In the process to the marketing of cultivars, identification of superior test locations within multi-environment variety trial schemes is of critical relevance. It is relevant to breeding organizations as well as to g...In the process to the marketing of cultivars, identification of superior test locations within multi-environment variety trial schemes is of critical relevance. It is relevant to breeding organizations as well as to governmental organizations in charge of cultivar registration. Where competition among breeding companies exists, effective and fair multi-environment variety trials are of utmost importance to motivate investment in breeding. The objective of this study was to use genotype main effect plus genotype by environment interaction（GGE） biplot analysis to evaluate test locations in terms of discrimination ability, representativeness and desirability, and to investigate the presence of multiple mega-environments in cotton production in the Yangtze River Valley（YaRV）, China. Four traits（cotton lint yield, fiber length, lint breaking tenacity, micronaire） and two composite selection indices were considered. It was found that the assumption of a single mega-environment in the YaRV for cotton production does not hold. The YaRV consists of three cotton mega-environments： a main one represented by 11 locations and two minor ones represented by two test locations each. This demands that the strategy of cotton variety registration or recommendation must be adjusted. GGE biplot analysis has also led to the identification of test location superior for cotton variety evaluation. Although test location desirable for selecting different traits varied greatly, Jinzhou, Hubei Province, China, was found to be desirable for selecting for all traits considered while Jianyang, Sichuan Province, China, was found to be desirable for none.展开更多
Peanut is a worldwide oilseed crop and the need to assess germplasm in a non-destructive manner is important for seed nutritional breeding.In this study,Near Infrared Spectroscopy(NIRS)was applied to rapidly assess ge...Peanut is a worldwide oilseed crop and the need to assess germplasm in a non-destructive manner is important for seed nutritional breeding.In this study,Near Infrared Spectroscopy(NIRS)was applied to rapidly assess germplasm variability from whole seed of 699 samples,field-collected and assembled in four genetic and environmentbased sets:one set of 300 varieties of a core-collection and three sets of 133 genotypes of an interspecific population,evaluated in three environments in a large spatial scale of two countries,Mbalmayo and Bafia in Cameroon and Nioro in Senegal,under rainfed conditions.NIR elemental spectra were gathered on six subsets of seeds of each sample,after three rotation scans,with a spectral resolution of 16 cm-1over the spectral range of867 nm to 2530 nm.Spectra were then processed by principal component analysis(PCA)coupled with Partial least squares-discriminant analysis(PLS-DA).As results,a huge variability was found between varieties and genotypes for all NIR wavelength within and between environments.The magnitude of genetic variation was particularly observed at 11 relevant wavelengths such as 1723 nm,usually related to oil content and fatty acid composition.PCA yielded the most chemical attributes in three significant PCs(i.e.,eigenvalues>10),which together captured 93%of the total variation,revealing genetic and environment structure of varieties and genotypes into four clusters,corresponding to the four samples sets.The pattern of genetic variability of the interspecific population covers,remarkably half of spectrum of the core-collection,turning out to be the largest.Interestingly,a PLS-DA model was developed and a strong accuracy of 99.6%was achieved for the four sets,aiming to classify each seed sample according to environment origin.The confusion matrix achieved for the two sets of Bafia and Nioro showed 100%of instances classified correctly with 100%at both sensitivity and specificity,confirming that their seed quality was different from each other and all other samples.Overall,NIR展开更多
The demand for food is tremendously increasing with the growth of the world population,which necessitates the development of sustainable agriculture under the impact of various factors,such as climate change.To fulfil...The demand for food is tremendously increasing with the growth of the world population,which necessitates the development of sustainable agriculture under the impact of various factors,such as climate change.To fulfill this challenge,we are developing Metaverses for agriculture,referred to as Agri Verse,under our Decentralized Complex Adaptive Systems in Agriculture(De CASA)project,which is a digital world of smart villages created alongside the development of Decentralized Sciences(De Sci)and Decentralized Autonomous Organizations(DAO)for Cyber-Physical-Social Systems(CPSSs).Additionally,we provide the architectures,operating modes and major applications of De CASA in AgriVerse.For achieving sustainable agriculture,a foundation model based on ACP theory and federated intelligence is envisaged.Finally,we discuss the challenges and opportunities.展开更多
Several components of predator functional diversity have been hypothesized to influence prey suppression through either niche complementarity or mass ratio effects.Nevertheless,most studies have used a functional grou...Several components of predator functional diversity have been hypothesized to influence prey suppression through either niche complementarity or mass ratio effects.Nevertheless,most studies have used a functional group approach when assessing the role of these predators in ecosystem functioning.By adopting a trait-based approach,we evaluated the relative contributions of carabid diversity components in predicting prey suppression.Our results highlight the importance of both taxonomic and functional diversity components of carabids as key drivers of prey suppression.Prey suppression was best predicted by carabid densities,with the dominance of Poecilus cupreus potentially driving the positive effect of community total abundance through the mass ratio effect.Prey suppression increased with increasing the density of large carabids.In addition,carabid eye diameter and antennal length were key functional traits for predicting prey suppression.Furthermore,prey suppression increased with increasing carabid functional richness following the niche complementarity effect.In contrast to functional richness,functional evenness and functional divergence of carabid communities were weakly correlated with prey suppression.By identifying which diversity components of carabid communities contribute the most to increase prey suppression,our results can guide efforts aiming to predict the relationship between diversity of these predators and ecosystem functioning.展开更多
Macadamia nuts (Macadamia integrifolia) grown in Venezuela have showed an average total fat content of 70%. Oleic acid (18:1) was the main monounsaturated fatty acid (MUFA) (51.3%), followed by palmitoleic acid (16:1,...Macadamia nuts (Macadamia integrifolia) grown in Venezuela have showed an average total fat content of 70%. Oleic acid (18:1) was the main monounsaturated fatty acid (MUFA) (51.3%), followed by palmitoleic acid (16:1, 22.6%). The content of polyunsaturated fatty acids (PUFAs), C18:2 and C18:3 represented 5.4%. Thus, MUFAs and PUFAs together constituted more than 80% of the total fatty acids present. Trans-vaccenic acid was also present (3%). As regards to other phytochemical compounds, tocopherols and tocotrienols were not found in the sample, but the presence of squalene was detected.The antioxidant activity (44.2%) of the extract was produced by the phytochemicals present.展开更多
