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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Effect of milk yield characteristics, breed, and parity on success of the first insemination in Dutch dairy cows
Inchaisri, C. ; Hogeveen, H. ; Vos, P.L.A.M. ; Weijden, G.C. van der; Jorritsma, R. - \ 2010
Journal of Dairy Science 93 (2010). - ISSN 0022-0302 - p. 5179 - 5187.
body condition score - reproductive-performance - conception rates - genetic-relationships - energy-balance - united-states - new-york - holstein - cattle - fertility
The objective of this study was to determine the contribution of cow factors to the probability of a successful first insemination (SFI). The investigation was performed with 51,791 lactations from 1,396 herds obtained from the Dutch dairy cow database of the Cattle Improvement Co-operative (CRV). Cows that had the first insemination (AI) between 40 and 150 d postpartum were selected. The first AI was classified as successful when cows were not reinseminated and either calved between 267 and 295 d later or were culled within 135 to 295 d after first AI. The lactation curve characteristics of individual lactations were estimated by Wilmink's curve using the test-day milk records from CRV. The lactation curve characteristics (peak milk yield, milk yield at the first-AI date, time of peak yield (PT), and milk persistency) were calculated. Breed, parity, interval from calving to first AI (CFI), lactation curve characteristics, milk production traits, moment of AI related to PT (before or after PT), calf status, month of AI, and month of calving were selected as independent variables for a model with SFI as a dependent variable. A multivariable logistic regression model was used with farm as a random effect. Overall SFI was 44%. The effect of parity on SFI depended on CFI. The first-parity cows had the greatest SFI (0.43) compared with other parities (0.32–0.39) at the same period of CFI before 60 d in milk (DIM), and cows in parity =5 had the least SFI (0.38–0.40) when AI was after 60 DIM. After 60 DIM, extending CFI did not improve SFI in the first-parity cows, but SFI was improved in multiparous cows. Holstein-Friesian cows had lesser SFI (0.37) compared with cross-breed cows (0.39–0.46). Twin and stillbirth calving reduced SFI (0.39) compared with a single female calf (0.45) or a male calf (0.43) calving. The SFI in different months of AI varied and depended on CFI. Cows that received AI before 60 DIM had a lesser SFI, especially in March, June, and July (0.18, 0.35, and 0.34, respectively). Artificial insemination before PT reduced SFI (0.39) in comparison with AI after PT (0.44). The effect of milk yield at the first-AI date on SFI varied depending on CFI. After 60 DIM at the same period of CFI, a high level of milk yield at the first-AI date reduced SFI. In conclusion, knowledge of the contribution of cow factors on SFI can be applied to support decision making on the moment of insemination of an individual cow in estrus. Key words: milk production; lactation curve; first insemination; successful calving
AFLP Markers as a tool to reconstruct complex relationships: a case study in Rosa (Rosaceae)
Koopman, W.J.M. ; Wissemann, V. ; Cock, K. de; Huylenbroeck, J. van; Riek, J. de; Sabatino, G.J.H. ; Visser, D.L. ; Vosman, B. ; Ritz, K. ; Maes, B. ; Werlemark, G. ; Nybom, H. ; Debener, T. ; Linde, M. ; Smulders, M.J.M. - \ 2008
American Journal of Botany 95 (2008)3. - ISSN 0002-9122 - p. 353 - 366.
bayesian phylogenetic inference - internal transcribed spacers - genus rosa - genetic-relationships - dna-sequences - chloroplast dna - reticulate evolution - molecular evidence - north-america - sect. caninae
The genus Rosa has a complex evolutionary history caused by several factors, often in conjunction: extensive hybridization, recent radiation, incomplete lineage sorting, and multiple events of polyploidy. We examined the applicability of AFLP markers for reconstructing (species) relationships in Rosa, using UPGMA clustering, Wagner parsimony, and Bayesian inference. All trees were well resolved, but many of the deeper branches were weakly supported. The cluster analysis showed that the rose cultivars can be separated into a European and an Oriental cluster, each being related to different wild species. The phylogenetic analyses showed that (1) two of the four subgenera (Hulthemia and Platyrhodon) do not deserve subgeneric status; (2) section Carolinae should be merged with sect. Cinnamomeae; (3) subsection Rubigineae is a monophyletic group within sect. Caninae, making sect. Caninae paraphyletic; and (4) there is little support for the distinction of the five other subsections within sect. Caninae. Comparison of the trees with morphological classifications and with previous molecular studies showed that all methods yielded reliable trees. Bayesian inference proved to be a useful alternative to parsimony analysis of AFLP data. Because of their genome-wide sampling, AFLPs are the markers of choice to reconstruct (species) relationships in evolutionary complex groups.
AFLP markers support separation of Solanum nodiflorum from Solanum americanum sensu strictio (Solanaceae)
Manoko, M.L.K. ; Berg, R.G. van den; Feron, R.M.C. ; Weerden, G.M. van der; Mariani, C. - \ 2007
Plant Systematics and Evolution 267 (2007)1-4. - ISSN 0378-2697 - p. 1 - 11.
genetic-relationships - l. - biosystematics - relatives - homology - barley - wild
This study was aimed at examining the relationships between the African material of Solanum americanum (also designated as S. nodiflorum), accessions of this taxon from other geographical areas, and American S. americanum using AFLP markers. 96 individuals representing 39 accessions of S. americanum sensu lato and related diploid species from the widest possible geographical range, and one accession of S. dulcamara (as outgroup) were used. The AFLP results suggested that American S. americanum differs from S. nodiflorum and that the material investigated in this study can be assigned to three different species: S. americanum sensu stricto, S. nodiflorum and a Solanum species from Brazil. These species can be differentiated based on a combination of floral and fruit characteristics.
