Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Quantitative trait loci (QTL) mapping of blush skin and flowering time in a European pear (Pyrus communis) progeny of ‘Flamingo’ × ‘Abate Fetel’
    Ntladi, Solomon M. ; Human, Jan P. ; Bester, Cecilia ; Vervalle, Jessica ; Roodt-Wilding, Rouvay ; Tobutt, Kenneth R. - \ 2018
    Tree Genetics and Genomes 14 (2018)5. - ISSN 1614-2942
    Blush skin - Candidate genes - European pear - Flowering time - QTLs - SSRs

    Blush skin and flowering time are agronomic traits of interest to the Agricultural Research Council (ARC) Infruitec-Nietvoorbij pear breeding programme. The genetic control of these traits was investigated in the pear progeny derived from ‘Flamingo’ (blush cultivar) × ‘Abate Fetel’ (slightly blush) made up of 121 seedlings. Blush skin was scored phenotypically over three seasons and flowering time was scored over two seasons. A total of 160 loci from 137 simple sequence repeat (SSR) markers were scored in the progeny and used to construct parental genetic linkage maps. Quantitative trait loci (QTL) analysis revealed two QTLs for blush skin, a major QTL on linkage group (LG) 5 in ‘Flamingo’, and a major QTL on LG9 in ‘Abate Fetel’. Two SSR markers, NB101a and SAmsCO865954, were closely linked with the major QTL on LG5 in ‘Flamingo’, with alleles 139 bp and 462 bp in coupling, respectively. These markers were present in approximately 90% of the seedlings scored as good blush (class 4) based on the average data set. These two markers were used to genotype other pear accessions to validate the QTL on LG5 with the view of marker-assisted selection. Two candidate genes, MYB86 and UDP-glucosyl transferase, were associated with the QTL on LG5 and MYB21 and MYB39 were associated with the QTL on LG9. QTL analysis for flowering time revealed a major QTL located on LG9 in both parents. Marker GD142 with allele 161 bp from ‘Flamingo’ was present in approximately 88% of the seedlings that flowered earlier than either parent, based on the average data set. The QTLs and linked markers will facilitate marker-assisted selection for the improvement of these complex traits.

    In-situ observations using tagged animals
    Roquet, F. ; Boehme, L. ; Bester, M.N. ; Bornemann, H. ; Brasseur, S.M.J.M. ; Charrassin, J.B. ; Costa, D. ; Fedak, M.A. ; Guinet, C. ; Hall, A. ; Harcourt, R. ; Hindell, M.A. ; Kovacs, K.M. ; Lea, M.A. ; Lovell, P. ; Lowther, A. ; Lyderson, C. ; Mcmahon, C. ; Picard, B. ; Reverdin, G. ; Vincent, C. - \ 2017
    - 5 p.
    Marine mammals help gather information on some of the harshest environments on the planet, through the use of miniaturized ocean sensors glued on their fur. Since 2004, hundreds of diving marine animals, mainly Antarctic and Arctic seals, have been fitted with a new generation of Argos tags developed by the Sea Mammal Research Unit of the University of St Andrews in Scotland, UK. These tags investigate the at-sea ecology of these animals while simultaneously collecting valuable oceanographic data. Some of the study species travel thousands of kilometres continuously diving to great depths (up to 2100 m). The resulting data are now freely available to the global scientific community at http://www.meop.net. Despite great progress in their reliability and data accuracy, the current generation of loggers while approaching standard ARGO quality specifications have yet to match them. Yet, improvements are underway; they involve updating the technology, implementing a more systematic phase of calibration and taking benefit of the recently acquired knowledge on the dynamical response of sensors. Together these efforts are rapidly transforming animal tagging into one of the most important sources of oceanographic data in polar regions and in many coastal areas
    When diving animals help us to observe the oceans: the MEOP data portal
    Roquet, F. ; Boehme, L. ; Bester, M.N. ; Bornemann, H. ; Brasseur, S.M.J.M. ; Charrassin, J.B. ; Costa, D. ; Fedak, M.A. ; Guinet, C. ; Hall, A. - \ 2016
    Detection of molecular signatures of selection at microsatellite loci in the South African abalone (Haliotis midae) using a population genomic approach
    Rhode, Clint ; Vervalle, Jessica ; Bester-van der Merwe, Aletta E. ; Roodt-Wilding, Rouvay - \ 2013
    Marine Genomics 10 (2013). - ISSN 1874-7787 - p. 27 - 36.
    Adaptation - F-outlier - Linkage disequilibrium - Neutrality - Population genomics - Selection