Agroecosystems in the Senegalese groundnut basin experience long periods of high temperatures and drought, which disrupt the stability of soil microbial communities. This study evaluated how that stability is affected...Agroecosystems in the Senegalese groundnut basin experience long periods of high temperatures and drought, which disrupt the stability of soil microbial communities. This study evaluated how that stability is affected by homefields and outfields’ agricultural practices and the duration of heat stress. Specifically, we collected soils from organically farmed fields that receive continual high inputs of manure (homefields), and from fields that are rarely manured (outfields). Soil samples were submitted to artificial heat stress at 60°C for 3, 14, and 28 days, followed by 28 days of recovery at 28°C. We examined the functional stability of microbial communities by quantifying C mineralization, and characterized the stability of the communities’ taxonomic compositions via high-throughput DNA sequencing. We found that the microbial communities have a low resistance to heat stress in soils from both types of fields. However, the manuring practice does affect how the functional stability of microbial communities responds to different durations of heat stress. Although functional stability was not recovered fully in either soil, microbial community resilience seemed to be greater in homefield soils. Differences in manuring practices also affected the structural taxonomic stability of microbial communities: relative abundances of Bacilli, Chloroflexia, Actinobacteria and Sordariomycetes increased in the homefield stressed-soils, but decreased significantly in outfield soils. In contrast, relative abundances of α-Proteobacteria, γ-Proteobacteria and Eurotiomycetes increased significantly in outfield stressed-soils, while decreasing significantly in the homefield soils. Relative abundances of Bacilli changed little in outfield soils, indicating that this taxon is resistant to heat stress. In summary, the microbial communities’ capacities to resist heat stress and recover from it depend upon the organic richness of the soil (i.e., manuring practice) and the adaptation of soil microbes to environmental conditions.展开更多
Several internet-based surveillance systems have been created to monitor the web for animal health surveillance.These systems collect a large amount of news dealing with outbreaks related to animal diseases.Automatica...Several internet-based surveillance systems have been created to monitor the web for animal health surveillance.These systems collect a large amount of news dealing with outbreaks related to animal diseases.Automatically identifying news articles that describe the same outbreak event is a key step to quickly detect relevant epidemiological information while alleviating manual curation of news content.This paper addresses the task of retrieving news articles that are related in epidemiological terms.We tackle this issue using text mining and feature fusion methods.The main objective of this paper is to identify a textual representation in which two articles that share the same epidemiological content are close.We compared two types of representations(i.e.,features)to represent the documents:(i)morphosyntactic features(i.e.,selection and transformation of all terms from the news,based on classical textual processing steps)and(ii)lexicosemantic features(i.e.,selection,transformation and fusion of epidemiological terms including diseases,hosts,locations and dates).We compared two types of term weighing(i.e.,Boolean and TF-IDF)for both representations.To combine and transform lexicosemantic features,we compared two data fusion techniques(i.e.,early fusion and late fusion)and the effect of features generalisation,while evaluating the relative importance of each type of feature.We conducted our analysis using a corpus composed of a subset of news articles in English related to animal disease outbreaks.Our results showed that the combination of relevant lexicosemantic(epidemiological)features using fusion methods improves classical morphosyntactic representation in the context of disease-related news retrieval.The lexicosemantic representation based on TF-IDF and feature generalisation(F-measure=0.92,r-precision=0.58)outperformed the morphosyntactic representation(F-measure=0.89,r-precision=0.45),while reducing the features space.Converting the features into lower granular features(i.e.,generalisation)contributed to impr展开更多
Various biological constraints including erratic and asynchronous flowering between male and female plants hinder successful hybrid development and genetic gains in greater yam breeding programs.Therefore,pollen stora...Various biological constraints including erratic and asynchronous flowering between male and female plants hinder successful hybrid development and genetic gains in greater yam breeding programs.Therefore,pollen storage has gained much attention to facilitate artificial pollinations and increase the genetic gains.This 4-year study aimed at developing a practical long-term pollen storage technique for the successful development of yam hybrids.Fresh pollens were collected from two Dioscorea alata males,then lyophilized(two lyophilization treatments were applied),followed by storage at room temperature(24℃–25℃)for 12 months.Moreover,the lyophilized and stored pollens were tested for viability by crossing with four female varieties.Our results showed that lyophilization is effective for achieving viable pollens after 12 months of storage.Treatment 1(48 h drying)showed higher pollen germination and fertility rates than Treatment 2(72 h drying).Although we observed a reduction in viability of lyophilized pollens after 12 months of storage,we generated hybrid seedlings with success rates from 12%to 21%compared to 21%–31%when using fresh pollens.Paternity testing based on molecular genotyping confirmed the hybrid status of the obtained seedlings,which grew well in a greenhouse.Lyophilization is a practical approach for a long-term storage of greater yam pollen samples.This protocol will positively impact yam breeding programs particularly in developing countries.展开更多
GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures.It allows long-term access to datasets following the FAIR principles:Findable,Acce...GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures.It allows long-term access to datasets following the FAIR principles:Findable,Accessible,Interoperable,and Reusable,by using a flexible and original approach.It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration,storage,and querying.It takes advantage of international standards including the Crop Ontology,MIAPPE,and the Breeding API.GnpIS allows handling data for a wide range of species and experiment types,including multiannual perennial plants experimental network or annual plant trials with either raw data,i.e.,direct measures,or computed traits.It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data.This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data.Our repository follows the Open Science data publication principles by ensuring citability of each dataset.Finally,GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types.GnpIS can therefore contribute to emerging international federations of information systems.展开更多
