scholarly journals Diversifying mechanisms in the on-farm evolution of crop mixtures

2014 ◽  
Author(s):  
Mathieu Thomas ◽  
Stéphanie Thépot ◽  
Sophie Jouanne-Pin ◽  
Nathalie Galic ◽  
Carine Remoué ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Heading Date ◽  
Common Garden ◽  
Initial Mixture ◽  
Crop Evolution ◽  
Mixture Component ◽  
Evolutionary Mechanisms ◽  
Modern Agriculture ◽  
Selection Processes ◽  
On Farm

While modern agriculture relies on genetic homogeneity in the field, some farmers grow genetically heterogeneous crops and exchange seeds. Such diversifying practices associated with seed recycling may allow adaptation of crops to their environment. This socio-genetical model constitutes an original experimental evolution design called On-Farm Dynamic Management (OFDM). Studying OFDM can help understanding how evolutionary mechanisms shape crop diversity submitted to diverse agro-environmental conditions. We studied a farmer-led initiative where a mixture of four French wheat landraces called "Mélange de Touselles" (MDT) was created and distributed within a farmers' network. Fifteen populations derived by farmers from the initial mixture were sampled after 2 to 7 generations of cultivation on their farm. Twenty-one space-time samples of 80 individuals were genotyped using 17 microsatellites markers and characterized for their heading date in a "common-garden" experiment. Gene polymorphism was studied using four markers located in earliness genes. An original network-based approach was developed to depict the particular and complex genetic structure of the landraces composing the mixture. A rapid differentiation of the mixture was detected, larger at the phenotypic and gene levels compared to the neutral genetic level, indicating a potential divergent selection. We identified two interacting selection processes: variation of the mixture component frequencies and evolution of the within-variety diversity, that shaped the standing variability available within the mixture. These results confirm that farmers' practices increase genetic diversity and allow crop evolution, which is critical in the context of global change. OFDM appears as a promising model of crop experimental evolution.

scholarly journals An increase in atypical petal numbers during a shift to autogamy in a coastal sand verbena and potential evolutionary mechanisms

2021 ◽  
Author(s):  
Eric F. LoPresti ◽  
James G. Mickley ◽  
Caroline L. Edwards ◽  
Marjorie G. Weber
Keyword(s):  
Reproductive Traits ◽  
Common Garden ◽  
Developmental Stability ◽  
Great Variability ◽  
Evolutionary Mechanisms ◽  
Science Project ◽  
Public Citizen ◽  
Coastal Sand ◽  
Abronia Umbellata ◽  
Citizen Science Project

AbstractPremiseThe evolution of variation in reproductive traits is of longstanding interest in biology. In plants, meristic traits, such as petal and sepal numbers, are usually considered invariant within taxa. However, certain species consistently exhibit great variability in these traits, though the factors contributing to “atypical” counts are not well-known. The sand verbenas, Abronia (Nyctaginaceae), usually have five perianth lobes (‘petals’) in their fused corollas and are self-incompatible, thus departures from either of these norms in populations, varieties, or species are of evolutionary interest.MethodsTo characterize and understand an increase in atypical petal numbers during a transition from xenogamy (outcrossing) to autogamy (selfing) in the coastal sand verbena Abronia umbellata, we integrated common garden studies with analysis of over 11,000 photographed flowers from iNaturalist, a citizen science project. Here we evaluate several adaptive and nonadaptive explanations for the production of these ‘atypical’ flowers.Key resultsOur photo analysis and common garden show that the nominate xenogamous variety has 5 petals with very little variation, however, an autogamous, geographically separated variety, A. u. var. breviflora has a high preponderance of four-petalled morphs. Flower morph did not affect successful autogamy, and petal numbers were not related to environmental factors, hybridization, or flower size in the ways hypothesized.ConclusionsWe conclude that this loss of petals is consistent with relaxation of selection on petal number in selfers, inbreeding leading to a loss of developmental stability, or correlated selection on another trait. This study strongly demonstrates the power of data available from public citizen databases for easily scored traits, such as petal number.

Maintenance and Analysis of Agricultural Data: A Challenge

2016 ◽  
Vol 5 (09) ◽  
pp. 4842
Author(s):  
Gupta N. K.* ◽  
Isaac R. K. ◽  
R. K. Singh
Keyword(s):  
Research And Development ◽  
Agricultural Research ◽  
Research Work ◽  
International Level ◽  
Modern Agriculture ◽  
Huge Data ◽  
Data Collecting ◽  
Agricultural Research And Development ◽  
On Farm

