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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    Ghost Introgression: Spooky Gene Flow in the Distant Past
    Ottenburghs, Jente - \ 2020
    Bioessays 42 (2020)6. - ISSN 0265-9247
    adaptation - demographic modelling - hybridization - macroevolution - phylogenetic networks - reproductive isolation - speciation

    Evolution is a continuous trial and error process in which most lineages go extinct without leaving fossil remains. Many of these lineages would be closely related and occasionally hybridized with lineages that gave rise to extant species. Hence, it is likely that one can find genetic signatures of these ancient introgression events in present-day genomes, so-called ghost introgression. The increasing availability of high-quality genome assemblies for non-model organisms and the development of more sophisticated methods for detecting introgression will undoubtedly reveal more cases of ghost introgression, indicating that the Tree of Life is even more reticulated than assumed. The presence of ghost introgression has important consequences for the study of numerous evolutionary processes, including adaptation, speciation, and macroevolutionary patterns. In addition, detailed studies of introgressed regions could provide insights into the morphology of the extinct lineage, providing an unexpected link between genomics and the fossil record. Hence, new methods that take into account ghost introgression will need to be developed.

    Review : Synergy between mechanistic modelling and data-driven models for modern animal production systems in the era of big data
    Ellis, J.L. ; Jacobs, M. ; Dijkstra, J. ; Laar, H. van; Cant, J.P. ; Tulpan, D. ; Ferguson, N. - \ 2020
    Animal (2020). - ISSN 1751-7311 - 15 p.
    animal production - digital agriculture - hybridization - machine learning - mechanistic modelling

    Mechanistic models (MMs) have served as causal pathway analysis and 'decision-support' tools within animal production systems for decades. Such models quantitatively define how a biological system works based on causal relationships and use that cumulative biological knowledge to generate predictions and recommendations (in practice) and generate/evaluate hypotheses (in research). Their limitations revolve around obtaining sufficiently accurate inputs, user training and accuracy/precision of predictions on-farm. The new wave in digitalization technologies may negate some of these challenges. New data-driven (DD) modelling methods such as machine learning (ML) and deep learning (DL) examine patterns in data to produce accurate predictions (forecasting, classification of animals, etc.). The deluge of sensor data and new self-learning modelling techniques may address some of the limitations of traditional MM approaches - access to input data (e.g. sensors) and on-farm calibration. However, most of these new methods lack transparency in the reasoning behind predictions, in contrast to MM that have historically been used to translate knowledge into wisdom. The objective of this paper is to propose means to hybridize these two seemingly divergent methodologies to advance the models we use in animal production systems and support movement towards truly knowledge-based precision agriculture. In order to identify potential niches for models in animal production of the future, a cross-species (dairy, swine and poultry) examination of the current state of the art in MM and new DD methodologies (ML, DL analytics) is undertaken. We hypothesize that there are several ways via which synergy may be achieved to advance both our predictive capabilities and system understanding, being: (1) building and utilizing data streams (e.g. intake, rumination behaviour, rumen sensors, activity sensors, environmental sensors, cameras and near IR) to apply MM in real-time and/or with new resolution and capabilities; (2) hybridization of MM and DD approaches where, for example, a ML framework is augmented by MM-generated parameters or predicted outcomes and (3) hybridization of the MM and DD approaches, where biological bounds are placed on parameters within a MM framework, and the DD system parameterizes the MM for individual animals, farms or other such clusters of data. As animal systems modellers, we should expand our toolbox to explore new DD approaches and big data to find opportunities to increase understanding of biological systems, find new patterns in data and move the field towards intelligent, knowledge-based precision agriculture systems.

