Publications by authors named "Domenico Rau"

25 Publications

  • Page 1 of 1

Pod indehiscence in common bean is associated with the fine regulation of PvMYB26.

J Exp Bot 2021 02;72(5):1617-1633

Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, via Brecce Bianche, Ancona, Italy.

In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris (L)., the major locus qPD5.1-Pv for pod indehiscence was identified recently. We developed a BC4/F4 introgression line population and narrowed the major locus down to a 22.5 kb region. Here, gene expression and a parallel histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest associated peak. Based on mapping and expression data, we propose early and fine up-regulation of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is associated with the lack of a functional abscission layer in the ventral sheath, and that the key anatomical modifications associated with pod shattering in common bean occur early during pod development. We finally propose that loss of pod shattering in legumes resulted from histological convergent evolution and that it is the result of selection at orthologous loci.
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http://dx.doi.org/10.1093/jxb/eraa553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7921299PMC
February 2021

GWAS Based on RNA-Seq SNPs and High-Throughput Phenotyping Combined with Climatic Data Highlights the Reservoir of Valuable Genetic Diversity in Regional Tomato Landraces.

Genes (Basel) 2020 11 23;11(11). Epub 2020 Nov 23.

Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy.

Tomato ( L.) is a widely used model plant species for dissecting out the genomic bases of complex traits to thus provide an optimal platform for modern "-omics" studies and genome-guided breeding. Genome-wide association studies (GWAS) have become a preferred approach for screening large diverse populations and many traits. Here, we present GWAS analysis of a collection of 115 landraces and 11 vintage and modern cultivars. A total of 26 conventional descriptors, 40 traits obtained by digital phenotyping, the fruit content of six carotenoids recorded at the early ripening (breaker) and red-ripe stages and 21 climate-related variables were analyzed in the context of genetic diversity monitored in the 126 accessions. The data obtained from thorough phenotyping and the SNP diversity revealed by sequencing of ripe fruit transcripts of 120 of the tomato accessions were jointly analyzed to determine which genomic regions are implicated in the expressed phenotypic variation. This study reveals that the use of fruit RNA-Seq SNP diversity is effective not only for identification of genomic regions that underlie variation in fruit traits, but also of variation related to additional plant traits and adaptive responses to climate variation. These results allowed validation of our approach because different marker-trait associations mapped on chromosomal regions where other candidate genes for the same traits were previously reported. In addition, previously uncharacterized chromosomal regions were targeted as potentially involved in the expression of variable phenotypes, thus demonstrating that our tomato collection is a precious reservoir of diversity and an excellent tool for gene discovery.
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http://dx.doi.org/10.3390/genes11111387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709041PMC
November 2020

Genome-Wide Association Mapping of Prostrate/Erect Growth Habit in Winter Durum Wheat.

Int J Mol Sci 2020 Jan 8;21(2). Epub 2020 Jan 8.

Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy.

By selecting for prostrate growth habit of the juvenile phase of the cycle, durum wheat cultivars could be developed with improved competitive ability against weeds, and better soil coverage to reduce the soil water lost by evaporation. A panel of 184 durum wheat ( subsp. ) genotypes, previously genotyped with DArT-seq markers, was used to perform association mapping analysis of prostrate/erect growth habit trait and to identify candidate genes. Phenotypic data of plant growth habit were recorded during three consecutive growing seasons (2014-2016), two different growth conditions (field trial and greenhouse) and two sowing periods (autumn and spring). Genome-wide association study revealed significant marker-trait associations, twelve of which were specific for a single environment/year, 4 consistent in two environments, and two MTAs for the LSmeans were identified across all environments, on chromosomes 2B and 5A. The co-localization of some MTAs identified in this study with known vernalization and photoperiod genes demonstrated that the sensitivity to vernalization and photoperiod response are actually not only key components of spring/winter growth habit, but they play also an important role in defining the magnitude of the tiller angle during the tillering stage. Many zinc-finger transcription factors, such as C2H2 or CCCH-domain zinc finger proteins, known to be involved in plant growth habit and in leaf angle regulation were found as among the most likely candidate genes. The highest numbers of candidate genes putatively related to the trait were found on chromosomes 3A, 4B, 5A and 6A. Moreover, a bioinformatic approach has been considered to search for functional ortholog genes in wheat by using the sequence of rice and barley tiller angle-related genes. The information generated could be used to improve the understanding of the mechanisms that regulate the prostrate/erect growth habit in wheat and the adaptive potential of durum wheat under resource-limited environmental conditions.
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http://dx.doi.org/10.3390/ijms21020394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7014441PMC
January 2020