Agriculture is the backbone of India and agriculture research is required for sustainable and modern agriculture. In India there are more than 1,00,000 agricultural scientists working for agricultural research and development ICAR, SAUs, KVKs, CSIR, IITs, NGOs, etc. large number of data are being produced by different scientist, researcher and student involved in various research work conducted on farm. The availability of huge data from the field of agriculture is needed to be translated in valuable and easily understandable format. Several data collecting agencies are working on state, central and international level. In spite of good no. of available software's, the information obtained through the analysis of data are, somehow, lacking in meeting their fate of serving the targeted communities-farmers, researcher and student. Loss of data means loss of national money. So there is need of proper Maintenance and analysis of agricultural data. Here vast information is collected related to the topic from different countries to evaluate what type of system are being used by them to solve the problem and also to prepare a strategy by adopting which maintenance and analysis of agricultural data in India will be possible. This will save not only the money but also the time for generating the same data and the valuable man power. 

scholarly journals Adaptation of Escherichia coli to Long-Term Serial Passage in Complex Medium: Evidence of Parallel Evolution

mSystems ◽  
2017 ◽  
Vol 2 (2) ◽  
Author(s):  
Karin E. Kram ◽  
Christopher Geiger ◽  
Wazim Mohammed Ismail ◽  
Heewook Lee ◽  
Haixu Tang ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Parallel Evolution ◽  
Microbial Evolution ◽  
Complex Medium ◽  
Evolutionary Mechanisms ◽  
Adaptive Mutations ◽  
Experimental Systems ◽  
Experimental Laboratory ◽  
Five Phases

ABSTRACT With a growing body of work directed toward understanding the mechanisms of evolution using experimental systems, it is crucial to decipher what effects the experimental setup has on the outcome. If the goal of experimental laboratory evolution is to elucidate underlying evolutionary mechanisms and trends, these must be demonstrated in a variety of systems and environments. Here, we perform experimental evolution in a complex medium allowing the cells to transition through all five phases of growth, including death phase and long-term stationary phase. We show that the swiftness of selection and the specific targets of adaptive evolution are different in this system compared to others. We also observe parallel evolution where different mutations in the same genes are under positive natural selection. Together, these data show that while some outcomes of microbial evolution experiments may be generalizable, many outcomes will be environment or system specific. Experimental evolution of bacterial populations in the laboratory has led to identification of several themes, including parallel evolution of populations adapting to carbon starvation, heat stress, and pH stress. However, most of these experiments study growth in defined and/or constant environments. We hypothesized that while there would likely continue to be parallelism in more complex and changing environments, there would also be more variation in what types of mutations would benefit the cells. In order to test our hypothesis, we serially passaged Escherichia coli in a complex medium (Luria-Bertani broth) throughout the five phases of bacterial growth. This passaging scheme allowed cells to experience a wide variety of stresses, including nutrient limitation, oxidative stress, and pH variation, and therefore allowed them to adapt to several conditions. After every ~30 generations of growth, for a total of ~300 generations, we compared both the growth phenotypes and genotypes of aged populations to the parent population. After as few as 30 generations, populations exhibit changes in growth phenotype and accumulate potentially adaptive mutations. There were many genes with mutant alleles in different populations, indicating potential parallel evolution. We examined 8 of these alleles by constructing the point mutations in the parental genetic background and competed those cells with the parent population; five of these alleles were found to be adaptive. The variety and swiftness of adaptive mutations arising in the populations indicate that the cells are adapting to a complex set of stresses, while the parallel nature of several of the mutations indicates that this behavior may be generalized to bacterial evolution. IMPORTANCE With a growing body of work directed toward understanding the mechanisms of evolution using experimental systems, it is crucial to decipher what effects the experimental setup has on the outcome. If the goal of experimental laboratory evolution is to elucidate underlying evolutionary mechanisms and trends, these must be demonstrated in a variety of systems and environments. Here, we perform experimental evolution in a complex medium allowing the cells to transition through all five phases of growth, including death phase and long-term stationary phase. We show that the swiftness of selection and the specific targets of adaptive evolution are different in this system compared to others. We also observe parallel evolution where different mutations in the same genes are under positive natural selection. Together, these data show that while some outcomes of microbial evolution experiments may be generalizable, many outcomes will be environment or system specific.

scholarly journals Development of Software for Soil Compaction Assessment

2012 ◽  
Vol 69 (1) ◽  
Author(s):  
Adrian MOLNAR ◽  
Ioan DROCAS ◽  
Ovidiu RANTA ◽  
Sorin STANILA
Keyword(s):  
Soil Compaction ◽  
Computer Applications ◽  
Agricultural Field ◽  
Modern Agriculture ◽  
Spatial Management ◽  
Farm Scale ◽  
Main Input ◽  
User Friendly ◽  
On Farm

In today modern agriculture are required specific computer applications for the monitoring of agricultural field status. This paper analyses the possibilities to develop user-friendly software for soil compaction assessment, which uses input data related to soil properties, in field agricultural traffic specific conditions and other parameters, in order to get the most accurate solutions for soil compaction spatial management. Within paper are mentioned the main requirements for proper structural design of the developed software, the main input parameters are defined and the main structure of the developed software is described. The designed software will be a useful tool for soil compaction management on long term, not only on farm scale but also on national scale.

