Annals of Applied Biology

Publications in this journal

• Article: The unconventional geminivirus Beet curly top Iran virus: satisfying Koch's postulates and determining vector and host range.

  SOLEIMANI R, MATIC S, TAHERI H, BEHJATNIA SAA, VECCHIATI M, IZADPANAH K, ACCOTTO G.P
  Annals of Applied Biology 12/2012;
• Article: Genetic and geographical structure in grapevines from northwestern Spain

  E. Díaz-Losada, A. Tato Salgado, A.M. Ramos-Cabrer, B. Díaz-Hernández, S. Pereira-Lorenzo
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  ABSTRACT: The grapevine germplasm bank from Estación de Viticultura e Enoloxía de Galicia contains 110 accessions collected from more than 100-year-old grapevines from northwestern Spain. We identified 60 different genotypes (among which ‘Pinot Noir’ and ‘Shyrah’ were included as references) with 32 polymorphic microsatellites (SSRs), 21 of which were unlinked SSRs and without null alleles, which were used to detect genetic structure. We found four reconstructed populations that were highly differentiated by analysis of molecular variance (18.3%): (i) western Galician group (‘Caíño Bravo’); (ii) eastern Galician group (‘Merenzao’); (iii) Castilian group (‘Garnacha’) and (iv) southern Spanish group (‘Moscatel’). The greatest genetic differentiation was found between the western Galician/eastern Galician groups and the southern Spanish/Castilian groups, with Fst > 0.13. Western and eastern Galician groups contained most of the ancient Galician cultivars (86%) and included ancestors from central Europe, such as ‘Pinot Noir’ and ‘Shyrah’ in the western Galician group and the introgressant ‘Merenzao’ (French ‘Trousseau’) in the eastern Galician group; the Castilian and southern Spain groups included traditional cultivars from central and southern Spanish and suggest a further introduction of those cultivars in northwestern plantations. Genetic structure corresponded with East-to-West geographical differentiation in the northern Iberian Peninsula, following the old path to Santiago de Compostela from France, with the southern Spanish and Castilian groups in the East (Castilian plateau and southern Spain), the eastern Galician group and the western Galician group in the West. Five new relationships were discovered: ‘Caíño Bravo’/‘Caíño Longo2’, ‘Albarín Tinto’/‘Torrontés1’, ‘Treixadura’/‘Treixadura Francesa’, ‘Moscatel’/‘Moscatel de Bago Miúdo’ and ‘Moscatel’/‘Moscatel de Hamburgo’, indicating that hybridisation and further selection by growers have been the origin of most of the genetic diversity found in northwestern Spain.
  Annals of Applied Biology 07/2012; 161:24-35.
• Article: Assessment of transgene flow in tomato and potential effects of genetically modified tomato expressing Cry3Bb1 toxins on bumblebee feeding behaviour

  Salvatore Arpaia, Rossella Battafarano, Liang-Yan Chen, Yann Devos, Grazia Maria Di Leo, Bao-Rong Lu
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  ABSTRACT: One of the concerns surrounding the commercial release of genetically modified (GM) crops is the escape of transgenes into agricultural or semi-natural habitats through vertical gene flow, as this may cause environmental or economic problems. There is also the concern that GM crops may affect pollinators and the pollination services they provide. Despite the growing commercial interest of GM tomato (Solanum lycopersicum), gene flow has been assessed only sparsely in tomato. To evaluate the likelihood of gene flow from GM tomato plants to sexually compatible plants, and to assess whether bumblebee activity is affected by GM tomato, three experiments were conducted under greenhouse conditions, using a Bt-tomato expressing the insecticidal Cry3Bb1 protein as model system: (a) artificial crosses between a GM tomato line, two wild tomato relatives (Solanum hirsutum and Solanum nigrum) and a non-GM tomato variety; (b) bumblebee-mediated crosses between GM and non-GM tomato plants and (c) visual observations of bumblebees’ feeding behaviour. No hybrids were obtained between the GM tomato line and S. hirsutum and S. nigrum. In an experimental design where non-GM receptor plants outnumbered GM plants by approximately 3:1, the bumblebee-mediated cross-fertilisation rate between GM and non-GM tomato plants was measured at 4.3 ± 5.47%. No significant differences in feeding behaviour of bumblebees foraging on GM and non-GM tomato plants were observed. Therefore, we conclude that: (a) the probability of transgene introgression between the GM tomato line used in this study and its wild relatives S. hirsutum and S. nigrum is negligible; (b) bumblebee activity can mediate cross-fertilisation between GM and non-GM tomato and (3) the Cry3Bb1-expressing tomato line tested does not adversely affect the feeding behaviour of bumblebees.
  Annals of Applied Biology 05/2012;
• Article: Ranking the value of germplasm: new oil palm (Elaeis guineensis) breeding stocks as a case study

