Publications by authors named "Roberto Papa"

66 Publications

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 Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Lupins.

Curr Protoc 2021 Jul;1(7):e191

Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland.

Well-characterized genetic resources are fundamental to maintain and provide the various genotypes for pre-breeding programs for the production of new cultivars (e.g., wild relatives, unimproved material, landraces). The aim of the current article is to provide protocols for the characterization of the genetic resources of two lupin crop species: the European Lupinus albus and the American Lupinus mutabilis. Intelligent nested collections of lupins derived from homozygous lines (single-seed descent) are being developed, established, and exploited using cutting-edge approaches for genotyping, phenotyping, data management, and data analysis within the INCREASE project (EU Horizon 2020). This will allow us to predict the phenotypic performance of genotyped lines, and will further boost research and development in lupins. Lupins stand out due to their high-quality seed protein (∼40% of seed dry weight) and other primary components in the seeds, which include fatty acids, dietary fiber, and minerals. The potential of lupins as a crop is highlighted by the multiple benefits of plant-based food in terms of food security, nutrition, human health, and sustainable production. The use of lupins in foods, along with other well-studied and widely used food legumes, will also provide a greatly diversified plant-based food palette to meet the Global Goals for Sustainable Development to improve people's lives by 2030. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Lupin seed phenotypic descriptors Basic Protocol 2: Lupin seed imaging Basic Protocol 3: Standardized phenotypic characterization of lupin genetic resources grown towards primary seed increase (development of single-seed descent genetic resources).
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http://dx.doi.org/10.1002/cpz1.191DOI Listing
July 2021

Contrasting Fake News in Oncology: The First Declaration of Good Communication.

JCO Glob Oncol 2021 05;7:740-746

General Direction, AOU Ospedali Riuniti of Ancona, Ancona, Italy.

Purpose: Nowadays, websites, online journals, and social media give access to an extraordinary amount of medical information. Misleading news are often disseminated generating false expectations, exaggerated anxiety, and confusion; in oncology setting, disinformation is perhaps more deleterious than in other fields, with a considerable impact on single patients as well as on families and, more in general, on Public Health. We aimed to promote a better interaction between the health care and the world of communication.

Materials And Methods: A regional technical table was established with the aim of drafting a shared document through the consensus conference method in the RAND/University of California Los Angeles variant, identifying strategies to overcome barriers between communication and health care as well as to propose common criteria for an effective dissemination of medical information.

Results: Sixteen articles met the inclusion criteria, from which 72 recommendations were drawn to the communication and health field (40 related to specific issues and 32 transversal to all the specific topics). Following an evaluation of relevance by the panel of experts, it was found that 57 recommendations scored more than 7, 13 between 4 and 6.9, and 2 below 4.

Conclusion: This consensus and the drawn up document represent a concrete attempt to find a renewed and strategic alliance between key figures in health care and communication operators. As the American Declaration of Independence, our Declaration of Good Communication has identified high-impact recommendations for the best management of patients, providing simple but fundamental concepts and recommendations about effectiveness especially in oncology setting.
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http://dx.doi.org/10.1200/GO.21.00003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8162956PMC
May 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

A common bean truncated CRINKLY4 kinase controls gene-for-gene resistance to the fungus Colletotrichum lindemuthianum.

J Exp Bot 2021 05;72(10):3569-3581

Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France.