Clonality, spatial structure, and pathogenic variation in Fusarium fujikuroi from rain-fed rice in southern Laos.

PLoS One 2019 23;14(12):e0226556. Epub 2019 Dec 23.

Dipartimento di Agraria, Sezione di Patologia ed Entomologia, Università degli Studi di Sassari, Sassari, Italy.

Bakanae disease, caused by the fungal phytopathogen Fusarium fujikuroi, can be detected in most rice (Oryza sativa L.) growing areas worldwide. In this study, we investigated the population structure of this fungus in southern Lao PDR, a country located near the geographic origin of rice domestication. Microsatellites (SSRs) and mating type (MAT) analyses, pathogenicity and fungicide sensitivity tests were integrated in the study. The first key finding is that the population genetic structure of F. fujikuroi in Lao PDR is consistent with high clonal reproduction. Indeed, (i) "true" clones were identified; (ii) within populations, MAT types were frequently skewed from 1:1 ratio, (iii) linkage disequilibrium (among SSRs as also among SSRs and MAT) was present, and (iv) gene-flow between opposite MAT types within the same population is restricted. The presence of genetic divergence among areas and populations and the occurrence of positive spatial autocorrelation of genetic variation, indicate that migration is restricted, and that genetic drift plays an important role in the evolution of this fungus. Two main well-defined groups of isolates were detected (FST = 0.213) that display a non-random spatial distribution. They differ in the ability to induce seedlings death but not seedlings elongation (the typical Bakanae symptom) suggesting that the pathogen's ability to induce the two symptoms is under different genetic control. Finally, we compared two agroecosystems with contrasting characteristics: low-input and traditional (Lao PDR) vs high-input and modern (Italy). We found differences in the level of population structuring and of spatial autocorrelation. This suggests that the evolutionary potential of the fungus not only depends on its intrinsic characteristics, but is strongly influenced by other external factors, most likely by the dynamics of infested seed exchange. Thus, quarantine and chemical treatments are a way to reduce population connectivity and hence the evolutionary potential of this pathogen.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0226556PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927642PMC
April 2020

Convergent Evolution of the Seed Shattering Trait.

Genes (Basel) 2019 01 19;10(1). Epub 2019 Jan 19.

Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.

Loss of seed shattering is a key trait in crop domestication, particularly for grain crops. For wild plants, seed shattering is a crucial mechanism to achieve greater fitness, although in the agricultural context, this mechanism reduces harvesting efficiency, especially under dry conditions. Loss of seed shattering was acquired independently in different monocotyledon and dicotyledon crop species by 'convergent phenotypic evolution', leading to similar low dehiscent and indehiscent phenotypes. Here, the main aim is to review the current knowledge about seed shattering in crops, in order to highlight the tissue modifications that underlie the convergent phenotypic evolution of reduced shattering in different types of fruit, from the silique of species, to the pods of legumes and spikes of cereals. Emphasis is given to legumes, with consideration of recent data obtained for the common bean. The current review also discusses to what extent convergent phenotypes arose from parallel changes at the histological and/or molecular levels. For this reason, an overview is included of the main findings relating to the genetic control of seed shattering in the model species and in other important crops.
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http://dx.doi.org/10.3390/genes10010068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356738PMC
January 2019

Genomic dissection of pod shattering in common bean: mutations at non-orthologous loci at the basis of convergent phenotypic evolution under domestication of leguminous species.

