J Allainguillaume

University of the West of England, Bristol, Bristol, England, United Kingdom

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Publications (32)116.14 Total impact

  • Andy Wetten, Colin Campbell, Joël Allainguillaume
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    ABSTRACT: Mealybugs (Hemiptera: Coccoidea: Pseudococcidae) are key vectors of badnaviruses, including Cacao Swollen Shoot Virus (CSSV) the most damaging virus affecting cacao (Theobroma cacao L.). The effectiveness of mealybugs as virus vectors is species dependent and it is therefore vital that CSSV resistance breeding programmes in cacao incorporate accurate mealybug identification. In this work the efficacy of a CO1-based DNA barcoding approach to species identification was evaluated by screening a range of mealybugs collected from cacao in seven countries. Morphologically similar adult females were characterised by scanning electron microscopy and then, following DNA extraction, were screened with CO1 barcoding markers. A high degree of CO1 sequence homology was observed for all 11 individual haplotypes including those accessions from distinct geographical regions. This has allowed for the design of a High Resolution Melt (HRM) assay capable of rapid identification of the commonly encountered mealybug pests of cacao. HRM Analysis (HRMA) readily differentiated between mealybug pests of cacao that can not necessarily be identified by conventional morphological analysis. This new approach, therefore, has potential to facilitate breeding for resistance to CSSV and other mealybug transmitted diseases. This article is protected by copyright. All rights reserved.
    Pest Management Science 04/2015; DOI:10.1002/ps.4017 · 2.74 Impact Factor
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    ABSTRACT: Paternal biocontainment methods (PBMs) act by preventing pollen-mediated transgene flow. They are compromised by transgene escape via the crop-maternal line. We therefore assess the efficacy of PBMs for transgenic rapeseed (Brassica napus) biocontainment across the United Kingdom by estimating crop-maternal hybridization with its two progenitor species.We used remote sensing, field surveys, agricultural statistics, and meta-analysis to determine the extent of sympatry between the crop and populations of riparian and weedy B. rapa and B. oleracea. We then estimated the incidence of crop-maternal hybridization across all settings to predict the efficacy of PBMs.Evidence of crop chloroplast capture by the progenitors was expanded to a national scale, revealing that crop-maternal gene flow occurs at widely variable rates and is dependent on both the recipient and setting.We use these data to explore the value that this kind of biocontainment can bring to genetic modification (GM) risk management in terms of reducing the impact that hybrids have on the environment rather than preventing or reducing hybrid abundance per se.
    New Phytologist 11/2014; 205(3). DOI:10.1111/nph.13131 · 6.55 Impact Factor
  • Ekemini OBOK, Andy WETTEN, Joël ALLAINGUILLAUME
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    ABSTRACT: The badnavirus Cacao swollen shoot virus (CSSV) is the causal pathogen of cacao swollen shoot virus disease (CSSVD), the most debilitating viral condition affecting Theobroma cacao. CSSVD is classified as a crowd disease and CSSV has been shown to move between T. cacao and alternative host species within the Malvaceae. Attempts to control the disease in West Africa using a cutting out approach have met with, at best, limited success while resistance breeding is hampered by fundamental gaps in our knowledge about CSSV transmission. CSSV is thought to be spread by at least 15 species of mealybugs (Hemiptera: Pseudococcidae). Reports are conflicting about the retention time of CSSV in mealybug vectors and because those studies were dependent on virus screening based on subjective interpretation of visual symptoms of the disease in T. cacao (vein clearing, shoot swelling) they are all inevitably problematic to interpret. In the present study we have monitored, via PCR, the presence of CSSV in the vector species Planococcus citri (Risso) and Pseudococcus longispinus (Targioni Tozzetti) following a virus acquisition access period (AAP) of 72 h spent on T. cacao seedlings infected with the CSSV severe strain New Juaben. Following the AAP mealybugs were transferred to a non-host food source (Solanum tuberosum) and then over a six day period individuals were sampled destructively. Sequencing of PCR products confirmed that both species can acquire the virus and that retention is highly variable between individuals. Viral retention by mealybugs is discussed with respect to the likely efficacy of the non-malvaceous barrier crops proposed for use as protective borders surrounding new T. cacao plantings.
