Evolutionary change in agriculture: the past, present and future

Bumblebees mediate landscape effects on a forest herb's population genetic structure in European agricultural landscapes

Spatially isolated plant populations in agricultural landscapes exhibit genetic responses not only to habitat fragmentation per se but also to the composition of the landscape matrix between habitat patches. These responses can only be understood by examining how the landscape matrix influences among-habitat movements of pollinators and seed vectors, which act as genetic linkers among populations. We studied the forest herb Polygonatum multiflorum and its associated pollinator and genetic linker, the bumblebee Bombus pascuorum, in three European agricultural landscapes. We aimed to identify which landscape features affect the movement activity of B. pascuorum between forest patches and to assess the relative importance of these features in explaining the forest herb's population genetic structure. We applied microsatellite markers to estimate the movement activity of the bumblebee as well as the population genetic structure of the forest herb. We modelled the movement activity as a function of various landscape metrics. Those metrics found to explain the movement activity best were then used to explain the population genetic structure of the forest herb. The bumblebee movement activity was affected by the cover of maize fields and semi-natural grasslands on a larger spatial scale and by landscape heterogeneity on a smaller spatial scale. For some measures of the forest herb's population genetic structure, that is, allelic richness, observed heterozygosity and the F-value, the combinations of landscape metrics, which explained the linker movement activity best, yielded lower AICc values than 95% of the models including all possible combinations of landscape metrics. Synthesis: The genetic linker, B. pascuorum, mediates landscape effects on the population genetic structure of the forest herb P. multiflorum. Our study indicates, that the movement of the genetic linker among forest patches, and thus the pollen driven gene flow of the herb, depends on the relative value of floral resources in the specific landscape setting. Noteworthy, the population genetic structure of the long-lived, clonal forest herb species correlated with recent land-use types such as maize, which have been existing for not more than a few decades within these landscapes. This underscores the short time in which land-use changes can influence the evolutionary potential of long-lived wild plants.

Potential Acetylcholinesterase Inhibitor Acting on the Pesticide Resistant and Susceptible Cotton Pests

Gossypium spp., produces economically important cotton fiber, and its yield is highly affected due to pest attacks. Insecticidal target site mutation is one of the reasons behind insecticide resistance to a wide range of pesticides. Acetylcholinesterase (AChE) protein sequences from major pests of cotton were analyzed to assess various physicochemical properties, presence of motifs, and understand evolutionary relationship. The impact of three mutant AChE1, A. lucorum A216S, B. tabaci F392W, and A. gossypii A302S, on the strucutral stability was assessed, and F392W_AChE1 was selected based on 100 ns molecular dynamics simulation. Virtual screening of the zinc database and high-throughput virtual screening, standard precision, and extra precision docking resulted in the identification of six compounds. The six identified compounds and six known commercial pesticdes were docked with three mutant and three wild type AChE1, and one (C1) was selected based on Tice criteria. The conformational and interaction stability of the AChE1-C1 and F392W_AChE1-C1 complexes were monitored at 100 ns Gromacs simulation and were found to be thermodynamically favorable. Therefore, C1 may have the potential to bind to the resistant and susceptible strains of cotton pest, and the resistance developed by insects could be arrested. Furthermore, synthesis and field study of C1 will lead us to a better understanding of the efficacy of the identified compound.

Opportunities from Unmanned Aerial Vehicles to Identify Differences in Weed Spatial Distribution between Conventional and Conservation Agriculture

Weeds are one of the major issues in agricultural production and they are present in most agricultural systems. Due to the heterogeneity of weed distribution, understanding spatial patterns is paramount for precision farming and improving sustainability in crop management. Nevertheless, limited information is currently available about the differences between conventional agricultural (CV) weed spatial patterns and weed spatial patterns in conservation agricultural systems (CA); moreover, opportunities to use unmanned aerial vehicles (UAV) and recognition algorithms to monitor these differences are still being explored and tested. In this work, the opportunity to use UAVs to detect changes in spatial distribution over time between CA and CV fields was assessed for data acquisition. Acquired data were processed using maximum likelihood classification to discriminate between weeds and surrounding elements; then, a similarity assessment was performed using the ‘equal to’ function of the raster calculator. The results show important differences in spatial distribution over time between CA and CV fields. In the CA field 56.18% of the area was infested in both years when the field margin effect was included, and 22.53% when this effect was excluded; on the other hand, in the CV field only 11.50% of the area was infested in both years. The results illustrate that there are important differences in the spatial distribution of weeds between CA and CV fields; such differences can be easily detected using UAVs and identification algorithms combined.

