Environmental biosafety and transgenic potato in a centre of diversity for this crop

Discovering trends and hotspots of biosafety and biosecurity research via machine learning

Coronavirus disease 2019 (COVID-19) has infected hundreds of millions of people and killed millions of them. As an RNA virus, COVID-19 is more susceptible to variation than other viruses. Many problems involved in this epidemic have made biosafety and biosecurity (hereafter collectively referred to as ‘biosafety’) a popular and timely topic globally. Biosafety research covers a broad and diverse range of topics, and it is important to quickly identify hotspots and trends in biosafety research through big data analysis. However, the data-driven literature on biosafety research discovery is quite scant. We developed a novel topic model based on latent Dirichlet allocation, affinity propagation clustering and the PageRank algorithm (LDAPR) to extract knowledge from biosafety research publications from 2011 to 2020. Then, we conducted hotspot and trend analysis with LDAPR and carried out further studies, including annual hot topic extraction, a 10-year keyword evolution trend analysis, topic map construction, hot region discovery and fine-grained correlation analysis of interdisciplinary research topic trends. These analyses revealed valuable information that can guide epidemic prevention work: (1) the research enthusiasm over a certain infectious disease not only is related to its epidemic characteristics but also is affected by the progress of research on other diseases, and (2) infectious diseases are not only strongly related to their corresponding microorganisms but also potentially related to other specific microorganisms. The detailed experimental results and our code are available at https://github.com/KEAML-JLU/Biosafety-analysis.

Next-generation sequencing of the soil nematode community enables the sustainability of banana plantations to be monitored

Uganda faces a considerable challenge to match its food production to an annual population growth rate of 3%. Cooking bananas are the country's most produced staple crop but the annual national harvest is not increasing. The crop grows on infertile soils that are normally fertilised organically and often susceptible to erosion. Soil nematodes are well-established as bioindicators of soil quality that can support environmental monitoring and assessment of the sustainability of agricultural systems. These invertebrates are a highly ranked indicator of biodiversity with molecular approaches available. Consequently, we have applied next-generation DNA sequencing of soil nematodes to evaluate soil quality of Ugandan banana plantations. The aim is to establish a method for constructing an aspect of an environmental biosafety dossier with the future aim of assessing the impact of transgenic crops and improving current cropping systems. The soil samples did not differ significantly in any of the measured soil chemistry factors, soil texture or percentage of organic matter. Thirty taxons of soil nematodes other than the plant parasites were recovered from soil supporting nine banana plantations plus three each from coffee and banana-coffee interplants from East and West Uganda. Cluster analysis correctly allocated each plantation to the crop/intercrop being grown when based on the abundance of taxa rather than taxa presence or absence. This indicates that the host has considerable effects on the abundance of specific nematode species within the soil. Overall, nematodes were more abundant in soil from coffee plantations than from banana-coffee interplants with the lowest values being from fields supporting just banana. Only the basal and trophic diversity indices and the percentage of nematodes that are rapid colonisers varied between the three plantation types. The soil of all fifteen plantations can be classified as having a mature soil web condition with low physical disturbance, limited chemical stressors, moderately high nutrient enrichment and balanced decomposition channels.

The origin and widespread occurrence of Sli-based self-compatibility in potato

Self-compatible (SC) diploid potatoes allow innovative potato breeding. Therefore, the Sli gene, originally described in S. chacoense, has received much attention. In elite S. tuberosum diploids, spontaneous berry set is occasionally observed. We aimed to map SC from S. tuberosum origin. Two full-sib mapping populations from non-inbred diploids were used. Bulks were composed based on both pollen tube growth and berry set upon selfing. After DNA sequencing of the parents and bulks, we generated k-mer tables. Set algebra and depth filtering were used to identify bulk-specific k-mers. Coupling and repulsion phase k-mers, transmitted from the SC parent, mapped in both populations to the distal end of chromosome 12. Intersection between the k-mers from both populations, in coupling phase with SC, exposed a shared haplotype of approximately 1.5 Mb. Subsequently, we screened read archives of potatoes and wild relatives for k-mers specific to this haplotype. The well-known SC clones US-W4 and RH89-039-16, but surprisingly, also S. chacoense clone M6 were positives. Hence, the S. tuberosum source of SC seems identical to Sli. Furthermore, the candidate region drastically reduced to 333 kb. Haplotype-specific KASP markers were designed and validated on a panel of diploid clones including another renown SC dihaploid G254. Interestingly, k-mers specific to the SC haplotype were common in tetraploid varieties. Pedigree information suggests that the SC haplotype was introduced into tetraploid varieties via the founder "Rough Purple Chili". We show that Sli is surprisingly widespread and indigenous to the cultivated gene pool of potato.

