Evolutionary relationships among the Aegilops-Triticum relatives of cultivated wheats have been d... more Evolutionary relationships among the Aegilops-Triticum relatives of cultivated wheats have been difficult to resolve owing to incomplete lineage sorting and reticulate evolution. Recent studies have suggested that the wheat D-genome lineage (progenitor of Ae. tauschii) originated through homoploid hybridization between the A-genome lineage (progenitor of Triticum s.str.) and the B-genome lineage (progenitor of Ae. speltoides). Scenarios of reticulation have been debated, calling for adequate phylogenetic analyses based on comprehensive sampling. To reconstruct the evolution of Aegilops-Triticum diploids, we here combined high-throughput sequencing of 38 nuclear low-copy loci of multiple accessions of all 13 species with inferences of the species phylogeny using the full-parameterized MCMC_SEQ method. Phylogenies recovered a monophyletic Aegilops-Triticum lineage that began diversifying ~6.5 Ma ago and gave rise to four sublineages, i.e. the A- (2 species), B- (1 species), D- (9 spec...
The phenology of flowering was studied in an experimental garden, on diploid and tetraploid popul... more The phenology of flowering was studied in an experimental garden, on diploid and tetraploid populations of Anthoxanthum alpinum A. & D. Löve and of A. odoratum L. of central and southern Europe and also in situ in a contact zone between diploid A. alpinum and tetraploid A. odoratum. In the experimental garden, the phenological parameters were studied at the individual level (onset of flowering) and at the population level (dates on which each population showed opened anthers for the first time on 40, 50, 60, 70, or 80% of the plants). Anthoxanthum alpinum flowered earlier than A. odoratum, regardless of the respective ploidy level of the two taxa. The average time lag between the appearance of the stigma and that of the stamens was about 2 days for the two A. alpinum taxa and 6 days for those of A. odoratum. Flowering was spread over the longest period for the tetraploid A. odoratum, which shows the great phenological variability of this taxon. The in situ study confirms the precoci...
The maintenance of species integrity despite pervasive hybridization is ruled by the interplay be... more The maintenance of species integrity despite pervasive hybridization is ruled by the interplay between reproductive barriers. Endogenous postzygotic isolation will shape patterns of introgression in hybrid zones, leading to variable outcomes depending on the genetic mechanism involved. Here, we analyzed experimental and natural hybrid populations of Aegilops geniculata and Ae. triuncialis to examine the genetics of species boundaries in the face of gene flow. Because long-terminal repeat retrotransposons (LTR-RTs) showing differential evolutionary trajectories are likely to affect hybrid dysgenesis and reproductive isolation between these wild wheat species, we addressed the impact of LTR-RTs in shaping introgression between them. Experimental settings involving artificial sympatry and enforced crossings quantified strong, but incomplete reproductive isolation, and highlighted asymmetrical endogenous postzygotic isolation between the two species. Natural hybrid zones located in the ...
The role of polyploidy in the evolution of plants is reviewed. The types of polyploids and their ... more The role of polyploidy in the evolution of plants is reviewed. The types of polyploids and their origins are defined. Instant consequences of polyploidy are described, as well as the relationships between polyploidy and distribution, ecology and breeding system. The conditions for the establishment of polyploids in a diploid population are discussed. Finally, the evolution from polyploid to diploid inheritance (diploidisation) is summarised.
The mountain birch, Betula pubescens ssp. tortuosa is a tetraploid tree species which forms the t... more The mountain birch, Betula pubescens ssp. tortuosa is a tetraploid tree species which forms the tree limit in northern Fennoscandia. We identified nine polymorphic microsatellite loci in order to characterize the genetic structure of populations at different elevations close to the treeline. The microsatellite loci were highly polymorphic, with 14–42 alleles per locus and an average expected heterozygosity of 0.73 ± 0.25 under random chromosome segregation and 0.68 ± 0.23 under random chromatid segregation.
Proceedings. Biological sciences / The Royal Society, Jan 7, 2015
Interspecific hybridization leads to new interactions among divergent genomes, revealing the natu... more Interspecific hybridization leads to new interactions among divergent genomes, revealing the nature of genetic incompatibilities having accumulated during and after the origin of species. Conflicts associated with misregulation of transposable elements (TEs) in hybrids expectedly result in their activation and genome-wide changes that may be key to species boundaries. Repetitive genomes of wild wheats have diverged under differential dynamics of specific long terminal repeat retrotransposons (LTR-RTs), offering unparalleled opportunities to address the underpinnings of plant genome reorganization by selfish sequences. Using reciprocal F1 hybrids between three Aegilops species, restructuring and epigenetic repatterning was assessed at random and LTR-RT sequences with amplified fragment length polymorphism and sequence-specific amplified polymorphisms as well as their methylation-sensitive counterparts, respectively. Asymmetrical reorganization of LTR-RT families predicted to cause co...