    2nd International Hemipteran-Plant Interactions Symposium, University of California, Riverside; 06/2014
  • Ekemini Obok, Andrew Wetten, Joël Allainguillaume
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    ABSTRACT: Cacao Swollen Shoot Virus (CSSV) is a mealybug‐transmitted badnavirus widely present in West Africa that can cause significant yield reduction to or death of, cacao trees within 3‐5 years of infection. Given the paucity of information about the pathogen in Nigeria (presently the world’s fifth largest producer of cocoa), this work set out to map the distribution of the virus and its mealybug vectors in key producing areas, using molecular screening. GPS‐aided surveys for the collection of symptomatic and asymptomatic cacao leaves in 2012 and 2013 followed by PCR‐based screening for CSSV, revealed virus presence from 7°29'43.9"N in the north to 6°49'44.8"N in the south and from 5°57'47.8"E in the east to 4°01'39.1"E in the west. Scanning electron microscopy combined with CO1‐based DNA barcoding of mealybugs collected from cacao during the survey also demonstrated the widespread presence of the most efficient vectors of the virus throughout the main cocoa producing areas of the country. These findings represent the first substantial molecular evidence of the extent of CSSV presence and its vectors in Nigeria and can be utilised for more effective prevention of its spread.
    Knowing your enemy – the future of crop protection, AHDB Crop Research Conference., The Queen Elizabeth II Conference Centre, Broad Sanctuary, London, Greater London SW1P 3EE; 09/2013
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    ABSTRACT: DNA- and RNA-based polymerase chain reaction (PCR) systems were used with Cacao swollen shoot virus (CSSV) primers designed from conserved regions of the six published genomic sequences of CSSV to investigate whether the virus is transmissible from infected trees through cross-pollination to seeds and seedlings. Pollen was harvested from CSSV infected cocoa trees and used to cross-pollinate flowers of healthy cocoa trees (recipient parents) to generate enough cocoa seeds for the PCR screening. Adequate precautions were taken to avoid cross-contamination during duplicated DNA extractions and only PCR results accompanied by effective positive and negative controls were scored. Results from the PCR analyses showed that samples of cocoa pod husk, mesocarp and seed tissues (testa, cotyledon and embryo) from the cross-pollinations were PCR negative for CSSV DNA. Sequential DNA samples from new leaves of seedlings resulting from the cross-pollinated trees were consistently PCR negative for presence of portions of CSSV DNA for over 36 months after germination. A reverse transcription-PCR analysis performed on the seedlings showed negative results, indicating absence of functional CSSV RNA transcripts in the seedlings. None of the seedlings exhibited symptoms characteristic of the CSSV disease, and all infectivity tests on the seedlings were also negative. Following these results, the study concluded that although CSSV DNA was detected in pollen from CSSV infected trees, there was no evidence of pollen transmission of the virus through cross-pollination from infected cocoa parents to healthy cocoa trees.
    Plant Pathology 04/2013; 62(2). DOI:10.1111/j.1365-3059.2012.02640.x · 2.97 Impact Factor
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    Proceedings of the Royal Society B: Biological Sciences 01/2013; 280(1754):20122854. DOI:10.1098/rspb.2012.2854 · 5.29 Impact Factor
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    ABSTRACT: Major histocompatibility complex (MHC) genes encode proteins that present pathogen-derived antigens to T-cells, initiating the adaptive immune response in vertebrates. Although populations with low MHC diversity tend to be more susceptible to pathogens, some bottlenecked populations persist and even increase in numbers despite low MHC diversity. Thus, the relative importance of MHC diversity versus genome-wide variability for the long-term viability of populations after bottlenecks and/or under high inbreeding is controversial. We tested the hypothesis that genome-wide inbreeding (estimated using microsatellites) should be more critical than MHC diversity alone in determining pathogen resistance in the self-fertilizing fish Kryptolebias marmoratus by analysing MHC diversity and parasite loads in natural and laboratory populations with different degrees of inbreeding. Both MHC and neutral diversities were lost after several generations of selfing, but we also found evidence of parasite selection acting on MHC diversity and of non-random loss of alleles, suggesting a possible selective advantage of those individuals with functionally divergent MHC, in accordance with the hypothesis of divergent allele advantage. Moreover, we found that parasite loads were better explained by including MHC diversity in the model than by genome-wide (microsatellites) heterozygosity alone. Our results suggest that immune-related overdominance could be the key in maintaining variables rates of selfing and outcrossing in K. marmoratus and other mixed-mating species.
