Microsatellite genotyping of apple (Malus × domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification
Treuren, R. van; Kemp, H. ; Ernsting, G. ; Jongejans, B. ; Houtman, H. ; Visser, L. - \ 2010
Genetic Resources and Crop Evolution 57 (2010)6. - ISSN 0925-9864 - p. 853 - 865.
appels - genenbanken - genotypen - genetische merkers - microsatellieten - genetische diversiteit - fenotypen - apples - gene banks - genotypes - genetic markers - microsatellites - genetic diversity - phenotypes - molecular characterization - ssr markers - construction - polymorphism - database - tomato - plants - dna
A highly informative set of 16 microsatellite markers was used to fingerprint 695 apple accessions from eight Dutch collections. Among the total sample, 475 different genotypes were distinguished based on multi-locus microsatellite variation, revealing a potential redundancy within the total sample of 32%. The majority of redundancies were found between collections, rather than within collections. No single collection covered the total observed diversity well, as each collection consisted of about 50% of unique accessions. These findings reflected the fact that most collection holders focus on common Dutch varieties, as well as on region-specific diversity. Based on the diversity patterns observed, maintenance of genetic resources by a network of co-operating collection holders, rather than by collecting the total diversity in a single collection appears to be an efficient approach. Comparison of microsatellite and passport data showed that for many accessions the marker data did not provide support for the registered variety names. Verification of accessions showed that discrepancies between passport and molecular data were largely due to documentation and phenotypic determination errors. With the help of the marker data the varietal names of 45 accessions could be corrected. Microsatellite genotyping of apple appears to be an efficient tool in the management of collections and in variety identification. The development of a marker database was considered relevant as a reference instrument in variety identification and as a source of information about thus far unexplored diversity that could be of interest in the development of new apple varieties
Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stabilty
Arens, P.F.P. ; Mansilla, C. ; Deinum, D. ; Cavellini, L. ; Moretti, A. ; Rolland, S. ; Schoot, H. van der; Calvache, D. ; Ponz, F. ; Collonnier, C. ; Mathis, R. ; Smilde, D. ; Caranta, C. ; Vosman, B. - \ 2010
Theoretical and Applied Genetics 120 (2010)3. - ISSN 0040-5752 - p. 655 - 664.
nucleotide-binding - genes - dissection - varieties - construction - database - network - tm-2(2) - family - locus
Molecular markers linked to phenotypically important traits are of great interest especially when traits are difficult and/or costly to be observed. In tomato where a strong focus on resistance breeding has led to the introgression of several resistance genes, resistance traits have become important characteristics in distinctness, uniformity and stability (DUS) testing for Plant Breeders Rights (PBR) applications. Evaluation of disease traits in biological assays is not always straightforward because assays are often influenced by environmental factors, and difficulties in scoring exist. In this study, we describe the development and/or evaluation of molecular marker assays for the Verticillium genes Ve1 and Ve2, the tomato mosaic virus Tm1 (linked marker), the tomato mosaic virus Tm2 and Tm2 2 genes, the Meloidogyne incognita Mi1-2 gene, the Fusarium I (linked marker) and I2 loci, which are obligatory traits in PBR testing. The marker assays were evaluated for their robustness in a ring test and then evaluated in a set of varieties. Although in general, results between biological assays and marker assays gave highly correlated results, marker assays showed an advantage over biological tests in that the results were clearer, i.e., homozygote/heterozygote presence of the resistance gene can be detected and heterogeneity in seed lots can be identified readily. Within the UPOV framework for granting of PBR, the markers have the potential to fulfil the requirements needed for implementation in DUS testing of candidate varieties and could complement or may be an alternative to the pathogenesis tests that are carried out at present.
