Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations

Large scale sampling of Mexican maize landraces for the presence of transgenes

The presence and levels of transgenic maize in Mexico and the effect this could have on local landraces or closely related species such as teosinte has been the subject of several previous reports, some showing contrasting results. Cultural, social and political factors all affect maize cultivation in Mexico and although since 1998 there has been a moratorium on the commercial cultivation of transgenic maize, Mexico imports maize, mainly from the USA where transgenic cultivars are widely grown. Additionally extensive migration between rural areas in Mexico and the USA and customs of seed exchange between farmers may also play an unintentional role in the establishment of transgenic seed. A comprehensive study of all Mexican maize landraces throughout the country is not feasible, however this report presents data based on analysis of 3204 maize accessions obtained from the central region of Mexico (where permits have never been authorized for cultivation of transgenic maize) and the northern region (where for a short period authorization for experimental plots was granted). The results of the study confirm that transgenes are present in all the geographical areas sampled and were more common in germplasm obtained in the northern region. However, there was no evidence that regions where field trials had been authorized showed higher levels of transgene presence or that the morphology of seed lots harboring transgenic material was significantly modified in favor of expected transgenic phenotypes.

Confirmation of 'Pollen- and Seed-Specific Gene Deletor' System Efficiency for Transgene Excision from Transgenic Nicotiana tabacum under Field Conditions

The commercial application of genetically modified plants has been seriously impeded by public concern surrounding the potential risks posed by such plants to the ecosystem and human health. Previously, we have developed a 'pollen- and seed-specific Gene Deletor' system that automatically excised all transgenes from the pollen and seeds of greenhouse-grown transgenic Nicotiana tabacum. In this study, we conducted seven field experiments over three consecutive years to evaluate the stability of transgene excision under field conditions. Our results showed that transgenes were stably excised from transgenic Nicotiana tabacum under field conditions with 100% efficiency. The stability of transgene excision was confirmed based on PCR, as well as the GUS staining patterns of various organs (roots, leaves, petiole, stem, flower, fruit, and seeds) from transgenic N. tabacum. In six transgenic lines (D4, D10, D31, D56, and D43), the transgenes were stably deleted in the T0 and T1 generations. Thus, the 'Gene Deletor' system is an efficient and reliable method to reduce pollen- and seed-mediated unintentional gene flow. This system might help to alleviate the food safety concerns associated with transgenic crops.

The Household Context of In Situ Conservation in a Center of Crop Diversity: Self-Reported Practices and Perceptions of Maize and Phaseolus Bean Farmers in Oaxaca, Mexico

Crop diversity conservation in situ is an ecosystem service with benefits at household, community, and global scales. These include risk reduction and adaptation to changing physical and sociocultural environments—both important given the accelerating changes in climate, human migration, and the industrialization of agriculture. In situ conservation typically occurs as part of small-scale, traditionally based agriculture and can support cultural identity and values. Although decisions regarding crop diversity occur at the household level, few data detail the household context of in situ crop diversity management. Our research addressed this data gap for maize and Phaseolus bean in Oaxaca, Mexico, a major center of diversity for those crops. We defined diversity as farmer-named varieties and interviewed 400 farming households across eight communities in two contrasting socioecological regions. Our research asked, “In a major center of maize and Phaseolus diversity, what are the demographic, production, and consumption characteristics of the households that are stewarding this diversity?” We describe the context of conservation and its variation within and between communities and regions and significant associations between diversity and various independent variables, including direct maize consumption, region, and marketing of crops. These results provide a benchmark for communities to understand and strengthen their maize and bean systems in ways they value and for scientists to support those communities in dynamically stewarding locally and globally significant diversity.

Transgene Flow: Challenges to the On-Farm Conservation of Maize Landraces in the Brazilian Semi-Arid Region

Brazil is one of the largest global producers of genetically modified crops and a center of origin and diversification of relevant species for agriculture and food. Transgenic monocultures occupy around 50 million hectares, whereas smallholder farmers, indigenous people, and traditional communities are responsible for in-situ/on-Farm conservation of local genetic resources. Based on 15 years of expertise in regulating GMOs and in cross-institutional agrobiodiversity conservation projects, this article discusses the challenges regarding the coexistence of these two agricultural models based on transgene flow detection in maize landraces. As part of a broad and unique participatory transgene-flow-monitoring process, 1098 samples of maize landraces were collected in the Brazilian Semi-arid Region between 2018 and 2021 and analyzed using immunochromatographic strips. The tests revealed 34% of samples with presence of GM proteins. It is concluded that the biosafety standards in force in Brazil do not allow the assurance of on-Farm conservation of maize. The sectors that contribute to agrobiodiversity conservation and do not benefit from using GM seeds are taking on the burden of this process. Transgene flow can be reduced by approving and enforcing more effective coexistence rules that consider maize landraces crop areas also as seed-producing areas added to full disclosure of commercial seeds origin.