Plant J 2019 02 12;97(4):693-714. Epub 2019 Jan 12.

Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.

The complete or partial loss of shattering ability occurred independently during the domestication of several crops. Therefore, the study of this trait can provide an understanding of the link between phenotypic and molecular convergent evolution. The genetic dissection of 'pod shattering' in Phaseolus vulgaris is achieved here using a population of introgression lines and next-generation sequencing techniques. The 'occurrence' of the indehiscent phenotype (indehiscent versus dehiscent) depends on a major locus on chromosome 5. Furthermore, at least two additional genes are associated with the 'level' of shattering (number of shattering pods per plant: low versus high) and the 'mode' of shattering (non-twisting versus twisting pods), with all of these loci contributing to the phenotype by epistatic interactions. Comparative mapping indicates that the major gene identified on common bean chromosome 5 corresponds to one of the four quantitative trait loci for pod shattering in Vigna unguiculata. None of the loci identified comprised genes that are homologs of the known shattering genes in Glycine max. Therefore, although convergent domestication can be determined by mutations at orthologous loci, this was only partially true for P. vulgaris and V. unguiculata, which are two phylogenetically closely related crop species, and this was not the case for the more distant P. vulgaris and G. max. Conversely, comparative mapping suggests that the convergent evolution of the indehiscent phenotype arose through mutations in different genes from the same underlying gene networks that are involved in secondary cell-wall biosynthesis and lignin deposition patterning at the pod level.
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http://dx.doi.org/10.1111/tpj.14155DOI Listing
February 2019

Beans ( ssp.) as a Model for Understanding Crop Evolution.

Front Plant Sci 2017 8;8:722. Epub 2017 May 8.

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy.

Here, we aim to provide a comprehensive and up-to-date overview of the most significant outcomes in the literature regarding the origin of genus, the geographical distribution of the wild species, the domestication process, and the wide spread out of the centers of origin. can be considered as a unique model for the study of crop evolution, and in particular, for an understanding of the convergent phenotypic evolution that occurred under domestication. The almost unique situation that characterizes the genus is that five of its ∼70 species have been domesticated (i.e., , and ), and in addition, for and , the wild forms are distributed in both Mesoamerica and South America, where at least two independent and isolated episodes of domestication occurred. Thus, at least seven independent domestication events occurred, which provides the possibility to unravel the genetic basis of the domestication process not only among species of the same genus, but also between gene pools within the same species. Along with this, other interesting features makes crops very useful in the study of evolution, including: (i) their recent divergence, and the high level of collinearity and synteny among their genomes; (ii) their different breeding systems and life history traits, from annual and autogamous, to perennial and allogamous; and (iii) their adaptation to different environments, not only in their centers of origin, but also out of the Americas, following their introduction and wide spread through different countries. In particular for this resulted in the breaking of the spatial isolation of the Mesoamerican and Andean gene pools, which allowed spontaneous hybridization, thus increasing of the possibility of novel genotypes and phenotypes. This knowledge that is associated to the genetic resources that have been conserved and represents a crucial tool in the hands of researchers, to preserve and evaluate this diversity, and at the same time, to identify the genetic basis of adaptation and to develop new improved varieties to tackle the challenges of climate change, and food security and sustainability.
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http://dx.doi.org/10.3389/fpls.2017.00722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420584PMC
May 2017

A Comprehensive Phenotypic Investigation of the "Pod-Shattering Syndrome" in Common Bean.

Front Plant Sci 2017 3;8:251. Epub 2017 Mar 3.

Dipartimento di Agraria, Sezione di Agronomia, Colture Erbacee e Genetica, Università degli Studi di Sassari Sassari, Italy.