A strong effect of growth medium and organ type on the identification of QTLs for phytate and mineral concentrations in three Arabidopsis thaliana RIL populations
Ghandilyan, A. ; Ilk, N. ; Hanhart, C.J. ; Mbengue, M. ; Barboza, L. ; Schat, H. ; Koornneef, M. ; El-Lithy, M.E.M. ; Vreugdenhil, D. ; Reymond, M. ; Aarts, M.G.M. - \ 2009
Journal of Experimental Botany 60 (2009)5. - ISSN 0022-0957 - p. 1409 - 1425.
quantitative trait loci - inbred line population - natural variation - erecta - seeds - construction - accumulation - efficiency - nutrition - ecotypes
The regulation of mineral accumulation in plants is genetically complex, with several genetic loci involved in the control of one mineral and loci affecting the accumulation of different minerals. To investigate the role of growth medium and organ type on the genetics of mineral accumulation, two existing (LerxKond, LerxAn-1) and one new (LerxEri-1) Arabidopsis thaliana Recombinant Inbred Line populations were raised on soil and hydroponics as substrates. Seeds, roots, and/or rosettes were sampled for the determination of their Ca, Fe, K, Mg, Mn, P or Zn concentrations. For seeds only, the concentration of phytate (IP6), a strong chelator of seed minerals, was determined. Correlations between minerals/IP6, populations, growth conditions, and organs were determined and mineral/IP6 concentration data were used to identify quantitative trait loci (QTLs) for these traits. A striking difference was found between QTLs identified for soil-grown versus hydroponics-grown populations and between QTLs identified for different plant organs. Three common QTLs were identified for several populations, growth conditions, and organs, one of which corresponded to the ERECTA locus, variation of which has a strong effect on plant morphology
Did the pile driving during the construction of the Offshore Wind Farm Egmond aan Zee, the Netherlands, impact porpoises?
Leopold, M.F. ; Camphuysen, C.J. - \ 2009
Texel : IMARES (Report / Wageningen IMARES C091/09) - 17
windenergie - windmolens - geluidsproductie - geluidshinder - akoestische emissie - civiele techniek - constructie - pijlers - milieueffect - noordzee - nederland - offshore - onderwaterakoestiek - phocoenidae - wind power - windmills - sound production - noise pollution - acoustic emissions - civil engineering - construction - piles - environmental impact - north sea - netherlands - offshore - underwater acoustics - phocoenidae
The Dutch consortium "NoordzeeWind" has built the first offshore wind farm in Dutch North Sea waters, known as "Offshore Wind farm Egmond aan Zee" (OWEZ) Part of the construction works consisted of driving 36 monopiles into the sea floor, during April-June 2006. The noise levels that attended this activity may have been detrimental to marine life forms. Cetaceans in particular are sensitive to very high noise levels and a possible impact on the most abundant cetacean living off the Dutch coast, the harbour porpoise was therefore studied. Direct observations were hard to conduct, given the low (summer) densities of porpoises around the construction site. Pathological observations on stranded specimen failed to produce clear results. Inner ears of freshly stranded porpoises were examined for possible damage, but before necropsies could be conducted the animals had been stored frozen and this had destroyed any visible signs of noise-induced damage to the inner ear. Thus, the spatiotemporal pattern of porpoise strandings was examined. Porpoises did not strand in higher numbers on the coastal stretch directly east of the construction site, or to the north-east of this location (downstream) compared to other parts of the country. Porpoises also did not strand in higher than expected numbers near the construction site, at the time of construction. It was therefore concluded that the construction did not lead to visibly increased mortality of harbour porpoises. In retrospect this might have been expected, given that densities of porpoises are normally very low in summer at the site, that the building process is noisy anyway, scaring porpoises off (to safe distances) before the actual pile driving commences. A ramp-up procedure and usage of a pinger further helped to ward off porpoises from the site, before full-power pile driving started. These factors combined (timing and high before-pile driving noise levels) made it very unlikely that porpoises got in harm’s way during the construction of OWEZ.
Accessing information in working memory: Can the focus of attention grasp two elements at the same time?