Sesame(Sesamum indicum L.) plays a crucial role in Ethiopian agriculture,serving both subsistence and commercial purposes.However,our understanding of the extensive genetic diversity and population structure of Ethiop...Sesame(Sesamum indicum L.) plays a crucial role in Ethiopian agriculture,serving both subsistence and commercial purposes.However,our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited.To address this knowledge gap,we genotyped 368 Ethiopian sesame germplasms,categorizing into four distinct breeding groups:Accessions,landraces,improved varieties,and wild types,using a comprehensive set of 28 polymorphic markers,including 23 simple sequence repeat(SSR) and five Insertion-Deletion(InDel) markers.These markers ensured robust genomic representation,with at least two markers per linkage group.Our results unveiled substantial genetic diversity,identifying a total of 535 alleles across all accessions.On average,each locus displayed 8.83 alleles,with observed and expected heterozygosity values of 0.30 and 0.36,respectively.Gene Diversity and Polymorphic Information Content(PIC) were recorded at 0.37 and 0.35.The percentage of polymorphic loci varied significantly among breeding groups,ranging from8.00% to 82.40%,indicating high diversity in accessions(82.4%),moderate diversity in improved varieties(31.20%) and landraces(29.60%),and limited diversity in wild types(8.00).Analysis of Molecular Variance(AMOVA) results emphasized significant genetic differentiation among populations,with substantial diversity(P<0.001) within each population.Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations,while the larger proportion of genetic diversity(92%) resided within each individual sesame population,showcasing heightened diversity within each group.Our study’s findings received support from both Bayesian clustering and Neighbor-joining(NJ) analysis,reaffirming the credibility of our genetic structure insights.Notably,Population structure analysis at its highest Δk value(k=2) revealed the existence of two primary genetic clusters,further subdivided into four sub-populations at k=4.Similarly,NJ analysis identified two promi展开更多
What is already known about this topic?Given the challenges presented by drug-resistant strains of tuberculosis(TB)and the rising mobility of the population,achieving the objective of eradicating TB appears uncertain....What is already known about this topic?Given the challenges presented by drug-resistant strains of tuberculosis(TB)and the rising mobility of the population,achieving the objective of eradicating TB appears uncertain.What is added by this report?The examination of TB incidence trends in 10 highburden countries(HBCs)indicated a steady rise in cases,with India and China jointly accounting for nearly 70%of the burden.Projections for the future show diverse trajectories in these countries,with potential difficulties in reaching the TB elimination target,especially in Nigeria,Congo,and South Africa.What are the implications for public health practice?The number of TB cases is on the rise.It is crucial to learn from successful strategies to improve TB prevention and control worldwide through collaborative efforts.展开更多
This study's goal is to present a dynamic portrait of the farm-buildings environment in Occitania,in Southern France,in order to better identify the transitions underway in agri-food chains.To this end,we undertoo...This study's goal is to present a dynamic portrait of the farm-buildings environment in Occitania,in Southern France,in order to better identify the transitions underway in agri-food chains.To this end,we undertook a ter-ritorial diagnosis based on actor statements,using 28 semi-structured interviews across Occitania.This diagnosis was enriched by graphic modelling,which enabled the spatialization of the dynamics described.We show that the process of standardisation of farm buildings prevails in the majority of the territories studied.This phenomenon has intensified in recent years with the development of vast photovoltaic-roofed sheds,accentuating the farm-land conversion and soil sealing.At the same time,in areas with strong environmental,landscape and heritage contexts,a'new adventure in farm buildings'(2022 survey)is taking shape.It is primarily driven by local short food chains,which rely on self-construction,repurposing and refurbishment,the sharing of tools and equipment,and which favour the use and reuse of local resources.This study shows that farm-buildings dynamics crystallise many challenges confronting the reterritorialisation of agriculture and food production.展开更多
Despite previous reports on the genotypic variation of architectural and functional traits in fruit trees,phenotyping large populations in the field remains challenging.In this study,we used high-throughput phenotypin...Despite previous reports on the genotypic variation of architectural and functional traits in fruit trees,phenotyping large populations in the field remains challenging.In this study,we used high-throughput phenotyping methods on an apple tree core-collection(1000 individuals)grown under contrasted watering regimes.First,architectural phenotyping was achieved using T-LiDAR scans for estimating convex and alpha hull volumes and the silhouette to total leaf area ratio(STAR).Second,a semi-empirical index(IPL)was computed from chlorophyll fluorescence measurements,as a proxy for leaf photosynthesis.Last,thermal infrared and multispectral airborne imaging was used for computing canopy temperature variations,water deficit,and vegetation indices.All traits estimated by these methods were compared to low-throughput in planta measurements.Vegetation indices and alpha hull volumes were significantly correlated with tree leaf area and trunk cross sectional area,while IPL values showed strong correlations with photosynthesis measurements collected on an independent leaf dataset.By contrast,correlations between stomatal conductance and canopy temperature estimated from airborne images were lower,emphasizing discrepancies across measurement scales.High heritability values were obtained for almost all the traits except leaf photosynthesis,likely due to large intra-tree variation.Genotypic means were used in a clustering procedure that defined six classes of architectural and functional combinations.Differences between groups showed several combinations between architectural and functional traits,suggesting independent genetic controls.This study demonstrates the feasibility and relevance of combining multi-scale high-throughput methods and paves the way to explore the genetic bases of architectural and functional variations in woody crops in field conditions.展开更多
Corynespora cassiicola is the causal agent of Corynespora Leaf Fall(CLF)disease.CLF is one of the most important fungal diseases of rubber trees in Asia and Africa but disease outbreaks have not been reported in South...Corynespora cassiicola is the causal agent of Corynespora Leaf Fall(CLF)disease.CLF is one of the most important fungal diseases of rubber trees in Asia and Africa but disease outbreaks have not been reported in South America.Cassiicolin,a small cysteine-rich glycoprotein secreted by the pathogenic C.cassiicola isolate CCP,was previously identified as a potential disease effector in rubber tree.Recently,the cassiicolin-encoding gene(Cas1)was characterized and shown to be expressed in the early phase of infection.In this study,we investigated whether previously undetected strains of C.cassiicola are present in South American rubber plantations by examining the fungal endophyte population found in asymptomatic rubber tree leaves.Four isolates were identified as C.cassiicola.Genes encoding new forms of the cassiicolin precursor protein(Cas3 and Cas4)were identified from these isolates.Three of four isolates were able to induce symptoms on the cultivar they were isolated from in a detached leaf assay,with different kinetics and intensities.One isolate had the same pathogenicity profile as the pathogenic isolate CCP;the other two isolates developed symptoms late during the course of infection,suggesting saprotrophic capabilities.However,no Cas3 or Cas4 transcripts could be detected upon inoculation with the endophytic isolates,whereas the reference gene Cas1 was expressed upon inoculation with the CCP isolate.This work demonstrated that C.cassiicola is present in South America in an endophytic form and that it may evolve from an endophytic to a saprophytic or even potentially pathogenic life style.展开更多