Glyphosate ban in Mexico: potential impacts on agriculture and weed management

Since glyphosate was classified as potentially carcinogenic by the International Agency for Research on Cancer, public debate regarding the environmental impact and health risks from its use has intensified. Almost all regulatory agencies throughout the world have concluded that the judicious use of glyphosate does not pose risks to the environment and human health. However, on the last day of 2020 the Mexican government decreed a ban of this herbicide beginning January, 2024. In current Mexican agriculture there are no safer chemical and/or other weed management technologies that allow for the economical substitution of glyphosate for weed control. Many Mexican weed scientists agree that glyphosate use should be reduced, but not banned outright. This decree could have more negative economic and social consequences as well as environmental and human health risks than benefits, which could compromise the country's food and public security. Crop yields are projected by some to decline by up to 40% with this ban, increasing food prices, making food less accessible to low-income consumers. In addition, a black market for the smuggling and illegal sale of glyphosate is possible. The possible environmental, economic and social impacts caused by the glyphosate ban in Mexico are discussed, emphasizing the impact on weed management. © 2021 Society of Chemical Industry.

Food safety, food security and genetically modified organisms in Africa: a current perspective

Moving forward from 2020, Africa faces an eminent challenge of food safety and security in the coming years. The World Food Programme (WFP) of the United Nations (UN) estimates that 20% of Africa's population of 1.2 billion people face the highest level of undernourishment in the world, likely to worsen due to COVID-19 pandemic that has brought the entire world to its knees. Factors such as insecurity and conflict, poverty, climate change and population growth have been identified as critical contributors to the food security challenges on the continent. Biotechnological research on Genetically Modified Organisms (GMOs) provides a range of opportunities (such as increased crop yields, resistance to pests and diseases, enhanced nutrient composition and food quality) in addressing the hunger, malnutrition and food security issues on the continent. However, the acceptance and adoption of GMOs on the continent has been remarkably slow, perhaps due to contrasting views about the benefits and safety concerns associated with them. With the reality of food insecurity and the booming population in Africa, there is an eminent need for a more pragmatic position to this debate. The present review presents an overview of the current situation of food safety and security and attempts to reconcile major viewpoints on GMOs research considering the current food safety and security crisis in the African continent.

Spatiotemporal Controllability and Environmental Risk Assessment of Genetically Engineered Gene Drive Organisms from the Perspective of European Union Genetically Modified Organism Regulation

Gene drive organisms are a recent development created by using methods of genetic engineering; they inherit genetic constructs that are passed on to future generations with a higher probability than with Mendelian inheritance. There are some specific challenges inherent to the environmental risk assessment (ERA) of genetically engineered (GE) gene drive organisms because subsequent generations of these GE organisms might show effects that were not observed or intended in the former generations. Unintended effects can emerge from interaction of the gene drive construct with the heterogeneous genetic background of natural populations and/or be triggered by changing environmental conditions. This is especially relevant in the case of gene drives with invasive characteristics and typically takes dozens of generations to render the desired effect. Under these circumstances, "next generation effects" can substantially increase the spatial and temporal complexity associated with a high level of uncertainty in ERA. To deal with these problems, we suggest the introduction of a new additional step in the ERA of GE gene drive organisms that takes 3 criteria into account: the biology of the target organisms, their naturally occurring interactions with the environment (biotic and abiotic), and their intended biological characteristics introduced by genetic engineering. These 3 criteria are merged to form an additional step in ERA, combining specific "knowns" and integrating areas of "known unknowns" and uncertainties, with the aim of assessing the spatiotemporal controllability of GE gene drive organisms. The establishment of assessing spatiotemporal controllability can be used to define so-called "cut-off criteria" in the risk analysis of GE gene drive organisms: If it is likely that GE gene drive organisms escape spatiotemporal controllability, the risk assessment cannot be sufficiently reliable because it is not conclusive. Under such circumstances, the environmental release of the GE gene drive organisms would not be compatible with the precautionary principle (PP). Integr Environ Assess Manag 2020;16:555-568. © 2020 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Contemporary evolution of maize landraces and their wild relatives influenced by gene flow with modern maize varieties

Mexico is recognized as the center of origin and domestication of maize. Introduction of modern maize varieties (MVs) into Mexico raised concerns regarding the possible effects of gene flow from MVs into maize landraces (LRs) and their wild relatives (WRs), teosintes. However, after more than 60 y from the release of the first MVs, the impact of the sympatry with LRs and their WRs has not been explored with genetic data. In this work, we assessed changes in the genomes of 7 maize LRs and 2 WR subspecies from collections spanning over 70 y. We compared the genotypes obtained by genotyping by sequencing (GBS) for LRs and WRs before and after the adoption of MVs, and observed introgression from sympatric MVs into LRs and into the WR Zea mays ssp. mexicana sampled after the year 2000. We also found a decrease in the paired divergence index (F _ST ) between MV-LR and MV-WR over the same time frame. Moreover, we determined that LR genetic diversity increased after 2000, probably as a result of gene flow from MVs introduced in the 1990s. Our findings allowed us to identify ongoing changes in the domesticated and wild maize genetic pools, and concur with previous works that have evaluated short-term gene flow from MVs into LRs in other crops. Our approach represents a useful tool for tracking evolutionary change in wild and domesticated genetic resources, as well as for developing strategies for their conservation.