  S. Wening, A.E. Croxford, C.S. Ford, W.T.B. Thomas, B.P. Forster, G. Okyere‐Boateng, S.P.C. Nelson, P.D.S. Caligari, M.J. Wilkinson
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  ABSTRACT: Plant breeders constantly need to introduce desirable new alleles to refresh breeding stocks. This first requires an assessment of potential new sources of material and then identification of genotypes most able to augment existing stocks. Genetic distance analysis is widely used for both purposes, although it measures both haplotype diversity and novel allele abundance. Here, we present a more tailored approach to address these problems. Using oil palm as an exemplar, simple metrics of allelic and genetic richness, graphical genotyping and multivariate analysis were deployed to determine the overall value of Ghanaian germplasm to supplement Sumatra Bioscience (SumBio) breeding material. We next compared three methods to rank individuals. The first was based on multivariate genetic distance. However, we also developed two new systems: Global Allelic Divergence (GAD), based on novel allele abundance, and Genome Scan Allelic (GSA) divergence, which additionally considers genome context. Ghanaian material exhibited increased allelic richness, higher heterozygosity and a higher proportion of private alleles than extant SumBio breeding stocks. Graphical genotyping revealed Ghanaian material as allele-rich in genomic regions that were allele-poor in SumBio breeding stocks. Multivariate analysis showed a collective distinctness and increased variability of Ghanaian plants. Ranks of individuals varied between GSA, GAD and genetic distance. The GAD and GSA ranks correlated strongly with each other but only poorly with the genetic distance-based ranks. We conclude that GSA and GAD are superior ranking systems to identify individuals most likely to introduce valuable new alleles, whilst genetic distance analysis identifies individuals likely to require least backcrossing.
  Annals of Applied Biology 01/2012; 160(2):145 - 156.
• Article: Ground beetle species (Carabidae, Coleoptera) activity and richness in relation to crop type, fertility management and crop protection in a farm management comparison trial

  Eyre, M.E, Luff, M.L, Atlihan, R. & Leifert
  Annals of Applied Biology 01/2012;
• Article: Farmland bird invertebrate food provision in arable crops

  Holland J.M, Smith B.M, Birkett T.C, Southway S
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  ABSTRACT: Invertebrates are an essential food source for most farmland birds yet their relative abundance and biomass in the most commonly grown arable crops are poorly understood. Dvac suction sampling was used to determine the abundance, biomass and community composition of those invertebrate groups considered important in the diet of farmland birds for the commonest arable crops. Approximately 40 fields were sampled at the edge and mid-field over 2 years in three different locations in England. In cereals, the fauna was primarily comprised of Araneae (10%), Coleoptera (30%) and Hemiptera (58%), whereas the oilseed rape fauna was dominated by Coleoptera (65%) and peas and potatoes by Hemiptera (89%). Beans contained a high proportion of Coleoptera (39%) and Hemiptera (49%). Aphididae were the most abundant family (20–86% of total), although in oilseed rape and beans, Chrysomelidae, Curculionidae and Nitidulidae formed ca 20% of the fauna. Aphids only formed a small proportion (7%) of the total biomass, except in peas (32%). Instead, Araneae, Carabidae, Heteroptera, Homoptera and Tipulidae formed much larger and more equal proportions. The highest abundance and biomass of invertebrates were recorded in cereals and least in potatoes. The Grey Partridge chick-food index in all crops was only a half or less of the level required to ensure that chick survival is sufficient to maintain numbers of this red-listed species. The total number of invertebrates, their biomass, diversity and the Grey Partridge chick-food index were higher at the crop edge compared to mid-field. Conservation measures are needed to help reverse the long-term declines of invertebrates on farmland, which should include developing further invertebrate-rich, agri-environment scheme options and management techniques to encourage invertebrates considered important as bird food within arable crops.
  Annals of Applied Biology 01/2012; 160(1):66-75.
• Article: Preliminary evidence of recovery from Tomato spotted wilt virus infection in Frankliniella occidentalis individuals.