    Data from: Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomes
    Moran, Peter A. ; Pascoal, Sonia ; Cezard, Timothee ; Risse, J.E. ; Ritchie, Michael G. ; Bailey, Nathan W. - \ 2018
    University College Cork
    hybridization - faster X effect - population genomics - sex chromosomes - RAD sequencing - Teleogryllus oceanicus - Teleogryllus commodus - Teleogryllus marini - Teleogryllus
    Linking intraspecific and interspecific divergence is an important challenge in speciation research. X chromosomes are expected to evolve faster than autosomes and disproportionately contribute to reproductive barriers, and comparing genetic variation on X and autosomal markers within and between species can elucidate evolutionary processes that shape genome variation. We performed RADseq on a 16-population transect of two closely-related Australian cricket species, Teleogryllus commodus and T. oceanicus, covering allopatry and sympatry. This classic study system for sexual selection provides a rare exception to Haldane’s rule, as hybrid females are sterile. We found no evidence of recent introgression, despite the fact that the species co-exist in overlapping habitats in the wild and interbreed in the laboratory. Putative X-linked loci showed greater differentiation between species compared to autosomal loci. However, population differentiation within species was unexpectedly lower on X-linked markers than autosomal markers, and relative X-to-autosomal genetic diversity was inflated above neutral expectations. Populations of both species showed genomic signatures of recent population expansions, but these were not strong enough to account for the inflated X/A diversity. Instead, most of the excess polymorphism on the X could better be explained by sex-biased processes that increase the relative effective population size of the X, such as interspecific variation in the strength of sexual selection among males. Taken together, the opposing patterns of diversity and differentiation at X versus autosomal loci implicate a greater role for sex-linked genes in maintaining species boundaries in this system.
    Political Consumerism: Research Challenges and Future Directions
    Boström, Magnus ; Micheletti, Michele ; Oosterveer, P.J.M. - \ 2018
    In: The Oxford Handbook of Political Consumerism / Boström, Magnus, Micheletti, Michele, Oosterveer, Peter, Oxford University Press - ISBN 9780190629038
    political consumerism - consumer research design - industry sectors - hybridization - supply and demand - infrastructure - moral dilemmas - democracy - religion - nationalism - research design
    This chapter highlights The Oxford Handbook of Political Consumerism’s most interesting findings and identifies major characteristics and conceptual/methodological topics for advancing research on the phenomenon of political consumerism. It emphasizes how scholars study the phenomenon’s multidimensionality in a more fragmented context and explains differences in the forms and spread of political consumerism across industry sectors. The wide diversity in the forms and spread of political consumerism across countries and regions is related to political and cultural traditions, levels of economic development, and the role of social media. The Handbook also puts stress on how all four forms of political consumerism are involved in democratically problematic types of political consumerism. Political consumerism’s effectiveness is evaluated from several perspectives along with a recommendation for further study of input, output, and outcome aspects. The chapter encourages new studies on undemocratic types of political consumerism as well as investigations into the absence of political consumerism in certain countries and industry sectors. All this requires innovative methodology, new theoretical conceptualization, and cross-disciplinary work.” through innovative methodology, conceptualization, and cross-disciplinary work.
    Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomes
    Moran, Peter A. ; Pascoal, Sonia ; Cezard, Timothee ; Risse, Judith E. ; Ritchie, Michael G. ; Bailey, Nathan W. - \ 2018
    Molecular Ecology 27 (2018)19. - ISSN 0962-1083 - p. 3905 - 3924.
    faster-X effect - hybridization - population genomics - RAD sequencing - sex chromosomes - Teleogryllus

    Linking intraspecific and interspecific divergence is an important challenge in speciation research. X chromosomes are expected to evolve faster than autosomes and disproportionately contribute to reproductive barriers, and comparing genetic variation on X and autosomal markers within and between species can elucidate evolutionary processes that shape genome variation. We performed RADseq on a 16 population transect of two closely related Australian cricket species, Teleogryllus commodus and T. oceanicus, covering allopatry and sympatry. This classic study system for sexual selection provides a rare exception to Haldane's rule, as hybrid females are sterile. We found no evidence of recent introgression, despite the fact that the species coexist in overlapping habitats in the wild and interbreed in the laboratory. Putative X-linked loci showed greater differentiation between species compared with autosomal loci. However, population differentiation within species was unexpectedly lower on X-linked markers than autosomal markers, and relative X-to-autosomal genetic diversity was inflated above neutral expectations. Populations of both species showed genomic signatures of recent population expansions, but these were not strong enough to account for the inflated X/A diversity. Instead, most of the excess polymorphism on the X could better be explained by sex-biased processes that increase the relative effective population size of the X, such as interspecific variation in the strength of sexual selection among males. Taken together, the opposing patterns of diversity and differentiation at X versus autosomal loci implicate a greater role for sex-linked genes in maintaining species boundaries in this system.

