Publications by authors named "Hans-Peter Koelewijn"

9 Publications

  • Page 1 of 1

Community genetics in the time of next-generation molecular technologies.

Mol Ecol 2013 Jun;22(12):3198-207

WSL Swiss Federal Research Institute, 8903, Birmensdorf, Switzerland.

Understanding the interactions of co-occurring species within and across trophic levels provides key information needed for understanding the ecological and evolutionary processes that underlie biological diversity. As genetics has only recently been integrated into the study of community-level interactions, the time is right for a critical evaluation of potential new, gene-based approaches to studying communities. Next-generation molecular techniques, used in parallel with field-based observations and manipulative experiments across spatio-temporal gradients, are key to expanding our understanding of community-level processes. Here, we introduce a variety of '-omics' tools, with recent studies of plant-insect herbivores and of ectomycorrhizal systems providing detailed examples of how next-generation approaches can revolutionize our understanding of interspecific interactions. We suggest ways that novel technologies may convert community genetics from a field that relies on correlative inference to one that reveals causal mechanisms of genetic co-variation and adaptations within communities.
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http://dx.doi.org/10.1111/mec.12300DOI Listing
June 2013

Cytoplasmic male sterility contributes to hybrid incompatibility between subspecies of Arabidopsis lyrata.

G3 (Bethesda) 2013 Oct 3;3(10):1727-40. Epub 2013 Oct 3.

Department of Biology, University of Oulu, FIN-90014 Oulu, Finland.

In crosses between evolutionarily diverged populations, genomic incompatibilities may result in sterile hybrids, indicating evolution of reproductive isolation. In several plant families, crosses within a population can also lead to male sterile progeny because of conflict between the maternally and biparentally inherited genomes. We examined hybrid fertility between subspecies of the perennial outcrossing self-incompatible Lyrate rockcress (Arabidopsis lyrata) in large reciprocal F2 progenies and three generations of backcrosses. In one of the reciprocal F2 progenies, almost one-fourth of the plants were male-sterile. Correspondingly, almost one-half of the plants in one of the four reciprocal backcross progenies expressed male sterility. In an additional four independent F2 and backcross families, three segregated male sterility. The observed asymmetrical hybrid incompatibility is attributable to male sterility factors in one cytoplasm, for which the other population lacks effective fertility restorers. Genotyping of 96 molecular markers and quantitative trait locus mapping revealed that only 60% of the plants having the male sterile cytoplasm and lacking the corresponding restorers were phenotypically male-sterile. Genotyping data showed that there is only one restorer locus, which mapped to a 600-kb interval at the top of chromosome 2 in a region containing a cluster of pentatricopeptide repeat genes. Male fertility showed no trade-off with seed production. We discuss the role of cytoplasm and genomic conflict in incipient speciation and conclude that cytoplasmic male sterility-lowering hybrid fitness is a transient effect with limited potential to form permanent reproductive barriers between diverged populations of hermaphrodite self-incompatible species.
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http://dx.doi.org/10.1534/g3.113.007815DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789797PMC
October 2013

Comparative mapping in the Fagaceae and beyond with EST-SSRs.

BMC Plant Biol 2012 Aug 29;12:153. Epub 2012 Aug 29.

INRA, UMR1202 BIOGECO, Cestas F-33610, France.

Background: Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species.

Results: We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype.

Conclusions: This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.
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http://dx.doi.org/10.1186/1471-2229-12-153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3493355PMC
August 2012

A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study.

BMC Genomics 2010 Oct 15;11:570. Epub 2010 Oct 15.

INRA, UMR1202 BIOGECO, F-33610 Cestas, France.

Background: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut).

Results: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.

Conclusion: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.
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http://dx.doi.org/10.1186/1471-2164-11-570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091719PMC
October 2010

Genetic impoverishment of the last black grouse (Tetrao tetrix) population in the Netherlands: detectable only with a reference from the past.

Mol Ecol 2008 Apr 10;17(8):1897-904. Epub 2008 Mar 10.

Population Biology and Conservation Biology, Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36, Uppsala, Sweden.

