Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that ar... more Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.
Evolutionary studies that are aimed at defining the processes behind the present level and organi... more Evolutionary studies that are aimed at defining the processes behind the present level and organization of crop genetic diversity represent the fundamental bases for biodiversity conservation and use. A Mesoamerican origin of the common bean Phaseolus vulgaris was recently suggested through analysis of nucleotide polymorphism at the nuclear level. Here, we have used chloroplast microsatellites to investigate the origin of the common bean, on the basis of the specific characteristics of these markers (no recombination, haploid genome, uniparental inheritance), to validate these recent findings. Indeed, comparisons of the results obtained through analysis of nuclear and cytoplasmic DNA should allow the resolution of some of the contrasting information available on the evolutionary processes. The main outcomes of the present study are: (i) confirmation at the chloroplast level of the results obtained through nuclear data, further supporting the Mesoamerican origin of P. vulgaris, with central Mexico representing the cradle of its diversity; (ii) identification of a putative ancestral plastidial genome, which is characteristic of a group of accessions distributed from central Mexico to Peru, but which have not been highlighted beforehand through analyses at the nuclear level. Finally, the present study suggests that when a single species is analyzed, there is the need to take into account the complexity of the relationships between P. vulgaris and its closely related and partially intercrossable species P. coccineus and P. dumosus. Thus, the present study stresses the importance for the investigation of the speciation processes of these taxa through comparisons of both plastidial and nuclear variability. This knowledge will be fundamental not only from an evolutionary point of view, but also to put P. coccineus and P. dumosus germplasm to better use as a source of useful diversity for P. vulgaris breeding.
A deeper understanding of random markers is important if they are to be employed for a range of o... more A deeper understanding of random markers is important if they are to be employed for a range of objectives. The sequence specific amplified polymorphism (S-SAP) technique is a powerful genetic analysis tool which exploits the high copy number of retrotransposon long terminal repeats (LTRs) in the plant genome. The distribution and inheritance of S-SAP bands in the barley genome was
Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that ar... more Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.
... In the Chinese sample, Zhang et al. (2008) found 5% hybrids, noting that average seed weight ... more ... In the Chinese sample, Zhang et al. (2008) found 5% hybrids, noting that average seed weight of the Andean types was lower than that of the American Andean beans, with the opposite for the Mesoamerican Chinese bean. ...
We have studied the nucleotide diversity of common bean, Phaseolus vulgaris, which is characteriz... more We have studied the nucleotide diversity of common bean, Phaseolus vulgaris, which is characterized by two independent domestications in two geographically distinct areas: Mesoamerica and the Andes. This provides an important model, as domestication can be studied as a replicate experiment. We used nucleotide data from five gene fragments characterized by large introns to analyse 214 accessions (102 wild and 112 domesticated). The wild accessions represent a cross-section of the entire geographical distribution of P. vulgaris. A reduction in genetic diversity in both of these gene pools was found, which was three-fold greater in Mesoamerica compared with the Andes. This appears to be a result of a bottleneck that occurred before domestication in the Andes, which strongly impoverished this wild germplasm, leading to the minor effect of the subsequent domestication bottleneck (i.e. sequential bottleneck). These findings show the importance of considering the evolutionary history of crop species as a major factor that influences their current level and structure of genetic diversity. Furthermore, these data highlight a single domestication event within each gene pool. Although the findings should be interpreted with caution, this evidence indicates the Oaxaca valley in Mesoamerica, and southern Bolivia and northern Argentina in South America, as the origins of common bean domestication.
We examined the local adaptation patterns in a system comprising several interconnected
heterogen... more We examined the local adaptation patterns in a system comprising several interconnected heterogeneous plant populations from which populations of two phylogenetically closely related pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal agents of barley net blotch. We integrated two approaches, the comparison between the population structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that two closely related pathogens with very similar niche specialisation and life-styles can give rise to different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the coevolutionary ‘arms race’ between the plant and the net-form pathogen. Moreover, data suggested latitudinal clines of host resistance and that different ecological conditions can result in differential selective pressures at different sites. Our data are of interest for on-farm conservation of plant genetic resources, as also in establishing efficient breeding programs and strategies for deployment of resistance genes of P. teres.
