G. Attene - Academia.edu (original) (raw)

Papers by G. Attene

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.

Theoretical and Applied Genetics, 2011

Evolutionary studies in plant and animal breeding are aimed at understanding the structure and or... more Evolutionary studies in plant and animal breeding are aimed at understanding the structure and organization of genetic variations of species. We have identiWed and characterized a genomic sequence in Phaseolus vulgaris of 1,200 bp (PvSHP1) that is homologous to SHATTER-PROOF-1 (SHP1), a gene involved in control of fruit shattering in Arabidopsis thaliana. The PvSHP1 fragment was mapped to chromosome Pv06 in P. vulgaris and is linked to the Xower and seed color gene V. AmpliWcation of the PvSHP1 sequence from the most agronomically important legume species showed a high degree of interspecies diversity in the introns within the Phaseoleae, while the coding region was conserved across distant taxa. Sequencing of the PvSHP1 sequence in a sample of 91 wild and domesticated genotypes that span the geographic distribution of this species in the centers of origin showed that PvSHP1 is highly polymorphic and, therefore, particularly useful to further investigate the origin and domestication history of P. vulgaris. Our data conWrm the gene pool structure seen in P. vulgaris along with independent domestication processes in the Andes and Mesoamerica; they provide additional evidence for a single domestication event in Mesoamerica. Moreover, our results support the Mesoamerican origin of this species. Finally, we have developed three indel-spanning markers that will be very useful for bean germplasm characterization, and particularly to trace the distribution of the domesticated Andean and Mesoamerican gene pools. Communicated by B. Diers.

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.

Genome, 2005

Pyrenophora teres f. sp. teres mating-type genes (MAT-1: 1190 bp; MAT-2: 1055 bp) have been ident... more Pyrenophora teres f. sp. teres mating-type genes (MAT-1: 1190 bp; MAT-2: 1055 bp) have been identified. Their predicted proteins, measuring 379 and 333 amino acids, respectively, are similar to those of other Pleosporales, such as Pleospora sp., Cochliobolus sp., Alternaria alternata, Leptosphaeria maculans, and Phaeosphaeria nodorum. The structure of the MAT locus is discussed in comparison with those of other fungi. A mating-type PCR assay has also been developed; with this assay we have analyzed 150 isolates that were collected from 6 Sardinian barley landrace populations. Of these, 68 were P. teres f. sp. teres (net form; NF) and 82 were P. teres f. sp. maculata (spot form; SF). Within each mating type, the NF and SF amplification products were of the same length and were highly similar in sequence. The 2 mating types were present in both the NF and the SF populations at the field level, indicating that they have all maintained the potential for sexual reproduction. Despite the 2 forms being sympatric in 5 fields, no intermediate isolates were detected with amplified fragment length polymorphism (AFLP) analysis. These results suggest that the 2 forms are genetically isolated under the field conditions. In all of the samples of P. teres, the ratio of the 2 mating types was consistently in accord with the 1:1 null hypothesis. This ratio is expected when segregation distortion and clonal selection among mating types are absent or asexual reproduction is rare. Overall, sexual reproduction appears to be the major process that equalizes the frequencies of the 2 mating types within populations.

Annals of Botany, 2007

Aims The main aim of this study was to use an amplified fragment length polymorphism (AFLP)-based... more Aims The main aim of this study was to use an amplified fragment length polymorphism (AFLP)-based, large-scale screening of the whole genome of Phaseolus vulgaris to determine the effects of selection on the structure of the genetic diversity in wild and domesticated populations. † Methods Using pooled DNA samples, seven each of wild and domesticated populations of P. vulgaris were studied using 2506 AFLP markers (on average, one every 250 kb). About 10 % of the markers were also analysed on individual genotypes and were used to infer allelic frequencies empirically from bulk data. In both data sets, tests were made to determine the departure from neutral expectation for each marker using an F ST -based method. † Key Results The most important outcome is that a large fraction of the genome of the common bean (16 %; P , 0 . 01) appears to have been subjected to effects of selection during domestication. Markers obtained in individual genotypes were also mapped and classified according to their proximities to known genes and quantitative trait loci (QTLs) of the domestication syndrome. Most of the markers that were found to be potentially under the effects of selection were located in the proximity of previously mapped genes and QTLs related to the domestication syndrome. † Conclusions. Overall, the results indicate that in P. vulgaris a large portion of the genome appears to have been subjected to the effects of selection, probably because of linkage to the loci selected during domestication. As most of the markers that are under the effects of selection are linked to known loci related to the domestication syndrome, it is concluded that population genomics approaches are very efficient in detecting QTLs. A method based on bulk DNA samples is presented that is effective in pre-screening for a large number of markers to determine selection signatures.

