peter Breyne - Academia.edu (original) (raw)

Papers by peter Breyne

Current Opinion in Plant Biology, 2001

Molecular and General Genetics, 1992

T-DNA vectors were constructed which carry a β-glucuronidase (gusA) gene fused to the promoter of... more T-DNA vectors were constructed which carry a β-glucuronidase (gusA) gene fused to the promoter of the nopaline synthase (nos) gene and the 3′ end of the octopine synthase (ocs) gene. This reporter gene was cloned at different locations and orientations towards the right T-DNA border. For each construct, between 30 and 60 stably transformed calli were analysed for β-glucuronidase activity. Depending on the T-DNA configuration, distinct populations of gusA-expressing calli were obtained. Placing the reporter gene in the middle of the T-DNA results in relatively low expression levels and a limited inter-transformant variability. Placing the gene with its promoter next to the right border led to an increase in both the mean activity and the variability level. With this construct, some of the calli expressed the gusA gene at levels four to five times higher than the mean. In all these series, at least 30% of the calli contained reporter gene activities that were less than half of the mean expression level. Separating the gusA gene from the right T-DNA border by an additional 3′-untranslated region, derived from the nos gene, resulted in an increase in the mean expression to a level almost four times higher than that of constructions carrying the reporter gene in the middle of the T-DNA. Moreover, the number of transformants with extremely low activities decreased by at least 50% and this resulted in significantly lower inter-transformant variability independently of the orientation of the reporter gene on the T-DNA.

Proceedings of The National Academy of Sciences, 2002

Using synchronized tobacco Bright Yellow-2 cells and cDNAamplified fragment length polymorphism-b... more Using synchronized tobacco Bright Yellow-2 cells and cDNAamplified fragment length polymorphism-based genomewide expression analysis, we built a comprehensive collection of plant cell cycle-modulated genes. Approximately 1,340 periodically expressed genes were identified, including known cell cycle control genes as well as numerous unique candidate regulatory genes. A number of plant-specific genes were found to be cell cycle modulated. Other transcript tags were derived from unknown plant genes showing homology to cell cycle-regulatory genes of other organisms. Many of the genes encode novel or uncharacterized proteins, indicating that several processes underlying cell division are still largely unknown.

Plant Molecular Biology Reporter, 1993

We have established a procedure for automated, kinetic analysis of β-glucuronidase (GUS) activiti... more We have established a procedure for automated, kinetic analysis of β-glucuronidase (GUS) activities using a colorimetric or fluorometric microtiter plate reader connected to a computer that directs the measurements and accesses the data. Compared with end-point measurements, the procedure saves time, is more accurate, and needs 20 times less material. It allows a more precise determination of GUS activities over a range of 400,000-fold, with a limit of detection of about 0.01 units of GUS per mL in the colorimetric assay and 0.1 milliunit of GUS in the fluorometric assay. A general protocol for the determination of GUS activities in transgenic plant tissue was worked out and applied to investigate the expression of a chimeric β-glucuronidase gene in stably transformed tobacco calli.

Molecular Breeding, 1999

Progress in the breeding of plantain and banana has been restricted by the complex genetic struct... more Progress in the breeding of plantain and banana has been restricted by the complex genetic structure and behaviour of cultivated polyploid Musa. Genetic improvement has been hindered due to the large amount of space required for growth and maintenance of plant populations, in addition to the long growth cycle and the low levels of fertility and seed viability characteristic of cultivated genotypes. Molecular marker assisted breeding has the potential to dramatically enhance the pace and efficiency of genetic improvement in Musa. This study was conducted to compare different PCR-based marker systems (RAPD, VNTR and AFLP) for the analysis of breeding populations generated from two diverse Musa breeding schemes. All three assays detected a high level of polymorphism between parental genotypes and within progeny populations. As expected, AFLP assays had by far the highest multiplex ratio while VNTR analysis detected the highest levels of polymorphism. AFLP analysis of a full-sib tetraploid hybrid population confirmed previous reports based on VNTR analysis, of a high frequency of recombination during 2n (3x) gamete formation by a triploid plantain landrace. In addition, both VNTR and RAPD analyses of a full-sib triploid hybrid population suggested a high frequency of homoeologous recombination during n (2x) gamete formation by tetraploid hybrids. In general, there was a poor correlation between estimates of genetic similarity based on different types of marker. The implications of these findings for the molecular breeding of Musa crops are discussed.