Oberauer, K. ; Bialkova, S.E. - \ 2009
Journal of Experimental Psychology. General 138 (2009)1. - ISSN 0096-3445 - p. 64 - 87.
short-term-memory - individual-differences - premise integration - task - capacity - comprehension - model - costs - representations - construction
Processing information in working memory requires selective access to a subset of working-memory contents by a focus of attention. Complex cognition often requires joint access to 2 items in working memory. How does the focus select 2 items? Two experiments with an arithmetic task and 1 with a spatial task investigate time demands for successive operations that involve 2 digits or 2 spatial positions, respectively. When both items used in an operation have been used in the preceding operation, latencies are shortened. No such repetition benefit (arithmetic) or a much smaller benefit (spatial) was found when only 1 item was repeated. The results rule out serial access to the 2 items, parallel access by expanding the focus, and parallel access by splitting the focus. They support the notion that 2 items are accessed by chunking them, so that they fit a focus limited to 1 chunk. Keywords: attention, working memory, relations
Ordering dominant markers in F2 populations
Jansen, J. - \ 2009
Euphytica 165 (2009)2. - ISSN 0014-2336 - p. 401 - 417.
genetic-linkage maps - construction - likelihood
Ordering dominant markers in F2 populations is considered a difficult problem. The difficulties arise from the fact that recombinations cannot be observed directly from the data. In general, the multi-point maximum likelihood would be the appropriate criterion for ordering markers. This criterion takes into account all available information present in marker data. However, calculation of multi-point maximum likelihoods is very time-demanding, especially if the number of markers is large. In this paper, ordering markers by minimising the number of recombinations between adjacent markers is used as a simple alternative to multi-point maximum likelihood. Contrary to multi-point maximum likelihood, this method does not involve any probability assumptions about the occurrence of recombination events. Simulated data indicate that the minimum number of recombinations between adjacent markers is approximately a linear function of the map length obtained by multi-point maximum likelihood. As a consequence, it will lead to more or less the same optimum marker orders. Optimisation of marker orders with regard to the number of recombinations between adjacent markers is carried out by a modified form of simulated annealing. The reliability of the resulting marker orders is studied by generating marker orders that are plausible with the data using a Metropolis algorithm
The Potential Of High-Resolution BAC-FISH In Banana Breeding
Capdeville, G. De; Souza, M.T. ; Szinay, D. ; Eugenio Cardamone Diniz, L. ; Wijnker, T.G. ; Swennen, R. ; Kema, G.H.J. ; Jong, J.H.S.G.M. de - \ 2009
Euphytica 166 (2009)3. - ISSN 0014-2336 - p. 431 - 443.
artificial chromosome library - in-situ hybridization - musa-acuminata - diploid bananas - genome structure - dna - hybrids - gene - construction - balbisiana
Abstract The genetic complexity in the genus Musa has been subject of study in many breeding programs worldwide. Parthenocarpy, female sterility, polyploidy in different cultivars and limited amount of genetic and genomic information make the production of new banana cultivars difficult and time consuming. In addition, it is known that part of the cultivars and related wild species in the genus contain numerous chromosomal rearrangements. In order to produce new cultivars more effectively breeders must better understand the genetic differences of the potential crossing parents for introgression hybridization, but extensive genetic information is lacking. As an alternative to achieve information on genetic collinearity we make use of modern chromosome map technology known as high-resolution fluorescent in situ hybridization (FISH). This article presents the technical aspects and applications of such a technology in Musa species. The technique deals with BAC clone positioning on pachytene chromosomes of Calcutta 4 (Musa acuminata ssp. burmanicoides, A genome group, section Eumusa) and M. velutina (section Rodochlamys). Pollen mother cells digestion with pectolytic enzymes and maceration with acetic acid were optimized for making cell spread preparations appropriate for FISH. As an example of this approach we chose BAC clones that contain markers to known resistance genes and hybridize them for establishing their relative positions on the two species. Technical challenges for adapting existing protocols to the banana cells are presented. We also discuss how this technique can be instrumental for validating collinearity between potential crossing parents and how the method can be helpful in future mapping initiatives, and how this method allows identification of chromosomal rearrangements between related Musa species and cultivars
Genetic mapping and transcription analyses of resistance gene loci in potato using NBS profiling
Brugmans, B.W. ; Wouters, D.C.A.E. ; Os, H. van; Hutten, R.C.B. ; Linden, C.G. van der; Visser, R.G.F. ; Eck, H.J. van; Vossen, E.A.G. van der - \ 2008
Theoretical and Applied Genetics 117 (2008)8. - ISSN 0040-5752 - p. 1379 - 1388.