  Mautino G.C, Sacco D, Ciuffo M, Turina M, Tavella L
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  ABSTRACT: In this study we analyzed the ability of individual thrips to transmit Tomato spotted wilt virus (TSWV) in a population of Frankliniella occidentalis over their lifespan as adults (about 10 days). In three experiments a total of 636 thrips were individually tested for their transmission capacity through leaf disc assays using four inoculation access periods (IAPs). Almost half of the transmitting thrips maintained the capacity to infect leaf discs in each of the four IAPs, confirming the persistent propagative nature of the transmission modality. Nevertheless, a relevant number of thrips (9.25% of transmitter thrips) was able to transmit in the early phases of their adult life (for the first two IAPs), but did not transmit the virus for the remainder of their lifetime. We compared the virus titer of these individuals at the end of the fourth IAP with that of individuals that maintained transmission ability in the four IAPs and showed a statistically significant difference. This difference could be evidence for recovery from TSWV infection in individual thrips.
  Annals of Applied Biology 01/2012; 161:266-276.
• Article: Genetic structure and preservation strategies of autochthonous vegetable crop landraces of north-western Italy

  Portis E, Baudino M, Magurno F, Lanteri S
  Annals of Applied Biology 01/2012; 160(1):76–85.
• Article: Grape phylloxera (Daktulosphaira vitifoliae) – a review of potential detection and alternative management options

  Benheim, D. Rochfort, S. Robertson, E. Potter, I. D. Powell, K. S
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  ABSTRACT: The management options for grape phylloxera, Daktulosphaira vitifoliae, a monophagous insect pest of Vitis species are reviewed. Although in a worldwide context, grape phylloxera is managed predominantly by the use of resistant rootstocks developed through conventional breeding of hybrid crosses of American Vitis species, this management aspect is largely excluded from the review so that emerging technologies in the field of detection, quarantine and alternative management are discussed. In some viticulture regions of the world, where grape phylloxera's geographic distribution is limited (e.g. Australia), the pest is managed through a combination of surveillance, detection and quarantine. Although some alternative management options for grape phylloxera exist they have received relatively limited research attention because of the relative success of resistant rootstocks. The resilience of resistant rootstocks as the primary management option could also be challenged in the future by host-plant interactions with diverse grape phylloxera clonal lineages and by potential impacts of climate change on both grapevine and grape phylloxera distribution. A range of control options exist which could be integrated into an improved management system for grape phylloxera. Priority areas for future evaluation and further development include early detection techniques, investigation into the use of biological control agents and development of an integrated approach to grapevine phylloxera management.
  Annals of Applied Biology 01/2012; 161(2):91-115.
• Article: Population structure of rice (Oryza sativa) landraces from high altitude area of Indian Himalayas

  Avinash Pandey, I.S. Bisht, K.V. bhat
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  ABSTRACT: This study examined the genetic diversity in 20 rice landrace populations from parts of traditional farming areas of the Indian Himalayas using 11 mapped simple sequence repeats (SSR) loci. Twenty-four individuals sampled from each of the 20 landraces (480 individuals), which were collected from farmers from Northwest to Northeast Himalaya, showed that all landraces showed within population variation and none were homogeneous. The number of polymorphic loci in a landrace population ranged from 5 to 11. A total of 71 alleles were recorded of which 58 were common and 13 were rare. Of the 71 alleles, 46 were common to both Northwest and Northeast regions, whereas 9 were unique to the former and 16 were unique to the latter. The mean number of alleles per locus was 6.45 and for landrace populations from Northwest and Northeast regions were 5.0 and 5.64, respectively. Population differentiation, as shown by a high FST value (0.61), was greater for Northeast populations. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram classified the populations into three major clusters: cluster I comprised seven populations from the Northwest region, cluster II comprised seven populations from the Northeast region and cluster III comprised populations from both regions. Investigating the population genetic structure can help monitor change in diversity over time and space, and also help devise a rational plan for management of crop landraces on-farm under farmer management.
  Annals of Applied Biology 01/2012; 160(1):16-24.
• Article: Egg exposure to pyriproxyfen in the tomato leaf miner Tuta absoluta: ovicidal activity or behavioural‐modulated hatching mortality?