A Natural infrageneric classification for Cicer (Leguminoseae, Cicereae)
Davies, A.M.R. ; Maxted, N. ; Maesen, L.J.G. van der - \ 2007
Blumea 52 (2007)2. - ISSN 0006-5196 - p. 379 - 400.
genetic-relationships - genus cicer - phylogenetic-relationships - isozyme polymorphism - sequences - turkey - rapd - dna - morphology - diversity
A comprehensive morphological survey and analysis of all taxonomically recognised wild species of Cicer L. (Leguminosae, Cicereae) is presented. The data (104 characters from 152 herbarium specimens representing 34 of the 44 recognised taxa in the genus Cicer with supplementary data for the remaining taxa taken from the literature) were analysed using multivariate statistics (cluster analysis, factor analysis and ordination techniques). The results are discussed in the context of extant classifications and the re-organisation of a novel infrageneric classification also incorporating information from published genetic data. A revised classification with 3 subgenera, 5 sections and 2 series is proposed.
AFLP data support the recognition of a new tuber-bearing Solanum species but are uninformative about its taxonomic relationships
Berg, R.G. van den; Groendijk-Wilders, N. - \ 2007
Plant Systematics and Evolution 269 (2007)3-4. - ISSN 0378-2697 - p. 133 - 143.
genetic-relationships - solanaceae - petota - boundaries - l.
Solanum section Petota, containing the cultivated potato and its wild relatives, is a group of around 200 species. Many of these species are morphologically very variable with unclear boundaries, and the group as a whole appears to be somewhat over-classified. Describing a new species in this group should only be undertaken with caution, and molecular data can be used to test the distinctness of any putative new taxon. AFLP markers have shown the ability to reliably distinguish species in several groups within the genus Solanum. We tested the distinctness of a new tuber-bearing Solanum species using morphological and AFLP data, and tried to establish its affiliation to the series within the section. There was clear support for the species status of the material known as Solanum hannemanii in genebank collections, but the AFLP data were inconclusive about its relationships to the other investigated species. Also, the distinction of the series Tuberosa and Megistacroloba, to which these species belong, was not supported.
Phylogenetic Signal in AFLP Data Sets
Koopman, W.J.M. - \ 2005
Systematic Biology 54 (2005)2. - ISSN 1063-5157 - p. 197 - 217.
fragment length polymorphism - internal transcribed spacer - maximum-likelihood estimate - dna-dna hybridizations - sequence data - genetic-relationships - confidence-limits - arbitrary primers - difference test - wild relatives
AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment of fragments, (c) asymmetry in the probability of losing and gaining fragments, and (d) problems in distinguishing heterozygote from homozygote bands. In the present study, AFLP data sets of Lactuca s.l. were examined for the presence of phylogenetic signal. An indication of this signal was provided by carrying out tree length distribution skewness (g1) tests, permutation tail probability (PTP) tests, and relative apparent synapomorphy analysis (RASA). A measure of the support for internal branches in the optimal parsimony tree (MPT) was made using bootstrap, jackknife, and decay analysis. Finally, the extent of congruence in MPTs for AFLP and internal transcribed spacer (ITS)-1 data sets for the same taxa was made using the partition homogeneity test (PHT) and the Templeton test. These analytical studies suggested the presence of phylogenetic signal in the AFLP data sets, although some incongruence was found between AFLP and ITS MPTs. An extensive literature survey undertaken indicated that authors report a general congruence of AFLP and ITS tree topologies across a wide range of taxonomic groups, suggesting that the present results and conclusions have a general bearing. In these earlier studies and those for Lactuca s.l., AFLP markers have been found to be informative at somewhat lower taxonomic levels than ITS sequences. Tentative estimates are suggested for the levels of ITS sequence divergence over which AFLP profiles are likely to be phylogenetically informative. [Amplified Fragment Length Polymorphism (AFLP) markers; congruence; Dollo parsimony; g1 statistic; internal transcribed spacer (ITS) sequences; Lactuca; partition homogeneity test (PHT); phylogenetic signal.]
Vegetative compatibility groups in Verticillium dahliae isolates from the Netherlands as compared to VCG diversity in Europe and in the USA
Hiemstra, J.A. ; Rataj-Guranowska, M. - \ 2003
European Journal of Plant Pathology 109 (2003)8. - ISSN 0929-1873 - p. 827 - 839.
genetic-relationships - fusarium-oxysporum - tester strains - pathogenicity - virulence - mutants - cotton - soil - differentiation - populations
In a study of vegetative compatibility in Verticillium dahliae in the Netherlands, a collection of 45 isolates including representatives from woody hosts, several horticultural crops and from the soil of potato fields was examined. In addition an effort was made to compare vegetative compatibility groups (VCGs) from different countries. The results of this study indicate that VCG diversity in V. dahliae in the Netherlands is limited. Only two VCGs were detected: VCG NL-I and VCG NL-II. The former is the predominant VCG for isolates from tree hosts. However, Verticillium wilt in trees can be caused by isolates from both VCGs. It is suggested that the predominance of VCG NL-I in tree hosts is the result of the origin of the tree and the cropping history of its growing site, rather than trees being preferential hosts for isolates from this VCG. Comparison of VCG testers from the Netherlands, from several other European countries and from the USA show that in Europe two major VCGs are present. The first one, including NL-I, is compatible with USA VCG 3 and VCG 4, whereas the second one, including NL-II, is compatible with USA VCG 1 and VCG 2. These groups are not completely separated; in some cases, testers formed heterokaryons with VCG testers from both main groups. Because of the presence of these bridge isolates and because mutants from the same isolate differ in ability to form heterokaryons, it is emphasised that careful selection of isolate testers is an essential step to get a clear picture of VCG diversity.
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