disease-resistance - confers resistance - map - tomato - genome - construction - arabidopsis - proteins - sequence - analogs
NBS profiling is a method for the identification of resistance gene analog (RGA) derived fragments. Here we report the use of NBS profiling for the genome wide mapping of RGA loci in potato. NBS profiling analyses on a minimal set of F1 genotypes of the diploid mapping population previously used to generate the ultra dense (UHD) genetic map of potato, allowed us to efficiently map polymorphic RGA fragments relative to 10,000 existing AFLP markers. In total, 34 RGA loci were mapped, of which only 13 contained RGA sequences homologous to RGAs genetically positioned at approximately similar positions in potato or tomato. The remaining RGA loci mapped either at approximate chromosomal regions previously shown to contain RGAs in potato or tomato without sharing homology to these RGAs, or mapped at positions not yet identified as RGA-containing regions. In addition to markers representing RGAs with unknown functions, segregating markers were detected that were closely linked to four functional R genes that segregate in the UHD mapping population. To explore the potential of NBS profiling in RGA transcription analyses, RNA isolated from different tissues was used as template for NBS profiling. Of all the fragments amplified approximately 15% showed putative intensity or absent/present differences between different tissues suggesting putative tissue specific RGA or R gene transcription. Putative absent/present differences between individuals were also found. In addition to being a powerful tool for generating candidate gene markers linked to R gene loci, NBS profiling, when applied to cDNA, can be instrumental in identifying those members of an R gene cluster that are transcribed, and thus putatively functional.
Marker-assisted optimization of an expert-based strategy for the acquisition of modern lettuce varieties to improve a genebank collection
Treuren, R. van; Hintum, T.J.L. van; Wiel, C.C.M. van de - \ 2008
Genetic Resources and Crop Evolution 55 (2008)2. - ISSN 0925-9864 - p. 319 - 330.
genetic-variation - bremia-lactucae - accessions - construction - resistance - database - tomato - aflps - rapd
To regularly improve the composition of the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN) with modern varieties, feedback from crop experts is used to select approximately 10% of the new material for incorporation in the collection. In the present study, assessments of six experts were compared to microsatellite data of 414 new varieties and 1408 existing accessions. Based on the microsatellite data, the extent to which the genetic diversity of the collection would be enriched (added value) was calculated for specific sets of new varieties. When individual assessments of experts were evaluated, the total added value of expert-based selections was not significantly higher compared to randomly chosen groups, except for a single expert. Unfamiliarity with new varieties was shown to be a crucial factor in the assessment of crop experts. According to the current acquisition protocol that seeks for consensus among experts, varieties are selected based on recommendations from at least three experts. This protocol also did not perform better than randomly chosen groups of new varieties. However, significantly better results were obtained with alternative protocols. It was concluded that breeding value was a more decisive criterion in the current acquisition protocol than maximal extension of the genetic diversity within the collection. A modified protocol addressing both commercial and diversity aspects was suggested in order to meet the demands of plant breeders as well as conservationists
Elkas levert gewas én stroom : kas met zonnecellen geopend in Wageningen
Vegter, B. ; Sonneveld, P.J. - \ 2008
Vakblad voor de Bloemisterij 63 (2008)26. - ISSN 0042-2223 - p. 36 - 37.
kassen - elektriciteitsgeneratoren - zonne-energie - elektriciteit - bouwtechnologie - constructie - glastuinbouw - kastechniek - greenhouses - electricity generators - solar energy - electricity - construction technology - construction - greenhouse horticulture - greenhouse technology
WUR Glastuinbouw heeft de Elkas gebouwd, die warmte en stroom kan leveren. Het gebogen glas kaatst het NIR-licht terug op zonnecellen, die elektriciteit opwekken. Het PAR-licht wordt doorgelaten voor de gewasgroei
Expressed sequence tag-derived microsatellite markers of perennial ryegrass (Lolium perenne L.).
