Publications by authors named "Tania Gioia"

18 Publications

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The INCREASE project: Intelligent Collections of Food-Legume Genetic Resources for European Agrofood Systems.

Plant J 2021 Aug 24. Epub 2021 Aug 24.

Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy.

Food legumes are crucial for all agriculture-related societal challenges including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. The transition to plant-based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co-benefits for human health. The characterization, maintenance and exploitation of food-legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and healthy food system. INCREASE will implement, on chickpea, common bean, lentil and lupin, a new approach to conserve, manage and characterise genetic resources,. Intelligent Collections, consisting of nested core collections, composed of single seed decent (SSD) purified accessions (i.e. inbred lines), will be developed, exploiting germplasm available both from genebanks, and on-farm, and subjected to different level of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via participatory approach, the needs of various actors including breeders, scientists, farmers, agri-food and non-food industry, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentalised approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield, and boosting the competitiveness of agriculture and food sector, INCREASE strategy will have a major impact on economy and society, and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.
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http://dx.doi.org/10.1111/tpj.15472DOI Listing
August 2021

Characterization of Nutritional Quality Traits of a Common Bean Germplasm Collection.

Foods 2021 Jul 6;10(7). Epub 2021 Jul 6.

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.

Food legumes are at the crossroads of many societal challenges that involve agriculture, such as climate change and food sustainability and security. In this context, pulses have a crucial role in the development of plant-based diets, as they represent a very good source of nutritional components and improve soil fertility, such as by nitrogen fixation through symbiosis with rhizobia. The main contribution to promotion of food legumes in agroecosystems will come from plant breeding, which is guaranteed by the availability of well-characterized genetic resources. Here, we analyze seeds of 25 American and European common bean purified accessions (i.e., lines of single seed descent) for different morphological and compositional quality traits. Significant differences among the accessions and superior genotypes for important nutritional traits are identified, with some lines showing extreme values for more than one trait. Heritability estimates indicate the importance of considering the effects of environmental growth conditions on seed compositional traits. They suggest the need for more phenotypic characterization in different environments over different years to better characterize combined effects of environment and genotype on nutritional trait variations. Finally, adaptation following the introduction and spread of common bean in Europe seems to have affected its nutritional profile. This finding further suggests the relevance of evolutionary studies to guide breeders in the choice of plant genetic resources.
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http://dx.doi.org/10.3390/foods10071572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8306501PMC
July 2021

Towards the Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Common Bean.

Curr Protoc 2021 May;1(5):e133

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

The optimal use of legume genetic resources represents a key prerequisite for coping with current agriculture-related societal challenges, including conservation of agrobiodiversity, agricultural sustainability, food security, and human health. Among legumes, the common bean (Phaseolus vulgaris) is the most economically important for human consumption, and its evolutionary trajectories as a species have been crucial to determining the structure and level of its present and available genetic diversity. Genomic advances are considerably enhancing the characterization and assessment of important genetic variants. For this purpose, the development and availability of, and access to, well-described and efficiently managed genetic resource collections that comprise pure lines derived by single-seed-descent cycles will be paramount for the use of the reservoir of common bean variability and for the advanced breeding of legume crops. This is one of the main aims of the new and challenging European project INCREASE, which is the implementation of Intelligent Collections with appropriate standardized protocols that must be characterized, maintained, and made available, along with the related data, to users such as breeders and researchers. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Characterizing common bean seeds for seed trait descriptors Basic Protocol 2: Bean seed imaging Basic Protocol 3: Characterizing bean lines for plant trait descriptors specific for common bean Primary Seed Increase.
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http://dx.doi.org/10.1002/cpz1.133DOI Listing
May 2021

Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well-Represented Collections.

Curr Protoc 2021 May;1(5):e134

Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.

