Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An integrated model to study varietal diversity in traditional agroecosystems.

ABSTRACT: Agricultural diversity is one of the bases of traditional agroecosystems, having great environmental and cultural importance. The current loss of agricultural diversity is causing serious concern, mainly because of its essential role in supporting global and local food security. Stopping this loss requires a better understanding of how diversity is managed locally and what mechanisms sustain agricultural diversity. Here we propose a generalist agent-based model that couples biological, cultural, and social dynamics to obtain varietal diversity as an emergent phenomenon at the community level. With a mechanistic approach, we explore how four of the model dynamics can shape systems diversity. To validate the model, we performed a bibliographic review on Manihot esculenta and Zea mays case studies. The model yielded compatible results for manioc and maize varietal richness at both community and household levels.

SUBMITTER: Hirata Sanches V

PROVIDER: S-EPMC8797245 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

An integrated model to study varietal diversity in traditional agroecosystems.

Hirata Sanches Vitor V Adams Cristina C Ferreira Fernando Fagundes FF

PloS one 20220128 1

Agricultural diversity is one of the bases of traditional agroecosystems, having great environmental and cultural importance. The current loss of agricultural diversity is causing serious concern, mainly because of its essential role in supporting global and local food security. Stopping this loss requires a better understanding of how diversity is managed locally and what mechanisms sustain agricultural diversity. Here we propose a generalist agent-based model that couples biological, cultural, ...[more]

PMID: 35089959

Similar Datasets

Traditional agroecosystems as conservatories and incubators of cultivated plant varietal diversity: the case of fig (Ficus carica L.) in Morocco.

Project description:BackgroundTraditional agroecosystems are known to host both large crop species diversity and high within crop genetic diversity. In a context of global change, this diversity may be needed to feed the world. Are these agroecosystems museums (i.e. large core collections) or cradles of diversity? We investigated this question for a clonally propagated plant, fig (Ficus carica), within its native range, in Morocco, but as far away as possible from supposed centers of domestication.ResultsFig varieties were locally numerous. They were found to be mainly highly local and corresponded to clones propagated vegetatively. Nevertheless these clones were often sufficiently old to have accumulated somatic mutations for selected traits (fig skin color) and at neutral loci (microsatellite markers). Further the pattern of spatial genetic structure was similar to the pattern expected in natural population for a mutation/drift/migration model at equilibrium, with homogeneous levels of local genetic diversity throughout Moroccan traditional agroecosystems.ConclusionsWe conclude that traditional agroecosystems constitue active incubators of varietal diversity even for clonally propagated crop species, and even when varieties correspond to clones that are often old. As only female fig is cultivated, wild fig and cultivated fig probably constitute a single evolutionary unit within these traditional agroecosystems. Core collections, however useful, are museums and hence cannot serve the same functions as traditional agroecosystems.

| S-EPMC2844065 | biostudies-literature

Effects of traditional agroecosystems and grazing areas on amphibian diversity in a region of central Mexico.

Project description:Habitat loss or degradation due to land cover change is regarded as one of the main drivers of amphibian decline; therefore, it is imperative to assess the effects of land-cover change on this group of vertebrates. In this study, we analyze changes in alpha and beta diversity of amphibian communities found in five land-cover types: mountain cloud forest, tropical evergreen forest, shade coffee, milpa huasteca, and grazing areas; six samples sites were established for each land-cover type, separated at least one km away. The study was conducted in the northwest part of the state of Hidalgo, in a transition zone between the Sierra Madre Oriental and the Gulf of Mexico, which is a region rich in amphibian species. The results indicate that alpha diversity decreases with loss of canopy cover, this being high in mountain cloud forest, tropical evergreen forest, and Shade coffee, and low in milpa huasteca and grazing areas. The land-cover type with the highest species evenness was found in milpa huasteca and the lowest in. The highest beta diversity was observed among tropical evergreen forest and grazing areas. Mountain cloud forest contains both exclusive species and the highest number of species currently regarded as threatened by national and international conservation assessment systems. In order to preserve amphibian diversity in the study area it is vital to protect the last remnants of native vegetation, especially mountain cloud forest, but also including Shade coffee, since the latter habitat harbors amphibian diversity similar to that found in native forests. Finally, implementation of policies that both reduce Grazing areas and increase their productivity is also necessary, since these highly modified areas turn out to be the ones that affect amphibian diversity the most.

| S-EPMC6378913 | biostudies-literature

Plant Diversity Reduces the Risk of Antibiotic Resistance Genes in Agroecosystems.

