Xavier Reboud

Evidence for a large-scale population structure among accessions of Arabidopsis thaliana : possible causes and consequences for the distribution of linkage disequilibrium

The existence of a large‐scale population structure was investigated in Arabidopsis thaliana by studying patterns of polymorphism in a set of 71 European accessions. We used sequence polymorphism surveyed in 10 fragments of ∼600 nucleotides and a set of nine microsatellite markers. Population structure was investigated using a model‐based inference framework. Among the accessions studied, the presence of four groups was inferred using genetic data, without using prior information on the geographical origin of the accessions. Significant genetic isolation by geographical distance was detected at the group level, together with a geographical gradient in allelic richness across groups. These results are discussed with respect to the previously proposed scenario of postglacial colonization of Europe from putative glacial refugia. Finally, the contribution of the inferred structure to linkage disequilibrium among 171 pairs of essentially unlinked markers was also investigated. Linkage disequilibrium analysis revealed that significant associations detected in the whole sample were mainly due to genetic differentiation among the inferred groups. We discuss the implication of this finding for future association studies in A. thaliana.

The Dominance of the Herbicide Resistance Cost in Several Arabidopsis thaliana Mutant Lines

Resistance evolution depends upon the balance between advantage and disadvantage (cost) conferred in treated and untreated areas. By analyzing morphological characters and simple fitness components, the cost associated with each of eight herbicide resistance alleles (acetolactate synthase, cellulose synthase, and auxin-induced target genes) was studied in the model plant Arabidopsis thaliana. The use of allele-specific PCR to discriminate between heterozygous and homozygous plants was used to provide insights into the dominance of the resistance cost, a parameter rarely described. Morphological characters appear more sensitive than fitness (seed production) because 6 vs. 4 differences between resistant and sensitive homozygous plants were detected, respectively. Dominance levels for the fitness cost ranged from recessivity (csr1-1, ixr1-2, and axr1-3) to dominance (axr2-1) to underdominance (aux1-7). Furthermore, the dominance level of the herbicide resistance trait did not predict the dominance level of the cost of resistance. The relationship of our results to theoretical predictions of dominance and the consequences of fitness cost and its dominance in resistance management are discussed.

Weeds in agricultural landscapes. A review

There is currently an increasing societal and political shift towards more sustainable agricultural systems to provide both food production and ecological biodiversity levels. This shift has recently modified scientific questioning and brought up new research challenges for agro-ecological research. This is the case in particular for weed management, where issues have so far largely focused on the conflict between weeds and crop productivity. Here, we review recent findings that have led to a changing perception on weeds in agro-ecosystems and upcoming areas in terms of weed management options. Our main findings are that weeds have numerous interactions with other organisms and, in turn, some of these interactions can have direct, either negative or positive, effects on the functioning of the agro-ecosystem. Many interactions are species-specific, and therefore assessing the role of weed communities in the agro-ecosystem would benefit from further development in the functional grouping of weed species. In terms of weed management our review shows that alternative cropping systems can deliver both good levels of crop productivity and of weed management at the field level. Weeds respond to landscape attributes and there is a need to fully assess the scope for utilizing the spatio-temporal organization of cropping systems and uncultivated habitats as a tool for minimizing weed infestations. Weeds are also submitted to biological regulation through the predation of their seeds and further research is required to assess the effect of cropping systems and landscape on levels of weed natural enemies, and therefore on the potential contribution of biological regulation in the management of weeds.

Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, Amplifluor and TaqMan, in diploid and polyploid plants

The application of high-throughput SNP genotyping is a great challenge for many research projects in the plant genetics domain. The GOOD assay for mass spectrometry, Amplifluor® and TaqMan® are three methods that rely on different principles for allele discrimination and detection, specifically, primer extension, allele-specific PCR and hybridization, respectively. First, with the goal of assessing allele frequencies by means of SNP genotyping, we compared these methods on a set of three SNPs present in the herbicide resistance genes CSR, AXR1 and IXR1 of Arabidopsis thaliana. In this comparison, we obtained the best results with TaqMan® based on PCR specificity, flexibility in primer design and success rate. We also used mass spectrometry for genotyping polyploid species. Finally, a combination of the three methods was used for medium- to high-throughput genotyping in a number of different plant species. Here, we show that all three genotyping technologies are successful in discriminating alleles in various plant species and discuss the factors that must be considered in assessing which method to use for a given application.