In vitro performance in cotton plants with different genetic backgrounds: the case of Gossypium hirsutum in Mexico, and its implications for germplasm conservation

One of the best ex situ conservation strategies for wild germplasm is in vitro conservation of genetic banks. The success of in vitro conservation relies heavily on the micropropagation or performance of the species of interest. In the context of global change, crop production challenges and climate change, we face a reality of intensified crop production strategies, including genetic engineering, which can negatively impact biodiversity conservation. However, the possible consequences of transgene presence for the in vitro performance of populations and its implications for biodiversity conservation are poorly documented. In this study we analyzed experimental evidence of the potential effects of transgene presence on the in vitro performance of Gossypium hirsutum L. populations, representing the Mexican genetic diversity of the species, and reflect on the implications of such presence for ex situ genetic conservation of the natural variation of the species. We followed an experimental in vitro performance approach, in which we included individuals from different wild cotton populations as well as individuals from domesticated populations, in order to differentiate the effects of domestication traits dragged into the wild germplasm pool via gene flow from the effects of transgene presence. We evaluated the in vitro performance of five traits related to plant establishment (N = 300): propagation rate, leaf production rate, height increase rate, microbial growth and root development. Then we conducted statistical tests (PERMANOVA, Wilcoxon post-hoc tests, and NMDS multivariate analyses) to evaluate the differences in the in vitro performance of the studied populations. Although direct causality of the transgenes to observed phenotypes requires strict control of genotypes, the overall results suggest detrimental consequences for the in vitro culture performance of wild cotton populations in the presence of transgenes. This provides experimental, statistically sound evidence to support the implementation of transgene screening of plants to reduce time and economic costs in in vitro establishment, thus contributing to the overarching goal of germplasm conservation for future adaptation.

Farmers prevailing perception profiles regarding GM crops: A classification proposal

Genetically modified organisms have been at the centre of a major public controversy, involving different interests and actors. While much attention has been devoted to consumer views on genetically modified food, there have been few attempts to understand the perceptions of genetically modified technology among farmers. By investigating perceptions of genetically modified organisms among Brazilian farmers, we intend to contribute towards filling this gap and thereby add the views of this stakeholder group to the genetically modified debate. A comparative analysis of our data and data from other studies indicate there is a complex variety of views on genetically modified organisms among farmers. Despite this diversity, we found variations in such views occur within limited parameters, concerned principally with expectations or concrete experiences regarding the advantages of genetically modified crops, perceptions of risks associated with them, and ethical questions they raise. We then propose a classification of prevailing profiles to represent the spectrum of perceptions of genetically modified organisms among farmers.

Transgene flow in Mexican maize revisited: Socio-biological analysis across two contrasting farmer communities and seed management systems

The flow of transgenes into landraces and wild relatives is an important biosafety concern. The case of transgene flow into local maize varieties in Mexico (the center of origin of maize) has been intensively debated over the past 15 years, including legal, political, and environmental disputes fanned by the existence of a significant scientific controversy over the methods used for the detection of transgenes. The use of diverse approaches and a lack of harmonized methods specific to the detection and monitoring of transgenes in landraces have generated both positive and negative results regarding contamination of Mexican maize with genetically modified material over the years. In this paper, we revisit the case of transgene contamination in Mexican maize and present a novel research approach based on socio‐biological analysis of contrasting communities and seed management systems. Two communities were used to investigate how different social and biological factors can affect transgene flow and impact transgene spread in Mexico. Our results show the presence of transgenes in one community and thus support the position that transgenes are highly likely to be present in Mexican maize landraces. However, our work also demonstrates that the extent and frequency with which transgenes can be found will significantly depend on the societal characteristics and seed management systems of the local communities. Therefore, we argue that future analysis of transgene presence should include social research on the seed management practices in the sampling area so that more robust and comprehensive understandings and conclusions can be drawn.

Environmental impacts of genetically modified plants: A review

Powerful scientific techniques have caused dramatic expansion of genetically modified crops leading to altered agricultural practices posing direct and indirect environmental implications. Despite the enhanced yield potential, risks and biosafety concerns associated with such GM crops are the fundamental issues to be addressed. An increasing interest can be noted among the researchers and policy makers in exploring unintended effects of transgenes associated with gene flow, flow of naked DNA, weediness and chemical toxicity. The current state of knowledge reveals that GM crops impart damaging impacts on the environment such as modification in crop pervasiveness or invasiveness, the emergence of herbicide and insecticide tolerance, transgene stacking and disturbed biodiversity, but these impacts require a more in-depth view and critical research so as to unveil further facts. Most of the reviewed scientific resources provide similar conclusions and currently there is an insufficient amount of data available and up until today, the consumption of GM plant products are safe for consumption to a greater extent with few exceptions. This paper updates the undesirable impacts of GM crops and their products on target and non-target species and attempts to shed light on the emerging challenges and threats associated with it. Underpinning research also realizes the influence of GM crops on a disturbance in biodiversity, development of resistance and evolution slightly resembles with the effects of non-GM cultivation. Future prospects are also discussed.

Impact on environment, ecosystem, diversity and health from culturing and using GMOs as feed and food

Modern agriculture provides the potential for sustainable feeding of the world's increasing population. Up to the present moment, genetically modified (GM) products have enabled increased yields and reduced pesticide usage. Nevertheless, GM products are controversial amongst policy makers, scientists and the consumers, regarding their possible environmental, ecological, and health risks. Scientific-and-political debates can even influence legislation and prospective risk assessment procedure. Currently, the scientifically-assessed direct hazardous impacts of GM food and feed on fauna and flora are conflicting; indeed, a review of literature available data provides some evidence of GM environmental and health risks. Although the consequences of gene flow and risks to biodiversity are debatable. Risks to the environment and ecosystems can exist, such as the evolution of weed herbicide resistance during GM cultivation. A matter of high importance is to provide precise knowledge and adequate current information to regulatory agencies, governments, policy makers, researchers, and commercial GMO-releasing companies to enable them to thoroughly investigate the possible risks.