Conservation Genetics, 2010

Rosa arvensis is a naturally rare and scattered indigenous wild rose species in Flanders, the nor... more Rosa arvensis is a naturally rare and scattered indigenous wild rose species in Flanders, the northern part of Belgium. As is the case for many light demanding woody species in this area, it is currently threatened by habitat fragmentation and destruction due to high human pressure. Recent inventories revealed a restricted distribution pattern for this rose, concentrated mainly in two regions of the south western part of Flanders. Surprisingly, strong differentiation was observed among natural populations in these two proximate regions in both an AFLP-based and a morphological analysis. A common garden experiment indicated a partly genetic basis for the morphological divergence. Additionally, the AFLP analysis of roses sampled in the same forested area within one of the two regions resulted in two differentiated gene pools. Possible causes for the observed differentiation can be adaptive divergence, founder effects and/or historical hybridisation with dogroses. Together, the congruent genetic and morphometric differentiation between the two geographic regions urges a cautious approach in conservation programs.

Biodiversity and Conservation, 2002

Eugenia uniflora L. (pitanga) is widely distributed in tropical areas. It is present in coastal v... more Eugenia uniflora L. (pitanga) is widely distributed in tropical areas. It is present in coastal vegetation from Ceara, in northeastern Brazil, to Rio Grande do Sul, at the southern tip of the country. Eugenia uniflora is of ecological importance, both as colonizing species on disturbed land and as food supplier for a wide variety of insects, birds and mammals. Pitanga plays a role in the maintenance of shrubby coastal ecosystems, especially at disturbed sites, and in 'restinga' ecosystems, at the interface between low forest and strand vegetation. To investigate the genetic diversity residing within the species, three neighboring populations at a distance of less than 24 km from each other, with varying degrees of human impact, were studied. The level of genetic diversity within and between populations was assessed with amplified fragment length polymorphism (AFLP) methodology. A total of 532 AFLP markers were analyzed in 66 individual trees. The polymorphism level varied from 61.2 to 96% depending on the primer combination used. Intra- and inter-population genetic diversity analysis showed that more than 88% of the variation resided within the populations, with a Gst of 0.123. Nevertheless, using neighbor joining (NJ) and principal component analysis (PCA), on the genetic distance (GD) data, permitted the three analyzed populations to be differentiated.

Molecular Genetics and Genomics, 2003

An improved cDNA-AFLP method for genome-wide expression analysis has been developed. We demonstra... more An improved cDNA-AFLP method for genome-wide expression analysis has been developed. We demonstrate that this method is an efficient tool for quantitative transcript profiling and a valid alternative to microarrays. Unique transcript tags, generated from reverse-transcribed messenger RNA by restriction enzymes, were screened through a series of selective PCR amplifications. Based on in silico analysis, an enzyme combination was chosen that ensures that at least 60% of all the mRNAs were represented by an informative sequence tag. The sensitivity and specificity of the method allows one to detect poorly expressed genes and distinguish between homologous sequences. Accurate gene expression profiles were determined by quantitative analysis of band intensities, and subtle differences in transcriptional activity were revealed. A detailed screen for cell cycle-modulated genes in tobacco demonstrates the usefulness of the technology for genome-wide expression analysis.

Plant Systematics and Evolution, 2009

Multivariate analysis of both endocarp and leaf morphometrics is combined with cluster analysis a... more Multivariate analysis of both endocarp and leaf morphometrics is combined with cluster analysis and Bayesian inference of AFLP markers to assess the morphologic and genetic variation of five European members of Prunus section Prunus (P. cerasifera, P. domestica, P. insititia, P. spinosa, and P. × fruticans). Endocarp morphometrics separate most Prunus taxa studied, but overlap remains between P. domestica and P. cerasifera, and P. spinosa and P. × fruticans. Leaf morphometrics yield better separation of P. domestica and P. cerasifera, but do not allow distinction between P. spinosa and P. × fruticans. Both cluster analysis and PCoA of AFLP markers equally produce three distinct clusters. A first consists of all P. cerasifera samples and the sole P. cocomilia; a second cluster includes all individuals of P. domestica and P. insititia; and a third group comprises all P. spinosa and P. × fruticans samples.