Seed shattering in crops is a key domestication trait due to its relevance for seed dispersal, yield, and fundamental questions in evolution (e.g., convergent evolution). Here, we focused on pod shattering in common bean ( L.), the most important legume crop for human consuption in the world. With this main aim, we developed a methodological pipeline that comprises a thorough characterization under field conditions, including also the chemical composition and histological analysis of the pod valves. The pipeline was developed based on the assumption that the shattering trait itself can be treated in principle as a "syndrome" (i.e., a set of correlated different traits) at the pod level. We characterized a population of 267 introgression lines that were developed to study shattering in common bean. Three main objectives were sought: (1) to dissect the shattering trait into its "components," of (percentage of shattering pods per plant) and (percentage of pods with twisting or non-twisting valves); (2) to test whether shattering is associated to the chemical composition and/or the histological characteristics of the pod valves; and (3) to test the associations between shattering and other plant traits. We can conclude the following: Very high shattering levels can be achieved in different modes; shattering resistance is mainly a qualitative trait; and high shattering levels is correlated with high carbon and lignin contents of the pod valves and with specific histological charaterstics of the ventral sheath and the inner fibrous layer of the pod wall. Our data also suggest that shattering comes with a "cost," as it is associated with low pod size, low seed weight per pod, high pod weight, and low seed to pod-valves ratio; indeed, it can be more exaustively described as a syndrome at the pod level. Our work suggests that the valve chemical composition (i.e., carbon and lignin content) can be used for a high troughput phenotyping procedures for shattering phenotyping. Finally, we believe that the application of our pipeline will greatly facilitate comparative studies among legume crops, and gene tagging.
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http://dx.doi.org/10.3389/fpls.2017.00251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5334323PMC
March 2017

High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits.

Front Plant Sci 2016 6;7:2005. Epub 2017 Jan 6.

Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche Ancona, Italy.

Crop species have been deeply affected by the domestication process, and there have been many efforts to identify selection signatures at the genome level. This knowledge will help geneticists to better understand the evolution of organisms, and at the same time, help breeders to implement successful breeding strategies. Here, we focused on domestication in the Mesoamerican gene pool of by sequencing 49 gene fragments from a sample of 45 wild and domesticated accessions, and as controls, two accessions each of the closely related species and . An excess of nonsynonymous mutations within the domesticated germplasm was found. Our data suggest that the cost of domestication alone cannot explain fully this finding. Indeed, the significantly higher frequency of polymorphisms in the coding regions observed only in the domesticated plants (compared to noncoding regions), the fact that these mutations were mostly nonsynonymous and appear to be recently derived mutations, and the investigations into the functions of their relative genes (responses to biotic and abiotic stresses), support a scenario that involves new functional mutations selected for adaptation during domestication. Moreover, consistent with this hypothesis, selection analysis and the possibility to compare data obtained for the same genes in different studies of varying sizes, data types, and methodologies allowed us to identify four genes that were strongly selected during domestication. Each selection candidate is involved in plant resistance/tolerance to abiotic stresses, such as heat, drought, and salinity. Overall, our study suggests that domestication acted to increase functional diversity at target loci, which probably controlled traits related to expansion and adaptation to new agro-ecological growing conditions.
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http://dx.doi.org/10.3389/fpls.2016.02005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5216878PMC
January 2017

Evolutionary Metabolomics Reveals Domestication-Associated Changes in Tetraploid Wheat Kernels.

Mol Biol Evol 2016 Jul 5;33(7):1740-53. Epub 2016 Apr 5.

Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy Dipartimento di Scienze Agrarie, Alimentari e Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy

Domestication and breeding have influenced the genetic structure of plant populations due to selection for adaptation from natural habitats to agro-ecosystems. Here, we investigate the effects of selection on the contents of 51 primary kernel metabolites and their relationships in three Triticum turgidum L. subspecies (i.e., wild emmer, emmer, durum wheat) that represent the major steps of tetraploid wheat domestication. We present a methodological pipeline to identify the signature of selection for molecular phenotypic traits (e.g., metabolites and transcripts). Following the approach, we show that a reduction in unsaturated fatty acids was associated with selection during domestication of emmer (primary domestication). We also show that changes in the amino acid content due to selection mark the domestication of durum wheat (secondary domestication). These effects were found to be partially independent of the associations that unsaturated fatty acids and amino acids have with other domestication-related kernel traits. Changes in contents of metabolites were also highlighted by alterations in the metabolic correlation networks, indicating wide metabolic restructuring due to domestication. Finally, evidence is provided that wild and exotic germplasm can have a relevant role for improvement of wheat quality and nutritional traits.
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http://dx.doi.org/10.1093/molbev/msw050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915355PMC
July 2016

Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris.

New Phytol 2016 Mar 3;209(4):1781-94. Epub 2015 Nov 3.

Dipartimento di Agraria, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy.

Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources.
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http://dx.doi.org/10.1111/nph.13713DOI Listing
March 2016

Co-evolution in a landrace meta-population: two closely related pathogens interacting with the same host can lead to different adaptive outcomes.

Sci Rep 2015 Aug 7;5:12834. Epub 2015 Aug 7.

Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy.

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 co-evolutionary '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.
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http://dx.doi.org/10.1038/srep12834DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528193PMC
August 2015

European flint landraces grown in situ reveal adaptive introgression from modern maize.

PLoS One 2015 8;10(4):e0121381. Epub 2015 Apr 8.

Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.

We have investigated the role of selection in the determination of the detected levels of introgression from modern maize hybrid varieties into maize landraces still cultivated in situ in Italy. We exploited the availability of a historical collection of landraces undertaken before the introduction and widespread use of modern maize, to analyse genomic changes that have occurred in these maize landraces over 50 years of co-existence with hybrid varieties. We have combined a previously published SSR dataset (n=21) with an AFLP loci dataset (n=168) to provide higher resolution power and to obtain a more detailed picture. We show that selection pressures for adaptation have favoured new alleles introduced by migration from hybrids. This shows the potential for analysis of historical introgression even over this short period of 50 years, for an understanding of the evolution of the genome and for the identification of its functionally important regions. Moreover, this demonstrates that landraces grown in situ represent almost unique populations for use for such studies when the focus is on the domesticated plant. This is due to their adaptation, which has arisen from their dynamic evolution under a continuously changing agro-ecological environment, and their capture of new alleles from hybridisation. We have also identified loci for which selection has inhibited introgression from modern germplasm and has enhanced the distinction between landraces and modern maize. These loci indicate that selection acted in the past, during the formation of the flint and dent gene pools. In particular, the locus showing the strongest signals of selection is a Misfit transposable element. Finally, molecular characterisation of the same samples with two different molecular markers has allowed us to compare their performances. Although the genetic-diversity and population-structure analyses provide the same global qualitative pattern, which thus provides the same inferences, there are differences related to their natures and characteristics.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121381PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390310PMC
April 2016

Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean.

Plant Cell 2014 May 21;26(5):1901-1912. Epub 2014 May 21.

Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy Consiglio per la Ricerca e Sperimentazione in Agricoltura, Cereal Research Centre (CRA-CER), 71122 Foggia, Italy

Using RNA sequencing technology and de novo transcriptome assembly, we compared representative sets of wild and domesticated accessions of common bean (Phaseolus vulgaris) from Mesoamerica. RNA was extracted at the first true-leaf stage, and de novo assembly was used to develop a reference transcriptome; the final data set consists of ∼190,000 single nucleotide polymorphisms from 27,243 contigs in expressed genomic regions. A drastic reduction in nucleotide diversity (∼60%) is evident for the domesticated form, compared with the wild form, and almost 50% of the contigs that are polymorphic were brought to fixation by domestication. In parallel, the effects of domestication decreased the diversity of gene expression (18%). While the coexpression networks for the wild and domesticated accessions demonstrate similar seminal network properties, they show distinct community structures that are enriched for different molecular functions. After simulating the demographic dynamics during domestication, we found that 9% of the genes were actively selected during domestication. We also show that selection induced a further reduction in the diversity of gene expression (26%) and was associated with 5-fold enrichment of differentially expressed genes. While there is substantial evidence of positive selection associated with domestication, in a few cases, this selection has increased the nucleotide diversity in the domesticated pool at target loci associated with abiotic stress responses, flowering time, and morphology.
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http://dx.doi.org/10.1105/tpc.114.124040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079357PMC
May 2014