Identifying the molecular basis of resistance to pathogens is critical to promote a chemical-free cropping system. In plants, nucleotide-binding leucine-rich repeat constitute the largest family of disease resistance (R) genes, but this resistance can be rapidly overcome by the pathogen, prompting research into alternative sources of resistance. Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is one of the most important diseases of common bean. This study aimed to identify the molecular basis of Co-x, an anthracnose R gene conferring total resistance to the extremely virulent C. lindemuthianum strain 100. To that end, we sequenced the Co-x 58 kb target region in the resistant JaloEEP558 (Co-x) common bean and identified KTR2/3, an additional gene encoding a truncated and chimeric CRINKLY4 kinase, located within a CRINKLY4 kinase cluster. The presence of KTR2/3 is strictly correlated with resistance to strain 100 in a diversity panel of common beans. Furthermore, KTR2/3 expression is up-regulated 24 hours post-inoculation and its transient expression in a susceptible genotype increases resistance to strain 100. Our results provide evidence that Co-x encodes a truncated and chimeric CRINKLY4 kinase probably resulting from an unequal recombination event that occurred recently in the Andean domesticated gene pool. This atypical R gene may act as a decoy involved in indirect recognition of a fungal effector.
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http://dx.doi.org/10.1093/jxb/erab082DOI Listing
May 2021

Domestication of Crop Metabolomes: Desired and Unintended Consequences.

Trends Plant Sci 2021 06 27;26(6):650-661. Epub 2021 Feb 27.

Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria. Electronic address:

The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.
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http://dx.doi.org/10.1016/j.tplants.2021.02.005DOI Listing
June 2021

Ancient genomes reveal early Andean farmers selected common beans while preserving diversity.

Nat Plants 2021 02 8;7(2):123-128. Epub 2021 Feb 8.

Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.

All crops are the product of a domestication process that started less than 12,000 years ago from one or more wild populations. Farmers selected desirable phenotypic traits (such as improved energy accumulation, palatability of seeds and reduced natural shattering) while leading domesticated populations through several more or less gradual demographic contractions. As a consequence, the erosion of wild genetic variation is typical of modern cultivars, making them highly susceptible to pathogens, pests and environmental change. The loss of genetic diversity hampers further crop improvement programmes to increase food production in a changing world, posing serious threats to food security. Using both ancient and modern seeds, we analysed the temporal dynamics of genetic variation and selection during the domestication process of the common bean (Phaseolus vulgaris) in the southern Andes. Here, we show that most domestic traits were selected for before 2,500 years ago, with no or only minor loss of whole-genome heterozygosity. In fact, most of the changes at coding genes and linked regions that differentiate wild and domestic genomes are already present in the ancient genomes analysed here, and all ancient domestic genomes dated between 600 and 2,500 years ago are highly variable (at least as variable as modern genomes from the wild). Single seeds from modern cultivars show reduced variation when compared with ancient seeds, indicating that intensive selection within cultivars in the past few centuries probably partitioned ancestral variation within different genetically homogenous cultivars. When cultivars from different Andean regions are pooled, the genomic variation of the pool is higher than that observed in the pool of ancient seeds from north and central western Argentina. Considering that most desirable phenotypic traits are probably controlled by multiple polymorphic genes, a plausible explanation of this decoupling of selection and genetic erosion is that early farmers applied a relatively weak selection pressure by using many phenotypically similar but genetically diverse individuals as parents. Our results imply that selection strategies during the past few centuries, as compared with earlier times, more intensively reduced genetic variation within cultivars and produced further improvements by focusing on a few plants carrying the traits of interest, at the cost of marked genetic erosion within Andean landraces.
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http://dx.doi.org/10.1038/s41477-021-00848-7DOI Listing
February 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

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

Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding.

Genes (Basel) 2020 10 30;11(11). Epub 2020 Oct 30.

Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil.

Brazil is the largest consumer and third highest producer of common beans ( L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 'diagnostic SNPs' that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.
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http://dx.doi.org/10.3390/genes11111298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7694079PMC
October 2020

Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm.

Front Genet 2020 21;11:217. Epub 2020 Apr 21.