    Proceedings of the Royal Society B: Biological Sciences 10/2012; DOI:10.1098/rspb.2012.1929 · 5.29 Impact Factor
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    ABSTRACT: We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.
    PLoS ONE 06/2012; 7(6):e37945. DOI:10.1371/journal.pone.0037945 · 3.53 Impact Factor
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    ABSTRACT: Aplochiton zebra (peladila, zebra trout) is a galaxiid fish endemic to Patagonia and the Falklands Islands, where populations are threatened by salmonid introductions. Here we describe the isolation and characterization of 13 polymorphic microsatellite DNA markers that can be used for assessing the genetic variation and conservation status of this species. The variability of these markers was assessed in six rivers in Chilean Patagonia. The number of alleles ranged from 5 to 80 per locus and observed heterozygosities varied between 0.168 and 0.910. A protocol for multiplexing these markers is described.
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    ABSTRACT: This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis × Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.
    Molecular Ecology Resources 01/2011; 11(1):219-22. DOI:10.1111/j.1755-0998.2010.02944.x · 5.63 Impact Factor
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    ABSTRACT: In the current Higher Education climate, there is a pressing need to integrate research and teaching in the student learning experience. In order to create synergy between research and teaching activities, to the benefit of students and instructors, we provided students with the opportunity to participate in a high profile collaboration between two scientific institutions. We planned and developed an integrated module leading the student through all the steps necessary in a large-scale, collaborative research project. Student feedback resulting from the intervention showed impressive levels of improvement in general appreciation of the course. Students also suggested that they would have liked a longer module, despite the intensive workload they experienced. All areas explored (general knowledge, research-based evaluation criteria, group and individual work) showed improvements in student evaluation after the module. We conclude that a residential, integrated experience of scientific research, from initial data collection to presentation at a scientific conference, can produce significant positive, active learning experiences to the students. A double bonus comes from the benefits towards research, both by compilation of data and long-term collaboration opportunities.
    Bioscience Education e-Journal 12/2010; DOI:10.3108/beej.16.6
  • Elliott LJ, Mason DC, Allainguillaume J, Wilkinson MJ
    Journal of Applied Remote Sensing 01/2010; · 0.89 Impact Factor
  • G.A. Ameyaw, A.C. Wetten, J. Allainguillaume
    Proceedings of the 16th International Cocoa Research Conference, Indonesia, Grand Hyatt Hotel, Bali,, Indonesia, Grand Hyatt Hotel, Bali,; 11/2009
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    ABSTRACT: Biocontainment methods for genetically modified crops closest to commercial reality (chloroplast transformation, male sterility) would be compromised (in absolute terms) by seed-mediated gene flow leading to chloroplast capture. Even in these circumstances, however, it can be argued that biocontainment still represses transgene movement, with the efficacy depending on the relative frequency of seed- and pollen-mediated gene flow. In this study, we screened for crop-specific chloroplast markers from rapeseed (Brassica napus) amongst sympatric and allopatric populations of wild B. oleracea in natural cliff-top populations and B. rapa in riverside and weedy populations. We found only modest crop chloroplast presence in wild B. oleracea and in weedy B. rapa, but a surprisingly high incidence in sympatric (but not in allopatric) riverside B. rapa populations. Chloroplast inheritance models indicate that elevated crop chloroplast acquisition is best explained if crop cytoplasm confers selective advantage in riverside B. rapa populations. Our results therefore imply that chloroplast transformation may slow transgene recruitment in two settings, but actually accelerate transgene spread in a third. This finding suggests that the appropriateness of chloroplast transformation for biocontainment policy depends on both context and geographical location.