Population structure of barley landrace populations and gene-flow with modern varieties.

PLoS One 2013 27;8(12):e83891. Epub 2013 Dec 27.

Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy ; Consiglio per la Ricerca e Sperimentazione in Agricoltura, Cereal Research Centre (CRA-CER), Foggia, Italy.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083891PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873955PMC
August 2014

European Phaseolus coccineus L. landraces: population structure and adaptation, as revealed by cpSSRs and phenotypic analyses.

PLoS One 2013 22;8(2):e57337. Epub 2013 Feb 22.

Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica, Università degli Studi di Sassari, Sassari, Italy.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057337PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3579852PMC
September 2013

Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes.

New Phytol 2013 Jan 5;197(1):300-313. Epub 2012 Nov 5.

Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.

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.
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http://dx.doi.org/10.1111/j.1469-8137.2012.04377.xDOI Listing
January 2013

Genetic structure and linkage disequilibrium in landrace populations of barley in Sardinia.

Theor Appl Genet 2012 Jun 13;125(1):171-84. Epub 2012 Mar 13.

Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy.

Multilocus digenic linkage disequilibria (LD) and their population structure were investigated in eleven landrace populations of barley (Hordeum vulgare ssp. vulgare L.) in Sardinia, using 134 dominant simple-sequence amplified polymorphism markers. The analysis of molecular variance for these markers indicated that the populations were partially differentiated (F(ST) = 0.18), and clustered into three geographic areas. Consistent with this population pattern, STRUCTURE analysis allocated individuals from a bulk of all populations into four genetic groups, and these groups also showed geographic patterns. In agreement with other molecular studies in barley, the general level of LD was low (13% of locus pairs, with P < 0.01) in the bulk of 337 lines, and decayed steeply with map distance between markers. The partitioning of multilocus associations into various components indicated that genetic drift and founder effects played a major role in determining the overall genetic makeup of the diversity in these landrace populations, but that epistatic homogenising or diversifying selection was also present. Notably, the variance of the disequilibrium component was relatively high, which implies caution in the pooling of barley lines for association studies. Finally, we compared the analyses of multilocus structure in barley landrace populations with parallel analyses in both composite crosses of barley on the one hand and in natural populations of wild barley on the other. Neither of these serves as suitable mimics of landraces in barley, which require their own study. Overall, the results suggest that these populations can be exploited for LD mapping if population structure is controlled.
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http://dx.doi.org/10.1007/s00122-012-1824-8DOI Listing
June 2012

Adaptation and diversity along an altitudinal gradient in Ethiopian barley (Hordeum vulgare L.) landraces revealed by molecular analysis.

BMC Plant Biol 2010 Jun 21;10:121. Epub 2010 Jun 21.

Dipartimento di Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche, 60131 Ancona, Italy.

Background: Among the cereal crops, barley is the species with the greatest adaptability to a wide range of environments. To determine the level and structure of genetic diversity in barley (Hordeum vulgare L.) landraces from the central highlands of Ethiopia, we have examined the molecular variation at seven nuclear microsatellite loci.

Results: A total of 106 landrace populations were sampled in the two growing seasons (Meher and Belg; the long and short rainy seasons, respectively), across three districts (Ankober, Mojanawadera and Tarmaber), and within each district along an altitudinal gradient (from 1,798 to 3,324 m a.s.l). Overall, although significant, the divergence (e.g. FST) is very low between seasons and geographical districts, while it is high between different classes of altitude. Selection for adaptation to different altitudes appears to be the main factor that has determined the observed clinal variation, along with population-size effects.