Transgene Biocontainment Strategies for Molecular Farming

Advances in plant synthetic biology promise to introduce novel agricultural products in the near future. 'Molecular farms' will include crops engineered to produce medications, vaccines, biofuels, industrial enzymes, and other high value compounds. These crops have the potential to reduce costs while dramatically increasing scales of synthesis and provide new economic opportunities to farmers. Current transgenic crops may be considered safe given their long-standing use, however, some applications of molecular farming may pose risks to human health and the environment. Unwanted gene flow from engineered crops could potentially contaminate the food supply, and affect wildlife. There is also potential for unwanted gene flow into engineered crops which may alter their ability to produce compounds of interest. Here, we briefly discuss the applications of molecular farming and explore the various genetic and physical methods that can be used for transgene biocontainment. As yet, no technology can be applied to all crop species, such that a combination of approaches may be necessary. Effective biocontainment is needed to enable large scale molecular farming.

Bee Community of Commercial Potato Fields in Michigan and Bombus impatiens Visitation to Neonicotinoid-Treated Potato Plants

We conducted a bee survey in neonicotinoid-treated commercial potato fields using bowl and vane traps in the 2016 growing season. Traps were placed outside the fields, at the field edges, and 10 and 30 m into the fields. We collected 756 bees representing 58 species, with Lasioglossum spp. comprising 73% of all captured bees. We found seven Bombus spp., of which B. impatiens was the only known visitor of potato flowers in our region. The majority of the bees (68%) were collected at the field edges and in the field margins. Blue vane traps caught almost four-times as many bees and collected 30% more species compared to bowl traps. Bee communities did not differ across trap locations but they were different among trap types. We tested B. impatiens visitation to neonicotinoid treated and untreated potato flowers in field enclosures. The amount of time bees spent at flowers and the duration of visits were not significantly different between the two treatments. Our results demonstrate that a diverse assemblage of bees is associated with an agroecosystem dominated by potatoes despite the apparent lack of pollinator resources provided by the crop. We found no difference in B. impatiens foraging behavior on neonicotinoid-treated compared to untreated 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.

Potato genetics, genomics, and applications

Potato has a variety of reproductive uniquenesses besides its clonal propagation by tubers. These traits are controlled by a different kind of genetic control. The reproductive information has been applied to enable interspecific hybridization to enhance valuable traits, such as disease and pest resistances, from the tuber-bearing Solanum gene pool. While progress has been made in potato breeding, many resources have been invested due to the requirements of large populations and long time frame. This is not only due to the general pitfalls in plant breeding, but also due to the complexity of polyploid genetics. Tetraploid genetics is the most prominent aspect associated with potato breeding. Genetic maps and markers have contributed to potato breeding, and genome information further elucidates questions in potato evolution and supports comprehensive potato breeding. Challenges yet remain on recognizing intellectual property rights to breeding and germplasm, and also on regulatory aspects to incorporate modern biotechnology for increasing genetic variation in potato breeding.

Ex-post analysis of landraces sympatric to a commercial variety in the center of origin of the potato failed to detect gene flow

The possible introduction of genetically modified potato in the Andean region raises concerns about the unintentional introduction of transgenes into the native potato germplasm because it is perceived to convey negative impacts on biodiversity. We investigated this question by an ex-post analysis of existing landraces resulting from natural hybridization between an unknown landrace and the fertile commercial variety ‘Yungay’. This variety can be regarded as exotic because it was bred in part from the southern Chilean germplasm of Solanum tuberosum Group Chilotanum. We sampled the landrace germplasm of 1,771 leaf samples comprising more than 400 different landraces from three regions where ‘Yungay’ and landraces have coexisted for 15–25 years in the Peruvian Andes. Simple sequence repeat (SSR) markers were used to identify putative hybrids based on allele sharing with those of ‘Yungay’. The exclusion procedure was iterative, starting with the SSR markers with highest discriminating capacity based on allele frequency of the variety ‘Yungay’ in our large database of 688 landraces by 24 SSR makers. With only 12 of the 24 SSR markers assayed, all of the samples could be rejected as possible hybrids with ‘Yungay’ as a parent. This result demonstrates that the unintentional introduction of a transgene, not under farmers’ selection, from a widely grown transgenic variety over a long period of time is unlikely to happen at a detectable scale. Our finding reinforces the prominent role of farmers in the selection and maintenance of landraces which, unlike hybrids, have specific characteristics that farmers appreciate.