Vanilla planifolia, the species cultivated to produce one of the world’s most popular flavors, is highly proneto partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report hereth...Vanilla planifolia, the species cultivated to produce one of the world’s most popular flavors, is highly proneto partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report herethe first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that thediploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequentlyobserved. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gbwith a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequenciesand the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linkinggene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complexmolecular regulation of endoreplication along the chromosomes. This high-quality, anchored assemblyrepresents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidationof this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a userfriendly integrated web portal that enables centralized access to high-throughput genomic and other omicsdata and interoperable use of bioinformatics tools.展开更多
The possibilities of combining the dissolution of short-range-order minerals （SROMs） like allophane and imogolite, by ammonium oxalate and a particle size distribution analysis performed by the pipette method were i...The possibilities of combining the dissolution of short-range-order minerals （SROMs） like allophane and imogolite, by ammonium oxalate and a particle size distribution analysis performed by the pipette method were investigated by tests on a soil sample from Reunion, a volcanic island located in the Indian Ocean, having a large SROMs content. The need to work with moist soil samples was again emphasized because the microaggregates formed during air-drying are resistant to the reagent. The SROM content increased, but irregularly, with the number of dissolutions by ammonium oxalate： 334 and 470 mg g-1 of SROMs were dissolved after one and three dissolutions respectively. Six successive dissolutions with ammonium oxalate on the same soil sample showed that 89% of the sum of oxides extracted by the 6 dissolutions were extracted by the first dissolution （mean 304 mg g-l）. A compromise needs to be found between the total removal of SROMs by large quantities of ammonium oxalate and the preservation of clay minerals, which were unexpectedly dissolved by this reagent. These tests enabled a description of the clay assemblage of the soil （gibbsite, smectite, and traces of kaolinite） in an area where such information was lacking due to the difficulties encountered in recuperation of the clay fraction.展开更多
Plants adjust their development in relation to the availability of nutrient sources. This necessitates signal- ing between root and shoot. Aside from the well-known systemic signaling processes mediated by auxin, cyto...Plants adjust their development in relation to the availability of nutrient sources. This necessitates signal- ing between root and shoot. Aside from the well-known systemic signaling processes mediated by auxin, cytokinin, and sugars, new pathways involving carotenoid-derived hormones have recently been identified. The auxin-responsive MAX pathway controls shoot branching through the biosynthesis of strigolactone in the roots. The BYPASSI gene affects the production of an as-yet unknown carotenoid-derived substance in roots that promotes shoot development. Novel local and systemic mechanisms that control adaptive root development in response to nitrogen and phosphorus starvation were recently discovered. Notably, the ability of the NITRATE TRANSPORTER 1.1 to transport auxin drew for the first time a functional link between auxin, root development, and nitrate availability in soil. The study of plant response to phos- phorus starvation allowed the identification of a systemic mobile miRNA. Deciphering and integrating these signaling pathways at the whole-plant level provide a new perspective for understanding how plants regulate their development in response to environmental cues.展开更多
Rain-induced fruit cracking is a major problem in sweet cherry cultivation.Basic research has been conducted to disentangle the physiological and mechanistic bases of this complex phenomenon,whereas genetic studies ha...Rain-induced fruit cracking is a major problem in sweet cherry cultivation.Basic research has been conducted to disentangle the physiological and mechanistic bases of this complex phenomenon,whereas genetic studies have lagged behind.The objective of this work was to disentangle the genetic determinism of rain-induced fruit cracking.We hypothesized that a large genetic variation would be revealed,by visual field observations conducted on mapping populations derived from well-contrasted cultivars for cracking tolerance.Three populations were evaluated over 7–8 years by estimating the proportion of cracked fruits for each genotype at maturity,at three different areas of the sweet cherry fruit:pistillar end,stem end,and fruit side.An original approach was adopted to integrate,within simple linear models,covariates potentially related to cracking,such as rainfall accumulation before harvest,fruit weight,and firmness.We found the first stable quantitative trait loci(QTLs)for cherry fruit cracking,explaining percentages of phenotypic variance above 20%,for each of these three types of cracking tolerance,in different linkage groups,confirming the high complexity of this trait.For these and other QTLs,further analyses suggested the existence of at least two-linked QTLs in each linkage group,some of which showed confidence intervals close to 5 cM.These promising results open the possibility of developing marker-assisted selection strategies to select cracking-tolerant sweet cherry cultivars.Further studies are needed to confirm the stability of the reported QTLs over different genetic backgrounds and environments and to narrow down the QTL confidence intervals,allowing the exploration of underlying candidate genes.展开更多
基金funded by the Jiangsu Agriculture Science and Technology Innovation Fund,China(CX(12)5035)the National Natural Science Foundation of China(30971735)+1 种基金the China Agriculture Research System(CARS-18-20)the Special Fund for Agro-Scientific Research in the Public Interest of China(Impact of Climate Change on Agriculture Production of China,200903003)
文摘In the process to the marketing of cultivars, identification of superior test locations within multi-environment variety trial schemes is of critical relevance. It is relevant to breeding organizations as well as to governmental organizations in charge of cultivar registration. Where competition among breeding companies exists, effective and fair multi-environment variety trials are of utmost importance to motivate investment in breeding. The objective of this study was to use genotype main effect plus genotype by environment interaction（GGE） biplot analysis to evaluate test locations in terms of discrimination ability, representativeness and desirability, and to investigate the presence of multiple mega-environments in cotton production in the Yangtze River Valley（YaRV）, China. Four traits（cotton lint yield, fiber length, lint breaking tenacity, micronaire） and two composite selection indices were considered. It was found that the assumption of a single mega-environment in the YaRV for cotton production does not hold. The YaRV consists of three cotton mega-environments： a main one represented by 11 locations and two minor ones represented by two test locations each. This demands that the strategy of cotton variety registration or recommendation must be adjusted. GGE biplot analysis has also led to the identification of test location superior for cotton variety evaluation. Although test location desirable for selecting different traits varied greatly, Jinzhou, Hubei Province, China, was found to be desirable for selecting for all traits considered while Jianyang, Sichuan Province, China, was found to be desirable for none.