Insights into the genomic evolution of insects from cricket genomes

Most of our knowledge of insect genomes comes from Holometabolous species, which undergo complete metamorphosis and have genomes typically under 2 Gb with little signs of DNA methylation. In contrast, Hemimetabolous insects undergo the presumed ancestral process of incomplete metamorphosis, and have larger genomes with high levels of DNA methylation. Hemimetabolous species from the Orthopteran order (grasshoppers and crickets) have some of the largest known insect genomes. What drives the evolution of these unusual insect genome sizes, remains unknown. Here we report the sequencing, assembly and annotation of the 1.66-Gb genome of the Mediterranean field cricket Gryllus bimaculatus, and the annotation of the 1.60-Gb genome of the Hawaiian cricket Laupala kohalensis. We compare these two cricket genomes with those of 14 additional insects and find evidence that hemimetabolous genomes expanded due to transposable element activity. Based on the ratio of observed to expected CpG sites, we find higher conservation and stronger purifying selection of methylated genes than non-methylated genes. Finally, our analysis suggests an expansion of the pickpocket class V gene family in crickets, which we speculate might play a role in the evolution of cricket courtship, including their characteristic chirping.

Ylla, Extavour et al. use genomic data from crickets to investigate the evolution of large genome sizes and DNA methylation events in insects. Their findings indicate that transposable element activity drove genome expansion in hemimetabolous insects, such as crickets and grasshoppers, and that DNA methylation is predominant in conserved genes.

Aqueous and Ethanolic Plant Extracts as Bio-Insecticides-Establishing a Bridge between Raw Scientific Data and Practical Reality

Global demand for food production is causing pressure to produce faster and bigger crop yields, leading to a rampant use of synthetical pesticides. To combat the nefarious consequences of its uses, a search for effective alternatives began in the last decades and is currently ongoing. Nature is seen as the main source of answers to crop protection problems, supported by several examples of plants/extracts used for this purpose in traditional agriculture. The literature reviewed allowed the identification of 95 plants whose extracts exhibit insecticide activity and can be used as bio-pesticides contributing to sustainable agriculture. The option for ethanol and/or water extracts is more environmentally friendly and resorts to easily accessible solvents, which can be reproduced by farmers themselves. This enables a bridge to be established between raw scientific data and a more practical reality. Azadirachta indica, Capsicum annuum, Nicotiana tabacum and Tagetes erecta are the most researched plants and have the potential to be viable options in the pest management approach. Azadirachta indica showed the most promising results and Brevicoryne brassicae was the most targeted pest species, being tested against the aqueous and/or ethanolic extracts of 23 different plants. Maceration using dried material (usually leaves) is the extraction method preferred by the majority of authors.

Genetically modified organisms and food security in Southern Africa: conundrum and discourse

The importance of food security and nourishment is recognized in Southern African region and in many communities, globally. However, the attainment of food security in Southern African countries is affected by many factors, including adverse environmental conditions, pests and diseases. Scientists have been insistently looking for innovative strategies to optimize crop production and combat challenges militating against attainment of food security. In agriculture, strategies of increasing crop production include but not limited to improved crop varieties, farming practices, extension services, irrigation services, mechanization, information technology, use of fertilizers and agrochemicals. Equally important is genetic modification (GM) technology, which brings new prospects in addressing food security problems. Nonetheless, since the introduction of genetically modified crops (GMOs) three decades ago, it has been a topic of public discourse across the globe, conspicuously so in Southern African region. This is regardless of the evidence that planting GMOs positively influenced farmer’s incomes, economic access to food and increased tolerance of crops to various biotic and abiotic stresses. This paper looks at the issues surrounding GMOs adoption in Southern Africa and lack thereof, the discourse, and its potential in contributing to the attainment of food security for the present as well as future generations.