    New Phytologist 07/2009; 183(4):1201-11. DOI:10.1111/j.1469-8137.2009.02877.x · 6.55 Impact Factor
  • Nadia Haider, Joel Allainguillaume, Mike J Wilkinson
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    ABSTRACT: Environmental concerns over the cultivation of Genetically Modified (GM) crops largely centre on the ecological consequences following gene flow to wild relatives. One attractive solution is to deploy biocontainment measures that prevent hybridization. Chloroplast transformation is the most advanced biocontainment method but is compromised by chloroplast capture (hybridization through the maternal lineage). To date, however, there is a paucity of information on the frequency of chloroplast capture in the wild. Oilseed rape (Brassica napus, AACC) frequently hybridises with wild Brassica rapa (AA, as paternal parent) and yields B. rapa-like introgressed individuals after only two generations. In this study we used chloroplast CAPS markers that differentiate between the two species to survey wild and weedy populations of B. rapa for the capture of B. napus chloroplasts. A total of 464 B. rapa plants belonging to 14 populations growing either in close proximity to B. napus (i.e. sympatric <5 m) or else were allopatric from the crop (>1 km) were assessed for chloroplast capture using PCR (trnL-F) and CAPS (trnT-L-Xba I) markers. The screen revealed that two sympatric B. rapa populations included 53 plants that possessed the chloroplast of B. napus. In order to discount these B. rapa plants as F(1) crop-wild hybrids, we used a C-genome-specific marker and found that 45 out of 53 plants lacked the C-genome and so were at least second generation introgressants. The most plausible explanation is that these individuals represent multiple cases of chloroplast capture following introgressive hybridisation through the female germ line from the crop. The abundance of such plants in sympatric sites thereby questions whether the use of chloroplast transformation would provide a sufficient biocontainment for GM oilseed rape in the United Kingdom.
    Current Genetics 02/2009; 55(2):139-50. DOI:10.1007/s00294-009-0230-5 · 1.71 Impact Factor
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    ABSTRACT: High resolution descriptions of plant distribution have utility for many ecological applications but are especially useful for predictive modeling of gene flow from transgenic crops. Difficulty lies in the extrapolation errors that occur when limited ground survey data are scaled up to the landscape or national level. This problem is epitomized by the wide confidence limits generated in a previous attempt to describe the national abundance of riverside Brassica rapa (a wild relative of cultivated rapeseed) across the United Kingdom. Here, we assess the value of airborne remote sensing to locate B. rapa over large areas and so reduce the need for extrapolation. We describe results from flights over the river Nene in England acquired using Airborne Thematic Mapper (ATM) and Compact Airborne Spectrographic Imager (CASI) imagery, together with ground truth data. It proved possible to detect 97% of flowering B. rapa on the basis of spectral profiles. This included all stands of plants that occupied >2m square (>5 plants), which were detected using single-pixel classification. It also included very small populations (<5 flowering plants, 1-2m square) that generated mixed pixels, which were detected using spectral unmixing. The high detection accuracy for flowering B. rapa was coupled with a rather large false positive rate (43%). The latter could be reduced by using the image detections to target fieldwork to confirm species identity, or by acquiring additional remote sensing data such as laser altimetry or multitemporal imagery. BBSRC
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    A K Quainoo, A C Wetten, J Allainguillaume
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    ABSTRACT: A study was undertaken to determine whether cocoa swollen shoot virus is transmitted by seeds, to improve the robustness of quarantine procedures for international exchange and long term conservation of cocoa germplasm. PCR/capillary electrophoresis, using cocoa swollen shoot virus primers designed from the most conserved regions of the six published cocoa genome sequences, allowed the detection of cocoa swollen shoot virus in all the component parts of cocoa seeds from cocoa swollen shoot virus-infected trees. PCR/capillary electrophoresis revealed the presence of cocoa swollen shoot virus in seedlings raised from seeds obtained from cocoa swollen shoot virus-infected trees. The high frequency with which the virus was transmitted through the seedlings suggested that cocoa swollen shoot virus is transmitted by seeds. This has serious implications for cocoa germplasm conservation and distribution.