The genetic and phenotypic characterization of crops allows us to elucidate their evolutionary and domestication history, the genetic basis of important traits, and the use of variation present in landraces and wild relatives to enhance resilience. In this context, we aim to provide an overview of the main genetic resources developed for lentil and their main outcomes, and to suggest protocols for continued work on this important crop. Lens culinaris is the third-most-important cool-season grain and its use is increasing as a quick-cooking, nutritious, plant-based source of protein. L. culinaris was domesticated in the Fertile Crescent, and six additional wild taxa (L. orientalis, L. tomentosus, L. odemensis, L. lamottei, L. ervoides, and L. nigricans) are recognized. Numerous genetic diversity studies have shown that wild relatives present high levels of genetic variation and provide a reservoir of alleles that can be used for breeding programs. Furthermore, the integration of genetics/genomics and breeding techniques has resulted in identification of quantitative trait loci and genes related to attributes of interest. Genetic maps, massive genotyping, marker-assisted selection, and genomic selection are some of the genetic resources generated and applied in lentil. In addition, despite its size (∼4 Gbp) and complexity, the L. culinaris genome has been assembled, allowing a deeper understanding of its architecture. Still, major knowledge gaps exist in lentil, and a deeper understanding and characterization of germplasm resources, including wild relatives, is critical to lentil breeding and improvement. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Recording of lentil seed descriptors Basic Protocol 2: Lentil seed imaging Basic Protocol 3: Lentil seed increase Basic Protocol 4: Recording of primary lentil seed INCREASE descriptors.
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http://dx.doi.org/10.1002/cpz1.134DOI Listing
May 2021

Comparative Analysis Based on Transcriptomics and Metabolomics Data Reveal Differences between Emmer and Durum Wheat in Response to Nitrogen Starvation.

Int J Mol Sci 2021 Apr 30;22(9). Epub 2021 Apr 30.

Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy.

Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We found that durum wheat exhibits broader and stronger response in comparison to emmer as seen from the expression pattern of both genes and metabolites and gene enrichment analysis. They showed major differences in the responses to N starvation for transcription factor families, emmer showed differential reduction in the levels of primary metabolites while durum wheat exhibited increased levels of most of them to N starvation. The correlation-based networks, including the differentially expressed genes and metabolites, revealed tighter regulation of metabolism in durum wheat in comparison to emmer. We also found that glutamate and γ-aminobutyric acid (GABA) had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and glutamate signaling modulating shoot vs. root growth in the two different wheat subspecies.
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http://dx.doi.org/10.3390/ijms22094790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8124848PMC
April 2021

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

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris).

PLoS One 2019 31;14(1):e0211342. Epub 2019 Jan 31.

Department of Plant Sciences/MS1, Section of Crop & Ecosystem Sciences, University of California, Davis, CA, United States of America.

Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA and include both dry bean and snap beans for the fresh and processing markets. Through population structure, principal components analyses, cluster analysis, and discriminant analysis of principal components (DAPC), Andean and Mesoamerican genotypes as well as most American commercial type classes could be distinguished. The genetic relationship among the commercial cultivars revealed by the SSR markers was generally in agreement with known pedigree data. The Mesoamerican cultivars were separated into three major groups-black, small white, and navy accessions clustered together in a distinct group, while great northern and pinto clustered in another group, showing mixed origin. The Andean cultivars were distributed in two different groups. The kidney market classes formed a single group, while the green bean accessions were distributed between the Andean and Mesoamerican groups, showing inter-gene pool genetic admixture. For a subset of 24 SSR markers, we compared and contrasted the genetic diversity of the commercial cultivars with those of wild and domesticated landrace accessions of common bean. An overall reduction in genetic diversity was observed in both gene pools, Andean and Mesoamerican, from wild to landraces to advanced cultivars. The limited diversity in the commercial cultivars suggests that an important goal of bean breeding programs should be to broaden the cultivated gene pool, particularly the genetic diversity of specific commercial classes, using the genetic variability present in common bean landraces.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0211342PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354994PMC
October 2019

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

Molecular Genotyping (SSR) and Agronomic Phenotyping for Utilization of Durum Wheat ( Desf.) Ex Situ Collection from Southern Italy: A Combined Approach Including Pedigreed Varieties.