Difference in leaf water use efficiency/photosynthetic nitrogen use efficiency of Bt-cotton and its conventional peer

This study is to test the effects of Bt gene introduction on the foliar water/nitrogen use efficiency in cotton. We measured leaf stomatal conductance, photosynthetic rate, and transpiration rate under light saturation condition at different stages of a conventional cultivar (zhongmian no. 16) and its counterpart Bt cultivar (zhongmian no. 30) that were cultured on three levels of fertilization, based on which leaf instantaneous water use efficiency was derived. Leaf nitrogen concentration was measured to calculate leaf photosynthetic nitrogen use efficiency, and leaf δ¹³C was used to characterize long term water use efficiency. Bt cultivar was found to have lower stomatal conductance, net photosynthetic rates and transpiration rates, but higher instantaneous and long time water use efficiency. In addition, foliar nitrogen concentration was found to be higher but net photosynthetic rate was lower in the mature leaves of Bt cultivar, which led to lower photosynthetic nitrogen use efficiency. This might result from the significant decrease of photosynthetic rate due to the decrease of stomatal conductance. In conclusion, our findings show that the introduction of Bt gene should significantly increase foliar water use efficiency but decrease leaf nitrogen use efficiency in cotton under no selective pressure.

Evolutionary Developmental Biology (Evo-Devo) Research in Latin America

Famous for its blind cavefish and Darwin's finches, Latin America is home to some of the richest biodiversity hotspots of our planet. The Latin American fauna and flora inspired and captivated naturalists from the nineteenth and twentieth centuries, including such notable pioneers such as Fritz Müller, Florentino Ameghino, and Léon Croizat who made a significant contribution to the study of embryology and evolutionary thinking. But, what are the historical and present contributions of the Latin American scientific community to Evo-Devo? Here, we provide the first comprehensive overview of the Evo-Devo laboratories based in Latin America and describe current lines of research based on endemic species, focusing on body plans and patterning, systematics, physiology, computational modeling approaches, ecology, and domestication. Literature searches reveal that Evo-Devo in Latin America is still in its early days; while showing encouraging indicators of productivity, it has not stabilized yet, because it relies on few and sparsely distributed laboratories. Coping with the rapid changes in national scientific policies and contributing to solve social and health issues specific to each region are among the main challenges faced by Latin American researchers. The 2015 inaugural meeting of the Pan-American Society for Evolutionary Developmental Biology played a pivotal role in bringing together Latin American researchers eager to initiate and consolidate regional and worldwide collaborative networks. Such networks will undoubtedly advance research on the extremely high genetic and phenotypic biodiversity of Latin America, bound to be an almost infinite source of amazement and fascinating findings for the Evo-Devo community.

Creating Completely Both Male and Female Sterile Plants by Specifically Ablating Microspore and Megaspore Mother Cells

Although genetically modified (GM) plants have improved commercially important traits, such as biomass and biofuel production, digestibility, bioremediation, ornamental value, and tolerance to biotic and abiotic stresses, there remain economic, political, or social concerns over potential ecological effects of transgene flow from GM plants. The current solution for preventing transgene flow from GM plants is genetically engineering sterility; however, approaches to generating both male and female sterility are limited. In addition, existing strategies for creating sterility lead to loss or modifications of entire flowers or floral organs. Here, we demonstrate that instead of the 1.5-kb promoter, the entire SOLO DANCERS (SDS) gene is required for its meiocyte-specific expression. We then developed an efficient method to specifically ablate microspore and megaspore mother cells using the SDS and BARNASE fusion gene, which resulted in complete sterility in both male and female reproductive organs in Arabidopsis (Arabidopsis thaliana) and tobacco (Nicotiana tabacum), but did not affect plant growth or development, including the formation of all flower organs. Therefore, our research provides a general and effective tool to prevent transgene flow in GM plants.

Transgene flow: facts, speculations and possible countermeasures

Convincing evidence has accumulated that unintended transgene escape occurs in oilseed rape, maize, cotton and creeping bentgrass. The escaped transgenes are found in variant cultivars, in wild type plants as well as in hybrids of sexually compatible species. The fact that in some cases stacked events are present that have not been planted commercially, implies unintended recombination of transgenic traits. As the consequences of this continuous transgene escape for the ecosystem cannot be reliably predicted, I propose to use more sophisticated approaches of gene technology in future. If possible GM plants should be constructed using either site-directed mutagenesis or cisgenic strategies to avoid the problem of transgene escape. In cases where a transgenic trait is needed, efficient containment should be the standard approach. Various strategies available or in development are discussed. Such a cautious approach in developing novel types of GM crops will enhance the sustainable potential of GM crops and thus increase the public trust in green gene technology.