Relatively few studies have extensively analysed the genetic diversity of the runner bean through... more Relatively few studies have extensively analysed the genetic diversity of the runner bean through molecular markers. Here, we used six chloroplast microsatellites (cpSSRs) to investigate the cytoplasmic diversity of 331 European domesticated accessions of the scarlet runner bean (Phaseolus coccineus L.), including the botanical varieties albiflorus, bicolor and coccineus, and a sample of 49 domesticated and wild accessions from Mesoamerica. We further explored the pattern of diversity of the European landraces using 12 phenotypic traits on 262 individuals. For 158 European accessions, we studied the relationships between cpSSR polymorphisms and phenotypic traits. Additionally, to gain insights into the role of gene flow and migration, for a subset of 115 accessions, we compared and contrasted the results obtained by cpSSRs and phenotypic traits with those obtained in a previous study with 12 nuclear microsatellites (nuSSRs). Our results suggest that both demographic and selective factors have roles in the shaping of the population genetic structure of the European runner bean. In particular, we infer the existence of a moderate-to-strong cytoplasmic bottleneck that followed the expansion of the crop into Europe, and we deduce multiple domestication events for this species. We also observe an adaptive population differentiation in the phenology across a latitudinal gradient, which suggests that selection led to the diversification of the runner bean in Europe. The botanical varieties albiflorus, bicolor and coccineus, which are based solely on flower colour, cannot be distinguished based on these cpSSRs and nuSSRs, nor according to the 12 quantitative traits.
Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that ar... more Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.
Evolutionary studies that are aimed at defining the processes behind the present level and organi... more Evolutionary studies that are aimed at defining the processes behind the present level and organization of crop genetic diversity represent the fundamental bases for biodiversity conservation and use. A Mesoamerican origin of the common bean Phaseolus vulgaris was recently suggested through analysis of nucleotide polymorphism at the nuclear level. Here, we have used chloroplast microsatellites to investigate the origin of the common bean, on the basis of the specific characteristics of these markers (no recombination, haploid genome, uniparental inheritance), to validate these recent findings. Indeed, comparisons of the results obtained through analysis of nuclear and cytoplasmic DNA should allow the resolution of some of the contrasting information available on the evolutionary processes. The main outcomes of the present study are: (i) confirmation at the chloroplast level of the results obtained through nuclear data, further supporting the Mesoamerican origin of P. vulgaris, with central Mexico representing the cradle of its diversity; (ii) identification of a putative ancestral plastidial genome, which is characteristic of a group of accessions distributed from central Mexico to Peru, but which have not been highlighted beforehand through analyses at the nuclear level. Finally, the present study suggests that when a single species is analyzed, there is the need to take into account the complexity of the relationships between P. vulgaris and its closely related and partially intercrossable species P. coccineus and P. dumosus. Thus, the present study stresses the importance for the investigation of the speciation processes of these taxa through comparisons of both plastidial and nuclear variability. This knowledge will be fundamental not only from an evolutionary point of view, but also to put P. coccineus and P. dumosus germplasm to better use as a source of useful diversity for P. vulgaris breeding.
A deeper understanding of random markers is important if they are to be employed for a range of o... more A deeper understanding of random markers is important if they are to be employed for a range of objectives. The sequence specific amplified polymorphism (S-SAP) technique is a powerful genetic analysis tool which exploits the high copy number of retrotransposon long terminal repeats (LTRs) in the plant genome. The distribution and inheritance of S-SAP bands in the barley genome was
Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that ar... more Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.
... In the Chinese sample, Zhang et al. (2008) found 5% hybrids, noting that average seed weight ... more ... In the Chinese sample, Zhang et al. (2008) found 5% hybrids, noting that average seed weight of the Andean types was lower than that of the American Andean beans, with the opposite for the Mesoamerican Chinese bean. ...