Low frequency transmission of a plastid-encoded trait in Setaria italica

It has been claimed that engineering traits into the chloroplast will prevent transgene transmission by pollen, precluding transgene flow from crops. A Setaria italica (foxtail or birdseed millet) with chloroplast-inherited atrazine resistance (bearing a nuclear dominant red-leaf base marker) was crossed with five male-sterile yellow- or green-leafed herbicide susceptible lines. Chloroplast-inherited resistance was consistently pollen transmitted at a 3×10−4 frequency in >780,000 hybrid offspring. The nuclear marker segregated in the F2, but resistance did not segregate, as expected. Pollen transmission of plastome traits can only be detected using both large samples and selectable genetic markers. The risk of pollen transmission at this frequency would be several orders of magnitude greater than spontaneous nuclear-genome mutation-rates. Chloroplast transformation may be an unacceptable means of preventing transgene outflow, unless stacked with additional mechanisms such as mitigating genes and/or male sterility.

A specialist-generalist classification of the arable flora and its response to changes in agricultural practices

BackgroundTheory in ecology points out the potential link between the degree of specialisation of organisms and their responses to disturbances and suggests that this could be a key element for understanding the assembly of communities. We evaluated this question for the arable weed flora as this group has scarcely been the focus of ecological studies so far and because weeds are restricted to habitats characterised by very high degrees of disturbance. As such, weeds offer a case study to ask how specialization relates to abundance and distribution of species in relation to the varying disturbance regimes occurring in arable crops.ResultsWe used data derived from an extensive national monitoring network of approximately 700 arable fields scattered across France to quantify the degree of specialisation of 152 weed species using six different ecological methods. We then explored the impact of the level of disturbance occurring in arable fields by comparing the degree of specialisation of weed communities in contrasting field situations.The classification of species as specialist or generalist was consistent between different ecological indices. When applied on a large-scale data set across France, this classification highlighted that monoculture harbour significantly more specialists than crop rotations, suggesting that crop rotation increases abundance of generalist species rather than sets of species that are each specialised to the individual crop types grown in the rotation. Applied to a diachronic dataset, the classification also shows that the proportion of specialist weed species has significantly decreased in cultivated fields over the last 30 years which suggests a biotic homogenization of agricultural landscapes.ConclusionsThis study shows that the concept of generalist/specialist species is particularly relevant to understand the effect of anthropogenic disturbances on the evolution of plant community composition and that ecological theories developed in stable environments are valid in highly disturbed environments such as agro-ecosystems. The approach developed here to classify arable weeds according to the breadth of their ecological niche is robust and applicable to a wide range of organisms. It is also sensitive to disturbance regime and we show here that recent changes in agricultural practices, i.e. increased levels of disturbance have favoured the most generalist species, hence leading to biotic homogenisation in arable landscapes.

A method to determine the mean pollen dispersal of individual plants growing within a large pollen source

Pollen dispersal has been recently focused on as a major issue in the risk assessment of transgenic crop plants. The shape of the pollen dispersal of individual plants is hard to determine since a very large number of plants must be monitored in order to track rare longdistance dispersal events. Conversely, studies using large plots as a pollen source provide a pollen distribution that depends on the shape of the source plot. We report here on a method based on the use of Fourier transforms by which the pollen dispersal of a single, average individual can be obtained from data using large plots as pollen sources, thus allowing the estimation of the probability of long-distance dispersal for single plants. This method is subsequently implemented on simulated data to test its susceptibility to random noise and edge effects. Its conditions of application and value for use in ecological studies, in particular risk assessment of the deliberate release of transgenic plants, are discussed.