Molecular and General Genetics, 1999

The degree of genetic diversity within and between 21 Arabidopsis thaliana (L.) Heynh ecotypes wa... more The degree of genetic diversity within and between 21 Arabidopsis thaliana (L.) Heynh ecotypes was estimated by AFLP analysis. Within seven of the 21 ecotypes, a low but significant level of polymorphism was detected, and for five of these ecotypes two or three distinct subgroups could be distinguished. As these ecotypes represent natural populations, this intra-ecotypic diversity reflects natural genetic variation and diversification within the ecotypes. The source of this diversity remains unclear but is intriguing in view of the predominantly self-fertilizing nature of Arabidopsis. Interrelationships between the different ecotypes were estimated after AFLP fingerprinting using two enzyme combinations (EcoRI/MseI and SacI/MseI) and a number of selective primer pairs. SacI recognition sites are less evenly distributed in the genome than EcoRI sites, and occur more frequently in coding sequences. In most cases, AFLP data from only one enzyme combination are used for genetic diversity analysis. Our results show that the use of two enzyme combinations can result in significantly different classifications of the ecotypes both in cluster and ordination analysis. This difference most probably reflects differences in the genomic distribution of the AFLP fragments generated, depending on the enzymes and selective primers used. For closely related varieties, as in the case of Arabidopsis ecotypes, this can preclude reliable classification.

Theoretical and Applied Genetics, 2002

The AFLP technique was used to assess the genetic relationships among the cultivated papaya (Cari... more The AFLP technique was used to assess the genetic relationships among the cultivated papaya (Carica papaya L.) and related species native to Ecuador. Genetic distances based on AFLP data were estimated for 95 accessions belonging to three genera including C. papaya, at least eight Vasconcella species and two Jacaratia species. Cluster analysis using different methods and principal co-ordinate analysis (PCO), based on the AFLP data from 496 polymorphic bands generated with five primer combinations, was performed. The resulted grouping of accessions of each species corresponds largely with their taxonomic classifications and were found to be consistent with other studies based on RAPD, isozyme and cpDNA data. The AFLP analysis supports the recent rehabilitation of the Vasconcella group as a genus; until recently Vasconcella was considered as a section within the genus Carica. Both cluster and PCO analysis clearly separated the species of the three genera and illustrated the large genetic distance between C. papaya accessions and the Vasconcella group. The specific clustering of the highly diverse group of Vasconcella × heilbornii accessions also suggests that these genotypes may be the result of bi-directional introgression events between Vasconcella stipulata and Vasconcella cundinamarcensis.

Transgenic Research, 1994

Studies on nuclear scaffolds and scaffold attachment regions (SARs) have recently been extended t... more Studies on nuclear scaffolds and scaffold attachment regions (SARs) have recently been extended to different plant species and indicate that SARs are involved in the structural and functional organization of the plant genome, as is the case for other eukaryotes. One type of SAR seems to delimit structural chromatin loops and may also border functional units of gene expression and DNA replication. Another group of SARs map close to regulatory elements and may be directly involved in gene expression. In this overview, we summarize the structural and functional properties of plant SARs in comparison with those of SARs from animals and yeast.

Wildlife Biology, 2007

T.J. 2007: Estimating social group size of Eurasian badgers Meles meles by genotyping remotely pl... more T.J. 2007: Estimating social group size of Eurasian badgers Meles meles by genotyping remotely plucked single hairs. -Wildl. Owing to the Eurasian badger's Meles meles role as an agricultural pest, its potential role in the transmission of bovine tuberculosis and other management problems, accurate estimation of badger abundance is required. At present, no censusing method exists that is accurate, cost-effective and relatively non-invasive. In this article, we test the feasibility of estimating badger social group and population size by genotyping DNA extracted from remotely plucked hair, obtained using unbaited barbed-wire traps suspended above runs and main sett entrances. Social group size was independently estimated by direct observation. The study was performed on 11 social groups in a population in Luxembourg, and hair samples were collected on alternate days during a four-week period. A total of 332 hair samples was collected, from which 303 single-hair extracts gave rise to a complete genetic profile after a single round of amplification. Of 48 multiple-hair extracts, 23% gave rise to a mixed profile from multiple contributors. Of samples collected from different barbs of the same trap on the same collection day, 53% originated from different individuals. After applying two error-checking protocols, an extended singles filter and a mismatch filter, 55 unique profiles were obtained. Mark-recapture analysis estimated the population to contain 61 badgers, whereas direct observation suggested a population of 49 badgers. By comparison with direct observation, hair-trapping yielded a higher estimate for six social groups, an equal estimate for four groups and a lower estimate for one group. We conclude that hair-trapping by means of unbaited barbed-wire traps, placed at sett entrances and well-used runs, offers a method of censusing badgers that is relatively accurate and precise, comparatively non-invasive, potentially applicable in a variety of habitats and at different population densities, and not prohibitively expensive. We suggest that DNA should be extracted from single hairs, rather than from hairs pooled from a single barb or a single trap, in order to avoid mixed profiles.