scholarly journals Herbicide injury induces DNA methylome alterations in Arabidopsis

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3560 ◽  
Author(s):  
Gunjune Kim ◽  
Christopher R. Clarke ◽  
Hailey Larose ◽  
Hong T. Tran ◽  
David C. Haak ◽  
...  
Keyword(s):  
Dependent Manner ◽  
Evolutionary Mechanisms ◽  
Herbicide Resistant ◽  
Modern Agriculture ◽  
Adaptive Mechanisms ◽  
History Of ◽  
Mock Treatment ◽  
Methylation Patterns ◽  
Dose Dependent ◽  
Herbicide Glyphosate

The emergence of herbicide-resistant weeds is a major threat facing modern agriculture. Over 470 weedy-plant populations have developed resistance to herbicides. Traditional evolutionary mechanisms are not always sufficient to explain the rapidity with which certain weed populations adapt in response to herbicide exposure. Stress-induced epigenetic changes, such as alterations in DNA methylation, are potential additional adaptive mechanisms for herbicide resistance. We performed methylC sequencing of Arabidopsis thaliana leaves that developed after either mock treatment or two different sub-lethal doses of the herbicide glyphosate, the most-used herbicide in the history of agriculture. The herbicide injury resulted in 9,205 differentially methylated regions (DMRs) across the genome. In total, 5,914 of these DMRs were induced in a dose-dependent manner, wherein the methylation levels were positively correlated to the severity of the herbicide injury, suggesting that plants can modulate the magnitude of methylation changes based on the severity of the stress. Of the 3,680 genes associated with glyphosate-induced DMRs, only 7% were also implicated in methylation changes following biotic or salinity stress. These results demonstrate that plants respond to herbicide stress through changes in methylation patterns that are, in general, dose-sensitive and, at least partially, stress-specific.

scholarly journals Benchmarking software tools for detecting and quantifying selection in Evolve and Resequencing studies

2019 ◽  
Author(s):  
Christos Vlachos ◽  
Claire Burny ◽  
Marta Pelizzola ◽  
Rui Borges ◽  
Andreas Futschik ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Time Series Data ◽  
Software Tools ◽  
Series Data ◽  
Test Statistics ◽  
Selection Processes ◽  
Study Selection ◽  
Powerful Approach ◽  
Future Data ◽  
Data Collections

AbstractThe combination of experimental evolution with whole genome re-sequencing of pooled individuals, also called Evolve and Resequence (E&R) is a powerful approach to study selection processes and to infer the architecture of adaptive variation. Given the large potential of this method, a range of software tools were developed to identify selected SNPs and to measure their selection coefficients. In this benchmarking study, we are comparing 15 test statistics implemented in 10 software tools using three different scenarios. We demonstrate that the power of the methods differs among the scenarios, but some consistently outperform others. LRT-1, which takes advantage of time series data consistently performed best for all three scenarios. Nevertheless, the CMH test, which requires only two time points had almost the same performance. This benchmark study will not only facilitate the analysis of already existing data, but also affect the design of future data collections.

scholarly journals Recombination and Selection in the Evolution of Picornaviruses and Other Mammalian Positive-Stranded RNA Viruses

2006 ◽  
Vol 80 (22) ◽  
pp. 11124-11140 ◽  
Author(s):  
Peter Simmonds
Keyword(s):  
Large Scale ◽  
Sequence Divergence ◽  
Purifying Selection ◽  
Sequence Evolution ◽  
Control Groups ◽  
Evolutionary Mechanisms ◽  
Virus Family ◽  
Selection Processes ◽  
Codon Use ◽  
Structural Region

ABSTRACT Picornaviridae are a large virus family causing widespread, often pathogenic infections in humans and other mammals. Picornaviruses are genetically and antigenically highly diverse, with evidence for complex evolutionary histories in which recombination plays a major part. To investigate the nature of recombination and selection processes underlying the evolution of serotypes within different picornavirus genera, large-scale analysis of recombination frequencies and sites, segregation by serotype within each genus, and sequence selection and composition was performed, and results were compared with those for other nonenveloped positive-stranded viruses (astroviruses and human noroviruses) and with flavivirus and alphavirus control groups. Enteroviruses, aphthoviruses, and teschoviruses showed phylogenetic segregation by serotype only in the structural region; lack of segregation elsewhere was attributable to extensive interserotype recombination. Nonsegregating viruses also showed several characteristic sequence divergence and composition differences between genome regions that were absent from segregating virus control groups, such as much greater amino acid sequence divergence in the structural region, markedly elevated ratios of nonsynonymous-to-synonymous substitutions, and differences in codon usage. These properties were shared with other picornavirus genera, such as the parechoviruses and erboviruses. The nonenveloped astroviruses and noroviruses similarly showed high frequencies of recombination, evidence for positive selection, and differential codon use in the capsid region, implying similar underlying evolutionary mechanisms and pressures driving serotype differentiation. This process was distinct from more-recent sequence evolution generating diversity within picornavirus serotypes, in which neutral or purifying selection was prominent. Overall, this study identifies common themes in the diversification process generating picornavirus serotypes that contribute to understanding of their evolution and pathogenicity.