基金supported by the GENES intra-Africa Academic Mobility scheme of the European Union(EU-GENES:EACEA/2917/2552)the DESIRA-ABEE project funded by European Union。
文摘Peanut is a worldwide oilseed crop and the need to assess germplasm in a non-destructive manner is important for seed nutritional breeding.In this study,Near Infrared Spectroscopy(NIRS)was applied to rapidly assess germplasm variability from whole seed of 699 samples,field-collected and assembled in four genetic and environmentbased sets:one set of 300 varieties of a core-collection and three sets of 133 genotypes of an interspecific population,evaluated in three environments in a large spatial scale of two countries,Mbalmayo and Bafia in Cameroon and Nioro in Senegal,under rainfed conditions.NIR elemental spectra were gathered on six subsets of seeds of each sample,after three rotation scans,with a spectral resolution of 16 cm-1over the spectral range of867 nm to 2530 nm.Spectra were then processed by principal component analysis(PCA)coupled with Partial least squares-discriminant analysis(PLS-DA).As results,a huge variability was found between varieties and genotypes for all NIR wavelength within and between environments.The magnitude of genetic variation was particularly observed at 11 relevant wavelengths such as 1723 nm,usually related to oil content and fatty acid composition.PCA yielded the most chemical attributes in three significant PCs(i.e.,eigenvalues>10),which together captured 93%of the total variation,revealing genetic and environment structure of varieties and genotypes into four clusters,corresponding to the four samples sets.The pattern of genetic variability of the interspecific population covers,remarkably half of spectrum of the core-collection,turning out to be the largest.Interestingly,a PLS-DA model was developed and a strong accuracy of 99.6%was achieved for the four sets,aiming to classify each seed sample according to environment origin.The confusion matrix achieved for the two sets of Bafia and Nioro showed 100%of instances classified correctly with 100%at both sensitivity and specificity,confirming that their seed quality was different from each other and all other samples.Overall,NIR
基金supported in part by the National Key Research and Development Program of China under Grant2021ZD0113701,2021ZD0113704the National Natural Science Foundation of China under Grant 62076239Chinese Academy of Sciences-Thailand National Science and Technology Development Agency Joint Research Program under Grant GJHZ2076。
文摘The demand for food is tremendously increasing with the growth of the world population,which necessitates the development of sustainable agriculture under the impact of various factors,such as climate change.To fulfill this challenge,we are developing Metaverses for agriculture,referred to as Agri Verse,under our Decentralized Complex Adaptive Systems in Agriculture(De CASA)project,which is a digital world of smart villages created alongside the development of Decentralized Sciences(De Sci)and Decentralized Autonomous Organizations(DAO)for Cyber-Physical-Social Systems(CPSSs).Additionally,we provide the architectures,operating modes and major applications of De CASA in AgriVerse.For achieving sustainable agriculture,a foundation model based on ACP theory and federated intelligence is envisaged.Finally,we discuss the challenges and opportunities.
基金supported by an INRAE/Lorraine Region(France)fellowshipthe“CASDAR Entomophages”Project(French Agricultural Ministry).
文摘Several components of predator functional diversity have been hypothesized to influence prey suppression through either niche complementarity or mass ratio effects.Nevertheless,most studies have used a functional group approach when assessing the role of these predators in ecosystem functioning.By adopting a trait-based approach,we evaluated the relative contributions of carabid diversity components in predicting prey suppression.Our results highlight the importance of both taxonomic and functional diversity components of carabids as key drivers of prey suppression.Prey suppression was best predicted by carabid densities,with the dominance of Poecilus cupreus potentially driving the positive effect of community total abundance through the mass ratio effect.Prey suppression increased with increasing the density of large carabids.In addition,carabid eye diameter and antennal length were key functional traits for predicting prey suppression.Furthermore,prey suppression increased with increasing carabid functional richness following the niche complementarity effect.In contrast to functional richness,functional evenness and functional divergence of carabid communities were weakly correlated with prey suppression.By identifying which diversity components of carabid communities contribute the most to increase prey suppression,our results can guide efforts aiming to predict the relationship between diversity of these predators and ecosystem functioning.