    Journal of Virological Methods 07/2008; 150(1-2):45-9. DOI:10.1016/j.jviromet.2008.03.009 · 1.88 Impact Factor
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    A K Quainoo, A C Wetten, J Allainguillaume
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    ABSTRACT: Investigations were undertaken on the use of somatic embryogenesis to generate cocoa swollen shoot virus (CSSV) disease free clonal propagules from infected trees. Polymerase chain reaction (PCR) capillary electrophoresis revealed the presence of CSSV in all the callus tissues induced from the CSSV-infected Amelonado cocoa trees (T1, T2 and T4). The virus was transmitted to primary somatic embryos induced from the infected callus tissues at the rate of 10 (19%), 18 (14%) and 16 (15%) for T1, T2 and T4, respectively. Virus free primary somatic embryos from the infected callus tissues converted into plantlets tested CSSV negative by PCR/capillary electrophoresis 2 years after weaning. Secondary somatic embryos induced from the CSSV-infected primary somatic embryos revealed the presence of viral fragments at the rate of 4 (4%) and 9 (9%) for T2 and T4, respectively. Real-time PCR revealed 23 of the 24 secondary somatic embryos contained no detectable virus. Based on these findings, it is proposed that progressive elimination of the CSSV in infected cocoa trees occurred from primary embryogenesis to secondary embryogenesis.
    Journal of Virological Methods 05/2008; 149(1):91-6. DOI:10.1016/j.jviromet.2008.01.007 · 1.88 Impact Factor
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    C J Allender, J Allainguillaume, J Lynn, G J King
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    ABSTRACT: Diversity in the chloroplast genome of 171 accessions representing the Brassica 'C' (n = 9) genome, including domesticated and wild B. oleracea and nine inter-fertile related wild species, was investigated using six chloroplast SSR (microsatellite) markers. The lack of diversity detected among 105 cultivated and wild accessions of B. oleracea contrasted starkly with that found within its wild relatives. The vast majority of B. oleracea accessions shared a single haplotype, whereas as many as six haplotypes were detected in two wild species, B. villosa Biv. and B. cretica Lam.. The SSRs proved to be highly polymorphic across haplotypes, with calculated genetic diversity values (H) of 0.23-0.87. In total, 23 different haplotypes were detected in C genome species, with an additional five haplotypes detected in B. rapa L. (A genome n = 10) and another in B. nigra L. (B genome, n = 8). The low chloroplast diversity of B. oleracea is not suggestive of multiple domestication events. The predominant B. oleracea haplotype was also common in B. incana Ten. and present in low frequencies in B. villosa, B. macrocarpa Guss, B. rupestris Raf. and B. cretica. The chloroplast SSRs reveal a wealth of diversity within wild Brassica species that will facilitate further evolutionary and phylogeographic studies of this important crop genus.
    Theoretical and Applied Genetics 03/2007; 114(4):609-18. DOI:10.1007/s00122-006-0461-5 · 3.51 Impact Factor
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    ABSTRACT: Research on the environmental risks of gene flow from genetically modified (GM) crops to wild relatives has traditionally emphasized recipients yielding most hybrids. For GM rapeseed (Brassica napus), interest has centred on the 'frequently hybridizing' Brassica rapa over relatives such as Brassica oleracea, where spontaneous hybrids are unreported in the wild. In two sites, where rapeseed and wild B. oleracea grow together, we used flow cytometry and crop-specific microsatellite markers to identify one triploid F1 hybrid, together with nine diploid and two near triploid introgressants. Given the newly discovered capacity for spontaneous introgression into B. oleracea, we then surveyed associated flora and fauna to evaluate the capacity of both recipients to harm cohabitant species with acknowledged conservational importance. Only B. oleracea occupies rich communities containing species afforded legislative protection; these include one rare micromoth species that feeds on B. oleracea and warrants further assessment. We conclude that increased attention should now focus on B. oleracea and similar species that yield few crop-hybrids, but possess scope to affect rare or endangered associates.
    Proceedings of the Royal Society B: Biological Sciences 01/2007; 273(1605):3111-5. DOI:10.1098/rspb.2006.3686 · 5.29 Impact Factor

Publication Stats

447 Citations
116.14 Total Impact Points

Institutions

  • 2012–2014
    • University of the West of England, Bristol
      • Department of Applied Sciences
      Bristol, England, United Kingdom
  • 1997–2009
    • University of Reading
      • • School of Biological Sciences
      • • Environmental Systems Science Centre (ESSC)
      Reading, England, United Kingdom