Conclusions: Our data show that barley landraces from Ethiopia are constituted by highly variable local populations (farmer's fields) that have large within-population diversity. These landraces are also shown to be locally adapted, with the major driving force that has shaped their population structure being consistent with selection for adaptation along an altitudinal gradient. Overall, our study highlights the potential of such landraces as a source of useful alleles. Furthermore, these landraces also represent an ideal system to study the processes of adaptation and for the identification of genes and genomic regions that have adaptive roles in crop species.
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http://dx.doi.org/10.1186/1471-2229-10-121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095281PMC
June 2010

Molecular differentiation of commercial varieties and feral populations of oilseed rape (Brassica napus L.).

BMC Evol Biol 2010 Mar 1;10:63. Epub 2010 Mar 1.

University of Vienna, Department of Conservation Biology, Vegetation Ecology and Landscape Ecology, Rennweg 14, Vienna, Austria.

Background: For assessing the risk of escape of transgenes from cultivation, the persistence of feral populations of crop plants is an important aspect. Feral populations of oilseed rape, Brassica napus, are well known, but only scarce information is available on their population dynamics, particularly in Central Europe. To investigate genetic diversity, origin and persistence of feral oilseed rape in Austria, we compared variation at nine polymorphic microsatellite loci in eight feral populations with 19 commercial varieties.

Results: Overall, commercial varieties and feral populations showed a similar pattern of genetic variation and a similar level of observed heterozygosity. The two groups, however, shared less than 50% of the alleles and no multilocus genotype. A significant among-group (commercial varieties versus feral populations) component of genetic variation was observed (AMOVA: FCT = 0.132). Pairwise comparisons between varieties and feral populations showed moderate to very high genetic differentiation (FST = 0.209 - 0.900). The software STRUCTURE also demonstrated a clear separation between commercial varieties and feral samples: out of 17 identified genetic clusters, only one comprised plants from both a commercial variety and feral sites.

Conclusions: The results suggest that feral oilseed rape is able to maintain persistent populations. The feral populations may have derived from older cultivars that were not included in our analyses or perhaps have already hybridised with related crops or wild relatives. Feral populations therefore have to be considered in ecological risk assessment and future coexistence measures as a potential hybridisation partner of transgenic oilseed rape.
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http://dx.doi.org/10.1186/1471-2148-10-63DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848156PMC
March 2010

Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L.

Evol Appl 2009 Nov 3;2(4):504-22. Epub 2009 Jul 3.

Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy.

Together with the knowledge of the population structure, a critical aspect for the planning of association and/or population genomics studies is the level of linkage disequilibrium (LD) that characterizes the species and the population used for such an analysis. We have analyzed the population structure and LD in wild and domesticated populations of Phaseolus vulgaris L. using amplified fragment length polymorphism markers, most of which were genetically mapped in two recombinant inbred populations. Our results reflect the previous knowledge of the occurrence of two major wild gene pools of P. vulgaris, from which two independent domestication events originated, one in the Andes and one in Mesoamerica. The high level of LD in the whole sample was mostly due to the gene pool structure, with a much higher LD in domesticated compared to wild populations. In relation to association studies, our results also suggest that whole-genome-scan approaches are feasible in the common bean. Interestingly, an excess of inter-chromosomal LD was found in the domesticated populations, which suggests an important role for epistatic selection during domestication. Moreover, our results indicate the occurrence of a strong bottleneck in the Andean wild population before domestication, suggesting a Mesoamerican origin of P. vulgaris. Finally, our data support the occurrence of a single domestication event in Mesoamerica, and the same scenario in the Andes.
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http://dx.doi.org/10.1111/j.1752-4571.2009.00082.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352449PMC
November 2009

Mutational biases and selective forces shaping the structure of Arabidopsis genes.