文摘Macadamia nuts (Macadamia integrifolia) grown in Venezuela have showed an average total fat content of 70%. Oleic acid (18:1) was the main monounsaturated fatty acid (MUFA) (51.3%), followed by palmitoleic acid (16:1, 22.6%). The content of polyunsaturated fatty acids (PUFAs), C18:2 and C18:3 represented 5.4%. Thus, MUFAs and PUFAs together constituted more than 80% of the total fatty acids present. Trans-vaccenic acid was also present (3%). As regards to other phytochemical compounds, tocopherols and tocotrienols were not found in the sample, but the presence of squalene was detected.The antioxidant activity (44.2%) of the extract was produced by the phytochemicals present.
文摘Agroecosystems in the Senegalese groundnut basin experience long periods of high temperatures and drought, which disrupt the stability of soil microbial communities. This study evaluated how that stability is affected by homefields and outfields’ agricultural practices and the duration of heat stress. Specifically, we collected soils from organically farmed fields that receive continual high inputs of manure (homefields), and from fields that are rarely manured (outfields). Soil samples were submitted to artificial heat stress at 60°C for 3, 14, and 28 days, followed by 28 days of recovery at 28°C. We examined the functional stability of microbial communities by quantifying C mineralization, and characterized the stability of the communities’ taxonomic compositions via high-throughput DNA sequencing. We found that the microbial communities have a low resistance to heat stress in soils from both types of fields. However, the manuring practice does affect how the functional stability of microbial communities responds to different durations of heat stress. Although functional stability was not recovered fully in either soil, microbial community resilience seemed to be greater in homefield soils. Differences in manuring practices also affected the structural taxonomic stability of microbial communities: relative abundances of Bacilli, Chloroflexia, Actinobacteria and Sordariomycetes increased in the homefield stressed-soils, but decreased significantly in outfield soils. In contrast, relative abundances of α-Proteobacteria, γ-Proteobacteria and Eurotiomycetes increased significantly in outfield stressed-soils, while decreasing significantly in the homefield soils. Relative abundances of Bacilli changed little in outfield soils, indicating that this taxon is resistant to heat stress. In summary, the microbial communities’ capacities to resist heat stress and recover from it depend upon the organic richness of the soil (i.e., manuring practice) and the adaptation of soil microbes to environmental conditions.
基金EU grant 874850 MOOD and is catalogued as MOOD009the French General Directorate for Food(DGAL),the French Agricultural Research Centre for International Development(CIRAD),the SONGES Project(FEDER and Occitanie),and the French National Research Agency under the Investments for the Future Program,referred to as ANR-16-CONV-0004(#DigitAg).
文摘Several internet-based surveillance systems have been created to monitor the web for animal health surveillance.These systems collect a large amount of news dealing with outbreaks related to animal diseases.Automatically identifying news articles that describe the same outbreak event is a key step to quickly detect relevant epidemiological information while alleviating manual curation of news content.This paper addresses the task of retrieving news articles that are related in epidemiological terms.We tackle this issue using text mining and feature fusion methods.The main objective of this paper is to identify a textual representation in which two articles that share the same epidemiological content are close.We compared two types of representations(i.e.,features)to represent the documents:(i)morphosyntactic features(i.e.,selection and transformation of all terms from the news,based on classical textual processing steps)and(ii)lexicosemantic features(i.e.,selection,transformation and fusion of epidemiological terms including diseases,hosts,locations and dates).We compared two types of term weighing(i.e.,Boolean and TF-IDF)for both representations.To combine and transform lexicosemantic features,we compared two data fusion techniques(i.e.,early fusion and late fusion)and the effect of features generalisation,while evaluating the relative importance of each type of feature.We conducted our analysis using a corpus composed of a subset of news articles in English related to animal disease outbreaks.Our results showed that the combination of relevant lexicosemantic(epidemiological)features using fusion methods improves classical morphosyntactic representation in the context of disease-related news retrieval.The lexicosemantic representation based on TF-IDF and feature generalisation(F-measure=0.92,r-precision=0.58)outperformed the morphosyntactic representation(F-measure=0.89,r-precision=0.45),while reducing the features space.Converting the features into lower granular features(i.e.,generalisation)contributed to impr
基金financially supported by the AfricaYam Project(Grant OPP1052998-Bill and Melinda Gates Foundation).
文摘Various biological constraints including erratic and asynchronous flowering between male and female plants hinder successful hybrid development and genetic gains in greater yam breeding programs.Therefore,pollen storage has gained much attention to facilitate artificial pollinations and increase the genetic gains.This 4-year study aimed at developing a practical long-term pollen storage technique for the successful development of yam hybrids.Fresh pollens were collected from two Dioscorea alata males,then lyophilized(two lyophilization treatments were applied),followed by storage at room temperature(24℃–25℃)for 12 months.Moreover,the lyophilized and stored pollens were tested for viability by crossing with four female varieties.Our results showed that lyophilization is effective for achieving viable pollens after 12 months of storage.Treatment 1(48 h drying)showed higher pollen germination and fertility rates than Treatment 2(72 h drying).Although we observed a reduction in viability of lyophilized pollens after 12 months of storage,we generated hybrid seedlings with success rates from 12%to 21%compared to 21%–31%when using fresh pollens.Paternity testing based on molecular genotyping confirmed the hybrid status of the obtained seedlings,which grew well in a greenhouse.Lyophilization is a practical approach for a long-term storage of greater yam pollen samples.This protocol will positively impact yam breeding programs particularly in developing countries.
文摘GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures.It allows long-term access to datasets following the FAIR principles:Findable,Accessible,Interoperable,and Reusable,by using a flexible and original approach.It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration,storage,and querying.It takes advantage of international standards including the Crop Ontology,MIAPPE,and the Breeding API.GnpIS allows handling data for a wide range of species and experiment types,including multiannual perennial plants experimental network or annual plant trials with either raw data,i.e.,direct measures,or computed traits.It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data.This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data.Our repository follows the Open Science data publication principles by ensuring citability of each dataset.Finally,GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types.GnpIS can therefore contribute to emerging international federations of information systems.