    Benefits from living together? Clades whose species use similar habitats may persist as a result of eco-evolutionary feedbacks
    Prinzing, Andreas ; Ozinga, Wim A. ; Brändle, Martin ; Courty, Pierre Emmanuel ; Hennion, Françoise ; Labandeira, Conrad ; Parisod, Christian ; Pihain, Mickael ; Bartish, Igor V. - \ 2017
    New Phytologist 213 (2017)1. - ISSN 0028-646X - p. 66 - 82.
    assembly of present and fossil communities - competition - conservation biology - enemy pressure and mutualism of coexisting species - evolution and conservatism - hybridization - niche breadth

    (Table presented.). Summary: Recent decades have seen declines of entire plant clades while other clades persist despite changing environments. We suggest that one reason why some clades persist is that species within these clades use similar habitats, because such similarity may increase the degree of co-occurrence of species within clades. Traditionally, co-occurrence among clade members has been suggested to be disadvantageous because of increased competition and enemy pressure. Here, we hypothesize that increased co-occurrence among clade members promotes mutualist exchange, niche expansion or hybridization, thereby helping species avoid population decline from environmental change. We review the literature and analyse published data for hundreds of plant clades (genera) within a well-studied region and find major differences in the degree to which species within clades occupy similar habitats. We tentatively show that, in clades for which species occupy similar habitats, species tend to exhibit increased co-occurrence, mutualism, niche expansion, and hybridization – and rarely decline. Consistently, throughout the geological past, clades whose species occupied similar habitats often persisted through long time-spans. Overall, for many plant species, the occupation of similar habitats among fellow clade members apparently reduced their vulnerability to environmental change. Future research should identify when and how this previously unrecognized eco-evolutionary feedback operates.

    Crossing species boundaries : the hybrid histories of the true geese
    Ottenburghs, Jente - \ 2016
    Wageningen University. Promotor(en): Herbert Prins; R.C. Ydenburg, co-promotor(en): Hendrik-Jan Megens. - Wageningen : Wageningen University - ISBN 9789462579781 - 268
    geese - anser - crossing - species - hybridization - speciation - phylogenomics - ganzen - anser - kruisen - soorten - hybridisatie - soortvorming - phylogenomica

    Hybridization, the interbreeding of different species, is a common phenomenon in birds: about 16% of bird species is known to have hybridized with at least one other species. Numerous avian hybrid zones have been studied from a morphological or genetic perspective, often documenting the interspecific exchange of genetic material by hybridization and backcrossing (i.e. introgression). The incidence of hybridization varies among bird orders with the Anseriformes (waterfowl: ducks, geese and swans) showing the highest propensity to hybridize. In this thesis, I provide a genomic perspective on the role of hybridization in the evolutionary history of one particular anseriform tribe, the Anserini or “True Geese”, which comprises 17 species divided over two genera: Anser and Branta . The diversification of this bird group took place in the late Pliocene and the early Pleistocene (between four and two million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of temperate grasslands. Most species show a steady population increase during this period, followed by population subdivision during the Last Glacial Maximum about 110,000 to 12,000 years ago. The combination of large effective population sizes and occasional range shifts facilitated contact between the diverging goose species, resulting in high levels of interspecific gene flow. Introgressive hybridization might have enabled these goose populations to quickly adapt to changing environments by transferring of advantageous alleles across species boundaries, increasing standing genetic variation or expanding phenotypic variation of certain traits (e.g., beak morphology). Hybridization seems to be a common and integral component in the evolution and diversification of geese. The pervasiveness of rapid speciation and hybridization in geese complicates the attempt to capture their evolutionary history in a phylogenetic tree, advocating a phylogenetic network approach. Indeed, trying to capture the complex diversification of the True Geese in a branching tree can be regarded as a wild goose chase.