  H.V.V. Tomé, E.M.G. Cordeiro, J.F. Rosado, R.N.C. Guedes
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  ABSTRACT: Insecticide susceptibility varies with the insect life stage and although the egg stage is sometimes perceived as the most vulnerable, it is a difficult target for insecticide application and little studied as such. Egg susceptibility to insecticides is generally considered important for insect growth regulators and insect pests of reduced mobility like leaf miners because of their placement on the host plant part targeted by the insecticidal application. The egg exposure to the juvenile hormone mimic pyriproxyfen was studied here in the tomato leaf miner Tuta absoluta (Lepidoptera: Gelechiidae), a key tomato insect pest, aiming to assess if mortality is achieved due to insecticide ovicidal activity or due to behavioural impairment of the larvae preventing egg hatching. Survival analysis of treated tomato leaves and/or eggs indicated the importance of egg exposure to pyriproxyfen leading to a significant decrease in survival with a nearly 50% reduction in survival time, which peaked at the first instar. Ovicidal activity of pyriproxyfen in the tomato leaf miner was negligible, but image recording and behaviour analysis indicated behavioural impairment of larval activity compromising hatching and leaf mining by early instar larvae leading to high mortality at this stage (ca 50%). The likely causes and management implications of such findings are discussed.
  Annals of Applied Biology 12/2011; 160(1):35 - 42.
• Article: Root colonisation of Pseudomonas aeruginosa strain UPMP3 and induction of defence‐related genes in oil palm (Elaeis guineensis)

  H. Sathyapriya, M. Sariah, A. Siti Nor Akmar, M. Wong
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  ABSTRACT: Pseudomonas aeruginosa strain UPMP3 labelled with β-glucuronidase (gusA) and green fluorescent protein (gfp) by electrotransformation yielded ca 1 × 107 transformants µg−1DNA. The data obtained from the dilution plate count showed that over 28 days both epiphytic and endophytic populations of P. aeruginosa strain UPMP3 increased from 5.76 log10 [colony forming unit (CFU) + 1] g−1 fresh weight (FW) to 8.19 log10 (CFU + 1) g−1FW and 4.10 log10 (CFU + 1) g−1FW to 6.23 (CFU + 1) g−1FW, respectively. Confocal laser scanning microscopic analysis of oil palm roots treated with gusA:gfp-tagged P. aeruginosa strain UPMP3 showed intense root colonisation over the sampling period. The root surface colonisation by P. aeruginosa strain UPMP3 was followed by a second stage, characterised by cortical infection, and a third stage, which involves xylem ingression. The colonisation of oil palm roots by the gusA:gfp-tagged strain was concentrated on root areas potentially rich in nutrients such as the elongation zones, ridges between epidermal cells and points of secondary adventitious root emergence. Different expression levels of defence-related genes, namely, chitinase and β-1,3-glucanase in the strain UPMP3–host interaction recorded over 28 days, suggested the potential role of P. aeruginosa strain UPMP3 in triggering the defence mechanism in oil palm. This is the first report on root colonisation and upregulation of defence-related genes on oil palm roots by P. aeruginosa strain UPMP3 and shows the potential of this strain to be used as a biocontrol agent in oil palm.
  Annals of Applied Biology 12/2011; 160(2):137 - 144.
• Article: Tritrophic interactions among Bt maize, an insect pest and entomopathogens: effects on development and survival of western corn rootworm

  J.L. Petzold‐Maxwell, S.T. Jaronski, A.J. Gassmann
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  ABSTRACT: Agricultural systems often provide a model for testing ecological hypotheses, while ecological theory can enable more effective pest management. One of the best examples of this is the interaction between host-plant resistance and natural enemies. With the advent of crops that are genetically modified to produce insecticidal toxins from the bacterium Bacillus thuringiensis (Bt), a new form of host-plant resistance has been introduced to agroecosystems. How Bt crops interact with natural enemies, especially insect pathogens in below-ground systems, is not well understood, but provides a unique opportunity to study below-ground tritrophic interactions. In this study, we used two species of entomopathogenic fungi and three species of entomopathogenic nematodes to determine how this community of soil-borne natural enemies might interact with Bt maize (event 59122, expressing the insecticidal protein Cry34/35Ab1) to affect survival and development of western corn rootworm (Diabrotica virgifera virgifera), which is an obligate root feeder and a serious pest of maize. We ran two experiments, one in a greenhouse and one in a growth chamber. Both experiments consisted of a fully crossed design with two maize treatments (Bt maize and non-Bt maize) and two entomopathogen treatments (present or absent). The community of entomopathogens significantly increased mortality of western corn rootworm, and Bt maize increased larval developmental time and mortality. Entomopathogens and Bt maize acted in an independent and additive manner, with both factors increasing the mortality of western corn rootworm. Results from this study suggest that entomopathogens may complement host-plant resistance from Bt crops.
  Annals of Applied Biology 11/2011; 160(1):43 - 55.
• Article: Detection of multiple sequence variants of Grapevine rupestris stem pitting‐associated virus using primers targeting the polymerase domain and partial genome sequencing of a novel variant