Broomrape Weeds. Underground Mechanisms of Parasitism and Associated Strategies for their Control: A Review

Broomrapes are plant-parasitic weeds which constitute one of the most difficult-to-control of all biotic constraints that affect crops in Mediterranean, central and eastern Europe, and Asia. Due to their physical and metabolic overlap with the crop, their underground parasitism, their achlorophyllous nature, and hardly destructible seed bank, broomrape weeds are usually not controlled by management strategies designed for non-parasitic weeds. Instead, broomrapes are in current state of intensification and spread due to lack of broomrape-specific control programs, unconscious introduction to new areas and may be decline of herbicide use and global warming to a lesser degree. We reviewed relevant facts about the biology and physiology of broomrape weeds and the major feasible control strategies. The points of vulnerability of some underground events, key for their parasitism such as crop-induced germination or haustorial development are reviewed as inhibition targets of the broomrape-crop association. Among the reviewed strategies are those aimed (1) to reduce broomrape seed bank viability, such as fumigation, herbigation, solarization and use of broomrape-specific pathogens; (2) diversion strategies to reduce the broomrape ability to timely detect the host such as those based on promotion of suicidal germination, on introduction of allelochemical interference, or on down-regulating host exudation of germination-inducing factors; (3) strategies to inhibit the capacity of the broomrape seedling to penetrate the crop and connect with the vascular system, such as biotic or abiotic inhibition of broomrape radicle growth and crop resistance to broomrape penetration either natural, genetically engineered or elicited by biotic- or abiotic-resistance-inducing agents; and (4) strategies acting once broomrape seedling has bridged its vascular system with that of the host, aimed to impede or to endure the parasitic sink such as those based on the delivery of herbicides via haustoria, use of resistant or tolerant varieties and implementation of cultural practices improving crop competitiveness.

MULTIGENERATIONAL VERSUS SINGLE GENERATION STUDIES TO ESTIMATE HERBICIDE RESISTANCE FITNESS COST IN ARABIDOPSIS THALIANA

Abstract The evolution of resistance in response to pesticide selection is expected to be delayed if fitness costs are associated with resistance genes. The estimate of fitness costs usually involves comparing major growth traits of resistant versus susceptible individuals in the absence of pesticide. Ideally, a measure of changes in resistance allele frequency over several generations would allow the best estimate of the overall fitness cost of a resistance gene. In greenhouse conditions, we monitored the dynamics of the evolution of the frequencies of six herbicide‐resistant mutations (acetolactate synthase, cellulose synthase, and auxin‐induced target genes) in the model species Arabidopsis thaliana in a multigenerational study covering five to seven nonoverlapping generations. The microevolutionary dynamics in experimental populations indicated a mean fitness cost of 38%, 73%, and 94% for the ixr1‐2, axr1‐3, and axr2‐1 resistances, respectively; no fitness cost for the csr1‐1, and ixr2‐1 resistances; and a transient advantage for the aux1‐7 resistance. The result for the csr1‐1 resistance contrasts with a cost of 37% based on total seed number in a previous study, demonstrating that single generation studies could have limitation for detecting cost. A positive frequency dependence for the fitness cost was also detected for the ixr1‐2 resistance. The results are discussed in relation are discussed in relation to the polymorphism at resistance loci.

Farmers' fears and agro-economic evaluation of sown grass strips in France

Since 2005, French farmers must set up sown grass strips along rivers in order to decrease pesticide levels and soil erosion. Farmers have thus parcelled out their fields, set aside 3% of their farm size and managed grass without herbicide. Consequently, this environmental policy may cause farmers’ fears due to economic losses and weed infestations of their field margins. Here, we studied farmers’ perception of sown grass strips. First, we interviewed 29 farmers in two French regions. Second, we evaluated the economic loss of gross margin when replacing crop by grass. Third, we evaluated the weed risk using flora surveys in sown grass strips. Our results showed that two thirds of interviewed farmers thought that sown grass strips affected their farm revenue and represented a weed risk. Concerning economy, we found that farmers loose from 358 to 853€/ha the year of installation and from 126 to 641€/ha next years. This economic loss is mainly due to the loss of crop production, with a minor impact of grass management cost. At the farm level, 3% of sown grass strips decreased the farm revenue by 7%. Concerning the weed risk, the farmers’ perception was linked with the presence of some competitive perennial weeds, e.g. Cirsium arvense, and wind-dispersing weeds, e.g. Asteraceae. Sown grass strips with high weed species richness of 26 species on average, or with dominance of non-sown species (16.7% of sown grass strips) did not affect the farmers’ perception. In our study, the economic loss was weak and acceptable at the farm level.