Life histories and fitness of two tuber moth species feeding on native Andean potatoes

In the inter-Andean valleys of central Perú, two species of tuber moth, Phthorimaea operculella (Zeller) and Symmetrischema tangolias (Gyen), often occur simultaneously in stored potatoes. Traditional farming communities in the region produce a variety of native potatoes for local consumption. These include Solanum tuberosum subsp. andigena, the presumed predecessor of commercial potatoes, S. tuberosum subsp. tuberosum. In this study, we examined resistance against P. operculella in ten native Peruvian potato varieties (Casa blanca, Chispiadita, Madre de vaca, Mamaco negro, Misha, Chorisa, Mamaco rosado, Occa papa, Vacapa jayllo, and Yana tornasol). We also compared resistance in the first five of these varieties against S. tangolias. Varieties with pigmented periderms showed moderate resistance (30-40% against P. operculella in Mamaco negro, Mamaco rosado, and Yana tornasol and 55% against S. tangolias in Mamaco negro). All the other varieties were susceptible to both moth species. Small tubers tended to be the most resistant to the attack by both moths; however, this was not related to the availability of food for developing larvae, since pupal weight and development time were unaffected by the size of tubers. Similar responses by the two moths to native potatoes indicate that tuber resistance could be used to control the complex of tuber moths that damage potatoes in the Andes. We suggest that native potatoes, which are often easily introgressed with commercial potatoes, are a potential source of resistance against tuber moths.

Transgenic potatoes for potato cyst nematode control can replace pesticide use without impact on soil quality

Current and future global crop yields depend upon soil quality to which soil organisms make an important contribution. The European Union seeks to protect European soils and their biodiversity for instance by amending its Directive on pesticide usage. This poses a challenge for control of Globodera pallida (a potato cyst nematode) for which both natural resistance and rotational control are inadequate. One approach of high potential is transgenically based resistance. This work demonstrates the potential in the field of a new transgenic trait for control of G. pallida that suppresses root invasion. It also investigates its impact and that of a second transgenic trait on the non-target soil nematode community. We establish that a peptide that disrupts chemoreception of nematodes without a lethal effect provides resistance to G. pallida in both a containment and a field trial when precisely targeted under control of a root tip-specific promoter. In addition we combine DNA barcoding and quantitative PCR to recognise nematode genera from soil samples without microscope-based observation and use the method for nematode faunal analysis. This approach establishes that the peptide and a cysteine proteinase inhibitor that offer distinct bases for transgenic plant resistance to G. pallida do so without impact on the non-target nematode soil community.

Informal "seed" systems and the management of gene flow in traditional agroecosystems: the case of cassava in Cauca, Colombia

Our ability to manage gene flow within traditional agroecosystems and their repercussions requires understanding the biology of crops, including farming practices' role in crop ecology. That these practices' effects on crop population genetics have not been quantified bespeaks lack of an appropriate analytical framework. We use a model that construes seed-management practices as part of a crop's demography to describe the dynamics of cassava (Manihot esculenta Crantz) in Cauca, Colombia. We quantify several management practices for cassava—the first estimates of their kind for a vegetatively-propagated crop—describe their demographic repercussions, and compare them to those of maize, a sexually-reproduced grain crop. We discuss the implications for gene flow, the conservation of cassava diversity, and the biosafety of vegetatively-propagated crops in centers of diversity. Cassava populations are surprisingly open and dynamic: farmers exchange germplasm across localities, particularly improved varieties, and distribute it among neighbors at extremely high rates vis-à-vis maize. This implies that a large portion of cassava populations consists of non-local germplasm, often grown in mixed stands with local varieties. Gene flow from this germplasm into local seed banks and gene pools via pollen has been documented, but its extent remains uncertain. In sum, cassava's biology and vegetative propagation might facilitate pre-release confinement of genetically-modified varieties, as expected, but simultaneously contribute to their diffusion across traditional agroecosystems if released. Genetically-modified cassava is unlikely to displace landraces or compromise their diversity; but rapid diffusion of improved germplasm and subsequent incorporation into cassava landraces, seed banks or wild populations could obstruct the tracking and eradication of deleterious transgenes. Attempts to regulate traditional farming practices to reduce the risks could compromise cassava populations' adaptive potential and ultimately prove ineffectual.