    Birds in a bush : Toward an avian phylogenetic network
    Ottenburghs, Jente ; Hooft, Pim van; Wieren, Sipke E. van; Ydenberg, Ronald C. ; Prins, Herbert H.T. - \ 2016
    The Auk : a quarterly journal of ornithology 133 (2016)4. - ISSN 0004-8038 - p. 577 - 582.
    adaptive radiation - genomics - hybridization - phylogenetic networks - Phylogenetics

    Reconstructing the avian tree of life has become one of the major goals in ornithology. The use of genomic tools seemed a promising approach to reach this goal, but, instead, phylogenetic analyses of large numbers of genes uncovered high levels of incongruence between the resulting gene trees. This incongruence can be caused by several biological processes, such as recombination, hybridization, and rapid speciation (which can lead to incomplete lineage sorting). These processes directly or indirectly amount to deviations from tree-like patterns, thereby thwarting the use of phylogenetic trees. Phylogenetic networks provide an ideal tool to deal with these difficulties. We illustrate the usefulness of phylogenetic networks to capture the complexity and subtleties of diversification processes by discussing several recent genomic analyses of birds in general and the well-known radiation of Darwin's finches. With the increasing amount of genomic data in avian phylogenetic studies, capturing the evolutionary history of a set of taxa in a phylogenetic tree will become increasingly difficult. Moreover, given the widespread occurrence of hybridization and the numerous adaptive radiations in birds, phylogenetic networks provide a powerful tool to display and analyse the evolutionary history of many bird groups. The genomic era might thus result in a paradigm shift in avian phylogenetics from trees to bushes.

    Data from: Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs
    Bosse, Mirte ; Soares Lopes, Marcos ; Madsen, Ole ; Megens, Hendrik-Jan ; Crooijmans, Richard ; Frantz, Laurent ; Harlizius, Barbara ; Bastiaansen, John ; Groenen, Martien - \ 2015
    Wageningen University & Research
    Commercial breeding - adaptive introgression - selection - domestication - hybridization - Sus scrofa
    Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.
    Production of interspecific Campanula hybrids by ovule culture: exploring the effecto of ovule isolation time
    Röper, A.C. ; Lütken, H. ; Christensen, B. ; Boutilier, K.A. ; Petersen, K.K. ; Müller, R. - \ 2015
    Euphytica 203 (2015). - ISSN 0014-2336 - p. 643 - 657.
    embryo rescue - inbreeding depression - breeding system - hybridization - incompatibility - trifolium - inheritance - phylogeny - endosperm - crosses
    The Campanula genus comprises several economically important ornamental plants species.Wide hybridisation is a method to increase phenotypic variability, but is limited due to interspecies hybridisation barriers.In this study we investigated whether ovule culture could be used to increase the success rate of interspecific hybridisation between C. portenschlagiana 9 C. poscharskyana and C. medium 9 C. formanekiana. The effect of different ovule isolation times on ovule germination in vitro was examined. In general, the number of collectible ovules and ovule germination was low. Interspecific hybrids between C. medium and C. formanekiana exhibited an increased number of viable ovules with later isolation time, but with different ovule germination rates. A parent-of-origin effect on both the number of collectible ovules and ovule germination was observed for C. medium 9 C. formanekiana. Histological analysis of embryo and endosperm development in collectible ovules isolated at different time points from interspecific crosses showed that the vast majority of ovules did not contain an embryo. When present, embryo development only progressed with ovule collection time in the C. medium and C. formanekiana crosses. The occurrence of miscoloured seedlings in interspecific crosses indicated incompatibilities between the parental lines that could not be prevented by reciprocal crossing. The low number of collectible ovules and germination rates might be inhibited due to fertilisation barriers.With this study, a protocol for ovule culture was established and the usefulness of ovule culture to obtain interspecific hybrids of selected Campanula species was demonstrated
    Testing the Generalist-Specialist Dilemma: The Role of Pyrrolizidine Alkaloids in Resistance to Invertebrate Herbivores in Jacobaea Species
    Wei, X. ; Vrieling, K. ; Mulder, P.P.J. ; Klinkhamer, P.G.L. - \ 2015
    Journal of Chemical Ecology 41 (2015). - ISSN 0098-0331 - p. 159 - 167.