    Identifying genomic regions that may be under selection is important for elucidating the genetic architecture of complex phenotypes underlying adaptation to heterogeneous environments. A population genomic approach, using a classical neutrality test and various Fst-outlier detection methods was employed to evaluate genome-wide polymorphism data in order to identify loci that may be candidates for selection amongst six populations (three cultured and three wild) of the South African abalone, Haliotis midae. Approximately 9% of the genome-wide microsatellite markers were putatively subject to directional selection, whilst 6-18% of the genome is thought to be influenced by balancing selection. Genetic diversity estimates for candidate loci under directional selection was significantly reduced in comparison to candidate neutral loci, whilst candidate balancing selection loci demonstrated significantly higher levels of genetic diversity (Kruskal-Wallis test, P<0.05). Pairwise Fst estimates based on candidate directional selection loci also demonstrated increased levels of differentiation between study populations. Various candidate loci under selection showed significant inter-chromosomal linkage disequilibrium, suggesting possible gene-networks underling adaptive phenotypes. Furthermore, several loci had significant hits to known genes when performing BLAST searches to NCBI's non-redundant databases, whilst others are known to be derived from expressed sequences even though homology to a known gene could not be established. A number of loci also demonstrated relatively high similarity to transposable elements. The association of these loci to functional and genomically active sequences could in part explain the observed signatures of selection.

    Isolation and validation of microsatellite markers from a depleted South African sciaenid species, the dusky kob (Argyrosomus japonicus), by means of the FIASCO/454 approach
    Mirimin, L. ; Ruiz Guajardo, J.C. ; Vervalle, J. ; Bester-Van der Merwe, Aletta ; Kerwath, S. ; Macey, B. ; Bloomer, P. ; Roodt-Wilding, R. - \ 2013
    Conservation Genetics Resources 5 (2013)3. - ISSN 1877-7252 - p. 841 - 844.
    454 GS-FLX - Argyrosomus spp - FIASCO - Microsatellites - Sciaenid

    The dusky kob (Argyrosomus japonicus) is a large, estuarine-dependent sciaenid fish that has been severely depleted in South African waters and that, in recent years, has received considerable attention from the local fish farming industry. Discovery and application of appropriate molecular markers is necessary to improve the understanding of wild population structure, assist the effectiveness of broodstock and breeding programmes, and ensure monitoring of potential interactions between wild and farmed fish. The present study uses a recently tested approach that combines the FIASCO enrichment protocol with 454 GS-FLX Next Generation Sequencing, to identify large numbers of microsatellite-containing sequences at a low cost and high discovery rate from the dusky kob genome. Following the FIASCO enrichment (targeting specifically tetranucleotide repeats), 2,355 potential tetranucleotide microsatellites (perfect repeat motifs including eight or more repeat units flanked by regions for primer design) were identified from 1/5th of a single 454 lane. From these sequences, a test panel of 60 potential markers was selected for validation. A total of eight (13 %) markers were successfully amplified from a test sample of wild dusky kob individuals and showed high levels of polymorphism (observed heterozygosity per locus ranging between 0.375 and 0.905). Cross-species amplification of seven of these markers was also successfully carried out in another closely related and commercially important South African sciaenid species, the silver kob (A. inodorus). The microsatellite markers developed in the present study are readily available tools suitable to address genetic variability of Argyrosomus species of southern Africa.

    A population genetic analysis of abalone domestication events in South Africa : Implications for the management of the abalone resource
    Rhode, Clint ; Hepple, Juli-Ann ; Jansen, Suzaan ; Davis, Tanja ; Vervalle, Jessica ; Bester-van der Merwe, Aletta Elizabeth ; Roodt-Wilding, Rouvay - \ 2012
    Aquaculture 356-357 (2012). - ISSN 0044-8486 - p. 235 - 242.
    Abalone - Aquaculture - Conservation - Domestication - Genetic diversity - Haliotis midae

    Abalone culture is South Africa's largest aquaculture sector in terms of revenue. Nonetheless, the industry is in its formative years and much scope remains for refinement and regulation of production practices. It is important to manage genetic diversity in terms of the particular breeding objectives pursued by respective facilities: selective breeding vs. ranching; whilst conserving the genetic integrity of wild populations remains a national imperative. The present study found no significant decrease in genetic diversity between wild and cultured populations as based on heterozygosity and allelic content of genomic- and EST-microsatellite loci. However, estimates for pairwise genotypic differentiation, F st, AMOVA and Factorial correspondence analysis suggest the genetic heterogeneity of cultured populations and their significant differentiation from the wild progenitor populations. As expected, the cultured population showed reduced effective population sizes, but relatedness remained low. It is postulated that both neutral and selective evolutionary forces are responsible for the observed patterns of genetic variability within and amongst populations. The implications of the results are discussed in terms of broad managerial objectives for the South African abalone and continued monitoring is advised.