We have studied a small isolated population of black grouse (Tetrao tetrix) in the Netherlands to examine the impact of isolation and reduction in numbers on genetic diversity. We compared the genetic diversity in the last extant Dutch population with Dutch museum samples and three other black grouse populations (from England, Austria and Norway, respectively) representing isolated and continuous populations. We found significantly lower allelic richness, observed and expected heterozygosities in the present Dutch population compared to the continuous populations (Austria and Norway) and also to the historical Dutch population. However, using a bottleneck test on each population, signs of heterozygosity excess were only found in the likewise isolated English population despite that strong genetic drift was evident in the present Dutch population in comparison to the reference populations, as assessed both in pairwise F(ST)and STRUCTURE analyses. Simulating the effect of a population reduction on the Dutch population from 1948 onwards, using census data and with the Dutch museum samples as a model for the genetic diversity in the initial population, revealed that the loss in number of alleles and observed heterozygosity was according to genetic drift expectations and within the standard error range of the present Dutch population. Thus, the effect of the strong decline in the number of grouse on genetic diversity was only detectable when using a reference from the past. The lack of evidence for a population reduction in the present Dutch population by using the program bottleneck was attributed to a rapidly found new equilibrium as a consequence of a very small effective population size.
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http://dx.doi.org/10.1111/j.1365-294X.2008.03717.xDOI Listing
April 2008

Rapid change in relative growth rate between the vegetative and reproductive stage of the life cycle in Plantago coronopus.

New Phytol 2004 Jul 13;163(1):67-76. Epub 2004 Apr 13.

Netherlands Institute of Ecology, Department of Plant Population Biology, Heteren, The Netherlands.

•  A growth experiment with seedlings from Plantago coronopus, originating from small (0.13 mg) and large (0.20 mg) seeds, was conducted under optimum nutrient conditions to gain insight into the physiological processes associated with the vegetative and generative phase of plant growth. •  The relative growth rate (RGR) during the vegetative stage was 300 mg g  d and dropped at the initiation of flowering buds to 60 mg g  d , a fivefold reduction, while remaining exponential. Investment in reproductive structures had prevalence over vegetative structures during the generative phase of the life cycle. The RGR of reproductive structures was 105 mg g  d . •  The initiation of flowering was stage-dependent. After the formation of about 14 leaves, plants started to form flowering buds, independent of weight or leaf size. The shoot : root ratio stayed the same during both the vegetative and generative stages. The change from a two-compartment system (shoot and root) to a three-compartment system (shoot, root and reproductive structures) did not change the balance or functional equilibrium between root and shoot. •  Seed size effects lasted until the end of the experiment and were reflected in all morphological measurements.
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http://dx.doi.org/10.1111/j.1469-8137.2004.01078.xDOI Listing
July 2004

Variation in restorer genes and primary sexual investment in gynodioecious Plantago coronopus: the trade-off between male and female function.

Proc Biol Sci 2003 Sep;270(1527):1939-45

Netherlands Institute of Ecology, Centre for Terrestrial Ecology, PO Box 40, 6666 ZG Heteren, The Netherlands.

In many gynodioecious species the nuclear inheritance of male fertility is complex and involves multiple (restorer) genes. In addition to restoring plants from the female (male sterile) to the hermaphrodite (male fertile) state, these genes are also thought to play a role in the determination of the quantity of pollen produced by hermaphrodites. The more restorer alleles a hermaphroditic plant possesses, the higher the pollen production. To test this hypothesis I combined the results of crossing studies of the genetics of male sterility with phenotypic data on investment in stamens and ovules among the progeny of plants involved in these studies. The sex ratio (i.e. the frequency of hermaphrodites among the progeny), being a measure of the number of restorer alleles of the maternal plant, was positively related to the investment in pollen (male function), but negatively related to the investment in ovules (female function), in both field and greenhouse experiments. Consequently, a negative correlation between male and female function was observed (trade-off) and it is suggested that antagonistic pleiotropic effects of restorer genes might be the cause. Phenotypic gender, a measure combining investment in both pollen and ovules, was highly repeatable between field and greenhouse, indicating genetic determination of a more male- or female-biased allocation pattern among the studied plants.
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http://dx.doi.org/10.1098/rspb.2003.2462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1691454PMC
September 2003

MAGNITUDE AND TIMING OF INBREEDING DEPRESSION IN SCOTS PINE (PINUS SYLVESTRIS L.).