    longitarsus flea beetles - senecio-jacobaea - secondary metabolites - natural-selection - chemical defense - ipomopsis-aggregata - plant defense - scarlet-gilia - host plants - hybridization
    Plants produce a diversity of secondary metabolites (SMs) to protect them from generalist herbivores. On the other hand, specialist herbivores use SMs for host plant recognition, feeding and oviposition cues, and even sequester SMs for their own defense. Therefore, plants are assumed to face an evolutionary dilemma stemming from the contrasting effects of generalist and specialist herbivores on SMs. To test this hypothesis, bioassays were performed with F2 hybrids from Jacobaea species segregating for their pyrrolizidine alkaloids (PAs), using a specialist flea beetle (Longitarsus jacobaeae) and a generalist slug (Deroceras invadens). Our study demonstrated that while slug feeding damage was negatively correlated with the concentration of total PAs and that of senecionine-like PAs, flea beetle feeding damage was not affected by PAs. It was positively correlated though, with leaf fresh weight. The generalist slug was deterred by senecionine-like PAs but the specialist flea beetle was adapted to PAs in its host plant. Testing other herbivores in the same plant system, it was observed that the egg number of the specialist cinnabar moth was positively correlated with jacobine-like PAs, while the silver damage of generalist thrips was negatively correlated with senecionine- and jacobine-like PAs, and the pupae number of generalist leaf miner was negatively correlated with otosenine-like PAs. Therefore, while the specialist herbivores showed no correlation whatsoever with PA concentration, the generalist herbivores all showed a negative correlation with at least one type of PA. We concluded that the generalist herbivores were deterred by different structural groups of PAs while the specialist herbivores were attracted or adapted to PAs in its host plants.
    The hybrid nature of pig genomes : unraveling the mosaic haplotype structure in wild and commercial Sus scrofa populations
    Bosse, M. - \ 2015
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Hendrik-Jan Megens; Ole Madsen. - Wageningen : Wageningen University - ISBN 9789462573000 - 253
    dieren - varkens - dierveredeling - genomen - hybridisatie - sus scrofa - haplotypen - genomica - populaties - genetische variatie - animals - pigs - animal breeding - genomes - hybridization - sus scrofa - haplotypes - genomics - populations - genetic variation - cum laude
    cum laude graduation
    Data from: Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations
    Bosse, M. ; Megens, H.J.W.C. ; Madsen, O. ; Frantz, L.A.F. ; Paudel, Y. ; Crooijmans, R.P.M.A. ; Groenen, M. - \ 2014
    pigs - phylogenetic tree - domestication - hybridization
    The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine-scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.
    Data from: Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations
    Frantz, L.A.F. ; Madsen, O. ; Megens, H.J.W.C. ; Groenen, M. ; Lohse, H. - \ 2014
    Wageningen UR
    speciation - hybridization - population genetics - empirical - phylogeography - genomics / proteomics - conservation genetics
    In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island Southeast Asia (ISEA). A previous study revealed signatures of inter-specific admixture between these Sus species (Frantz et al. (2013) Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. Genome biology, 14, R107). However, the timing, directionality and extent of this admixture remain unknown. Here we use a likelihood based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that inter-specific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture.
    Ploidy manipulation and introgression breeding in Darwin hybrid tulips
    Marasek-Ciolakowska, A. ; Xie, S.L. ; Arens, P. ; Tuyl, J.M. van - \ 2014
    Euphytica 198 (2014)3. - ISSN 0014-2336 - p. 389 - 400.
    asiatic lilies lilium - gish analysis - sexual polyploidization - interspecific hybrids - garden tulips - genome - recombination - gesneriana - hybridization - fosteriana
    Meiotic polyploidisation via crossing with 2n gamete producing genotypes and interploidy crosses are two of the main methods currently used to obtain polyploid tulips. In our study diploid 2n gamete producing F-1 hybrids of Darwin hybrids (Tulipa gesneriana x Tulipa fosteriana) and triploid hybrid resulting from 'Rhodos' x 'Princeps' cross were used as pollen donor and crossed with cultivars of T. gesneriana in the following combination: 2x x 2x, 3x x 2x, 2x x 3x, and 3x x 3x. The progenies resulting from crosses at diploid level were mostly diploid, whereas a few seedlings were triploid. In 3x x 2x crosses aneuploids with chromosome constitution in between triploid and tetraploid (43-45 chromosomes) were predominant, but also one tetraploid (2n = 4x = 48) and four pentaploids (2n = 5x = 60) were obtained. In 2x x 3x crosses most progenies were triploid with the exception of a few aneuploids (3x + 1 and 3x - 1), whereas in 3x x 3x cross diploid and aneuploid genotypes were recorded with chromosome number varied from 27 to 34. These results indicate that triploid parents produced aneuploid as well as euploid (x, 2x, 3x) gametes and that success in ploidy manipulation in tulip depends to a large degree on the ploidy level of the parental genotypes used for hybridization. Genome constitution of selected population of F1 and BC1 hybrids was analyzed through genomic in situ hybridization (GISH). GISH analysis of the BC1 showed a considerable amount of intergenomic recombination which is desirable for introgression breeding.