基金supported by the French Agence Nationale de la Recherche(project MARIS ANR-14-CE03-0007-01andprojectSWATCHANR-18-PRIM-0006)by the'Institut national de recherche pour I'agriculture,I'alimentation et I'environnement'(INRAE)supported by the Conseil Regional de La Réunion,the French Ministry of Agriculture and Food,the European Union(Feader program,grant n°AG/974/DAAF/2016-00096 and Feder program,grant n°GURTDI20151501-0000735).
基金funded by the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-ASTIP-2021-OCRI)China Agriculture Research System(CARS14)+2 种基金Hubei International Science and Technology Cooperation Project(2022EHB034)the Science and Technology Innovation Project of Hubei Province(2021-620-000-001-035)the Fundamental Research Funds for Central Non-profit Scientific Institution(2013).
文摘Sesame(Sesamum indicum L.) plays a crucial role in Ethiopian agriculture,serving both subsistence and commercial purposes.However,our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited.To address this knowledge gap,we genotyped 368 Ethiopian sesame germplasms,categorizing into four distinct breeding groups:Accessions,landraces,improved varieties,and wild types,using a comprehensive set of 28 polymorphic markers,including 23 simple sequence repeat(SSR) and five Insertion-Deletion(InDel) markers.These markers ensured robust genomic representation,with at least two markers per linkage group.Our results unveiled substantial genetic diversity,identifying a total of 535 alleles across all accessions.On average,each locus displayed 8.83 alleles,with observed and expected heterozygosity values of 0.30 and 0.36,respectively.Gene Diversity and Polymorphic Information Content(PIC) were recorded at 0.37 and 0.35.The percentage of polymorphic loci varied significantly among breeding groups,ranging from8.00% to 82.40%,indicating high diversity in accessions(82.4%),moderate diversity in improved varieties(31.20%) and landraces(29.60%),and limited diversity in wild types(8.00).Analysis of Molecular Variance(AMOVA) results emphasized significant genetic differentiation among populations,with substantial diversity(P<0.001) within each population.Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations,while the larger proportion of genetic diversity(92%) resided within each individual sesame population,showcasing heightened diversity within each group.Our study’s findings received support from both Bayesian clustering and Neighbor-joining(NJ) analysis,reaffirming the credibility of our genetic structure insights.Notably,Population structure analysis at its highest Δk value(k=2) revealed the existence of two primary genetic clusters,further subdivided into four sub-populations at k=4.Similarly,NJ analysis identified two promi
基金This study was supported by Selfsupporting Program of Guangzhou Laboratory(grant number:No.SRPG22-007).
文摘What is already known about this topic?Given the challenges presented by drug-resistant strains of tuberculosis(TB)and the rising mobility of the population,achieving the objective of eradicating TB appears uncertain.What is added by this report?The examination of TB incidence trends in 10 highburden countries(HBCs)indicated a steady rise in cases,with India and China jointly accounting for nearly 70%of the burden.Projections for the future show diverse trajectories in these countries,with potential difficulties in reaching the TB elimination target,especially in Nigeria,Congo,and South Africa.What are the implications for public health practice?The number of TB cases is on the rise.It is crucial to learn from successful strategies to improve TB prevention and control worldwide through collaborative efforts.
文摘This study's goal is to present a dynamic portrait of the farm-buildings environment in Occitania,in Southern France,in order to better identify the transitions underway in agri-food chains.To this end,we undertook a ter-ritorial diagnosis based on actor statements,using 28 semi-structured interviews across Occitania.This diagnosis was enriched by graphic modelling,which enabled the spatialization of the dynamics described.We show that the process of standardisation of farm buildings prevails in the majority of the territories studied.This phenomenon has intensified in recent years with the development of vast photovoltaic-roofed sheds,accentuating the farm-land conversion and soil sealing.At the same time,in areas with strong environmental,landscape and heritage contexts,a'new adventure in farm buildings'(2022 survey)is taking shape.It is primarily driven by local short food chains,which rely on self-construction,repurposing and refurbishment,the sharing of tools and equipment,and which favour the use and reuse of local resources.This study shows that farm-buildings dynamics crystallise many challenges confronting the reterritorialisation of agriculture and food production.
基金funded by the ApCoreStress project(INRA-BAP department)and supported by GIS Fruit(Bilan Yonis-Omar’s internship).
文摘Despite previous reports on the genotypic variation of architectural and functional traits in fruit trees,phenotyping large populations in the field remains challenging.In this study,we used high-throughput phenotyping methods on an apple tree core-collection(1000 individuals)grown under contrasted watering regimes.First,architectural phenotyping was achieved using T-LiDAR scans for estimating convex and alpha hull volumes and the silhouette to total leaf area ratio(STAR).Second,a semi-empirical index(IPL)was computed from chlorophyll fluorescence measurements,as a proxy for leaf photosynthesis.Last,thermal infrared and multispectral airborne imaging was used for computing canopy temperature variations,water deficit,and vegetation indices.All traits estimated by these methods were compared to low-throughput in planta measurements.Vegetation indices and alpha hull volumes were significantly correlated with tree leaf area and trunk cross sectional area,while IPL values showed strong correlations with photosynthesis measurements collected on an independent leaf dataset.By contrast,correlations between stomatal conductance and canopy temperature estimated from airborne images were lower,emphasizing discrepancies across measurement scales.High heritability values were obtained for almost all the traits except leaf photosynthesis,likely due to large intra-tree variation.Genotypic means were used in a clustering procedure that defined six classes of architectural and functional combinations.Differences between groups showed several combinations between architectural and functional traits,suggesting independent genetic controls.This study demonstrates the feasibility and relevance of combining multi-scale high-throughput methods and paves the way to explore the genetic bases of architectural and functional variations in woody crops in field conditions.