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

The first breeding program in the world for durum wheat was conceived in Italy in the early 1900s. Over the decades, pressure exerted by natural and artificial selection could have progressively reduced the genetic diversity of the durum wheat germplasm. In the present study, a large panel of Italian durum wheat accessions that includes landraces, old and modern cultivars was subjected to genotyping using the Illumina iSelect 15K wheat SNP array. The aim was to assess the impact that selection has in shaping Italian durum wheat genetic diversity and to exploit the patterns of genetic diversity between populations to identify molecular signatures of divergence and selection. Relatively small differences in genetic diversity have been observed among accessions, which have been selected and cultivated in Italy over the past 150 years. Indeed, directional selection combined with that operated by farmers/breeders resulted in the increase of linkage disequilibrium (LD) and in changes of the allelic frequencies in DNA regions that control important agronomic traits. Results from this study also show that major well-known genes and/or QTLs affecting plant height (RHT), earliness (VRN, PPD) and grain quality (GLU, PSY, PSD, LYC, PPO, LOX3) co-localized with outlier SNP loci. Interestingly, many of these SNPs fall in genomic regions where genes involved in nitrogen metabolism are. This finding highlights the key role these genes have played in the transition from landraces to modern cultivars. Finally, our study remarks on the need to fully exploit the genetic diversity of Italian landraces by intense pre-breeding activities aimed at introducing a new source of adaptability and resistance in the genetic background of modern cultivars, to contrast the effect of climate change. The list of divergent loci and loci under selection associated with useful agronomic traits represents an invaluable resource to detect new allelic variants for target genes and for guiding new genomic selection programs in durum wheat.
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http://dx.doi.org/10.3389/fgene.2020.00217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7187681PMC
April 2020

Development of a model care pathway for the management of Hymenoptera venom allergy: evidence-based key interventions and indicators.

Clin Transl Allergy 2020 4;10. Epub 2020 Mar 4.

11S.O. Hospital Medical Management, University Hospital Ospedali Riuniti di Ancona, Ancona, Italy.

Background: Hymenoptera venom allergy (HVA) is an underestimated condition representing an important cause of morbidity and mortality worldwide. Preventing future allergic reactions in patients who have already developed a systemic reaction is based on the correct management of the acute phase of the reaction followed by a correct diagnosis and, where indicated, prescription of adrenaline autoinjectors and VIT. A possible strategy to optimize care processes and to improve outcomes is the implementation of a Diagnostic and Therapeutic Care Pathways, also known as Integrated Care Pathways or Clinical Pathways (CPWs). The aim of the care pathway is to enhance the quality of care by improving risk-adjusted patient outcomes, promoting patient safety, increasing patient satisfaction, and optimizing the use of resources. To our knowledge, currently in Italy as well as in Europe, there is no CPWs codified for the management of HVA patients. This paper describes the development of the clinical content of a care pathway for the management of HVA.

Methods: The methodology applied is based on the eight step method to build the clinical content of an evidence-based care pathway suggested by Lodewijckx et al.

Results: Three hundred and seventeen different clinical activities were extracted from the selected literature. The expert panel was involved in their evaluation, expressing a judgment of relevance through the Delphi study. As a result, 126 clinical activities were appraised to be valid and feasible. The final recommendations (126) were translated into 123 key interventions. Six indicators were produced by the clinical activities.

Conclusion: A set of 123 key interventions and of six process indicators were found to be appropriate for the development and standardization of the clinical content of the Hymenoptera venom allergy care pathway.
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http://dx.doi.org/10.1186/s13601-020-00312-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7055031PMC
March 2020

Current State and Perspectives in Population Genomics of the Common Bean.

Plants (Basel) 2020 Mar 5;9(3). Epub 2020 Mar 5.

Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.

Correspondence: r [...].
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http://dx.doi.org/10.3390/plants9030330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7154925PMC
March 2020

Adaptation to novel environments during crop diversification.

Curr Opin Plant Biol 2020 08 10;56:203-217. Epub 2020 Feb 10.