    Long-term acclimation of anaerobic sludges for high-rate methanogenesis from LCFA
    Silva, S.A. ; Cavaleiro, A.J. ; Pereira, M.A. ; Stams, A.J.M. ; Alves, M.M. ; Sousa, D.Z. - \ 2014
    Biomass and Bioenergy 67 (2014). - ISSN 0961-9534 - p. 297 - 303.
    chain fatty-acids - oleic-acid - oxidizing bacteria - methane production - waste-water - digestion - lipids - quantification - hybridization - accumulation
    Inhibition of methanogens by long chain fatty acids (LCFA) and the low numbers of LCFA-degrading bacteria are limitations to exploit biogas production from fat-rich wastewaters. Generally reactors fail due to excessive LCFA accumulation onto the sludge. Here, long-term acclimation and bioaugmentation with a LCFA-degrading coculture were hypothesized as strategies to enhance methanogenic conversion of these compounds. Anaerobic sludges previously exposed to LCFA for more than 100 days converted a specific biomass-associated substrate of (3.2 ± 0.1) kg·kg-1 with very short lag phases (
    Cytogenetic studies on meiotic chromosome behaviors in sterile Oriental x Trumpet lily
    Luo, J.R. ; Tuyl, J.M. van; Arens, P. ; Niu, L.X. - \ 2013
    Genetics and Molecular Research 12 (2013)4. - ISSN 1676-5680 - p. 6673 - 6684.
    immature hybrid embryos - u-type exchange - crosses - lilies - meiosis - culture - inversions - spindle - hybridization - aberrations
    In order to determine the reasons for pollen sterility in lily hybrids, four diploid sterile Oriental x Trumpet (OT) lily cultivars ('Nymph', 'Gluhwein', 'Yelloween', and 'Shocking') were used to investigate the meiotic chromosome behaviors in pollen mother cells (PMCs), using genomic in situ hybridization and conventional cytological methods. At metaphase I, chromosome associations were quite variable, not only among different genotypes but also in different PMCs of the same genotype. In addition to bivalents, a certain amount of univalent, trivalents, and quadrivalents were observed in all of the investigated genotypes. In addition, ring octavalents and ring hexavalents were observed in 'Nymph'. Even dodecavalents were observed in 'Nymph'. These abnormal chromosome associations at metaphase I implied the occurrence of chromosome interchanges (translocation) in these intersectional hybrids. At anaphase-telophase, a large number of laggard chromosomes and different kinds of chromosome bridge configurations were observed. At the tetrad stage, micronuclei and polyads were also found in many PMCs. All of these abnormal chromosome behaviors in PMCs were responsible for the pollen sterility in lily hybrids.
    Epigenetic changes and transposon reactivation in Thai rice hybrids. Molecular Breeding
    Kantama, L. ; Junbuathong, S. ; Sakulkoo, J. ; Jong, J.H.S.G.M. de; Apisitwanich, S. - \ 2013
    Molecular Breeding 31 (2013)4. - ISSN 1380-3743 - p. 815 - 827.