  F. Terlizzi, C. Li, C. Ratti, W. Qiu, R. Credi, B. Meng
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  ABSTRACT: Grapevine rupestris stem pitting-associated virus (GRSPaV) is a member of the genus Foveavirus within the new family Betaflexiviridae. GRSPaV is distributed among grapevines worldwide and is implicated in the disease rupestris stem pitting (RSP) of the rugose wood complex and two other disorders. GRSPaV is composed of a wide range of sequence variants, and so far, the complete genomes of five sequence variants have been sequenced. Quick and reliable detection of different GRSPaV variants is a critical step in the elimination and control of GRSPaV. Previously, primers designed from various genomic regions have been used in RT-PCR for the detection of GRSPaV variants. The efficiency of RT-PCR varied widely depending on the spectrum of the primers that were used. In this study, we designed a pair of degenerate primers based on the consensus sequence of the genomic region encoding the highly conserved RNA-dependent RNA polymerase domain from five reference isolates of GRSPaV for which the genome sequence are available. We demonstrate that this set of primers is comparable, if not superior, to the broad-spectrum primers RSP13&14 in detecting multiple GRSPaV variants. Using these degenerate primers, we identified two new and distinct sequence variants. The 3′ terminal genomic region of one of the new variants, GRSPaV-ML, spanning the 3′ part of ORF1, through the entire open reading frames 2–4, and the 5′ region of ORF5 were sequenced. Sequence comparison demonstrates that GRSPaV-ML is distinct from each of the five reference isolates.
  Annals of Applied Biology 10/2011; 159(3):478 - 490.
• Article: Cost analysis in choosing group size when group testing for Potato virus Y in the presence of classification errors

  S.C. Liu, K.S. Chiang, C.H. Lin, W.C. Chung, S.H. Lin, T.C. Yang
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  ABSTRACT: In many areas of the world, Potato virus Y (PVY) is one of the most economically important disease problems in seed potatoes. In Taiwan, generation 2 (G2) class certified seed potatoes are required by law to be free of detectable levels of PVY. To meet this standard, it is necessary to perform accurate tests at a reasonable cost. We used a two-stage testing design involving group testing which was performed in Taiwan's Seed Improvement and Propagation Station to identify plants infected with PVY. At the first stage of this two-stage testing design, plants are tested in groups. The second stage involves no retesting for negative test groups and exhaustive testing of all constituent individual samples from positive test groups. In order to minimise costs while meeting government standards, it is imperative to estimate optimal group size. However, because of limited test accuracy, classification errors for diagnostic tests are inevitable; to get a more accurate estimate, it is necessary to adjust for these errors. Therefore, this paper describes an analysis of diagnostic test data in which specimens are grouped for batched testing to offset costs. The optimal batch size is determined by various cost parameters as well as test sensitivity, specificity and disease prevalence. Here, the Bayesian method is employed to deal with uncertainty in these parameters. Moreover, we developed a computer program to determine optimal group size for PVY tests such that the expected cost is minimised even when using imperfect diagnostic tests of pooled samples. Results from this research show that, compared with error free testing, when the presence of diagnostic testing errors is taken into account, the optimal group size becomes smaller. Higher diagnostic testing costs, lower costs of false negatives or smaller prevalence can all lead to a larger optimal group size. Regarding the effects of sensitivity and specificity, optimal group size increases as sensitivity increases; however, specificity has little effect on determining optimal group size. From our simulated study, it is apparent that the Bayesian method can truly update the prior information to more closely approximate the intrinsic characteristics of the parameters of interest. We believe that the results of this study will be useful in the implementation of seed potato certification programmes, particularly those which require zero tolerance for quarantine diseases in certified tubers.
  Annals of Applied Biology 10/2011; 159(3):491 - 502.