Molecular Ecology, 2005

The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics ... more The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift–dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies.

Scientia Horticulturae, 2007

Genetic stability of grafted marula trees within seven lines, some of which exhibiting interline ... more Genetic stability of grafted marula trees within seven lines, some of which exhibiting interline phenotypic variations, was evaluated using the AFLP technique. The study was conducted in two-fold using samples from the DR, LP, MR, OS, PH, SW and TR lines. The genetic analysis using leaf materials indicated varying levels of genetic variations between genotypes within the OS, MR, LP

The fine-scale pattern of correlated paternity was characterized within a population of the narro... more The fine-scale pattern of correlated paternity was characterized within a population of the narrow-endemic model plant species, Centaurea corymbosa, using microsatellites and natural progeny arrays. We used classical approaches to assess correlated mating within sibships and developed a new method based on pairwise kinship coefficients to assess correlated paternity within and among sibships in a spatio-temporal perspective. We also performed numerical simulations to assess the relative significance of different mechanisms promoting correlated paternity and to compare the statistical properties of different estimators of correlated paternity. Our new approach proved very informative to assess which factors contributed most to correlated paternity and presented good statistical properties. Within progeny arrays, we found that about one-fifth of offspring pairs were full-sibs. This level of correlated mating did not result from correlated pollen dispersal events (i.e., pollen codispersion) but rather from limited mate availability, the latter being due to limited pollen dispersal distances, the heterogeneity of pollen production among plants, phenological heterogeneity and, according to simulations, the self-incompatibility system. We point out the close connection between correlated paternity and the "TwoGener" approach recently developed to infer pollen dispersal and discuss the conditions to be met when applying the latter. Corresponding author: Laboratoire d'Eco-éthologie Evolutive, Uni-Sampson 1998). Variation in pollen viability among polversité Libre de Bruxelles, CP 160/12,

Heredity, 2003

Fine-scale structure of genetic diversity and gene flow were analysed in three Costa Rican popula... more Fine-scale structure of genetic diversity and gene flow were analysed in three Costa Rican populations of mahogany, Swietenia macrophylla. Population differentiation estimated using AFLPs and SSRs was low (38.3 and 24%) and only slightly higher than previous estimates for Central American populations based on RAPD variation (20%). Significant finescale spatial structure was found in all of the surveyed mahogany populations and is probably strongly influenced by the limited seed dispersal range of the species. Furthermore, a survey of progeny arrays from selected mother trees in two of the plots indicated that most pollinations involved proximate trees. These data indicate that very little gene flow, via either pollen or seed, is occurring between blocks of mahogany within a continuous or disturbed forest landscape. Thus, once diversity is removed from a forest population of mahogany, these data suggest that recovery would be difficult via seed or pollen dispersal, and provides an explanation for mahogany's apparent susceptibility to the pressures of logging. Evidence is reviewed from other studies of gene flow and seedling regeneration to discuss alternative extraction strategies that may maintain diversity or allow recovery of genetic resources.

The subgenus Rosa is very intriguing but complex. Nowadays, many European taxonomists apply the t... more The subgenus Rosa is very intriguing but complex. Nowadays, many European taxonomists apply the taxonomical structure of Henker (2000), although other classifications and views are still considered. In order to gain insight in the taxonomical structure, 1,144 individuals belonging to 27 different wild rose species and some spontaneous hybrids were sampled in Belgium, France, Germany, The Netherlands and Scandinavian countries.