Project description:Despite advances in dispersal mechanisms and risk assessment of antibiotic resistance genes (ARGs), how plants influence ARG contamination in agricultural soils remains underexplored. Here, the impacts of plant species and diversity on ARGs and mobile genetic elements (MGEs) in three agricultural soils are comprehensively investigated in a pot experiment. The results indicate that increased plant diversity reduces ARGs and MGEs abundance by 19.2%-51.2%, whereas plant species exhibit inconsistent and soil-dependent effects. Potential bacterial hosts harboring abundant ARGs have greater relative abundance than nonhosts, and both their richness and cumulative relative abundance are reduced by plant diversity. Notably, hosts inhibited by plant diversity present a greater relative abundance than the other hosts. The enriched compounds in root exudates due to plant diversity play a more important role in the metabolic network and contribute to rebalancing of the abundance of potential hosts and nonhosts. An independent test using pure organics reveals that higher resource diversity, resulting from increased plant diversity, reduces the relative abundance and mobility of abundant and high-risk ARGs. This study highlights the resource-mediated mitigation of the risks posed by ARG contamination and indicates that ensuring plant and resource diversity is a promising strategy for controlling ARGs in agroecosystems.

| S-EPMC11923964 | biostudies-literature

Approach to the Chemotaxonomic Characterization of Traditional Cultivation Grape Varieties through Their Varietal Aroma Profile.

Project description:In this study, the aroma profile of 12 minority grape varieties of Vitis vinifera L., included in the 'Caiño group', was defined along three vintages by solid phase microextraction followed by the gas chromatography-mass spectrometry method (SPME-GC-MS). Principal objectives were to assess the aromatic profile as a useful fingerprint to differentiate them, recover traditionally cultivated grape varieties for the differentiation of an important wine-growing area and discover their chemotaxonomic potential. In each variety, free and bound volatile profile was carried out by grouping varietal compounds into thirteen families. In total, 339 volatile compounds were identified, 230 as free forms and 205 as aromatic precursors. Remarkable quantitative differences were observed between aromatic profiles for terpenes in the free fraction and for C6 compounds, alcohols, sesquiterpenes and phenols in the glycosidic fraction. Principal component analysis based on their aromatic profile highlights a good differentiation between varieties and suggests a certain degree of aromatic chemotaxonomic proximity between previously known parental varieties, 'Caiño Blanco' with respect to 'Caiño Bravo' and 'Albariño'. This study shows the preliminary results of a large research project involving a larger number of grape varieties and thus a broader spectrum of genetic relationships between them.

| S-EPMC9140530 | biostudies-literature

De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity.

Project description:BackgroundPlants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to disentangle genetic and environmental factors.ResultsWe have shown that cDNA sequencing by RNA-seq is a robust approach for the characterization of varietal diversity between a local grapevine cultivar (Corvina) and the PN40024 reference genome. We detected 15,161 known genes including 9463 with novel splice isoforms, and identified 2321 potentially novel protein-coding genes in non-annotated or unassembled regions of the reference genome. We also discovered 180 apparent private genes in the Corvina genome which were missing from the reference genome.ConclusionsThe de novo assembly approach allowed a substantial amount of the Corvina transcriptome to be reconstructed, improving known gene annotations by robustly defining gene structures, annotating splice isoforms and detecting genes without annotations. The private genes we discovered are likely to be nonessential but could influence certain cultivar-specific characteristics. Therefore, the application of de novo transcriptome assembly should not be restricted to species lacking a reference genome because it can also improve existing reference genome annotations and identify novel, cultivar-specific genes.

| S-EPMC3556335 | biostudies-literature

Scientific selection: A century of increasing crop varietal diversity in US wheat.

Project description:A prevalent and persistent biodiversity concern is that modern cropping systems lead to an erosion in crop genetic diversity. Although certain trait uniformity provides advantages in crop management and marketing, farmers facing risks from change in climate, pests, and markets are also incentivized to adopt new varieties to address complex and spatially variable genetics, environment, and crop management interactions to optimize crop performance. In this study, we applied phylogenetically blind and phylogenetically informed diversity metrics to reveal significant increases in both the spatial and temporal diversity of the US wheat crop over the past century. Contrary to commonly held perceptions on the negative impact of modern cropping systems on crop genetic diversity, our results demonstrated a win-win outcome where the widespread uptake of scientifically selected varieties increased both crop production and crop diversity.

| S-EPMC9907116 | biostudies-literature

Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat.

Project description:Crop genetic diversity is essential for adaptation and productivity in agriculture. A previous study revealed that poor allele diversity in wheat commercial cultivars is a major barrier to its further improvement. Homologs within a variety, including paralogs and orthologs in polyploid, account for a large part of the total genes of a species. Homolog diversity, intra-varietal diversity (IVD), and their functions have not been elucidated. Common wheat, an important food crop, is a hexaploid species with three subgenomes. This study analyzed the sequence, expression, and functional diversity of homologous genes in common wheat based on high-quality reference genomes of two representative varieties, a modern commercial variety Aikang 58 (AK58) and a landrace Chinese Spring (CS). A total of 85,908 homologous genes, accounting for 71.9% of all wheat genes, including inparalogs (IPs), outparalogs (OPs), and single-copy orthologs (SORs), were identified, suggesting that homologs are an important part of the wheat genome. The levels of sequence, expression, and functional variation in OPs and SORs were higher than that of IPs, which indicates that polyploids have more homologous diversity than diploids. Expansion genes, a specific type of OPs, made a great contribution to crop evolution and adaptation and endowed crop with special characteristics. Almost all agronomically important genes were from OPs and SORs, demonstrating their essential functions for polyploid evolution, domestication, and improvement. Our results suggest that IVD analysis is a novel approach for evaluating intra-genomic variations, and exploitation of IVD might be a new road for plant breeding, especially for polyploid crops, such as wheat.

| S-EPMC10299346 | biostudies-literature

Integrated Approach from Sample-to-Answer for Grapevine Varietal Identification on a Portable Graphene Sensor Chip.