Transposable elements (TEs) are expectedly central to genome evolution. To assess the impact of T... more Transposable elements (TEs) are expectedly central to genome evolution. To assess the impact of TEs in driving genome turnover, we used allopolyploid genomes, showing considerable deviation from the predicted additivity of their diploid progenitors and thus having undergone major restructuring. Genome survey sequencing was used to select 17 putatively active families of long terminal repeat retrotransposons. Genome-wide TE insertions were genotyped with sequence-specific amplified polymorphism (SSAP) in diploid progenitors and their derived polyploids, and compared with changes in random sequences to assess restructuring of four independent Aegilops allotetraploid genomes. Generally, TEs with different evolutionary trajectories from those of random sequences were identified. Thus, TEs presented family-specific and species-specific dynamics following polyploidy, as illustrated by Sabine showing proliferation in particular polyploids, but massive elimination in others. Contrasting wit...
Advances in biochemical engineering/biotechnology, 2007
Gene flow from crops to wild relatives by sexual reproduction is one of the major issues in risk ... more Gene flow from crops to wild relatives by sexual reproduction is one of the major issues in risk assessment for the cultivation of genetically engineered (GE) plants. The main factors which influence hybridization and introgression, the two processes of gene flow, as well as the accompanying containment measures of the transgene, are reviewed. The comparison of risks between Switzerland and Europe highlights the importance of regional studies. Differences were assessed for barley, beet and wheat. Moreover, transgene flow through several wild species acting as bridge (bridge species) has been up to now poorly investigated. Indeed, transgene flow may go beyond the closest wild relative, as in nature several wild species complexes hybridize. Its importance is assessed by several examples in Poaceae. Finally, the transgene itself has genetic and ecological consequences that are reviewed. Transgenic hybrids between crops and wild relatives may have lower fitness than the wild relatives, ...
Extensive gene flow between wheat (Triticum sp.) and several wild relatives of the genus Aegilops... more Extensive gene flow between wheat (Triticum sp.) and several wild relatives of the genus Aegilops has recently been detected despite notoriously high levels of selfing in these species. Here, we assess and model the spread of wheat alleles into natural populations of the barbed goatgrass (Aegilops triuncialis), a wild wheat relative prevailing in the Mediterranean flora. Our sampling, based on an extensive survey of 31 Ae. triuncialis populations collected along a 60 km × 20 km area in southern Spain (Grazalema Mountain chain, Andalousia, totalling 458 specimens), is completed with 33 wheat cultivars representative of the European domesticated pool. All specimens were genotyped with amplified fragment length polymorphism with the aim of estimating wheat admixture levels in Ae. triuncialis populations. This survey first confirmed extensive hybridization and backcrossing of wheat into the wild species. We then used explicit modelling of populations and approximate Bayesian computation to estimate the selfing rate of Ae. triuncialis along with the magnitude, the tempo and the geographical distance over which wheat alleles introgress into Ae. triuncialis populations. These simulations confirmed that extensive introgression of wheat alleles (2.7 × 10(-4) wheat immigrants for each Ae. triuncialis resident, at each generation) into Ae. triuncialis occurs despite a high selfing rate (Fis ≈ 1 and selfing rate = 97%). These results are discussed in the light of risks associated with the release of genetically modified wheat cultivars in Mediterranean agrosystems.
ABSTRACT Summary Variability between and within spontaneous populations of Hordeum murinum in Swi... more ABSTRACT Summary Variability between and within spontaneous populations of Hordeum murinum in Switzerland was studied by enzyme electrophoresis. Most of the variation (61.5%) occurred within populations, while 38.5% occurred between populations. Absence of cleistogamy was observed. The results suggest evidence for a mixed mating system in H. murinum. Isozyme diagnostic bands for H. murinum and cultivated barley were established, allowing the detection of putative hybrids between them. No hybrids were obtained after performing experimental hybridization in the field and in the greenhouse. None was detected in the progeny of H. murinum growing in spontaneous contact zones either, confirming the existence of strong genetic barriers against hybridization. Our results are discussed in the context of the risk of transgene escape, associated with the cultivation of transgenic crops.