European flint landraces grown in situ reveal adaptive introgression from modern maize

We have investigated the role of selection in the determination of the detected levels of introgression from modern maize hybrid varieties into maize landraces still cultivated in situ in Italy. We exploited the availability of a historical collection of landraces undertaken before the introduction and widespread use of modern maize, to analyse genomic changes that have occurred in these maize landraces over 50 years of co-existence with hybrid varieties. We have combined a previously published SSR dataset (n=21) with an AFLP loci dataset (n=168) to provide higher resolution power and to obtain a more detailed picture. We show that selection pressures for adaptation have favoured new alleles introduced by migration from hybrids. This shows the potential for analysis of historical introgression even over this short period of 50 years, for an understanding of the evolution of the genome and for the identification of its functionally important regions. Moreover, this demonstrates that landraces grown in situ represent almost unique populations for use for such studies when the focus is on the domesticated plant. This is due to their adaptation, which has arisen from their dynamic evolution under a continuously changing agro-ecological environment, and their capture of new alleles from hybridisation. We have also identified loci for which selection has inhibited introgression from modern germplasm and has enhanced the distinction between landraces and modern maize. These loci indicate that selection acted in the past, during the formation of the flint and dent gene pools. In particular, the locus showing the strongest signals of selection is a Misfit transposable element. Finally, molecular characterisation of the same samples with two different molecular markers has allowed us to compare their performances. Although the genetic-diversity and population-structure analyses provide the same global qualitative pattern, which thus provides the same inferences, there are differences related to their natures and characteristics.

Detection of transgenes in local maize varieties of small-scale farmers in eastern cape, South Africa

Small-scale subsistence farmers in South Africa have been introduced to genetically modified (GM) crops for more than a decade. Little is known about i) the extent of transgene introgression into locally recycled seed, ii) what short and long-term ecological and socioeconomic impacts such mixing of seeds might have, iii) how the farmers perceive GM crops, and iv) to what degree approval conditions are followed and controlled. This study conducted in the Eastern Cape, South Africa, aims primarily at addressing the first of these issues. We analysed for transgenes in 796 individual maize plants (leaves) and 20 seed batches collected in a village where GM insect resistant maize was previously promoted and grown as part of an governmental agricultural development program over a seven year period (2001–2008). Additionally, we surveyed the varieties of maize grown and the farmers’ practices of recycling and sharing of seed in the same community (26 farmers were interviewed). Recycling and sharing of seeds were common in the community and may contribute to spread and persistence of transgenes in maize on a local or regional level. By analysing DNA we found that the commonly used transgene promoter p35s occurred in one of the 796 leaf samples (0.0013%) and in five of the 20 seed samples (25%). Three of the 20 seed samples (15%) included herbicide tolerant maize (NK603) intentionally grown by the farmers from seed bought from local seed retailers or acquired through a currently running agricultural development program. The two remaining positive seed samples (10%) included genes for insect resistance (from MON810). In both cases the farmers were unaware of the transgenes present. In conclusion, we demonstrate that transgenes are mixed into seed storages of small-scale farming communities where recycling and sharing of seeds are common, i.e. spread beyond the control of the formal seed system.

Genetic fallout in biocultural landscapes: molecular imperialism and the cultural politics of (not) seeing transgenes in Mexico

This article explores the trajectory of the global controversy over the introgression (or not) of transgenes from genetically modified maize into Mexican indigenous maize landraces. While a plurality of knowledge-making processes were deployed to render transgenes visible or invisible, we analyze how a particular in vitro based DNA-centered knowledge came to marginalize other forms of knowledge, thus obscuring other bio-cultural dimensions key to the understanding of gene flow and maize diversity. We show that dominant molecular norms of proof and standards of detection, which co-developed with the world of industrial monocropping and gene patenting, discarded and externalized non-compliant actors (i.e. complex maize genomes, human dimensions of gene flow). Operating in the name of high science, they hence obscured the complex biological and cultural processes that maintain crop diversity and enacted a cultural-political domination over the world of Mexican landraces and indigenous communities.

A parameter to quantify the degree of genetic mixing among individuals in hybrid populations

Hybridization between genetically distinct taxa is a complex evolutionary process. One challenge to studying hybrid populations is quantifying the degree to which non-native genes have become evenly mixed among individuals in the population. In this paper, we present a variance-based parameter, md, that measures the degree to which non-native genes are evenly distributed among individuals in a population. The parameter has a minimum value of 0 for populations in which individuals from multiple taxa are present but have not interbred, and a maximum value of 1 for populations in which all individuals have the same amount of non-native ancestry. A recurrence equation showed that relatively few generations of random mating are required for md to approach 1 (indicating a well-mixed population), and that md is independent of initial amounts of non-native ancestry. The parameter is mathematically equivalent to FST and we show how existing formulae for FST can be used to estimate md when diagnostic loci are available. Computer simulations showed this estimator to have very little bias for realistic amounts of data.

The contribution of genetic and genomic approaches to plant domestication studies

The application of genomic approaches to the phenomenon of plant domestication promises a better understanding of the origins of agriculture, but also of the way plant genomes in general are organized and expressed. Building on earlier genetic research, more detailed information has become available on the organization of genetic diversity at the genome level and the effects of gene flow on diversity in different regions of the genome. In addition, putative domestication genes have been identified through population genomics approaches (selective sweeps or divergence scanning). Further information has been obtained on the origin of domestication syndrome mutations and the dispersal and adaptation of crops after domestication. For the future, increasingly multidisciplinary approaches using combinations of genomics and other approaches will prevail.