PLoS One 2009 Jul 27;4(7):e6356. Epub 2009 Jul 27.

Dipartimento di Scienze Agronomiche e Genetica Vegetale Agraria (DISAGEVA), Università degli Studi di Sassari, Sassari, Italy.

Recently features of gene expression profiles have been associated with structural parameters of gene sequences in organisms representing a diverse set of taxa. The emerging picture indicates that natural selection, mediated by gene expression profiles, has a significant role in determining genic structures. However the current situation is less clear in plants as the available data indicates that the effect of natural selection mediated by gene expression is very weak. Moreover, the direction of the patterns in plants appears to contradict those observed in animal genomes. In the present work we analized expression data for >18000 Arabidopsis genes retrieved from public datasets obtained with different technologies (MPSS and high density chip arrays) and compared them with gene parameters. Our results show that the impact of natural selection mediated by expression on genes sequences is significant and distinguishable from the effects of regional mutational biases. In addition, we provide evidence that the level and the breadth of gene expression are related in opposite ways to many structural parameters of gene sequences. Higher levels of expression abundance are associated with smaller transcripts, consistent with the need to reduce costs of both transcription and translation. Expression breadth, however, shows a contrasting pattern, i.e. longer genes have higher breadth of expression, possibly to ensure those structural features associated with gene plasticity. Based on these results, we propose that the specific balance between these two selective forces play a significant role in shaping the structure of Arabidopsis genes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006356PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712092PMC
July 2009

Tagging the signatures of domestication in common bean (Phaseolus vulgaris) by means of pooled DNA samples.

Ann Bot 2007 Nov 1;100(5):1039-51. Epub 2007 Aug 1.

Dipartimento di Scienze degli Alimenti, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.

Background And 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.
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http://dx.doi.org/10.1093/aob/mcm151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759209PMC
November 2007

Use of a complexation of tebuconazole with beta-cyclodextrin for controlling foot and crown rot of durum wheat incited by Fusarium culmorum.

J Agric Food Chem 2006 Jan;54(2):480-4

Dipartimento di Protezione delle Piante and Centro Interdisciplinare di Eccellenza per lo Sviluppo della Ricerca Biotecnologica e per lo Studio della Biodiversità della Sardegna e dell'Area Mediterranea, Università di Sassari, I-07100 Sassari, Italy.

The methodology for the inclusion of tebuconazole (TBC) in beta-cyclodextrin (betaCD), spectroscopic characterization of the inclusion complex, and its activity for the control of a major soilborne disease of wheat caused by Fusarium culmorum are reported. Controlled release measured by chemical shift of the diagnostic protons H(3) and H(5) of betaCD confirmed stability of the complex at the solid state and in aqueous solution. Greenhouse and field experiments were conducted on durum wheat (Triticum durum cv. Prometeo) sown in substrate or in soil artificially infested with a virulent strain of F. culmorum. The inclusion complex betaCD-TBC, applied as seed dressing in combination or not with carboxymethylcellulose, reduced the disease incidence caused by F. culmorum and improved grain yield, showing effects that were generally comparable to those observed upon application of a commercial formulation of TBC. In the field experiment, only seed treatment with the inclusion complex betaCD-TBC allowed yield that was not different from that obtained from the uninoculated control. These results prove that by the use of the betaCD-TBC complex it is possible to obtain release of TBC and bioavailabilty of the fungicide without compromising its effectiveness.
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http://dx.doi.org/10.1021/jf0523014DOI Listing
January 2006

Isolation and characterization of the mating-type locus of the barley pathogen Pyrenophora teres and frequencies of mating-type idiomorphs within and among fungal populations collected from barley landraces.

Genome 2005 Oct;48(5):855-69

Dipartimento di Scienze degli Alimenti, Università Politecnica delle Marche, Ancona, Italy.

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.
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http://dx.doi.org/10.1139/g05-046DOI Listing
October 2005
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