    cytosine methylation - dna methylation - elements mites - genome - retrotransposons - hybridization - markers - inheritance - activation - expression
    Inter- or intraspecific hybridization is the first step in transferring exogenous traits to the germplasm of a recipient crop. One of the complicating factors is the occurrence of epigenetic modifications of the hybrids, which in turn can change their gene expression and phenotype. In this study we present an analysis of epigenome changes in rice hybrids that were obtained by crossing rice cultivars, most of them of indica type and Thai origin. Comparing amplified fragment length polymorphism (AFLP) fingerprints of twenty-four cultivars, we calculated Nei’s indexes for measuring genetic relationships. Epigenetic changes in their hybrids were established using methylation-sensitive AFLP fingerprinting and transposon display of the rice transposable elements (TEs) Stowaway Os-1 and Mashu, leading to the question whether the relationship between parental genomes is a predictor of epigenome changes, TE reactivation and changes in TE methylation. Our study now reveals that the genetic relationship between the parents and DNA methylation changes in their hybrids is not significantly correlated. Moreover, genetic distance correlates only weakly with Mashu reactivation, whereas it does not correlate with Stowaway Os-1 reactivation. Our observations also suggest that epigenome changes in the hybrids are localized events affecting specific chromosomal regions and transposons rather than affecting the genomic methylation landscape as a whole. The weak correlation between genetic distance and Mashu methylation and reactivation points at only limited influence of genetic background on the epigenetic status of the transposon. Our study further demonstrates that hybridizations between and among specific japonica and indica cultivars induce both genomic DNA methylation and reactivation/methylation change in the Stowaway Os-1 and Mashu transposons. The observed epigenetic changes seem to affect the transposons in a clear manner, partly driven by stochastic processes, which may account for a broader phenotypic plasticity of the hybrids. A better understanding of the epigenome changes leading to such transposon activation can lead to the development of novel tools for more variability in future rice breeding
    Cross-sectoral conflicts for water under climate change: the need to include water quality impacts
    Vliet, M.T.H. van; Ludwig, F. ; Kabat, P. - \ 2013
    planten - polyploïdie - hybriden - hybridisatie - genomica - evolutie - drosophila - plants - polyploidy - hybrids - hybridization - genomics - evolution - drosophila
    Climate change is expected to increase pressures on water use between different sectors (e.g. agriculture, energy, industry, domestic uses) and ecosystems. While climate change impacts on water availability have been studied widely, less work has been done to assess impacts on water quality. This study proposes a modelling framework to incorporate water quality in analyses of cross-sectoral conflicts for water between human uses and ecosystems under climate change and socio-economic changes. We illustrate this with an example that shows that increasing river temperatures and declines in summer low flow under climate change are likely to increase environmental restrictions on cooling water use, with substantial reductions in power plant capacities in Europe and the US. Hence, conflicts between environmental objectives and electricity supply are expected to increase due to both changes in water availability and water quality (water temperature) under climate change. A new impact modelling framework is proposed, which integrates relations between water availability, water quality and cross-sectoral water uses, including water requirements for ecosystems. This could provide improved understanding of how climate change and socioeconomic developments will affect the ‘water-energy-food-ecosystem nexus’. Index Terms—river flow, water temperature, water quality, climate change, socio-economic developments, human water use, ecosystems
    Pyrrolizidine Alkaloid Composition Influences Cinnabar Moth Oviposition Preferences in Jacobaea Hybrids
    Cheng, D. ; Meijden, E. van der; Mulder, P.P.J. ; Vrieling, K. ; Klinkhamer, P.G.L. - \ 2013
    Journal of Chemical Ecology 39 (2013)3. - ISSN 0098-0331 - p. 430 - 437.
    host-plant choice - senecio-jacobaea - specialist herbivore - generalist herbivores - tyria-jacobaeae - chemical defense - evolution - hybridization - populations - performance
    Plants produce a variety of secondary metabolites (PSMs) that may be selective against herbivores. Yet, specialist herbivores may use PSMs as cues for host recognition, oviposition, and feeding stimulation, or for their own defense against parasites and predators. This summarizes a dual role of PSMs: deter generalists but attract specialists. It is not clear yet whether specialist herbivores are a selective force in the evolution of PSM diversity. A prerequisite for such a selective force would be that the preference and/or performance of specialists is influenced by PSMs. To investigate these questions, we conducted an oviposition experiment with cinnabar moths (Tyria jacobaeae) and plants from an artificial hybrid family of Jacobaea vulgaris and Jacobaea aquatica. The cinnabar moth is a specialist herbivore of J. vulgaris and is adapted to pyrrolizidine alkaloids (PAs), defensive PSMs of these plants. The number of eggs and egg batches oviposited by the moths were dependent on plant genotype and positively correlated to concentrations of tertiary amines of jacobine-like PAs and some otosenine-like PAs. The other PAs did not correlate with oviposition preference. Results suggest that host plant PAs influence cinnabar moth oviposition preference, and that this insect is a potential selective factor against a high concentration of some individual PAs, especially those that are also involved in resistance against generalist herbivores
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