Studer, B. ; Asp, T. ; Frei, U. ; Hentrup, S. ; Meally, H. ; Guillard, A. ; Barth, S. ; Muylle, H. ; Roldan-Ruiz, I. ; Barre, P. ; Boucoiran, C.F.S. ; Stunnenberg, G. ; Dolstra, O. ; Skot, L. ; Skot, K.P. ; Turner, B. ; Humphreys, M. ; Kolliker, R. ; Roulund, N. ; Nielsen, K.K. ; Lubberstedt, T. - \ 2008
Molecular Breeding 21 (2008)4. - ISSN 1380-3743 - p. 533 - 548.
repeat ssr markers - multiflorum lam. - linkage map - plants - transferability - construction - reveals - qtl
An expressed sequence tag (EST) library of the key grassland species perennial ryegrass (Lolium perenne L.) has been exploited as a resource for microsatellite marker development. Out of 955 simple sequence repeat (SSR) containing ESTs, 744 were used for primer design. Primer amplification was tested in eight genotypes of L. perenne and L. multiflorum representing (grand-) parents of four mapping populations and resulted in 464 successfully amplified EST-SSRs. Three hundred and six primer pairs successfully amplified products in the mapping population VrnA derived from two of the eight genotypes included in the original screening and revealed SSR polymorphisms for 143 ESTs. Here, we report on 464 EST-derived SSR primer sequences of perennial ryegrass established in laboratory assays, providing a dedicated tool for marker assisted breeding and comparative mapping within and among forage and turf grasses. Electronic supplementary material The online version of this article (doi:10.1007/s11032-007-9148-0) contains supplementary material, which is available to authorized users.
Conversion of chromosome-specific RAPDs into SCAR-based anchor markers for onion linkage maps and its application to genetic analyses inother Allium species
Masuzaki, S. ; Miyazaki, T. ; McCallum, J. ; Heusden, A.W. van; Kik, C. ; Yamashita, K. ; Tashiro, Y. - \ 2008
Scientia Horticulturae 115 (2008)4. - ISSN 0304-4238 - p. 323 - 328.
amplified polymorphic dna - monosomic addition lines - l. aggregatum group - cepa l. - construction - assignment - sequences - aflp - locations - reveals
Integration of previously developed Allium cepa linkage maps requires the availability of anchor markers for each of the eight chromosomes of shallot (A. cepa L. common group Aggregatum). To this end, eight RAPD markers originating from our previous research were converted into SCAR markers via cloning and sequencing of RAPD amplicons and designing of 24-mer oligonucleotide primers. Of the eight pairs of SCAR primers, seven resulted in the amplification of single bands of the original RAPDs, and the remaining primer set amplified an additional band. The results of Southern hybridization using RAPD amplicons from genomic DNA of Japanese bunching onion (Allium fistulosum L.)¿shallot monosomic addition lines indicated that five SCAR markers were single shallot chromosome-specific markers and were not detected in genomic DNA of A. fistulosum. The eight SCAR primer pairs were applied to other Allium species and exhibited three types of amplification profiles, namely RAPD amplicons observed only in shallot, in shallot and Allium vavilovii, and in several Allium species. A mapping study using 65 F2 plants generated by the selfing of one interspecific cross A. cepa × Allium roylei individual integrated the SCAR marker SAOE17500 into chromosome 5 as expected. The results of the present study show that the eight SCAR primer sets specific to shallot can facilitate the mapping in A. cepa and can also serve as anchor points between maps of different Allium species
Underwater sound emissions and effects of the pile driving of the OWEZ windfarm facility near Egmond aan Zee (Tconstruct)
Haan, D. de; Burggraaf, D. ; Ybema, M.S. ; Hille Ris Lambers, R. - \ 2007
IJmuiden : IMARES (Report / Wageningen IMARES no. C106/07) - 75
windenergie - windmolens - geluidsproductie - geluidshinder - akoestische emissie - civiele techniek - constructie - pijlers - milieueffect - noordzee - nederland - offshore - onderwaterakoestiek - wind power - windmills - sound production - noise pollution - acoustic emissions - civil engineering - construction - piles - environmental impact - north sea - netherlands - offshore - underwater acoustics
The aim of this part of the Monitoring and Evaluation Program NSW (MEP-NSW), i.e. “acoustic measurements”, is to measure and analyze underwater sound emissions from the construction of the OWEZ wind farm and to investigate the effects to marine animals (in particular fish, harbour porpoises and seals) from other relevant studies. The Off-Shore Wind farm Egmond aan Zee (OWEZ) was built in the Dutch coastal zone 8 - 18 km off the coast from Egmond aan Zee. It consists of an arrangement of 36 wind turbines with a total capacity of 108 MW.