    Growth kinetics of hydrogen sulfide oxidizing bacteria in corroded concrete from sewers
    Jensen, H.S. ; Lens, P.N.L. ; Nielsen, J.L. ; Bester, K. ; Nielsen, A.H. ; Hvitved-Jacobsen, Th. ; Vollertsen, J. - \ 2011
    Journal of Hazardous Materials 189 (2011)3. - ISSN 0304-3894 - p. 685 - 691.
    thiobacillus-thiooxidans - elemental sulfur - corrosion - pipes - oxidation - systems
    Hydrogen sulfide oxidation by microbes present on concrete surfaces of sewer pipes is a key process in sewer corrosion. The growth of aerobic sulfur oxidizing bacteria from corroded concrete surfaces was studied in a batch reactor. Samples of corrosion products, containing sulfur oxidizing bacteria, were suspended in aqueous solution at pH similar to that of corroded concrete. Hydrogen sulfide was supplied to the reactor to provide the source of reduced sulfur. The removal of hydrogen sulfide and oxygen was monitored. The utilization rates of both hydrogen sulfide and oxygen suggested exponential bacterial growth with median growth rates of 1.25 d(-1) and 1.33 d(-1) as determined from the utilization rates of hydrogen sulfide and oxygen, respectively. Elemental sulfur was found to be the immediate product of the hydrogen sulfide oxidation. When exponential growth had been achieved, the addition of hydrogen sulfide was terminated leading to elemental sulfur oxidation. The ratio of consumed sulfur to consumed oxygen suggested that sulfuric acid was the ultimate oxidation product. To the knowledge of the authors, this is the first study to determine the growth rate of bacteria involved in concrete corrosion with hydrogen sulfide as source of reduced sulfur.
    Nematoda from the terrestrial deep subsurface of South Africa
    Borgonie, G. ; García-Moyano, A. ; Litthauer, D. ; Bert, W. ; Bester, A. ; Heerden, E. van; Möller, C. ; Erasmus, M. ; Onstott, T.C. - \ 2011
    Nature 474 (2011)7349. - ISSN 0028-0836 - p. 79 - 82.
    caenorhabditis-elegans - witwatersrand basin - evolution - shield - water
    Since its discovery over two decades ago, the deep subsurface biosphere has been considered to be the realm of single-cell organisms, extending over three kilometres into the Earth’s crust and comprising a significant fraction of the global biosphere1–4. The constraints of temperature, energy, dioxygen and space seemed to preclude the possibility of more-complex, multicellular organisms from surviving at these depths. Here we report species of the phylumNematoda that have been detected in or recovered from 0.9–3.6-kilometredeep fracture water in the deep mines of South Africa but have not been detected in the mining water. These subsurfacenematodes, including a new species, Halicephalobus mephisto, tolerate high temperature, reproduce asexually and preferentially feed upon subsurface bacteria. Carbon-14 data indicate that the fracture water in which the nematodes reside is 3,000–12,000-year-old palaeometeoric water. Our data suggest that nematodes should be found in other deep hypoxic settings where temperature permits, and that theymay control themicrobial population density by grazing on fracture surface biofilm patches. Our results expand the known metazoan biosphere and demonstrate that deep ecosystems are more complex than previously accepted. The discovery of multicellular life in the deep subsurface of the Earth also has important implications for the search for subsurface life on other planets in our Solar System.
    First Report of Lasiodiplodia crassispora as a pathogen of grapevine trunks in South Africa
    Niekerk, J.M. van; Bester, W. ; Halleen, F. ; Crous, P.W. ; Fourie, P.H. - \ 2010
    Plant Disease 94 (2010)8. - ISSN 0191-2917 - p. 1063 - 1063.
    morphology - spp.
    In 2003 and 2004, a survey of grapevine (Vitis vinifera L.) trunk pathogens was conducted in 30 vineyards in the Western and Northern Cape and Limpopo provinces of South Africa. In each vineyard, 20 visually healthy plants were sampled randomly by removing the distal part of one cordon arm. Isolations were made onto potato dextrose agar (PDA) from the internal wood decay symptoms observed in the cordon samples. Seven Botryosphaeriaceae spp. were identified, including Lasiodiplodia crassispora (1). Other Botryosphaeriaceae spp. are known grapevine trunk pathogens (2). Species identity was confirmed by DNA sequence data of the partial translation factor 1-a gene (1) and sequences deposited in GenBank (GU233658 and GU233659). The L. crassispora isolates (CBS 125626 and 125627) were associated with brown internal necrosis, a known symptom of grapevine Botryosphaeriaceae spp. infection (3), in the cordon arms of Ruby Cabernet grapevines occurring in two vineyards in the Northern Cape Province. L. crassispora was described from cankered wood of Santalum album in Western Australia and endophytically from Eucalyptus urophylla in Venezuela (1). Its grapevine pathogen status was determined using both isolates in a repeated pathogenicity test that included three isolates each of Botryosphaeria