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Somenzi E, Partel E, Barbato M, Chero Osorio AM, Colli L, Franceschi N, Mantovani R, Pilla F, Komjanc M, Achilli A, Hauffe HC, Ajmone Marsan P. Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics. Genet Sel Evol 2024; 56:32. [PMID: 38698323 PMCID: PMC11064358 DOI: 10.1186/s12711-024-00900-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Rendena is a dual-purpose cattle breed, which is primarily found in the Italian Alps and the eastern areas of the Po valley, and recognized for its longevity, fertility, disease resistance and adaptability to steep Alpine pastures. It is categorized as 'vulnerable to extinction' with only 6057 registered animals in 2022, yet no comprehensive analyses of its molecular diversity have been performed to date. The aim of this study was to analyse the origin, genetic diversity, and genomic signatures of selection in Rendena cattle using data from samples collected in 2000 and 2018, and shed light on the breed's evolution and conservation needs. RESULTS Genetic analysis revealed that the Rendena breed shares genetic components with various Alpine and Po valley breeds, with a marked genetic proximity to the Original Braunvieh breed, reflecting historical restocking efforts across the region. The breed shows signatures of selection related to both milk and meat production, environmental adaptation and immune response, the latter being possibly the result of multiple rinderpest epidemics that swept across the Alps in the eighteenth century. An analysis of the Rendena cattle population spanning 18 years showed an increase in the mean level of inbreeding over time, which is confirmed by the mean number of runs of homozygosity per individual, which was larger in the 2018 sample. CONCLUSIONS The Rendena breed, while sharing a common origin with Brown Swiss, has developed distinct traits that enable it to thrive in the Alpine environment and make it highly valued by local farmers. Preserving these adaptive features is essential, not only for maintaining genetic diversity and enhancing the ability of this traditional animal husbandry to adapt to changing environments, but also for guaranteeing the resilience and sustainability of both this livestock system and the livelihoods within the Rendena valley.
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Affiliation(s)
- Elisa Somenzi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Erika Partel
- Unità risorse foraggere e produzioni zootecniche, Centro Trasferimento Tecnologico, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Mario Barbato
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Department of Veterinary Science, Università degli Studi di Messina, Messina, Italy
| | - Ana María Chero Osorio
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Centro di Ricerca Sulla Biodiversità e sul DNA Antico, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Niccolò Franceschi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Fabio Pilla
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
| | - Matteo Komjanc
- Unità risorse foraggere e produzioni zootecniche, Centro Trasferimento Tecnologico, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Heidi Christine Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Paolo Ajmone Marsan
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Centro di Ricerca Nutrigenomica e Proteomica-PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Mota LFM, Giannuzzi D, Pegolo S, Sturaro E, Gianola D, Negrini R, Trevisi E, Ajmone Marsan P, Cecchinato A. Genomic prediction of blood biomarkers of metabolic disorders in Holstein cattle using parametric and nonparametric models. Genet Sel Evol 2024; 56:31. [PMID: 38684971 PMCID: PMC11057143 DOI: 10.1186/s12711-024-00903-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Metabolic disturbances adversely impact productive and reproductive performance of dairy cattle due to changes in endocrine status and immune function, which increase the risk of disease. This may occur in the post-partum phase, but also throughout lactation, with sub-clinical symptoms. Recently, increased attention has been directed towards improved health and resilience in dairy cattle, and genomic selection (GS) could be a helpful tool for selecting animals that are more resilient to metabolic disturbances throughout lactation. Hence, we evaluated the genomic prediction of serum biomarkers levels for metabolic distress in 1353 Holsteins genotyped with the 100K single nucleotide polymorphism (SNP) chip assay. The GS was evaluated using parametric models best linear unbiased prediction (GBLUP), Bayesian B (BayesB), elastic net (ENET), and nonparametric models, gradient boosting machine (GBM) and stacking ensemble (Stack), which combines ENET and GBM approaches. RESULTS The results show that the Stack approach outperformed other methods with a relative difference (RD), calculated as an increment in prediction accuracy, of approximately 18.0% compared to GBLUP, 12.6% compared to BayesB, 8.7% compared to ENET, and 4.4% compared to GBM. The highest RD in prediction accuracy between other models with respect to GBLUP was observed for haptoglobin (hapto) from 17.7% for BayesB to 41.2% for Stack; for Zn from 9.8% (BayesB) to 29.3% (Stack); for ceruloplasmin (CuCp) from 9.3% (BayesB) to 27.9% (Stack); for ferric reducing antioxidant power (FRAP) from 8.0% (BayesB) to 40.0% (Stack); and for total protein (PROTt) from 5.7% (BayesB) to 22.9% (Stack). Using a subset of top SNPs (1.5k) selected from the GBM approach improved the accuracy for GBLUP from 1.8 to 76.5%. However, for the other models reductions in prediction accuracy of 4.8% for ENET (average of 10 traits), 5.9% for GBM (average of 21 traits), and 6.6% for Stack (average of 16 traits) were observed. CONCLUSIONS Our results indicate that the Stack approach was more accurate in predicting metabolic disturbances than GBLUP, BayesB, ENET, and GBM and seemed to be competitive for predicting complex phenotypes with various degrees of mode of inheritance, i.e. additive and non-additive effects. Selecting markers based on GBM improved accuracy of GBLUP.