What can we learn from tobacco and other Solanaceae about horizontal DNA transfer?

In eukaryotic organisms, horizontal gene transfer (HGT) is regarded as an important though infrequent source of reticulate evolution. Many confirmed instances of natural HGT involving multicellular eukaryotes come from flowering plants. This review intends to provide a synthesis of present knowledge regarding HGT in higher plants, with an emphasis on tobacco and other species in the Solanaceae family because there are numerous detailed reports concerning natural HGT events, involving various donors, in this family. Moreover, in-depth experimental studies using transgenic tobacco are of great importance for understanding this process. Valuable insights are offered concerning the mechanisms of HGT, the adaptive role and regulation of natural transgenes, and new routes for gene trafficking. With an increasing amount of data on HGT, a synthetic view is beginning to emerge.

Greenhouse and field cultivations of antigen-expressing potatoes focusing on the variability in plant constituents and antigen expression

The production of plant-derived pharmaceuticals essentially requires stable concentrations of plant constituents, especially recombinant proteins; nonetheless, soil and seasonal variations might drastically interfere with this stability. In addition, variability might depend on the plant organ used for production. Therefore, we investigated the variability in plant constituents and antigen expression in potato plants under greenhouse and field growth conditions and in leaves compared to tubers. Using potatoes expressing VP60, the only structural capsid protein of the rabbit haemorrhagic disease virus (RHDV), CTB, the non-toxic B subunit (CTB) of the cholera toxin (CTA-CTB(5)) and the marker protein NPTII (neomycinphosphotransferase) as a model, we compare greenhouse and field production of potato-derived antigens. The influence of the production organ turned out to be transgene specific. In general, yield, plant quality and transgene expression levels in the field were higher than or similar to those observed in the greenhouse. The variation (CV) of major plant constituents and the amount of transgene-encoded protein was not influenced by the higher variation of soil properties observed in the field. Amazingly, for specific events, the variability in the model protein concentrations was often lower under field than under greenhouse conditions. The changes in gene expression under environmental stress conditions in the field observed in another event do not reduce the positive influence on variability since events like these should excluded from production. Hence, it can be concluded that for specific applications, field production of transgenic plants producing pharmaceuticals is superior to greenhouse production, even concerning the stability of transgene expression over different years. On the basis of our results, we expect equal or even higher expression levels with lower variability of recombinant pharmaceuticals in the field compared to greenhouse production combined with approximately 10 times higher tuber yield in the field.

The evolutionary ecology of clonally propagated domesticated plants

While seed-propagated crops have contributed many evolutionary insights, evolutionary biologists have often neglected clonally propagated crops. We argue that widespread notions about their evolution under domestication are oversimplified, and that they offer rich material for evolutionary studies. The diversity of their wild ancestors, the diverse ecologies of the crop populations themselves, and the intricate mix of selection pressures, acting not only on the parts harvested but also on the parts used by humans to make clonal propagules, result in complex and diverse evolutionary trajectories under domestication. We examine why farmers propagate some plants clonally, and discuss the evolutionary dynamics of sexual reproduction in clonal crops. We explore how their mixed clonal/sexual reproductive systems function, based on the sole example studied in detail, cassava (Manihot esculenta). Biotechnology is now expanding the number of clonal crops, continuing the 10 000-yr-old trend to increase crop yields by propagating elite genotypes. In an era of rapid global change, it is more important than ever to understand how the adaptive potential of clonal crops can be maintained. A key component of strategies for preserving this adaptive potential is the maintenance of mixed clonal/sexual systems, which can be achieved by encouraging and valuing farmer knowledge about the sexual reproductive biology of their clonal crops.