Project description:Identifying grape varieties in wine, related products, and raw materials is of great interest for enology and to ensure its authenticity. However, these matrices' complexity and low DNA content make this analysis particularly challenging. Integrating DNA analysis with 2D materials, such as graphene, offers an advantageous pathway toward ultrasensitive DNA detection. Here, we show that monolayer graphene provides an optimal test bed for nucleic acid detection with single-base resolution. Graphene's ultrathinness creates a large surface area with quantum confinement in the perpendicular direction that, upon functionalization, provides multiple sites for DNA immobilization and efficient detection. Its highly conjugated electronic structure, high carrier mobility, zero-energy band gap with the associated gating effect, and chemical inertness explain graphene's superior performance. For the first time, we present a DNA-based analytic tool for grapevine varietal discrimination using an integrated portable biosensor based on a monolayer graphene field-effect transistor array. The system comprises a wafer-scale fabricated graphene chip operated under liquid gating and connected to a miniaturized electronic readout. The platform can distinguish closely related grapevine varieties, thanks to specific DNA probes immobilized on the sensor, demonstrating high specificity even for discriminating single-nucleotide polymorphisms, which is hard to achieve with a classical end-point polymerase chain reaction or quantitative polymerase chain reaction. The sensor was operated in ultralow DNA concentrations, with a dynamic range of 1 aM to 0.1 nM and an attomolar detection limit of ∼0.19 aM. The reported biosensor provides a promising way toward developing decentralized analytical tools for tracking wine authenticity at different points of the food value chain, enabling data transmission and contributing to the digitalization of the agro-food industry.

| S-EPMC9973367 | biostudies-literature

Assessment of bacterial diversity of Rhipicephalus microplus ticks from two livestock agroecosystems in Antioquia, Colombia.

Project description:Rhipicephalus microplus is recognized as a tick species highly prevalent in cattle, with a wide pantropical distribution that seems to continue spreading geographically. However, its role as a biological vector has been scarcely studied in the livestock context. In this study, a 16S rRNA next-generation sequencing analysis was used to determine bacterial diversity in salivary glands and gut of R. microplus from two contrasting livestock agroecosystems in Antioquia, Colombia. Both the culture-independent approach (CI) and the culture-dependent (CD) approach were complementarily adopted in this study. A total of 341 unique OTUs were assigned, the richness showed to be higher in the Northern than in the Middle Magdalena region, and a high diversity was found at the phylum and genus levels in the samples obtained. With the CI approach, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most common phylum of bacteria regardless of the organ, or geographic origin of the specimens analyzed. While the relative abundance of bacteria at a phylum level with the CD approach varied between analyzed samples, the data obtained suggest that a high diversity of species of bacteria occurs in R. microplus from both livestock agroecosystems. Bacterial genera such as Anaplasma, Coxiella, and Ehrlichia, recognized for their implications in tick-borne diseases, were also detected, together with endosymbionts such as Lysinibacillus, previously reported as a potential tool for biological control. This information is useful to deepen the knowledge about microbial diversity regarding the relations between endosymbionts and pathogens and could facilitate the future development of epidemiological surveillance in livestock systems.

| S-EPMC7329104 | biostudies-literature

Meta-Analysis of Organic Fertilization Effects on Soil Bacterial Diversity and Community Composition in Agroecosystems.

Project description:Application of organic fertilizers or their combination with chemical fertilizers is a feasible practice for improving soil fertility and reducing soil degradation in agroecosystems, and these regulations are mainly mediated though soil microbial communities. Despite bacteria ranking among the most abundant and diverse groups of soil microorganisms, the effects of long-term organic fertilization (OF) and chemical-organic fertilization (COF) on soil bacterial diversity and community composition remain unclear. In this study, we conducted a meta-analysis and demonstrated that OF had no significant effect on bacterial alpha diversity. Application of chemical fertilizer and crop residue significantly decreased bacterial Richness index. Both OF and COF significantly altered bacterial community structure, with these changes being predominately attributed to shifts in soil pH. For bacterial phyla, both OF and COF significantly increased the relative abundance of Proteobacteria and Bacteroidetes, suggesting that OF and COF may cause the enrichment of copiotrophic taxa. In addition, COF significantly increased the relative abundance of Gammaproteobacteria but decreased the relative abundance of Acidobacteria. Overall, our results suggest that organic and chemical-organic fertilization can effectively maintain bacterial diversity and enhance soil fertility in agroecosystems, and the alteration of soil bacterial community structure is closely intertwined with soil pH.

| S-EPMC10675672 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data