Biological diversity in the patent system

Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI) established by the Global Biodiversity Information Facility (GBIF) and Encyclopedia of Life (EOL). We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8–1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on Intellectual Property and Genetic Resources, Traditional Knowledge and Folklore at the World Intellectual Property Organization.

Randomly detected genetically modified (GM) maize (Zea mays L.) near a transport route revealed a fragile 45S rDNA phenotype

Monitoring of genetically modified (GM) crops has been emphasized to prevent their potential effects on the environment and human health. Monitoring of the inadvertent dispersal of transgenic maize in several fields and transport routes in Korea was carried out by qualitative multiplex PCR, and molecular analyses were conducted to identify the events of the collected GM maize. Cytogenetic investigations through fluorescence in situ hybridization (FISH) of the GM maize were performed to check for possible changes in the 45S rDNA cluster because this cluster was reported to be sensitive to replication and transcription stress. Three GM maize kernels were collected from a transport route near Incheon port, Korea, and each was found to contain NK603, stacked MON863 x NK603, and stacked NK603 x MON810 inserts, respectively. Cytogenetic analysis of the GM maize containing the stacked NK603 x MON810 insert revealed two normal compact 5S rDNA signals, but the 45S rDNA showed a fragile phenotype, demonstrating a “beads-on-a-string” fragmentation pattern, which seems to be a consequence of genetic modification. Implications of the 45S rDNA cluster fragility in GM maize are also discussed.

Tracing the geographic origins of weedy Ipomoea purpurea in the southeastern United States

Ipomoea purpurea (common morning glory) is an annual vine native to Mexico that is well known for its large, showy flowers. Humans have spread morning glories worldwide, owing to the horticultural appeal of morning glory flowers. Ipomoea purpurea is an opportunistic colonizer of disturbed habitats including roadside and agricultural settings, and it is now regarded as a noxious weed in the Southeastern US. Naturalized populations in the Southeastern United States are highly polymorphic for a number of flower color morphs, unlike native Mexican populations that are typically monomorphic for the purple color morph. Although I. purpurea was introduced into the United States from Mexico, little is known about the specific geographic origins of US populations relative to the Mexican source. We use resequencing data from 11 loci and 30 I. purpurea accessions collected from the native range of the species in Central and Southern Mexico and 8 accessions from the Southeastern United States to infer likely geographic origins in Mexico. Based on genetic assignment analysis, haplotype composition, and the degree of shared polymorphism, I. purpurea samples from the Southeastern United States are genetically most similar to samples from the Valley of Mexico and Veracruz State. This supports earlier speculation that I. purpurea in the Southeastern United States was likely to have been introduced by European colonists from sources in Central Mexico.

Spatial structure and climatic adaptation in African maize revealed by surveying SNP diversity in relation to global breeding and landrace panels

Background

Climate change threatens maize productivity in sub-Saharan Africa. To ensure food security, access to locally adapted genetic resources and varieties is an important adaptation measure. Most of the maize grown in Africa is a genetic mix of varieties introduced at different historic times following the birth of the trans-Atlantic economy, and knowledge about geographic structure and local adaptations is limited.

Methodology

A panel of 48 accessions of maize representing various introduction routes and sources of historic and recent germplasm introductions in Africa was genotyped with the MaizeSNP50 array. Spatial genetic structure and genetic relationships in the African panel were analysed separately and in the context of a panel of 265 inbred lines representing global breeding material (based on 26,900 SNPs) and a panel of 1127 landraces from the Americas (270 SNPs). Environmental association analysis was used to detect SNPs associated with three climatic variables based on the full 43,963 SNP dataset.

Conclusions

The genetic structure is consistent between subsets of the data and the markers are well suited for resolving relationships and admixture among the accessions. The African accessions are structured in three clusters reflecting historical and current patterns of gene flow from the New World and within Africa. The Sahelian cluster reflects original introductions of Meso-American landraces via Europe and a modern introduction of temperate breeding material. The Western cluster reflects introduction of Coastal Brazilian landraces, as well as a Northeast-West spread of maize through Arabic trade routes across the continent. The Eastern cluster most strongly reflects gene flow from modern introduced tropical varieties. Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season. The associations located in genes of known importance for abiotic stress tolerance are interesting candidates for local adaptations.

New genes in traditional seed systems: diffusion, detectability and persistence of transgenes in a maize metapopulation

Gene flow of transgenes into non-target populations is an important biosafety concern. The case of genetically modified (GM) maize in Mexico has been of particular interest because of the country’s status as center of origin and landrace diversity. In contrast to maize in the U.S. and Europe, Mexican landraces form part of an evolving metapopulation in which new genes are subject to evolutionary processes of drift, gene flow and selection. Although these processes are affected by seed management and particularly seed flow, there has been little study into the population genetics of transgenes under traditional seed management. Here, we combine recently compiled data on seed management practices with a spatially explicit population genetic model to evaluate the importance of seed flow as a determinant of the long-term fate of transgenes in traditional seed systems. Seed flow between farmers leads to a much wider diffusion of transgenes than expected by pollen movement alone, but a predominance of seed replacement over seed mixing lowers the probability of detection due to a relative lack of homogenization in spatial frequencies. We find that in spite of the spatial complexities of the modeled system, persistence probabilities under positive selection are estimated quite well by existing theory. Our results have important implications concerning the feasibility of long term transgene monitoring and control in traditional seed systems.