Origin and genetic diversity of Western European populations of the potato cyst nematode (Globodera pallida) inferred from mitochondrial sequences and microsatellite loci

Native to South America, the potato cyst nematode Globodera pallida is one of the principal pests of Andean potato crops and is also an important global pest following its introduction to Europe, Africa, North America, Asia and Oceania. Building on earlier work showing a clear south to north phylogeographic pattern in Peruvian populations, we have been able to identify the origin of Western European populations with high accuracy. They are all derived from a single restricted area in the extreme south of Peru, located between the north shore of the Lake Titicaca and Cusco. Only four cytochrome b haplotypes are found in Western Europe, one of them being also found in some populations of this area of southern Peru. The allelic richness at seven microsatellite loci observed in the Western European populations, although only one-third of that observed in this part of southern Peru, is comparable to the allelic richness observed in the northern region of Peru. This result could be explained by the fact that most of the genetic variability observed at the scale of a field or even of a region is already observed at the scale of a single plant within a field. Thus, even introduction via a single infected potato plant could result in the relatively high genetic variability observed in Western Europe. This finding has important consequences for the control of this pest and the development of quarantine measures.

Will transgenic plants adversely affect the environment?

Transgenic insecticidal plants based on Bacillus thuringiensis (Bt) endotoxins, on proteinase inhibitors and on lectins, and transgenic herbicide tolerant plants are widely used in modern agriculture. The results of the studies on likelihood and non-likelihood of adverse effects of transgenic plants on the environment including: (i) effects on nontarget species; (ii) invasiveness; (iii) potential for transgenes to 'escape' into the environment by horizontal gene transfer; and (iv) adverse effects on soil biota are reviewed. In general, it seems that large-scale implementation of transgenic insecticidal and herbicide tolerant plants do not display considerable negative effects on the environments and, moreover, at least some transgenic plants can improve the corresponding environments and human health because their production considerably reduces the load of chemical insecticides and herbicides.

Nematode resistance

Plant-parasitic nematodes are major pests of both temperate and tropical agriculture. Many of the most damaging species employ an advanced parasitic strategy in which they induce redifferentiation of root cells to form specialized feeding structures able to support nematode growth and reproduction over several weeks. Current control measures, particularly in intensive agriculture systems, rely heavily on nematicides but alternative strategies are required as effective chemicals are withdrawn from use. Here, we review the different approaches that are being developed to provide resistance to a range of nematode species. Natural, R gene-based resistance is currently exploited in traditional breeding programmes and research is ongoing to characterize the molecular basis for the observed resistant phenotypes. A number of transgenic approaches hold promise, the best described being the expression of proteinase inhibitors to disrupt nematode digestion. The application of plant-delivered RNA interference (RNAi) to silence essential nematode genes has recently emerged as a potentially valuable resistance strategy.

Facilitating co-existence by tracking gene dispersal in conventional potato systems with microsatellite markers

Based on international findings, Irish co-existence guidelines for the cultivation of GM potato stipulate that an isolation distance of 20 m is required to minimize the spread of transgenic pollen in accordance with required labeling thresholds. As potato tolerant to Phytophthora infestans is the most applicable GM crop from an Irish context, we tested the efficacy of this isolation distance under Irish environmental conditions using the conventional variety Désirée as a pollen donor and the male-sterile variety British Queen as a pollen receptor. Gene flow was determined by scoring for berry presence on receptor plants and confirmed using a microsatellite marker system designed to assess paternity in F(1) seedlings. 99.1% of seedlings recovered were identified as having Désirée paternity. Whereas 19.9% (140/708) of total berries formed on receptor plants occurred at a distance of 21 m from the pollen source, only 4 of these berries bore viable true potato seed (TPS), from which 23 TPS germinated. TPS-bearing berry formation was negatively correlated with distance from the pollen source, and although overall distribution of berries and seeds was non-random across the plot, no significant correlation was evident with respect to wind direction. Microsatellite markers were also used to confirm that the foraging beetle Meligethes aeneus is a vector for the transmission of potato pollen, but a more detailed statistical analysis of this dataset was limited by inclement weather during the trial. To conclude, we recommend that a two-tiered system be established in regard to establishing isolation distances for the experimental trial and commercial cultivation of GM potato in Ireland, and that responsible crop management be adopted to minimize the establishment of TPS-derived volunteers, which we have noted will emerge through a rotation as a result of pollen-mediated gene flow.

