and Development Program of China(2023YFD1701403,2022YFD1601103)the Central Public-interest Scientific Institution Basal Research Fund(Y2024QC28)+1 种基金Basic Research Foundation of Yunnan Province of China(202401AT070304)the Science&Technology Innovation Program of the Chinese Academy of Agricultural Sciences.
文摘Tetracycline(TC),which is widely employed in agriculture,constitutes a serious source of environmental pollution.In this study,mechanical ball-milling(B)treated iron/manganese-nitrogen(Fe/Mn-N)doped hydrochars(Fe/Mn-BNHT)synthesized using saponin-containing seed meal(T)as a carbon source,showed excellent removal ability of tetracycline with a removal efficiency 95%.The Fe/Mn-BNHT showed superior performance in batch experiments with solution pH(3-9),coexisting ions,and after 5 cycles of application.Further analysis showed that Fe/Mn-BNHT mediated the degradation of adsorbed tetracycline with a degradation efficiency 87%.Surface complexation,electrostatic interactions,and hydrogen bonding facilitated the adsorption of tetracycline.・OH induced by oxygen vacancy(O_(V))was identified as the main reactive oxidation species in tetracycline degradation.Fe(III)-tetracycline complexes gained electrons through graphitic N,leading to tetracycline degradation and Fe(III)reduction.The degradation pathways for tetracycline are shown through density functional theory calculation and intermediate identification,and the ecological toxicity risk of 10 degradation intermediates is evaluated.This research provides a new perspective on the development of environmentally friendly materials that can simultaneously adsorb and degrade pollutants.
基金supported by the National Natural Science Foundation of China(32372558)National Natural Science Foundation of China-The Royal Society(32061130211)the Rural and Environment Science and Analytical Services Division of the Scottish Government through project JHI-B1-1,the Biotechnology and Biological Sciences Research Council(BBSRC)through award BB/SO15663/1,the Royal Society through award NAF/R1/201061.
文摘Host-pathogen co-evolution shapes resistance(R)proteins and their recognition of pathogen avirulence factors.However,little attention has been paid to naturally occurring genetic diversity in R genes.In this study,12 Solanum bulbocastanum accessions from the Commonwealth Potato Collection were screened for resistance to Phytophthora infestans,identifying 11 resistant and one susceptible accession.Targeted enrichment sequencing of nucleotide-binding leucine-rich repeat(NLR)genes using RenSeq,followed by diagnostic RenSeq(dRenSeq)analysis,revealed that all accessions except 7650 contained Rpi-blb1/RB variants.Variants in accessions 7641 and 7648 were non-functional,while three novel functional variants were identified.Cloning and functional analysis of Rpi-blb1/RB variants assessed their recognition of the avirulence factor IPI-O1.Three variants were functional,conferring resistance to P.infestans.Variants in accessions 7644 and 7647 also recognized IPI-O4,confirmed in transgenic potatoes.Analysis of a non-functional variant in S.bulbocastanum accession 7648 identified amino acid Ser347 in the nucleotide-binding(NB-ARC)domain as critical for cell-death initiation following IPI-O1 recognition.Predictions from the FunFOLD2 protein-ligand interaction model suggested that Ser347 is essential for ATP binding,suggesting potential inhibition on pentameric resistosome assembly.Western blot analysis revealed that the mutation of Ser347 to Asn markedly compromises the Rpi-blb1/RB protein stability,and co-immunoprecipitation assay further confirmed that this mutation severely disrupts the self-association of CCNB,thereby preventing Rpi-blb1/RB activation.Consistently,substituting Asn347 with serine restored function,underscoring its key role in Rpi-blb1/RB activity.Cell biology experiments demonstrated that Rpi-blb1/RB relocalize to the plasma membrane in response to IPI-O1.This relocalization depends on Ser347,further supporting the idea that its mutation affects resistosome formation,impairing resistance.This study provides an in-depth functional analysis of natural Rpi-blb1/RB diversity,offering insights into NLR protein evolution and resistance mechanisms in potatoes.
基金supported by funding from the National Key Research and Development Program of China(2021YFD1201400)the Inner Mongolia Autonomous Region Science and Technology Innovation Guide Award Fund,Special Project for First-Class Discipline Research of Department of Education,Inner Mongolia Autonomous Region(YLXKZX-ND-028)+7 种基金the Central Guidance on Local Science and Technology Development Fund(2022ZY0141)the Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region(NMGIRT2410)to J.Q.the Agricultural Science and Technology Innovation Program(CAAS-ZDXT201804)and Shenzhen Outstanding Talent Training Fund to S.H.the National Natural Science Foundation of China(32372720)to J.Z.Yunnan Science Fund(202105AF150028)to Y.S.the National Key Research and Development Program of China(2023YFF1000100)to T.L.China Agriculture Research System of MOF and MARA(CARS-09-P17)Key Technology Research Project of Inner Mongolia Autonomous Region(2020GG0054)to R.Z.
文摘Hybrid potato breeding based on diploid inbred lines is transforming the way of genetic improvement of this staple food crop,which requires a deep understanding of potato domestication and differentiation.In the present study,we resequenced 314 diploid wild and landrace accessions to generate a variome map of 47,203,407 variants.Using the variome map,we discovered the reshaping of tuber transcriptome during potato domestication,characterized genome-wide differentiation between landrace groups Stenotomum and Phureja.We identified a jasmonic acid biosynthetic gene possibly affecting the tuber dormancy period.Genome-wide association studies revealed a UDP-glycosyltransferase gene for the biosynthesis of anti-nutritional steroidal glycoalkaloids(SGAs),and a Dehydration Responsive Element Binding(DREB)transcription factor conferring increased average tuber weight.In addition,genome similarity and group-specific SNP analyses indicated that tetraploid potatoes originated from the diploid Solanum tuberosum group Stenotomum.These findings shed light on the evolutionary trajectory of potato domestication and improvement,providing a solid foundation for advancing hybrid potato-breeding practices.
基金supported by the Food and Agriculture Organization’s“SoilFER-VACS Framework-Enhancing Integrated Soil-Crop Management for Sustainable Food Systems in Africa”project,funded by the Ministry of Foreign Affairs of Japan.
文摘While global efforts to operationalize soil spectroscopy are progressing,cooperation is needed to fully leverage its potential for generating digital soil information to support sustainable soil management worldwide.The Global Soil Laboratory Network’s soil spectroscopy initiative(GLOSOLANSpec),led by the Food and Agriculture Organization of the United Nations(FAO)through its Global Soil Partnership(GSP),is dedicated to the further development and adoption of soil spectroscopy by fostering international collaboration via a scientific community of practice to produce accurate and reliable soil information for sustainable soil management and decision-making.To support this effort,we,a global consortium of soil scientists under the auspices of the International Union of Soil Sciences(IUSS)and GLOSOLAN-Spec,aim to address seven key challenges hindering the adoption of soil spectroscopy worldwide.Here,we offer perspectives on what is needed to advance soil spectroscopy as a routine soil analysis method,emphasizing its potential to generate new and reliable spatial and temporal soil data.