Assignment tests for variety identification compared to genetic similarity-based methods using experimental datasets from different marker systems in sugar beet
Riek, J. de; Everaert, I. ; Esselink, D. ; Calsyn, E. ; Smulders, M.J.M. ; Vosman, B. - \ 2007
Crop Science 47 (2007)5. - ISSN 0011-183X - p. 1964 - 1974.
beta-vulgaris l - linkage map - aflp - construction - regression - database - rapd - l.
High genetic variation within sugar beet (Beta vulgaris L.) varieties hampers reliable classification procedures independent of the type of marker technique applied. Datasets on amplified fragment length polymorphisms, sequence tagged microsatellite sites, and cleaved amplified polymorphic sites markers in eight sugar beet varieties were subjected to supervised classifiers, methods in which individual assignments are made to predefined classes, and unsupervised classifiers, defined afterward on the similarity in marker composition from sampled individuals. Major issues addressed are (i) which classification method gives the most consistent results when three marker techniques are compared, and (ii) given different classification techniques available, for which marker technique is the output generated least constrained by the way data analysis is performed. Assignment tests showed a higher consistency across classifications independent from the marker technique. A good allocation to the proper variety was obtained, together with a reliable allocation pattern among the other varieties. Both aspects deal with the variation within a variety and the distance to other varieties. Assignment data were transformed into an average similarity measure, similarity by assignment (Sax,y), which is a new genetic distance measure with interesting properties
A high-density, integrated genetic linkage map of lettuce (Lactuca spp.)
Truco, M.J. ; Antonise, R. ; Lavelle, D. ; Ochoa, O. ; Kozik, A. ; Witsenboer, H. ; Fort, S.B. ; Jeuken, M.J.W. ; Kesseli, R.V. ; Lindhout, P. ; Michelmore, R. ; Peleman, J. - \ 2007
Theoretical and Applied Genetics 115 (2007)6. - ISSN 0040-5752 - p. 735 - 746.
brassica-napus - aflp markers - recombination - sativa - populations - construction - genome - rflp - identification - exploitation
An integrated map for lettuce comprising of 2,744 markers was developed from seven intra- and inter-specific mapping populations. A total of 560 markers that segregated in two or more populations were used to align the individual maps. 2,073 AFLP, 152 RFLP, 130 SSR, and 360 RAPD as well as 29 other markers were assigned to nine chromosomal linkage groups that spanned a total of 1,505 cM and ranged from 136 to 238 cM. The maximum interval between markers in the integrated map is 43 cM and the mean interval is 0.7 cM. The majority of markers segregated close to Mendelian expectations in the intra-specific crosses. In the two L. saligna × L. sativa inter-specific crosses, a total of 155 and 116 markers in 13 regions exhibited significant segregation distortion. Data visualization tools were developed to curate, display and query the data. The integrated map provides a framework for mapping ESTs in one core mapping population relative to phenotypes that segregate in other populations. It also provides large numbers of markers for marker assisted selection, candidate gene identification, and studies of genome evolution in the Compositae
Did the pile driving during the construction of the Offshore Wind Farm Egmond aan Zee, the Netherlands, imapct local seabirds?