Theoretical and Applied Genetics, 2011

Phaseolus coccineus L. is closely related to P. vulgaris and is the third most important cultivat... more Phaseolus coccineus L. is closely related to P. vulgaris and is the third most important cultivated Phaseolus species. Little is known about the patterns of its diversity. In this work, a representative collection of its worldwide diversity was initially developed. The collection includes 28 wild forms (WFs) and 52 landraces (LRs) from Mesoamerica (the crop domestication area), and 148 LRs from Europe (where the crop was introduced in the sixteenth century). The collection was studied by using 12 SSR molecular markers that were developed for the P. vulgaris genome. They were proved to be effective and reliable in P. coccineus in this work. Fourteen LRs of P. dumosus (previously identified as a subspecies of P. coccineus) were also studied. The genetic diversity, population structure and phylogenetic relationships were investigated. The results indicate that: (a) the European and Mesoamerican gene pools are clearly differentiated, (b) a certain reduction of diversity occurred with introduction into Europe, and (c) the Mesoamerican LRs (P. dumosus included) and WFs are closely related and are connected by a high gene flow. Inferences on the domestication process of P. coccineus are also presented. This study provides a picture of the genetic diversity distribution and outcomes with introduction into the Old World, which was not available before. It also underlines that the genetic diversity of both WFs and LRs is an important source for Phaseolus spp. breeding programs and deserves to be preserved in situ and ex situ. Communicated by R. Varshney. Electronic supplementary material The online version of this article (

Theoretical and Applied Genetics, 2010

This study focuses on the expansion of Phaseolus vulgaris in Europe. The pathways of distribution... more This study focuses on the expansion of Phaseolus vulgaris in Europe. The pathways of distribution of beans into and across Europe were very complex, with several introductions from the New World that were combined with direct exchanges between European and other Mediterranean countries. We have analyzed here six chloroplast microsatellite (cpSSR) loci and two unlinked nuclear loci (for phaseolin types and Pv-shatterproof1). We have assessed the genetic structure and level of diversity of a large collection of European landraces of P. vulgaris (307) in comparison to 94 genotypes from the Americas that are representative of the Andean and Mesoamerican gene pools. First, we show that most of the European common bean landraces (67%

Molecular Breeding, 2006

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

PLoS ONE, 2013

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.

The introduction of next generation sequencing technologies has revolutionised genetic analysis, ... more The introduction of next generation sequencing technologies has revolutionised genetic analysis, creating new opportunities for plant research that can also be applied to non-model species. Among the applications of next generation sequencing, genotyping by sequencing aims at the identification of structural variants and polymorphisms in target regions or whole genomes. We used RNA sequencing (RNA-Seq) technology to investigate the whole common bean (Phaseolus vulgaris L.) transcriptome of 21 wild and domesticated accessions, mostly from Mesoamerica. The materials were chosen on the basis of previous molecular analyses carried out using both multilocus molecular markers and nucleotide data, which had highlighted greater genetic diversity in the Mesoamerican than the Andean gene pool. We identified an high number of single nucleotide polymorphisms and we used this large dataset for population genetics inference. In particular, variable RNA fragments in wild and domesticated forms were analysed, and we were able to identify genes under selection during the domestication process. This information is crucial not only to reconstruct the evolutionary history of this species, but also for a more efficient conservation of the existing germplasm and for selective breeding programmes.

Plant Genetic Resources, 2011

... 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. ...

New Phytologist, 2013

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.

Theoretical and Applied Genetics, 2011

Genome, 2005

Annals of Botany, 2007

Theoretical and Applied Genetics, 2011

Theoretical and Applied Genetics, 2010

Molecular Breeding, 2006

PLoS ONE, 2013

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.

Plant Genetic Resources, 2011

New Phytologist, 2013

Theoretical and Applied Genetics, 2011