Natural hybridization between a clonally propagated crop, cassava (Manihot esculenta Crantz) and a wild relative in French Guiana

Because domestication rarely leads to speciation, domesticated populations often hybridize with wild relatives when they occur in close proximity. Little work has focused on this question in clonally propagated crops. If selection on the capacity for sexual reproduction has been relaxed, these crops would not be expected to hybridize with their wild relatives as frequently as seed-propagated crops. Cassava is one of the most important clonally propagated plants in tropical agriculture. Gene flow between cassava and wild relatives has often been postulated, but never demonstrated in nature. We studied a population of a wild Manihot sp. in French Guiana, which was recently in contact with domesticated cassava, and characterized phenotypes (10 morphological traits) and genotypes (six microsatellite loci) of individuals in a transect parallel to the direction of hypothesized gene flow. Wild and domesticated populations were strongly differentiated at microsatellite loci. We identified many hybrids forming a continuum between these two populations, and phenotypic variation was strongly correlated with the degree of hybridization as determined by molecular markers. Analysis of linkage disequilibrium and of the diversity of hybrid pedigrees showed that hybridization has gone on for at least three generations and that no strong barrier prevents admixture of the populations. Hybrids were more heterozygous than either wild or domesticated individuals, and phenotypic comparisons suggested heterosis in vegetative traits. Our results also suggest that this situation is not uncommon, at least in French Guiana, and demonstrate the need for integrated management of wild and domesticated populations even in clonally propagated crops.

The complex network of non-cellulosic carbohydrate metabolism

Partitioning of carbon dominates intracellular fluxes in both photosynthetic and heterotrophic plant tissues, and has vast influence on both plant growth and development. Recently, much progress has been made in elucidating the structures of the biosynthetic and degradative pathways that link the major and minor pools of soluble carbohydrates to cellular polymers such as starch, heteroglycans and fructans. In most cases, the regulatory properties of these pathways have been elucidated and the enzymes involved have been investigated using reverse genetics approaches. Although many of the results from these approaches were merely confirmatory, several of them were highly unexpected. The challenge ahead is to achieve better understanding of metabolic regulation at the network level in order to develop more rational strategies for metabolic engineering.

Assessing environmental risks of transgenic plants

By the end of the 1980s, a broad consensus had developed that there were potential environmental risks of transgenic plants requiring assessment and that this assessment must be done on a case-by-case basis, taking into account the transgene, recipient organism, intended environment of release, and the frequency and scale of the intended introduction. Since 1990, there have been gradual but substantial changes in the environmental risk assessment process. In this review, we focus on changes in the assessment of risks associated with non-target species and biodiversity, gene flow, and the evolution of resistance. Non-target risk assessment now focuses on risks of transgenic plants to the intended local environment of release. Measurements of gene flow indicate that it occurs at higher rates than believed in the early 1990s, mathematical theory is beginning to clarify expectations of risks associated with gene flow, and management methods are being developed to reduce gene flow and possibly mitigate its effects. Insect pest resistance risks are now managed using a high-dose/refuge or a refuge-only strategy, and the present research focuses on monitoring for resistance and encouraging compliance to requirements. We synthesize previous models for tiering risk assessment and propose a general model for tiering. Future transgenic crops are likely to pose greater challenges for risk assessment, and meeting these challenges will be crucial in developing a scientifically coherent risk assessment framework. Scientific understanding of the factors affecting environmental risk is still nascent, and environmental scientists need to help improve environmental risk assessment.

Origin and evolution of Andigena potatoes revealed by chloroplast and nuclear DNA markers