Evolutionary relationships among the Aegilops-Triticum relatives of cultivated wheats have been d... more Evolutionary relationships among the Aegilops-Triticum relatives of cultivated wheats have been difficult to resolve owing to incomplete lineage sorting and reticulate evolution. Recent studies have suggested that the wheat D-genome lineage (progenitor of Ae. tauschii) originated through homoploid hybridization between the A-genome lineage (progenitor of Triticum s.str.) and the B-genome lineage (progenitor of Ae. speltoides). Scenarios of reticulation have been debated, calling for adequate phylogenetic analyses based on comprehensive sampling. To reconstruct the evolution of Aegilops-Triticum diploids, we here combined high-throughput sequencing of 38 nuclear low-copy loci of multiple accessions of all 13 species with inferences of the species phylogeny using the full-parameterized MCMC_SEQ method. Phylogenies recovered a monophyletic Aegilops-Triticum lineage that began diversifying ~6.5 Ma ago and gave rise to four sublineages, i.e. the A- (2 species), B- (1 species), D- (9 spec...
The phenology of flowering was studied in an experimental garden, on diploid and tetraploid popul... more The phenology of flowering was studied in an experimental garden, on diploid and tetraploid populations of Anthoxanthum alpinum A. & D. Löve and of A. odoratum L. of central and southern Europe and also in situ in a contact zone between diploid A. alpinum and tetraploid A. odoratum. In the experimental garden, the phenological parameters were studied at the individual level (onset of flowering) and at the population level (dates on which each population showed opened anthers for the first time on 40, 50, 60, 70, or 80% of the plants). Anthoxanthum alpinum flowered earlier than A. odoratum, regardless of the respective ploidy level of the two taxa. The average time lag between the appearance of the stigma and that of the stamens was about 2 days for the two A. alpinum taxa and 6 days for those of A. odoratum. Flowering was spread over the longest period for the tetraploid A. odoratum, which shows the great phenological variability of this taxon. The in situ study confirms the precoci...
The maintenance of species integrity despite pervasive hybridization is ruled by the interplay be... more The maintenance of species integrity despite pervasive hybridization is ruled by the interplay between reproductive barriers. Endogenous postzygotic isolation will shape patterns of introgression in hybrid zones, leading to variable outcomes depending on the genetic mechanism involved. Here, we analyzed experimental and natural hybrid populations of Aegilops geniculata and Ae. triuncialis to examine the genetics of species boundaries in the face of gene flow. Because long-terminal repeat retrotransposons (LTR-RTs) showing differential evolutionary trajectories are likely to affect hybrid dysgenesis and reproductive isolation between these wild wheat species, we addressed the impact of LTR-RTs in shaping introgression between them. Experimental settings involving artificial sympatry and enforced crossings quantified strong, but incomplete reproductive isolation, and highlighted asymmetrical endogenous postzygotic isolation between the two species. Natural hybrid zones located in the ...
The role of polyploidy in the evolution of plants is reviewed. The types of polyploids and their ... more The role of polyploidy in the evolution of plants is reviewed. The types of polyploids and their origins are defined. Instant consequences of polyploidy are described, as well as the relationships between polyploidy and distribution, ecology and breeding system. The conditions for the establishment of polyploids in a diploid population are discussed. Finally, the evolution from polyploid to diploid inheritance (diploidisation) is summarised.
The mountain birch, Betula pubescens ssp. tortuosa is a tetraploid tree species which forms the t... more The mountain birch, Betula pubescens ssp. tortuosa is a tetraploid tree species which forms the tree limit in northern Fennoscandia. We identified nine polymorphic microsatellite loci in order to characterize the genetic structure of populations at different elevations close to the treeline. The microsatellite loci were highly polymorphic, with 14–42 alleles per locus and an average expected heterozygosity of 0.73 ± 0.25 under random chromosome segregation and 0.68 ± 0.23 under random chromatid segregation.
Proceedings. Biological sciences / The Royal Society, Jan 7, 2015
Interspecific hybridization leads to new interactions among divergent genomes, revealing the natu... more Interspecific hybridization leads to new interactions among divergent genomes, revealing the nature of genetic incompatibilities having accumulated during and after the origin of species. Conflicts associated with misregulation of transposable elements (TEs) in hybrids expectedly result in their activation and genome-wide changes that may be key to species boundaries. Repetitive genomes of wild wheats have diverged under differential dynamics of specific long terminal repeat retrotransposons (LTR-RTs), offering unparalleled opportunities to address the underpinnings of plant genome reorganization by selfish sequences. Using reciprocal F1 hybrids between three Aegilops species, restructuring and epigenetic repatterning was assessed at random and LTR-RT sequences with amplified fragment length polymorphism and sequence-specific amplified polymorphisms as well as their methylation-sensitive counterparts, respectively. Asymmetrical reorganization of LTR-RT families predicted to cause co...