Gene flow in genetically modified wheat

Understanding gene flow in genetically modified (GM) crops is critical to answering questions regarding risk-assessment and the coexistence of GM and non-GM crops. In two field experiments, we tested whether rates of cross-pollination differed between GM and non-GM lines of the predominantly self-pollinating wheat Triticum aestivum. In the first experiment, outcrossing was studied within the field by planting "phytometers" of one line into stands of another line. In the second experiment, outcrossing was studied over distances of 0.5-2.5 m from a central patch of pollen donors to adjacent patches of pollen recipients. Cross-pollination and outcrossing was detected when offspring of a pollen recipient without a particular transgene contained this transgene in heterozygous condition. The GM lines had been produced from the varieties Bobwhite or Frisal and contained Pm3b or chitinase/glucanase transgenes, respectively, in homozygous condition. These transgenes increase plant resistance against pathogenic fungi. Although the overall outcrossing rate in the first experiment was only 3.4%, Bobwhite GM lines containing the Pm3b transgene were six times more likely than non-GM control lines to produce outcrossed offspring. There was additional variation in outcrossing rate among the four GM-lines, presumably due to the different transgene insertion events. Among the pollen donors, the Frisal GM line expressing a chitinase transgene caused more outcrossing than the GM line expressing both a chitinase and a glucanase transgene. In the second experiment, outcrossing after cross-pollination declined from 0.7-0.03% over the test distances of 0.5-2.5 m. Our results suggest that pollen-mediated gene flow between GM and non-GM wheat might only be a concern if it occurs within fields, e.g. due to seed contamination. Methodologically our study demonstrates that outcrossing rates between transgenic and other lines within crops can be assessed using a phytometer approach and that gene-flow distances can be efficiently estimated with population-level PCR analyses.

Transgene excision in pollen using a codon optimized serine resolvase CinH-RS2 site-specific recombination system

Transgene escape, a major environmental and regulatory concern in transgenic crop cultivation, could be alleviated by removing transgenes from pollen, the most frequent vector for transgene flow. A transgene excision vector containing a codon optimized serine resolvase CinH recombinase (CinH) and its recognition sites RS2 were constructed and transformed into tobacco (Nicotiana tabacum cv. Xanthi). CinH recombinase recognized 119 bp of nucleic acid sequences, RS2, in pollen and excised the transgene flanked by the RS2 sites. In this system, the pollen-specific LAT52 promoter from tomato was employed to control the expression of CinH recombinase. Loss of expression of a green fluorescent protein (GFP) gene under the control of the LAT59 promoter from tomato was used as an indicator of transgene excision. Efficiency of transgene excision from pollen was determined by flow cytometry (FCM)-based pollen screening. While a transgenic event in the absence of CinH recombinase contained about 70% of GFP-synthesizing pollen, three single-copy transgene events contained less than 1% of GFP-synthesizing pollen based on 30,000 pollen grains analyzed per event. This suggests that CinH-RS2 recombination system could be effectively utilized for transgene biocontainment.

Cross-fertilization between genetically modified and non-genetically modified maize crops in Uruguay

The cultivation of genetically modified (GM) Bt maize (Zea mays L.) events MON810 and Bt11 is permitted in Uruguay. Local regulations specify that 10% of the crop should be a non-GM cultivar as refuge area for biodiversity, and the distance from other non-GM maize crops should be more than 250 m in order to avoid cross-pollination. However, the degree of cross-fertilization between maize crops in Uruguay is unknown. The level of adventitious presence of GM material in non-GM crops is a relevant issue for organic farming, in situ conservation of genetic resources and seed production. In the research reported here, the occurrence and frequency of cross-fertilization between commercial GM and non-GM maize crops in Uruguay was assessed. The methodology comprised field sampling and detection using DAS-ELISA and PCR. Five field-pair cases where GM maize crops were grown near non-GM maize crops were identified. These cases had the potential to cross-fertilize considering the distance between crops and the similarity of the sowing dates. Adventitious presence of GM material in the offspring of non-GM crops was found in three of the five cases. Adventitious presence of event MON810 or Bt11 in non-GM maize, which were distinguished using specific primers, matched the events in the putative sources of transgenic pollen. Percentages of transgenic seedlings in the offspring of the non-GM crops were estimated as 0.56%, 0.83% and 0.13% for three sampling sites with distances of respectively 40, 100 and 330 m from the GM crops. This is a first indication that adventitious presence of transgenes in non-GM maize crops will occur in Uruguay if isolation by distance and/or time is not provided. These findings contribute to the evaluation of the applicability of the "regulated coexistence policy" in Uruguay.

Transgene introgression in crop relatives: molecular evidence and mitigation strategies

Incorporation of crop genes into wild and weedy relative populations (i.e. introgression) has long been of interest to ecologists and weed scientists. Potential negative outcomes that result from crop transgene introgression (e.g. extinction of native wild relative populations; invasive spread by wild or weedy hosts) have not been documented, and few examples of transgene introgression exist. However, molecular evidence of introgression from non-transgenic crops to their relatives continues to emerge, even for crops deemed low-risk candidates for transgene introgression. We posit that transgene introgression monitoring and mitigation strategies are warranted in cases in which transgenes are predicted to confer selective advantages and disadvantages to recipient hosts. The utility and consequences of such strategies are examined, and future directions provided.