Problems of implementing compulsory integrated pest management

Compulsory integrated pest management poses a number of challenges and issues for debate. Some of are discussed with reference to European Union requirements set out in Annex III of Directive 128/2009. Requirements on the use of plant protection products bring with them problems with dose reduction in the light of a resistance prevention strategy, the lack of threshold levels, the necessity of chemical treatments and the limited availability of effective products of biological origin. Use of preventive measures of pest control faces barriers related to profitability and a lack of knowledge on the part of farmers. Challenges to control the system, as well as the fact that some legally enforced rules are not suitable for all crops, seem also to be an issue. © 2019 Society of Chemical Industry.

Permaculture: Challenges and benefits in improving rural livelihoods in South Africa and Zimbabwe

Feeding a growing global population using conventional agricultural practices is leading toadverse environmental impacts. There is a call for alternative forms of agriculture that address social,economic, and environmental aspects of sustainability. Permaculture is a holistic design frameworkthat incorporates sustainable agricultural practices, potentially improving livelihoods. This studylooked at the challenges and benefits of permaculture in improving rural livelihoods in Zimbabweand South Africa. We used semi-structured interviews to collect data. Permaculture contributed over40% to total income for participants in both countries. However, permaculture was not the dominantsource of income and periodically straddled multiple livelihood strategies. The main benefits ofpermaculture were identified as improved human health, increased resilience to environmentalchanges, and reduction of input costs. The key challenges included high labour input, infestationof pests and diseases, and lack of knowledge on permaculture practices. Although permaculturepresents significant challenges, its integration with other forms of sustainable agricultural practicescan contribute to improved rural livelihoods.

Plant grafting: new mechanisms, evolutionary implications

Grafting, an old plant propagation practice, is still widely used with fruit trees and in recent decades also with vegetables. Taxonomic proximity is a general prerequisite for successful graft-take and long-term survival of the grafted, composite plant. However, the mechanisms underlying interspecific graft incompatibility are as yet insufficiently understood. Hormonal signals, auxin in particular, are believed to play an important role in the wound healing and vascular regeneration within the graft union zone. Incomplete and convoluted vascular connections impede the vital upward and downward whole plant transfer routes. Long-distance protein, mRNA and small RNA graft-transmissible signals currently emerge as novel mechanisms which regulate nutritional and developmental root/top relations and may play a pivotal role in grafting physiology. Grafting also has significant pathogenic projections. On one hand, stock to scion mechanical contact enables the spread of diseases, even without a complete graft union. But, on the other hand, grafting onto resistant rootstocks serves as a principal tool in the management of fruit tree plagues and vegetable soil-borne diseases. The 'graft hybrid' historic controversy has not yet been resolved. Recent evidence suggests that epigenetic modification of DNA-methylation patterns may account for certain graft-transformation phenomena. Root grafting is a wide spread natural phenomenon; both intraspecific and interspecific root grafts have been recorded. Root grafts have an evolutionary role in the survival of storm-hit forest stands as well as in the spread of devastating diseases. A more fundamental evolutionary role is hinted by recent findings that demonstrate plastid and nuclear genome transfer between distinct Nicotiana species in the graft union zone, within a tissue culture system. This has led to the formation of alloploid cells that, under laboratory conditions, gave rise to a novel, alloploid Nicotiana species, indicating that natural grafts may play a role in plant speciation, under certain circumstances.