文摘Corynespora cassiicola is the causal agent of Corynespora Leaf Fall(CLF)disease.CLF is one of the most important fungal diseases of rubber trees in Asia and Africa but disease outbreaks have not been reported in South America.Cassiicolin,a small cysteine-rich glycoprotein secreted by the pathogenic C.cassiicola isolate CCP,was previously identified as a potential disease effector in rubber tree.Recently,the cassiicolin-encoding gene(Cas1)was characterized and shown to be expressed in the early phase of infection.In this study,we investigated whether previously undetected strains of C.cassiicola are present in South American rubber plantations by examining the fungal endophyte population found in asymptomatic rubber tree leaves.Four isolates were identified as C.cassiicola.Genes encoding new forms of the cassiicolin precursor protein(Cas3 and Cas4)were identified from these isolates.Three of four isolates were able to induce symptoms on the cultivar they were isolated from in a detached leaf assay,with different kinetics and intensities.One isolate had the same pathogenicity profile as the pathogenic isolate CCP;the other two isolates developed symptoms late during the course of infection,suggesting saprotrophic capabilities.However,no Cas3 or Cas4 transcripts could be detected upon inoculation with the endophytic isolates,whereas the reference gene Cas1 was expressed upon inoculation with the CCP isolate.This work demonstrated that C.cassiicola is present in South America in an endophytic form and that it may evolve from an endophytic to a saprophytic or even potentially pathogenic life style.
基金This work was supported by France Genomique National infrastructure,funded as part of“Investissement d’avenir”program managed by Agence Nationale pour la Recherche(contrat ANR-10-INBS-09)and has also benefited from Imagerie-Gif core facility supported by l’Agence Nationale de la Recherche(ANR-11-EQPX-0029/Morphoscope,ANR-10-INBS-04/FranceBioImagingANR-11-IDEX-0003-02/Saclay Plant Sciences).
文摘Vanilla planifolia, the species cultivated to produce one of the world’s most popular flavors, is highly proneto partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report herethe first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that thediploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequentlyobserved. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gbwith a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequenciesand the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linkinggene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complexmolecular regulation of endoreplication along the chromosomes. This high-quality, anchored assemblyrepresents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidationof this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a userfriendly integrated web portal that enables centralized access to high-throughput genomic and other omicsdata and interoperable use of bioinformatics tools.
基金Supported by the Center for International Cooperation in Agronomic Research for Developmentthe French Ministry of Overseas Departments and Territories+1 种基金the European Agricultural Guidance and Guarantee Fundthe Regional Direction of Environment,France
文摘The possibilities of combining the dissolution of short-range-order minerals （SROMs） like allophane and imogolite, by ammonium oxalate and a particle size distribution analysis performed by the pipette method were investigated by tests on a soil sample from Reunion, a volcanic island located in the Indian Ocean, having a large SROMs content. The need to work with moist soil samples was again emphasized because the microaggregates formed during air-drying are resistant to the reagent. The SROM content increased, but irregularly, with the number of dissolutions by ammonium oxalate： 334 and 470 mg g-1 of SROMs were dissolved after one and three dissolutions respectively. Six successive dissolutions with ammonium oxalate on the same soil sample showed that 89% of the sum of oxides extracted by the 6 dissolutions were extracted by the first dissolution （mean 304 mg g-l）. A compromise needs to be found between the total removal of SROMs by large quantities of ammonium oxalate and the preservation of clay minerals, which were unexpectedly dissolved by this reagent. These tests enabled a description of the clay assemblage of the soil （gibbsite, smectite, and traces of kaolinite） in an area where such information was lacking due to the difficulties encountered in recuperation of the clay fraction.
文摘Plants adjust their development in relation to the availability of nutrient sources. This necessitates signal- ing between root and shoot. Aside from the well-known systemic signaling processes mediated by auxin, cytokinin, and sugars, new pathways involving carotenoid-derived hormones have recently been identified. The auxin-responsive MAX pathway controls shoot branching through the biosynthesis of strigolactone in the roots. The BYPASSI gene affects the production of an as-yet unknown carotenoid-derived substance in roots that promotes shoot development. Novel local and systemic mechanisms that control adaptive root development in response to nitrogen and phosphorus starvation were recently discovered. Notably, the ability of the NITRATE TRANSPORTER 1.1 to transport auxin drew for the first time a functional link between auxin, root development, and nitrate availability in soil. The study of plant response to phos- phorus starvation allowed the identification of a systemic mobile miRNA. Deciphering and integrating these signaling pathways at the whole-plant level provide a new perspective for understanding how plants regulate their development in response to environmental cues.
基金the INRAE sweet cherry breeding program,which is supported by INRAE BAP division and by INRAE’s private partner,CEP Innovation.
文摘Rain-induced fruit cracking is a major problem in sweet cherry cultivation.Basic research has been conducted to disentangle the physiological and mechanistic bases of this complex phenomenon,whereas genetic studies have lagged behind.The objective of this work was to disentangle the genetic determinism of rain-induced fruit cracking.We hypothesized that a large genetic variation would be revealed,by visual field observations conducted on mapping populations derived from well-contrasted cultivars for cracking tolerance.Three populations were evaluated over 7–8 years by estimating the proportion of cracked fruits for each genotype at maturity,at three different areas of the sweet cherry fruit:pistillar end,stem end,and fruit side.An original approach was adopted to integrate,within simple linear models,covariates potentially related to cracking,such as rainfall accumulation before harvest,fruit weight,and firmness.We found the first stable quantitative trait loci(QTLs)for cherry fruit cracking,explaining percentages of phenotypic variance above 20%,for each of these three types of cracking tolerance,in different linkage groups,confirming the high complexity of this trait.For these and other QTLs,further analyses suggested the existence of at least two-linked QTLs in each linkage group,some of which showed confidence intervals close to 5 cM.These promising results open the possibility of developing marker-assisted selection strategies to select cracking-tolerant sweet cherry cultivars.Further studies are needed to confirm the stability of the reported QTLs over different genetic backgrounds and environments and to narrow down the QTL confidence intervals,allowing the exploration of underlying candidate genes.