A flexible quantitative methodology for the analysis of gene-flow between conventionally bred maize populations using microsatellite markers

Previous studies of gene-flow in agriculture have used a range of physical and biochemical markers, including transgenes. However, physical and biochemical markers are not available for all commercial varieties, and transgenes are difficult to use when trying to estimate gene flow in the field where the use of transgenes is often restricted. Here, we demonstrate the use of simple sequence repeat microsatellite markers (SSRs) to study gene flow in maize. Developing the first quantitative analysis of pooled SSR samples resulted in a high sampling efficiency which minimised the use of resources and greatly enhanced the possibility of hybrid detection. We were able to quantitatively distinguish hybrids in pools of ten samples from non-hybrid parental lines in all of the 24 pair-wise combinations of commercial varieties tested. The technique was used to determine gene flow in field studies, from which a simple model describing gene flow in maize was developed.

Impact of interspecific hybridization between crops and weedy relatives on the evolution of flowering time in weedy phenotypes

BACKGROUND

Like conventional crops, some GM cultivars may readily hybridize with their wild or weedy relatives. The progressive introgression of transgenes into wild or weedy populations thus appears inevitable, and we are now faced with the challenge of determining the possible evolutionary effects of these transgenes. The aim of this study was to gain insight into the impact of interspecific hybridization between transgenic plants and weedy relatives on the evolution of the weedy phenotype.

METHODOLOGY/PRINCIPAL FINDINGS

Experimental populations of weedy birdseed rape (Brassica rapa) and transgenic rapeseed (B. napus) were grown under glasshouse conditions. Hybridization opportunities with transgenic plants and phenotypic traits (including phenological, morphological and reproductive traits) were measured for each weedy individual. We show that weedy individuals that flowered later and for longer periods were more likely to receive transgenic pollen from crops and weed × crop hybrids. Because stem diameter is correlated with flowering time, plants with wider stems were also more likely to be pollinated by transgenic plants. We also show that the weedy plants with the highest probability of hybridization had the lowest fecundity.

CONCLUSION/SIGNIFICANCE

Our results suggest that weeds flowering late and for long periods are less fit because they have a higher probability of hybridizing with crops or weed × crop hybrids. This may result in counter-selection against this subset of weed phenotypes, and a shorter earlier flowering period. It is noteworthy that this potential evolution in flowering time does not depend on the presence of the transgene in the crop. Evolution in flowering time may even be counter-balanced by positive selection acting on the transgene if the latter was positively associated with maternal genes promoting late flowering and long flowering periods. Unfortunately, we could not verify this association in the present experiment.

A European perspective on maize history

Maize was domesticated at least 8700 years ago in the highlands of Mexico. Genome-wide studies have greatly contributed to shed light into the diffusion of maize through the Americas from its center of origin. Also the presence of two European introductions in southern and northern Europe is now established. Such a spread was accompanied by an extreme diversification, and adaptation to the long days and low temperatures of temperate climates has been a key step in maize evolution. Linkage mapping and association mapping have successfully led to the identification of a handful set of the genetic factors that have contributed to maize adaptation, opening the way to new discoveries. Ultimately, these alleles will contribute to sustain breeding efforts to meet the new challenges raised by the evolution of mankind.

The Anthropology of Genetically Modified Crops

By late in the twentieth century, scientists had succeeded in manipulating organisms at the genetic level, mainly by gene transfer. The major impact of this technology has been seen in the spread of genetically modified (GM) crops, which has occurred with little controversy in some areas and with fierce controversy elsewhere. GM crops raise a very wide range of questions, and I address three areas of particular interest for anthropology and its allied fields. First are the political-economic aspects of GM, which include patenting of life forms and new relationships among agriculture, industry, and the academy. Second is the wide diversity in response and resistance to the technology. Third is the much-debated question of GM crops for the developing world. This analysis is approached first by determining what controls research agendas and then by evaluating actual impacts of crops to date.

Genetic diversity in a crop metapopulation

The need to protect crop genetic resources has sparked a growing interest in the genetic diversity maintained in traditional farming systems worldwide. Although traditional seed management has been proposed as an important determinant of genetic diversity and structure in crops, no models exist that can adequately describe the genetic effects of seed management. We present a metapopulation model that accounts for several features unique to managed crop populations. Using traditional maize agriculture as an example, we develop a coalescence-based model of a crop metapopulation undergoing pollen and seed flow as well as seed replacement. In contrast to metapopulation work on natural systems, we model seed migration as episodic and originating from a single source per population rather than as a constant immigration from the entire metapopulation. We find that the correlated origin of migrants leads to surprising results, including a loss of invariance of within-deme diversity and a parabolic relationship between F(ST) and migration quantity. In contrast, the effects of migration frequency on diversity and structure are more similar to classical predictions, suggesting that seed migration in managed crop populations cannot be described by a single parameter. In addition to migration, we investigate the effects of deme size and extinction rates on genetic structure, and show that high levels of pollen migration may mask the effects of seed management on structure. Our results highlight the importance of analytically evaluating the effects of deviations from classical metapopulation models, especially in systems for which data are available to estimate specific model parameters.