Transposable elements (TEs) are expectedly central to genome evolution. To assess the impact of T... more Transposable elements (TEs) are expectedly central to genome evolution. To assess the impact of TEs in driving genome turnover, we used allopolyploid genomes, showing considerable deviation from the predicted additivity of their diploid progenitors and thus having undergone major restructuring. Genome survey sequencing was used to select 17 putatively active families of long terminal repeat retrotransposons. Genome-wide TE insertions were genotyped with sequence-specific amplified polymorphism (SSAP) in diploid progenitors and their derived polyploids, and compared with changes in random sequences to assess restructuring of four independent Aegilops allotetraploid genomes. Generally, TEs with different evolutionary trajectories from those of random sequences were identified. Thus, TEs presented family-specific and species-specific dynamics following polyploidy, as illustrated by Sabine showing proliferation in particular polyploids, but massive elimination in others. Contrasting wit...
Advances in biochemical engineering/biotechnology, 2007
Gene flow from crops to wild relatives by sexual reproduction is one of the major issues in risk ... more Gene flow from crops to wild relatives by sexual reproduction is one of the major issues in risk assessment for the cultivation of genetically engineered (GE) plants. The main factors which influence hybridization and introgression, the two processes of gene flow, as well as the accompanying containment measures of the transgene, are reviewed. The comparison of risks between Switzerland and Europe highlights the importance of regional studies. Differences were assessed for barley, beet and wheat. Moreover, transgene flow through several wild species acting as bridge (bridge species) has been up to now poorly investigated. Indeed, transgene flow may go beyond the closest wild relative, as in nature several wild species complexes hybridize. Its importance is assessed by several examples in Poaceae. Finally, the transgene itself has genetic and ecological consequences that are reviewed. Transgenic hybrids between crops and wild relatives may have lower fitness than the wild relatives, ...
Extensive gene flow between wheat (Triticum sp.) and several wild relatives of the genus Aegilops... more Extensive gene flow between wheat (Triticum sp.) and several wild relatives of the genus Aegilops has recently been detected despite notoriously high levels of selfing in these species. Here, we assess and model the spread of wheat alleles into natural populations of the barbed goatgrass (Aegilops triuncialis), a wild wheat relative prevailing in the Mediterranean flora. Our sampling, based on an extensive survey of 31 Ae. triuncialis populations collected along a 60 km × 20 km area in southern Spain (Grazalema Mountain chain, Andalousia, totalling 458 specimens), is completed with 33 wheat cultivars representative of the European domesticated pool. All specimens were genotyped with amplified fragment length polymorphism with the aim of estimating wheat admixture levels in Ae. triuncialis populations. This survey first confirmed extensive hybridization and backcrossing of wheat into the wild species. We then used explicit modelling of populations and approximate Bayesian computation to estimate the selfing rate of Ae. triuncialis along with the magnitude, the tempo and the geographical distance over which wheat alleles introgress into Ae. triuncialis populations. These simulations confirmed that extensive introgression of wheat alleles (2.7 × 10(-4) wheat immigrants for each Ae. triuncialis resident, at each generation) into Ae. triuncialis occurs despite a high selfing rate (Fis ≈ 1 and selfing rate = 97%). These results are discussed in the light of risks associated with the release of genetically modified wheat cultivars in Mediterranean agrosystems.
ABSTRACT Summary Variability between and within spontaneous populations of Hordeum murinum in Swi... more ABSTRACT Summary Variability between and within spontaneous populations of Hordeum murinum in Switzerland was studied by enzyme electrophoresis. Most of the variation (61.5%) occurred within populations, while 38.5% occurred between populations. Absence of cleistogamy was observed. The results suggest evidence for a mixed mating system in H. murinum. Isozyme diagnostic bands for H. murinum and cultivated barley were established, allowing the detection of putative hybrids between them. No hybrids were obtained after performing experimental hybridization in the field and in the greenhouse. None was detected in the progeny of H. murinum growing in spontaneous contact zones either, confirming the existence of strong genetic barriers against hybridization. Our results are discussed in the context of the risk of transgene escape, associated with the cultivation of transgenic crops.
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Papers by François Felber