scholarly journals Re-Introduction of Ancient Wheat Cultivars into Organic Agriculture—Emmer and Einkorn Cultivation Experiences under Marginal Conditions

2020 ◽  
Vol 12 (4) ◽  
pp. 1584 ◽  
Author(s):  
Szilvia Bencze ◽  
Marianna Makádi ◽  
Tibor J. Aranyos ◽  
Mihály Földi ◽  
Péter Hertelendy ◽  
...  
Keyword(s):  
Nutritive Value ◽  
Food System ◽  
Phenolic Content ◽  
Total Phenolic ◽  
Crop Species ◽  
Wheat Varieties ◽  
Hulled Wheat ◽  
Modern Agriculture ◽  
Organic Farmers ◽  
On Farm

Modern agriculture depends on the production of very few crop species, which provide lower nutritive value for consumers. The present work summarizes the results of a three-year experiment on hulled wheat varieties as potential candidates for food system diversification. The organic field cultivation tests with 10 emmer and five einkorn landraces and varieties were conducted on ~10m2 plots on sandy soil, and from 2017, under on-farm conditions in eastern Hungary. Most accessions adapted well to the marginal conditions, with some landraces even yielding higher than registered varieties—over 3 t per ha on average over three years. Compared to emmer, einkorn had higher maximum grain yields, but its yield performance varied more than that of emmer. Grain protein and the total phenolic content were high in both species. Compared to emmer, einkorn seeds exhibited a 3.8 times higher content of bound flavonoids and had 3.4 times higher antioxidant activity. Four einkorn accessions were resistant to leaf spot, as well as yellow and leaf rusts. Fusarium infected both species similarly. Our findings indicate that not only registered varieties of ancient wheat species but also their landraces can provide sustainable alternatives both for organic farmers and also for the diversification of agriculture.

Experimental evolution in photoautotrophic microorganisms as a means of enhancing chloroplast functions

2017 ◽  
Vol 62 (1) ◽  
pp. 77-84 ◽  
Author(s):  
Dario Leister
Keyword(s):  
Escherichia Coli ◽  
Green Algae ◽  
Experimental Evolution ◽  
Whole Genome ◽  
Model Species ◽  
Short Term ◽  
Evolutionary Mechanisms ◽  
Photosynthetic Microorganisms ◽  
Novel Targets ◽  
Abiotic Environmental Factors

The term ‘experimental evolution’ refers to short-term evolutionary experiments with microorganisms under controlled conditions in which selection is expected to occur. In combination with whole-genome sequencing and genetic engineering, the method has become a powerful tool to study evolutionary mechanisms and engineer new microbial variants. It has been most extensively used in the model species Escherichia coli and Saccharomyces cerevisiae, but more recently photosynthetic microorganisms have been subjected to experimental evolution. In such assays, strains were generated that had become more tolerant to certain abiotic environmental factors or evolved new traits during co-propagation with other organisms. These strains were viable under conditions that were lethal to the non-adapted progenitor and in a few cases, the causative mutations were identified. Because cyanobacteria like Synechocystis or green algae like Chlamydomonas reinhardtii share many features with crop plants – which are not amenable to such experiments – experimental evolution with photosynthetic microorganisms has the potential to identify novel targets for improving the capacity of plants to acclimate to environmental change. Here, I provide a survey of the experiments performed so far in cyanobacteria and green algae, focusing on Synechocystis and C. reinhardtii, and discuss the promise and the challenges of such approaches.

scholarly journals Automated guidance of agricultural machinery

2020 ◽  
pp. 12
Author(s):  
Guillermo P. Moreda
Keyword(s):  
Unmanned Vehicles ◽  
Agricultural Machinery ◽  
Farm Machinery ◽  
Modern Agriculture ◽  
Current State ◽  
On Farm

In modern agriculture, tractors have been fitted with accessories and technologies to help the tractor guidance. In this topic, these technologies will be explained describing different possibilities for the adoption of farm machinery guidance aids. Differences between systems helping the guidance and autosteering systems will be defined, along with current state of legislation concerning unmanned vehicles. Levels of precision in the track of the machinery will be explained, related with the GNSS technology onboard. Consequences of a better tractor guidance on farm tasks and economy will be outlined

Sign in / Sign up

Export Citation Format

Share Document