Leopold, M.F. ; Camphuysen, C.J. - \ 2007
Texel : IMARES Texel (Report / Wageningen IMARES nr. C062/07) - 26
zeevogels - ecologische verstoring - constructie - bouwtechnologie - windmolens - geluidshinder - voedingsgedrag - voedingsgewoonten - noordzee - nadelige gevolgen - sea birds - ecological disturbance - construction - construction technology - windmills - noise pollution - feeding behaviour - feeding habits - north sea - adverse effects
In this study, possible effects on sensitive seabirds are considered. Bird species most likely to be vulnerable to underwater sound are those that forage by diving after fish of shellfish. Diving birds that may occur in relatively high densities at the OWEZ location include auks, and possibly divers and seaduck. Terns, that feed by shallow dives are considered less vulnerable and mostly occur closer to the mainland coast. Several gull species may occur in the area in high densities, but they feed at the surface only, and are considered the least vulnerable. Pile driving took place from 17 April to 28 July 2007. The potentially vulnerable divers, seaduck and auks had largely left the area by the time the pile driving started. Migration commenced early in 2006 and any birds still left in the area by mid-April would have been scared away by the shipping activities long before actual pile driving started. Further mitigation of possible effects on sensitive seabirds included a ramp-up procedure that ensured that full hamming power was only administered after a period of low-energy blows that were unlikely to cause lethal effects on any birds still present. Furthermore, an underwater pinger, aimed at scaring off marine mammals, was put into operation 3-4 hours before pile driving started. Visual observations before and during three pile driving sessions failed to detect any of the seabirds deemed sensitive to pile driving noise in the vicinity of the construction work. Birds that did fly by the construction site (mainly gulls and terns) did not show a noticeable reaction to the activities. It is therefore concluded that effects of underwater noise on seabirds, though potentially detrimental, were negligible during construction of OWEZ. This was due to fortunate timing of the work and to appropriate mitigation measures.
QTL analysis of variation for vigour in rose
Yan, Z. ; Visser, P.B. ; Hendriks, T. ; Prins, T.W. ; Stam, P. ; Dolstra, O. - \ 2007
Euphytica 154 (2007)1-2. - ISSN 0014-2336 - p. 53 - 62.
genetic-linkage maps - quantitative trait loci - aflp markers - construction - rflp - rapd
The improvement of energy efficiency in the greenhouse production of cut rose and pot rose can be achieved through the use of rose cultivars having vigorous growth. A better understanding of the inheritance of vigour and its related traits will assist the breeding activities. Quantitative trait locus (QTL) analyses were performed with the help of an integrated linkage map of a diploid rose population originating from a cross between Rosa multiflora-derived genotypes. The underlying datasets for ten vigour-related traits were collected in an evaluation study of this population in two greenhouse experiments with suboptimal temperatures for growth. We identified ten chromosomal regions, scattered over the seven linkage groups, containing QTLs for these traits. Considering each trait separately, we detected a total of 42 QTLs. Among these QTLs, 24 were found in both of the experiments, eight and ten were specific to either of the two experiments. The number of QTLs for individual traits varied from three to five with a respective contribution to the phenotypic variation from 12 to 35%. QTLs for highly correlated traits frequently co-localized, indicating a common genetic basis. Clustering of QTLs for different traits was noted in some chromosome regions, for instance, one on chromosome 2 included major QTLs for eight of ten traits under study, suggesting co-localization of several separate genes or/and the occurrence of various genes having pleiotropic effects. The discovery of markers associated to QTL regions is in roses the first step towards marker-assisted selection for vigour improvement enabling the transfer of useful QTL-alleles of R. multiflora to pot and cut roses
Belang van bodemleven bij de aanleg van natuurgras sportvelden
Postma, J. ; Moonen, B. ; Nijhuis, E.H. ; Pastoor, R. - \ 2006
Wageningen [etc.] : Plant Research International [etc.] (Nota / Plant Research International 388) - 58
bodemfauna - sportveldgronden - sportterreinen - bodemkwaliteit - constructie - soil fauna - sports turf soils - sports grounds - soil quality - construction
De diverse groepen organismen in de bodem reageren op elkaar, maar ook op het gewas en op de fysische en chemische bodemeigenschappen van de bodem. Ten aanzien van bodemleven in sportvelden is echter betrekkelijk weinig kennis aanwezig. Nader onderzocht is de welke bodemorganismen bij de aanleg van sportvelden van belang kunnen zijn ter bevordering van de bodemkwaliteit.
Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme
Kiekens, R. ; Vercauteren, A. ; Moerkerke, B. ; Goetghebeur, E. ; Daele, H. Van Den; Sterken, R. ; Kuiper, M. ; Eeuwijk, F.A. van; Vuylsteke, M. - \ 2006
Nucleic acids research 34 (2006)13. - ISSN 0305-1048 - p. 3677 - 3686.
human gene-expression - allelic variation - transcriptional regulation - arabidopsis-thaliana - functional genomics - sequence tags - microarray - model - identification - construction
Large-scale screening studies carried out to date for genetic variants that affect gene regulation are generally limited to descriptions of differences in allele-specific expression (ASE) detected in vivo. Allele-specific differences in gene expression provide evidence for a model whereby cis-acting genetic variation results in differential expression between alleles. Such gene surveys for regulatory variation are a first step in identifying the specific nucleotide changes that govern gene expression differences, but they leave the underlying mechanisms unexplored. Here, we propose a quantitative genetics approach to perform a genome-wide analysis of ASE differences (GASED). The GASED approach is based on a diallel design that is often used in plant breeding programs to estimate general combining abilities (GCA) of specific inbred lines and to identify high-yielding hybrid combinations of parents based on their specific combining abilities (SCAs). In a context of gene expression, the values of GCA and SCA parameters allow cis- and trans-regulatory changes to be distinguished and imbalances in gene expression to be ascribed to cis-regulatory variation. With this approach, a total of 715 genes could be identified that are likely to carry allelic polymorphisms responsible for at least a 1.5-fold allelic expression difference in a total of 10 diploid Arabidopsis thaliana hybrids. The major strength of the GASED approach, compared to other ASE detection methods, is that it is not restricted to genes with allelic transcript variants. Although a false-positive rate of 9/41 was observed, the GASED approach is a valuable pre-screening method that can accelerate systematic surveys of naturally occurring cis-regulatory variation among inbred lines for laboratory species, such as Arabidopsis, mouse, rat and fruitfly, and economically important crop species, such as corn.
Molecular cytogenetics and DNA sequence analysis of an apomixis-linked BAC in Paspalum simplex reveal a non pericentromere location and partial microcolinearity with rice
Calderini, O. ; Chang, S.B. ; Jong, J.H.S.G.M. de; Busti, A. ; Paolocci, F. ; Arcioni, S. ; Vries, S.C. de; Abma-Henkens, M.H.C. ; Klein Lankhorst, R.M. ; Donnison, I.S. ; Pupilli, F. - \ 2006
Theoretical and Applied Genetics 112 (2006)6. - ISSN 0040-5752 - p. 1179 - 1191.
in-situ hybridization - oryza-sativa l - pennisetum-squamulatum - cenchrus-ciliaris - controlling locus - genomic region - apospory - plants - gene - construction
Apomixis in plants is a form of clonal reproduction through seeds. A BAC clone linked to apomictic reproduction in Paspalum simplex was used to locate the apomixis locus on meiotic chromosome preparations. Fluorescent in situ hybridisation revealed the existence of a single locus embedded in a heterochromatin-poor region not adjacent to the centromere. We report here for the first time information regarding the sequencing of a large DNA clone from the apomixis locus. The presence of two genes whose rice homologs were mapped on the telomeric part of the long arm of rice chromosome 12 confirmed the strong synteny between the apomixis locus of P. simplex with the related area of the rice genome at the map level. Comparative analysis of this region with rice as representative of a sexual species revealed large-scale rearrangements due to transposable elements and small-scale rearrangements due to deletions and single point mutations. Both types of rearrangements induced the loss of coding capacity of large portions of the ¿apomictic¿ genes compared to their rice homologs. Our results are discussed in relation to the use of rice genome data for positional cloning of apomixis genes and to the possible role of rearranged supernumerary genes in the apomictic process of P. simplex.