We have studied the nucleotide diversity of common bean, Phaseolus vulgaris, which is characteriz... more We have studied the nucleotide diversity of common bean, Phaseolus vulgaris, which is characterized by two independent domestications in two geographically distinct areas: Mesoamerica and the Andes. This provides an important model, as domestication can be studied as a replicate experiment. We used nucleotide data from five gene fragments characterized by large introns to analyse 214 accessions (102 wild and 112 domesticated). The wild accessions represent a cross-section of the entire geographical distribution of P. vulgaris. A reduction in genetic diversity in both of these gene pools was found, which was three-fold greater in Mesoamerica compared with the Andes. This appears to be a result of a bottleneck that occurred before domestication in the Andes, which strongly impoverished this wild germplasm, leading to the minor effect of the subsequent domestication bottleneck (i.e. sequential bottleneck). These findings show the importance of considering the evolutionary history of crop species as a major factor that influences their current level and structure of genetic diversity. Furthermore, these data highlight a single domestication event within each gene pool. Although the findings should be interpreted with caution, this evidence indicates the Oaxaca valley in Mesoamerica, and southern Bolivia and northern Argentina in South America, as the origins of common bean domestication.
We examined the local adaptation patterns in a system comprising several interconnected
heterogen... more We examined the local adaptation patterns in a system comprising several interconnected heterogeneous plant populations from which populations of two phylogenetically closely related pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal agents of barley net blotch. We integrated two approaches, the comparison between the population structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that two closely related pathogens with very similar niche specialisation and life-styles can give rise to different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the coevolutionary ‘arms race’ between the plant and the net-form pathogen. Moreover, data suggested latitudinal clines of host resistance and that different ecological conditions can result in differential selective pressures at different sites. Our data are of interest for on-farm conservation of plant genetic resources, as also in establishing efficient breeding programs and strategies for deployment of resistance genes of P. teres.
Relatively few studies have extensively analysed the genetic diversity of the runner bean through... more Relatively few studies have extensively analysed the genetic diversity of the runner bean through molecular markers. Here, we used six chloroplast microsatellites (cpSSRs) to investigate the cytoplasmic diversity of 331 European domesticated accessions of the scarlet runner bean (Phaseolus coccineus L.), including the botanical varieties albiflorus, bicolor and coccineus, and a sample of 49 domesticated and wild accessions from Mesoamerica. We further explored the pattern of diversity of the European landraces using 12 phenotypic traits on 262 individuals. For 158 European accessions, we studied the relationships between cpSSR polymorphisms and phenotypic traits. Additionally, to gain insights into the role of gene flow and migration, for a subset of 115 accessions, we compared and contrasted the results obtained by cpSSRs and phenotypic traits with those obtained in a previous study with 12 nuclear microsatellites (nuSSRs). Our results suggest that both demographic and selective factors have roles in the shaping of the population genetic structure of the European runner bean. In particular, we infer the existence of a moderate-to-strong cytoplasmic bottleneck that followed the expansion of the crop into Europe, and we deduce multiple domestication events for this species. We also observe an adaptive population differentiation in the phenology across a latitudinal gradient, which suggests that selection led to the diversification of the runner bean in Europe. The botanical varieties albiflorus, bicolor and coccineus, which are based solely on flower colour, cannot be distinguished based on these cpSSRs and nuSSRs, nor according to the 12 quantitative traits.