dothidea and Neofusicoccum australe as positive controls (2), Trichoderma harzianum as a nonpathogen treatment, and an uncolonized agar plug as a negative control. The Botryosphaeriaceae spp. and T. harzianum were plated on PDA and incubated at 25°C for 7 days. Lignified, 6-month-old shoots of grapevine cv. Chardonnay were excised from grapevines with internodes 4 to 6 used for inoculations. Before wounding, shoots were disinfected by submersion for 1 min in a 1 ml/liter solution of a quaternary ammonium compound (Sporekill; ICA International Chemicals (Pty) Ltd, Stellenbosch, South Africa). Twelve shoots were used for each isolate or control treatment. Wounds were made 2 mm deep on the fifth internode of the shoots with a 5-mm flame-sterilized cork borer (2,3). Wounds were inoculated with a pathogen colonized agar plug (5 mm in diameter) or an uncolonized agar plug and then covered with Parafilm (2,3). Inoculated shoots were incubated in the dark in moist chambers for 14 days at 25°C. After incubation, the bark of the shoots was peeled from the area around the wound and the lengths of any resultant lesions were measured under sterile conditions. The inoculum effect was assessed by analysis of variance and Student's t-test. Results showed that significantly (P <0.0001) longer lesions were caused by L. crassispora (13.36 mm) compared with N. australe (9.27 mm) and B. dothidea (5.28 mm) and also significantly longer than lesions caused by the nonpathogen and negative controls (3.23 and 2.90 mm, respectively). To determine if lesions were caused by inoculated fungi, isolations were made from the tissue at the edges of the lesions by aseptically removing five 0.5 × 1 mm pieces of wood and placing them on PDA dishes amended with 0.04 g/liter of streptomycin sulfate. Dishes were incubated under normal fluorescent light at 25°C for 14 days before identifying isolated fungi based on morphological and cultural characteristics (1). To our knowledge, this is the first report of L. crassispora as a grapevine pathogen.
    Evaluation of fungicides as potential grapevine pruning wound protectants against Botryosphaeria species
    Bester, W. ; Crous, P.W. ; Fourie, P.H. - \ 2007
    Australasian Plant Pathology 36 (2007)1. - ISSN 0815-3191 - p. 73 - 77.
    biological-control - eutypa-lata - south-africa - phomopsis - phaeoacremonium - infection - temperature - phylogeny - esca
    Protection of wounds against infection by trunk disease pathogens is the most efficient and cost-effective means to prevent grapevine trunk diseases. Studies done to determine the effectiveness of chemical pruning wound protectants have mostly focused on the control of Eutypa lata. However, other important wound pathogens, such as Phaeomoniella chlamydospora, Phaeoacremonium spp., Phomopsis spp. and species of Botryosphaeriaceae ( including Botryosphaeria and aggregate genera), pose just as significant a threat to sustainable grape production. Fungicide sensitivity studies have been conducted for Pa. chlamydospora, P. viticola and E. lata. However, no such studies have been conducted for the pathogenic species of Botryosphaeriaceae from grapevines in South Africa. Ten fungicides were, therefore, tested in vitro for their efficacy on mycelial inhibition of the four most common or pathogenic species of Botryosphaeriaceae in South Africa, 'B.' obtusa, Neofusicoccum australe, N. parvum and Lasiodiplodia theobromae. Iprodione, pyrimethanil, copper ammonium acetate, kresoxim-methyl and boscalid were ineffective in inhibiting the mycelial growth at the highest concentrations tested ( 20 mu g/mL for copper ammonium acetate, 5 mu g/mL for other agents tested). Benomyl, tebuconazole, prochloraz manganese chloride and flusilazole were the most effective fungicides with EC50 values for the different species ranging from 0.36-0.55, 0.07-0.17, 0.07-1.15 and 0.04-0.36 mu g/mL, respectively. These fungicides, except prochloraz manganese chloride, are registered for use on grapes in South Africa and were also reported to be effective against Pa. chlamydospora, P. viticola and E. lata. Results from bioassays on 1-year-old Chenin Blanc grapevine shoots indicated that benomyl, tebuconazole and prochloraz manganese chloride were most effective in limiting lesion length in pruning wounds that were inoculated with species of Botryosphaeriaceae after fungicide treatment. The bioassay findings were, however, inconclusive due to low and varied re-isolation incidences. Benomyl, tebuconazole, prochloraz manganese chloride and flusilazole can be identified as fungicides to be evaluated as pruning wound protectants in additional bioassays and vineyard trials against species of Botryosphaeriaceae as well as the other grapevine trunk disease pathogens.
    Polymorphism of bovine MHC class I genes.
    Davies, C.J. ; Joosten, I. ; Bernoco, D. ; Arriens, M.A. ; Bester, J. - \ 1994
    European journal of immunogenetics 21 (1994). - ISSN 0960-7420 - p. 239 - 258.
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