Evolution 1999 Jun;53(3):758-768

Department of Biology, University of Oulu, SF-90570, Oulu, Finland.

Inbreeding depression is a major selective force favoring outcrossing in flowering plants. However, some self-fertilization should weaken the harmful effects of inbreeding by exposing deleterious alleles to selection. This study examines the maintenance of inbreeding depression in the predominantly outcrossing species Pinus sylvestris L. (Scots pine). Open-pollinated and self-fertilized progeny of 23 maternal trees, originating from a natural stand in southern Finland, were grown at two sites. We observed significant inbreeding depression in two of the four life stages measured. Inbreeding depression was largest for seed maturation (δ = 0.74), where seedset in open-pollinated strobili (70.9%) was about four times higher than in selfed strobili (18.3%). Inbreeding depression in postgermination survival (upto an age of 23 years) was also high (δ = 0.62-0.75). No significant differences in height (δ = 0.05) or flowering (δ = 0.14) of the trees after 23 years were observed. Cumulative inbreeding depression was high (δ = 0.90-0.94) and differed significantly among maternal families (range 0.45-1.00). The magnitude of inbreeding depression among the 23 maternal parents was not significantly correlated between early (seed maturation) and later (postgermination survival) life stages, suggesting that its genetic basis varies across the life cycle. Size differences among the progeny types diminished in time due to nonrandom size-specific mortality, causing a decrease in the inbreeding depression estimates for height over time. Our results indicate that Scots pine exhibits high levels of inbreeding depression during both early and later stages of the life cycle. It is argued that self-fertilization in Scots pine is inefficient in purging the genetic load caused by highly deleterious mutations because of the nearly complete loss of selfed individuals over time. This results in an effectively random mating outcrossing population.
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http://dx.doi.org/10.1111/j.1558-5646.1999.tb05370.xDOI Listing
June 1999

EFFECTS OF DIFFERENT LEVELS OF INBREEDING ON PROGENY FITNESS IN PLANTAGO CORONOPUS.

Evolution 1998 Jun;52(3):692-702

Netherlands Institute of Ecology, Department of Plant Population Biology, Boterhoeksestraat 22, P.O. Box 40, 6666 ZG Heteren.

Inbreeding depression (δ) is a major selective force favoring outcrossing in flowering plants. Many phenotypic and genetic models of the evolution of selfing conclude that complete outcrossing should evolve whenever inbreeding depression is greater than one-half, otherwise selfing should evolve. Recent theoretical work, however, has challenged this view and emphasized (1) the importance of variation in inbreeding depression among individuals within a population; and (2) the nature of gene action between deleterious mutations at different loci (epistasis) as important determinants for the evolution of plant mating systems. The focus of this study was to examine the maintenance of inbreeding depression and the relationship between inbreeding level and inbreeding depression at both the population and the individual level in one population of the partially self-fertilizing plant Plantago coronopus (L.). Maternal plants, randomly selected from an area of about 50 m in a natural population, were used to establish lines with expected inbreeding coefficients (f) of 0, 0.25, 0.50, 0.75, and 0.875. Inbreeding depression was estimated both in the greenhouse and at the site of origin of the maternal plants by comparing growth, survival, flowering, and seed production of the progeny with different inbreeding coefficients. No significant inbreeding depression for these fitness traits was detected in the greenhouse after 16 weeks. This was in strong contrast to the field, where the traits all displayed significant inbreeding depression and declined with increased inbreeding. The results were consistent with the view that mutation to mildly deleterious alleles is the primary cause of inbreeding depression. At the family level, significantly different maternal line responses (maternal parent × inbreeding level interaction) provide a mechanism for the invasion of a selfing variant into the population through any maternal line exhibiting purging of its genetic load. At the population level, evidence for synergistic epistasis was detected for the probability of flowering, but not for total seed production. At the family level, however, a significant interaction between inbreeding level and maternal families for both traits was observed, indicating that epistasis could play a role in the expression of inbreeding depression among maternal lines.
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http://dx.doi.org/10.1111/j.1558-5646.1998.tb03694.xDOI Listing
June 1998
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