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

In the context of the global challenge of climate change, mitigation strategies are needed to adapt crops to novel environments. The main goal to address this is an understanding of the genetic basis of crop adaptation to different agro-ecological conditions. The movement of crops during the Colombian Exchange that started with the travels of Columbus in 1492 is an example of rapid adaptation to novel environments. Many diversification-related traits have been characterised in multiple crop species, and association-mapping analyses have identified loci involved in these. Here, we present an overview of current knowledge regarding the molecular basis related to the complex patterns of crop adaptation and dissemination, particularly outside their centres of origin. Investigation of the genomic basis of crop expansion offers a powerful contribution to the development of tools to identify and exploit valuable genetic diversity and to improve and design novel resilient crop varieties.
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http://dx.doi.org/10.1016/j.pbi.2019.12.011DOI Listing
August 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

An Early Tailored Approach Is the Key to Effective Rehabilitation in the Intensive Care Unit.

Arch Phys Med Rehabil 2019 08 21;100(8):1506-1514. Epub 2019 Feb 21.

Department of Experimental and Clinical Medicine, Neurorehabilitation Clinic, Marche Polytechnic University, Ancona, Italy.

Objective: To investigate the effectiveness, feasibility, and safety of an evidence-based rehabilitation care pathway in the intensive care unit (ICU) in different patient populations.

Design: Observational prospective cohort study, with retrospective controls.

Setting: ICUs of a university hospital.

Participants: Patients admitted between April 1, 2015, and June 30, 2015, were compared to a retrospective cohort admitted to the same ICUs during the same 3-month period in 2014. The number of patients studied (N=285) included 152 in the prospective group and 133 in the retrospective group.

Interventions: The prospective cohort benefited of a rehabilitation care pathway based on (1) interdisciplinary teamwork; (2) early customized and goal-oriented rehabilitation; (3) daily functional monitoring and treatment revision; (4) agreed discharge policy; and (5) continuity of care. The retrospective cohort underwent usual care.

Main Outcome Measures: Included the following: (1) proportions of patients undergoing rehabilitation team evaluation; (2) latency between patient admission to ICUs and rehabilitation team assessment; (3) proportions of patients undergoing rehabilitation treatment during ICU stay; (4) latency between the patient admission to ICUs and rehabilitation start; (5) ICU stay and total acute hospital stay; and (5) proportion of ventilator-free days out of ICU stay.

Results: The novel rehabilitation care pathway led to (1) an increased proportion of patients receiving rehabilitative assessment (P<.0001); (2) a decreased latency from ICU admission to both rehabilitation team assessment and rehabilitation start (P<.0001); (3) an increased proportion of patients undergoing rehabilitation (P<.0001); (4) a shorter length of stay in ICUs (P<.0001) and in hospital (P=.047); and (5) a shorter mechanical ventilation duration (P<.02). A direct relationship between rehabilitation start latency and ICU length of stay was observed.

Conclusions: An early, interdisciplinary team approach, providing a customized dynamic planning of physiotherapy programs, increases ventilator-free time and reduces total hospital stay, especially in patients admitted to the ICU after general surgery. This rehabilitation care pathway can be generalized to different geopolitical scenarios, being feasible, safe and cost effective.
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http://dx.doi.org/10.1016/j.apmr.2019.01.015DOI Listing
August 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

Multi-tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome.

Plant J 2019 03 15;97(6):1132-1153. Epub 2019 Jan 15.

Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, Potsdam-Golm, 14476, Germany.

Common bean (Phaseolus vulgaris L.) is an important legume species with a rich natural diversity of landraces that originated from the wild forms following multiple independent domestication events. After the publication of its genome, several resources for this relevant crop have been made available. A comprehensive characterization of specialized metabolism in P. vulgaris, however, is still lacking. In this study, we used a metabolomics approach based on liquid chromatography-mass spectrometry to dissect the chemical composition at a tissue-specific level in several accessions of common bean belonging to different gene pools. Using a combination of literature search, mass spectral interpretation, C-labeling, and correlation analyses, we were able to assign chemical classes and/or putative structures for approximately 39% of all measured metabolites. Additionally, we integrated this information with transcriptomics data and phylogenetic inference from multiple legume species to reconstruct the possible metabolic pathways and identify sets of candidate genes involved in the biosynthesis of specialized metabolites. A particular focus was given to flavonoids, triterpenoid saponins and hydroxycinnamates, as they represent metabolites involved in important ecological interactions and they are also associated with several health-promoting benefits when integrated into the human diet. The data are presented here in the form of an accessible resource that we hope will set grounds for further studies on specialized metabolism in legumes.
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http://dx.doi.org/10.1111/tpj.14178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6850281PMC
March 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