Genes (Basel) 2018 Sep 20;9(10). Epub 2018 Sep 20.

Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, viale dell'Ateneo Lucano 10, 85100 Potenza, Italy.

In South Italy durum wheat ( Desf.) has a long-time tradition of growing and breeding. Accessions collected and now preserved ex situ are a valuable genetic resource, but their effective use in agriculture and breeding programs remains very low. In this study, a small number (44) of simple sequence repeats (SSR) molecular markers were used to detect pattern of diversity for 136 accessions collected in South Italy over time, to identify the genepool of origin, and establish similarities with 28 Italian varieties with known pedigree grown in Italy over the same time-period. Phenotyping was conducted for 12 morphophysiological characters of agronomic interest. Based on discriminant analysis of principal components (DAPC) and STRUCTURE analysis six groups were identified, the assignment of varieties reflected the genetic basis and breeding strategies involved in their development. Some "old" varieties grown today are the result of evolution through natural hybridization and conservative pure line selection. A small number of molecular markers and little phenotyping coupled with powerful statistical analysis and comparison to pedigreed varieties can provide enough information on the genetic structure of durum wheat germplasm for a quick screening of the germplasm collection able to identify accessions for breeding or introduction in low input agriculture.
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http://dx.doi.org/10.3390/genes9100465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211131PMC
September 2018

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

GrowScreen-PaGe, a non-invasive, high-throughput phenotyping system based on germination paper to quantify crop phenotypic diversity and plasticity of root traits under varying nutrient supply.

Funct Plant Biol 2016 Feb;44(1):76-93

Institute of Biosciences and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.

New techniques and approaches have been developed for root phenotyping recently; however, rapid and repeatable non-invasive root phenotyping remains challenging. Here, we present GrowScreen-PaGe, a non-invasive, high-throughput phenotyping system (4 plants min-1) based on flat germination paper. GrowScreen-PaGe allows the acquisition of time series of the developing root systems of 500 plants, thereby enabling to quantify short-term variations in root system. The choice of germination paper was found to be crucial and paper☓root interaction should be considered when comparing data from different studies on germination paper. The system is suitable for phenotyping dicot and monocot plant species. The potential of the system for high-throughput phenotyping was shown by investigating phenotypic diversity of root traits in a collection of 180 rapeseed accessions and of 52 barley genotypes grown under control and nutrient-starved conditions. Most traits showed a large variation linked to both genotype and treatment. In general, root length traits contributed more than shape and branching related traits in separating the genotypes. Overall, results showed that GrowScreen-PaGe will be a powerful resource to investigate root systems and root plasticity of large sets of plants and to explore the molecular and genetic root traits of various species including for crop improvement programs.
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http://dx.doi.org/10.1071/FP16128DOI Listing
February 2016

Impact of domestication on the phenotypic architecture of durum wheat under contrasting nitrogen fertilization.

J Exp Bot 2015 Sep 12;66(18):5519-30. Epub 2015 Jun 12.

Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria Centro di Ricerca per la Cerealicoltura (CRA-CER), S.S. 673 km 25,200, 71122, Foggia, Italy Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy

The process of domestication has led to dramatic morphological and physiological changes in crop species due to adaptation to cultivation and to the needs of farmers. To investigate the phenotypic architecture of shoot- and root-related traits and quantify the impact of primary and secondary domestication, we examined a collection of 36 wheat genotypes under optimal and nitrogen-starvation conditions. These represented three taxa that correspond to key steps in the recent evolution of tetraploid wheat (i.e. wild emmer, emmer, and durum wheat). Overall, nitrogen starvation reduced the shoot growth of all genotypes, while it induced the opposite effect on root traits, quantified using the automated phenotyping platform GROWSCREEN-Rhizo. We observed an overall increase in all of the shoot and root growth traits from wild emmer to durum wheat, while emmer was generally very similar to wild emmer but intermediate between these two subspecies. While the differences in phenotypic diversity due to the effects of primary domestication were not significant, the secondary domestication transition from emmer to durum wheat was marked by a large and significant decrease in the coefficient of additive genetic variation. In particular, this reduction was very strong under the optimal condition and less intense under nitrogen starvation. Moreover, although under the optimal condition both root and shoot traits showed significantly reduced diversity due to secondary domestication, under nitrogen starvation the reduced diversity was significant only for shoot traits. Overall, a considerable amount of phenotypic variation was observed in wild emmer and emmer, which could be exploited for the development of pre-breeding strategies.
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http://dx.doi.org/10.1093/jxb/erv289DOI Listing
September 2015

Evidence for introduction bottleneck and extensive inter-gene pool (Mesoamerica x Andes) hybridization in the European common bean (Phaseolus vulgaris L.) germplasm.

PLoS One 2013 1;8(10):e75974. Epub 2013 Oct 1.

Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy.

Common bean diversity within and between Mesoamerican and Andean gene pools was compared in 89 landraces from America and 256 landraces from Europe, to elucidate the effects of bottleneck of introduction and selection for adaptation during the expansion of common bean (Phaseolus vulgaris L.) in Europe. Thirteen highly polymorphic nuclear microsatellite markers (nuSSRs) were used to complement chloroplast microsatellite (cpSSRs) and nuclear markers (phaseolin and Pv-shatterproof1) data from previous studies. To verify the extent of the introduction bottleneck, inter-gene pool hybrids were distinguished from "pure" accessions. Hybrids were identified on the basis of recombination of gene pool specific cpSSR, phaseolin and Pv-shatterproof1 markers with a Bayesian assignments based on nuSSRs, and with STRUCTURE admixture analysis. More hybrids were detected than previously, and their frequency was almost four times larger in Europe (40.2%) than in America (12.3%). The genetic bottleneck following the introduction into Europe was not evidenced in the analysis including all the accessions, but it was significant when estimated only with "pure" accessions, and five times larger for Mesoamerican than for Andean germplasm. The extensive inter-gene pool hybridization generated a large amount of genotypic diversity that mitigated the effects of the bottleneck that occurred when common bean was introduced in Europe. The implication for evolution and the advantages for common bean breeding are discussed.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075974PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3788063PMC
June 2014

Identification and characterization of a homologue to the Arabidopsis INDEHISCENT gene in common Bean.

J Hered 2013 Mar 12;104(2):273-86. Epub 2012 Dec 12.

Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy.

Reduction in pod shattering represents a key component of the domestication syndrome in common bean (Phaseolus vulgaris) and makes this domesticate dependent upon the farmer for seed dispersal. Attempts to elucidate the genetic control of this process have led to the identification of a major gene (St) linked to the presence/absence of pod suture fibers affecting pod shattering. Although St has been placed on the common bean genetic map, the sequence and the specific functions of this gene remain unknown. The purpose of this study was to identify a candidate gene for St. In Arabidopsis thaliana, INDEHISCENT gene (IND) is the primary factory required for silique shattering. A sequence homologous to IND was successfully amplified in P. vulgaris and placed on the common bean map using two recombinant inbred populations (BAT93 × Jalo EEP558; Midas × G12873). Although PvIND maps near the St locus, the lack of complete cosegregation between PvIND and St and the lack of polymorphisms at the PvIND locus correlated with the dehiscent/indehiscent phenotype suggests that PvIND may not be directly involved in pod shattering and may not be the gene underlying the St locus. However, PvIND may be closely linked to an as yet unidentified regulatory element at the St locus. Alternatively, a more precise phenotyping method taking into account quantitative trait variation needs to be developed to more accurately map the St locus.
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http://dx.doi.org/10.1093/jhered/ess102DOI Listing
March 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
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