Migrate or evolve: options for plant pathogens under climate change

Findings on climate change influence on plant pathogens are often inconsistent and context dependent. Knowledge of pathogens affecting agricultural crops and natural plant communities remains fragmented along disciplinary lines. By broadening the perspective beyond agriculture, this review integrates cross-disciplinary knowledge to show that at scales relevant to climate change, accelerated evolution and changing geographic distribution will be the main implications for pathogens. New races may evolve rapidly under elevated temperature and CO2 , as evolutionary forces act on massive pathogen populations boosted by a combination of increased fecundity and infection cycles under favourable microclimate within enlarged canopy. Changing geographic distribution will bring together diverse lineages/genotypes that do not share common ecological niche, potentially increasing pathogen diversity. However, the uncertainty of model predictions and a lack of synthesis of fragmented knowledge remain as major deficiencies in knowledge. The review contends that the failure to consider scale and human intervention through new technology are major sources of uncertainty. Recognizing that improved biophysical models alone will not reduce uncertainty, it proposes a generic framework to increase focus and outlines ways to integrate biophysical elements and technology change with human intervention scenarios to minimize uncertainty. To synthesize knowledge of pathogen biology and life history, the review borrows the concept of 'fitness' from population biology as a comprehensive measure of pathogen strengths and vulnerabilities, and explores the implications of pathogen mode of nutrition to fitness and its interactions with plants suffering chronic abiotic stress under climate change. Current and future disease management options can then be judged for their ability to impair pathogenic and saprophytic fitness. The review pinpoints improving confidence in model prediction by minimizing uncertainty, developing management strategies to reduce overall pathogen fitness, and finding new sources of data to trawl for climate signatures on pathogens as important challenges for future research.

The Evolution of Fruit Tree Productivity: A Review

The Evolution of Fruit Tree Productivity: A Review. Domestication of fruit trees has received far less attention than that of annual crop plants. In particular, very little is known about the evolution of fruit tree productivity. In the wild, most tree species reach reproductive maturity after a long period of juvenility and even then, sexual reproduction appears sporadically, often in a mode of masting. Environmental constraints limit trees' reproductive activity in their natural, wild habitats, resulting in poor, irregular productivity. Early fructification and regular, high rates of productivity have been selected by people, unconsciously and consciously. The reviewed evidence indicates an evolutionary continuum of productivity patterns among trees of wild habitats, intermediary domesticates, and the most advanced domesticates. Alternate bearing appears to represent an intermediate step in the fruit tree evolutionary pathway. The existence of a molecular, genetic mechanism that controls trees' sexual reproduction and fruiting pattern is suggested.

Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops

Domesticated food crops are derived from a phylogenetically diverse assemblage of wild ancestors through artificial selection for different traits. Our understanding of domestication, however, is based upon a subset of well-studied 'model' crops, many of them from the Poaceae family. Here, we investigate domestication traits and theories using a broader range of crops. We reviewed domestication information (e.g. center of domestication, plant traits, wild ancestors, domestication dates, domestication traits, early and current uses) for 203 major and minor food crops. Compiled data were used to test classic and contemporary theories in crop domestication. Many typical features of domestication associated with model crops, including changes in ploidy level, loss of shattering, multiple origins, and domestication outside the native range, are less common within this broader dataset. In addition, there are strong spatial and temporal trends in our dataset. The overall time required to domesticate a species has decreased since the earliest domestication events. The frequencies of some domestication syndrome traits (e.g. nonshattering) have decreased over time, while others (e.g. changes to secondary metabolites) have increased. We discuss the influences of the ecological, evolutionary, cultural and technological factors that make domestication a dynamic and ongoing process.

The Red Queen and the seed bank: pathogen resistance of ex situ and in situ conserved barley

Plant geneticists have proposed that the dynamic conservation of crop plants in farm environments (in situ conservation) is complementary to static conservation in seed banks (ex situ conservation) because it may help to ensure adaptation to changing conditions. Here, we test whether collections of a traditional variety of Moroccan barley (Hordeum vulgare ssp. vulgare) conserved ex situ showed differences in qualitative and quantitative resistance to the endemic fungal pathogen, Blumeria graminis f.sp. hordei, compared to collections that were continuously cultivated in situ. In detached-leaf assays for qualitative resistance, there were some significant differences between in situ and ex situ conserved collections from the same localities. Some ex situ conserved collections showed lower resistance levels, while others showed higher resistance levels than their in situ conserved counterparts. In field trials for quantitative resistance, similar results were observed, with the highest resistance observed in situ. Overall, this study identifies some cases where the Red Queen appears to drive the evolution of increased resistance in situ. However, in situ conservation does not always result in improved adaptation to pathogen virulence, suggesting a more complex evolutionary scenario, consistent with several published examples of plant-pathogen co-evolution in wild systems.