Uploads
Papers by G. Attene
and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow
different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace
populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the
population diversity of the landraces that were collected at field level (population). We used a representative pool of barley
varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the
Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but
significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian
landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative
sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these
populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics
studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data
also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate
change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while
allowing adaptation to local environments.
heterogeneous plant populations from which populations of two phylogenetically closely related
pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are
Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal
agents of barley net blotch. We integrated two approaches, the comparison between the population
structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that
two closely related pathogens with very similar niche specialisation and life-styles can give rise to
different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for
the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori
well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the coevolutionary
‘arms race’ between the plant and the net-form pathogen. Moreover, data suggested
latitudinal clines of host resistance and that different ecological conditions can result in differential
selective pressures at different sites. Our data are of interest for on-farm conservation of plant
genetic resources, as also in establishing efficient breeding programs and strategies for deployment
of resistance genes of P. teres.
we used six chloroplast microsatellites (cpSSRs) to investigate the cytoplasmic diversity of 331 European domesticated
accessions of the scarlet runner bean (Phaseolus coccineus L.), including the botanical varieties albiflorus, bicolor and
coccineus, and a sample of 49 domesticated and wild accessions from Mesoamerica. We further explored the pattern of
diversity of the European landraces using 12 phenotypic traits on 262 individuals. For 158 European accessions, we studied
the relationships between cpSSR polymorphisms and phenotypic traits. Additionally, to gain insights into the role of gene
flow and migration, for a subset of 115 accessions, we compared and contrasted the results obtained by cpSSRs and
phenotypic traits with those obtained in a previous study with 12 nuclear microsatellites (nuSSRs). Our results suggest that
both demographic and selective factors have roles in the shaping of the population genetic structure of the European
runner bean. In particular, we infer the existence of a moderate-to-strong cytoplasmic bottleneck that followed the
expansion of the crop into Europe, and we deduce multiple domestication events for this species. We also observe an
adaptive population differentiation in the phenology across a latitudinal gradient, which suggests that selection led to the
diversification of the runner bean in Europe. The botanical varieties albiflorus, bicolor and coccineus, which are based solely
on flower colour, cannot be distinguished based on these cpSSRs and nuSSRs, nor according to the 12 quantitative traits.
and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow
different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace
populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the
population diversity of the landraces that were collected at field level (population). We used a representative pool of barley
varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the
Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but
significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian
landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative
sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these
populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics
studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data
also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate
change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while
allowing adaptation to local environments.
heterogeneous plant populations from which populations of two phylogenetically closely related
pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are
Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal
agents of barley net blotch. We integrated two approaches, the comparison between the population
structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that
two closely related pathogens with very similar niche specialisation and life-styles can give rise to
different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for
the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori
well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the coevolutionary
‘arms race’ between the plant and the net-form pathogen. Moreover, data suggested
latitudinal clines of host resistance and that different ecological conditions can result in differential
selective pressures at different sites. Our data are of interest for on-farm conservation of plant
genetic resources, as also in establishing efficient breeding programs and strategies for deployment
of resistance genes of P. teres.
we used six chloroplast microsatellites (cpSSRs) to investigate the cytoplasmic diversity of 331 European domesticated
accessions of the scarlet runner bean (Phaseolus coccineus L.), including the botanical varieties albiflorus, bicolor and
coccineus, and a sample of 49 domesticated and wild accessions from Mesoamerica. We further explored the pattern of
diversity of the European landraces using 12 phenotypic traits on 262 individuals. For 158 European accessions, we studied
the relationships between cpSSR polymorphisms and phenotypic traits. Additionally, to gain insights into the role of gene
flow and migration, for a subset of 115 accessions, we compared and contrasted the results obtained by cpSSRs and
phenotypic traits with those obtained in a previous study with 12 nuclear microsatellites (nuSSRs). Our results suggest that
both demographic and selective factors have roles in the shaping of the population genetic structure of the European
runner bean. In particular, we infer the existence of a moderate-to-strong cytoplasmic bottleneck that followed the
expansion of the crop into Europe, and we deduce multiple domestication events for this species. We also observe an
adaptive population differentiation in the phenology across a latitudinal gradient, which suggests that selection led to the
diversification of the runner bean in Europe. The botanical varieties albiflorus, bicolor and coccineus, which are based solely
on flower colour, cannot be distinguished based on these cpSSRs and nuSSRs, nor according to the 12 quantitative traits.