Andigena potatoes (Solanum tuberosum L. subsp. andigena Hawkes) (2n = 4x = 48) are important, native-farmer-selected cultivars in the Andes, which form a primary gene pool for improving a worldwide grown potato (S. tuberosum subsp. tuberosum). To elucidate the origin of Andigena, 196 Andigena accessions were compared with 301 accessions of 33 closely related cultivated and wild species using several types of chloroplast DNA (ctDNA) markers and nuclear DNA (nDNA) restriction fragment length polymorphism (RFLP) markers. Fourteen ctDNA types (haplotypes) and 115 RFLP bands were detected in Andigena, of which the main haplotypes and frequent RFLP bands were mostly shared with a cultivated diploid species, S. stenotomum Juz. et Buk. Principal component analysis of nDNA polymorphisms revealed a progressive and continuous variation from Peruvian wild species with C-type ctDNA to a group of wild species having S-type ctDNA in its variation range (S. bukasovii, S. canasense, S. candolleanum, and S. multidissectum), to cultivated diploid potatoes (S. phureja and S. stenotomum), and to cultivated tetraploid potatoes (Andigena and Chilean S. tuberosum subsp. tuberosum). These results suggest that the initial Andigena population arose with multiple origins exclusively from S. stenotomum. The overall evolutionary process toward the present-day Andigena was discussed.

A northward colonisation of the Andes by the potato cyst nematode during geological times suggests multiple host-shifts from wild to cultivated potatoes

The cyst nematode Globodera pallida is a major pest of potato in South America where this specialist parasite is native. To investigate its phylogeography, we have genotyped individuals from 42 Peruvian populations using mitochondrial and nuclear molecular markers. A clear south-to-north phylogeographical pattern was revealed with five well-supported clades. The clade containing the southern populations is genetically more diverse and forms the most basal branch. The large divergence among cytochrome b haplotypes suggests that they diverged before human domestication of potato. As the nematodes studied have been sampled on cultivated potato, multiple host-shifts from wild to cultivated potatoes must have occurred independently in each clade. We hypothesise that this south-to-north pattern took place during the uplift of the Andes beginning 20 My ago and following the same direction. To our knowledge, this is the first study of a plant parasite sampled on cultivated plants revealing an ancient phylogeographical pattern.

An in-built proteinase inhibitor system for the protection of recombinant proteins recovered from transgenic plants

Proteolytic degradation represents a significant barrier to the efficient production of several recombinant proteins in plants, both in vivo during their expression and in vitro during their recovery from source tissues. Here, we describe a strategy to protect recombinant proteins during the recovery process, based on the coexpression of a heterologous proteinase inhibitor acting as a 'mouse trap' against the host proteases during extraction. After confirming the importance of trypsin- and chymotrypsin-like activities in crude protein extracts of potato (Solanum tuberosum L.) leaves, transgenic lines of potato expressing either tomato cathepsin D inhibitor (CDI) or bovine aprotinin, both active against trypsin and chymotrypsin, were generated by Agrobacterium tumefaciens-mediated genetic transformation. Leaf crude protein extracts from CDI-expressing lines, showing decreased levels of cathepsin D-like and ribulose 1,5-bisphosphate carboxylase/oxygenase hydrolysing activities in vitro, conducted decreased turnover rates of the selection marker protein neomycin phosphotransferase II (NPTII) relative to the turnover rates measured for transgenic lines expressing only the marker protein. A similar stabilizing effect on NPTII was observed in leaf protein extracts from plant lines coexpressing bovine aprotinin, confirming the ability of ectopically expressed broad-spectrum serine proteinase inhibitors to reproduce the protein-stabilizing effect of low-molecular-weight proteinase inhibitors generally added to protein extraction media.

Potential adoption and management of insect-resistant potato in Peru, and implications for genetically engineered potato

This paper analyzes some important issues surrounding possible deployment of genetically engineered (GE) insect-resistant potato in Peru, based on a large farmer survey held in Peru in 2003. We found that the formal seed system plays a limited role compared with the informal seed system, especially for smallholder farmers. Although 97% of smallholder farmers would buy seed of an insect-resistant variety, a majority would buy it only once every 2 to 4 years. Survey data show that farmers would be willing to pay a premium of 50% on seed cost for insect resistant varieties. Paying price premiums of 25% to 50%, farmers would still increase their net income, assuming insect resistance is high and pesticide use will be strongly reduced. Of all farmers, 55% indicated preference for insect-resistant potato in varieties other than their current varieties. The survey indicates that smallholder farmers are interested to experiment with new varieties and have a positive perception of improved varieties. Based on these findings, and considering the difficulties implementing existing biosafety regulatory systems such as those in place in the U.S. and E.U., we propose to develop a variety-based segregation system to separate GE from conventionally bred potatoes. In such a system, which would embrace the spread of GE potatoes through informal seed systems, only a limited number of sterile varieties would be introduced that are easily distinguishable from conventional varieties.