Analysis of metabolic and mineral changes in response to salt stress in durum wheat (Triticum turgidum ssp. durum) genotypes, which differ in salinity tolerance.

Plant Physiol Biochem 2018 Dec 26;133:57-70. Epub 2018 Oct 26.

Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673, Km 25,200, 71122, Foggia, Italy. Electronic address:

The key mechanisms of salinity tolerance (ST) in durum wheat were investigated, with five genotypes used to determine changes in morpho-physiological traits and mineral and metabolite contents after exposure to 50, 100 and 200 mM NaCl. Plant growth impairment was evident at the highest salt level. Under this condition, a wide range of shoot Na contents and ST were observed within genotypes. However, no significant correlation was seen between ST and Na exclusion from the shoots, which indicates that tissue tolerance also has a role. Consistent with this, there was significant correlation between ST and the Na:K ratio in the shoots. Indeed, the maintenance of the shoot Na and K homeostasis was found to be essential to achieve osmotic adjustment, which relied substantially on inorganic osmolytes, and to avoid toxicity symptoms, such as chlorophyll loss, which appeared only at the highest salinity level. Consistently, the metabolite changes occurred mainly in the shoots, with a dual response to salinity: (i) a conserved response that was common to all the genotypes and resulted in the accumulation of proline and in the depletion of organic acids, including some intermediates of the Krebs cycle; and (ii) a genotype-specific response that involved the accumulation of GABA, threonine, leucine, glutamic acid, glycine, mannose and fructose and appeared related to the different tolerance of genotypes to salinity. The lower magnitude of response to salinity detected in the roots confirmed the major role of the shoots in the determination of ST of durum wheat.
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http://dx.doi.org/10.1016/j.plaphy.2018.10.025DOI Listing
December 2018

Adapting legume crops to climate change using genomic approaches.

Plant Cell Environ 2019 01 13;42(1):6-19. Epub 2018 Jun 13.

School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia.

Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.
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http://dx.doi.org/10.1111/pce.13203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334278PMC
January 2019

Evolution of the Crop Rhizosphere: Impact of Domestication on Root Exudates in Tetraploid Wheat ( L.).

Front Plant Sci 2017 13;8:2124. Epub 2017 Dec 13.

Centro di Ricerca per la Cerealicoltura e le Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia Agraria (CREA-CI), Foggia, Italy.

Domestication has induced major genetic changes in crop plants to satisfy human needs and as a consequence of adaptation to agroecosystems. This adaptation might have affected root exudate composition, which can influence the interactions in the rhizosphere. Here, using two different soil types (sand, soil), we provide an original example of the impact of domestication and crop evolution on root exudate composition through metabolite profiling of root exudates for a panel of 10 wheat genotypes that correspond to the key steps in domestication of tetraploid wheat (wild emmer, emmer, durum wheat). Our data show that soil type can dramatically affect the composition of root exudates in the rhizosphere. Moreover, the composition of the rhizosphere metabolites is associated with differences among the genotypes of the wheat domestication groups, as seen by the high heritability of some of the metabolites. Overall, we show that domestication and breeding have had major effects on root exudates in the rhizosphere, which suggests the adaptive nature of these changes.
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http://dx.doi.org/10.3389/fpls.2017.02124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5733359PMC
December 2017

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
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