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Affiliation(s)
- Lucio F M Mota
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro, PD, Italy.
| | - Diana Giannuzzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro, PD, Italy
| | - Sara Pegolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro, PD, Italy.
| | - Enrico Sturaro
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro, PD, Italy
| | - Daniel Gianola
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, 53706, USA
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition (DIANA) and the Romeo and Enrica Invernizzi Research Center for Sustainable Dairy Production (CREI), Faculty of Agricultural, Food, and Environmental Sciences, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | - Erminio Trevisi
- Department of Animal Science, Food and Nutrition (DIANA) and the Romeo and Enrica Invernizzi Research Center for Sustainable Dairy Production (CREI), Faculty of Agricultural, Food, and Environmental Sciences, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
- Nutrigenomics and Proteomics Research Center, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Nutrition (DIANA) and the Romeo and Enrica Invernizzi Research Center for Sustainable Dairy Production (CREI), Faculty of Agricultural, Food, and Environmental Sciences, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
- Nutrigenomics and Proteomics Research Center, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | - Alessio Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro, PD, Italy
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Possenti M, Sessa G, Alfè A, Turchi L, Ruzza V, Sassi M, Morelli G, Ruberti I. HD-Zip II transcription factors control distal stem cell fate in Arabidopsis roots by linking auxin signaling to the FEZ/SOMBRERO pathway. Development 2024; 151:dev202586. [PMID: 38563568 DOI: 10.1242/dev.202586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
In multicellular organisms, specialized tissues are generated by specific populations of stem cells through cycles of asymmetric cell divisions, where one daughter undergoes differentiation and the other maintains proliferative properties. In Arabidopsis thaliana roots, the columella - a gravity-sensing tissue that protects and defines the position of the stem cell niche - represents a typical example of a tissue whose organization is exclusively determined by the balance between proliferation and differentiation. The columella derives from a single layer of stem cells through a binary cell fate switch that is precisely controlled by multiple, independent regulatory inputs. Here, we show that the HD-Zip II transcription factors (TFs) HAT3, ATHB4 and AHTB2 redundantly regulate columella stem cell fate and patterning in the Arabidopsis root. The HD-Zip II TFs promote columella stem cell proliferation by acting as effectors of the FEZ/SMB circuit and, at the same time, by interfering with auxin signaling to counteract hormone-induced differentiation. Overall, our work shows that HD-Zip II TFs connect two opposing parallel inputs to fine-tune the balance between proliferation and differentiation in columella stem cells.
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Affiliation(s)
- Marco Possenti
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Rome 00178, Italy
| | - Giovanna Sessa
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Altea Alfè
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Luana Turchi
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Valentino Ruzza
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Massimiliano Sassi
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Giorgio Morelli
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Rome 00178, Italy
| | - Ida Ruberti
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
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Bleve G, Trivellin N, Chirizzi D, Tarantini A, Orlandi VT, Milano F. Sensitivity of Xylella fastidiosa subsp. pauca Salento-1 to light at 410 nm. Photochem Photobiol Sci 2024; 23:793-801. [PMID: 38578539 DOI: 10.1007/s43630-024-00556-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/14/2024] [Indexed: 04/06/2024]
Abstract
All over the world, from America to the Mediterranean Sea, the plant pathogen Xylella fastidiosa represents one of the most difficult challenges with many implications at ecological, agricultural, and economic levels. X. fastidiosa is a rod-shaped Gram-negative bacterium belonging to the family of Xanthomonadaceae. It grows at very low rates and infects a wide range of plants thanks to different vectors. Insects, through their stylets, suck a sap rich in nutrients and inject bacteria into xylem vessels. Since, until now, no antimicrobial treatment has been successfully applied to kill X. fastidiosa and/or prevent its diffusion, in this study, antimicrobial blue light (aBL) was explored as a potential anti-Xylella tool. Xylella fastidiosa subsp. pauca Salento-1, chosen as a model strain, showed a certain degree of sensitivity to light at 410 nm. The killing effect was light dose dependent and bacterial concentration dependent. These preliminary results support the potential of blue light in decontamination of agricultural equipment and/or plant surface; however, further investigations are needed for in vivo applications.
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Affiliation(s)
- Gianluca Bleve
- Istituto di Scienze delle Produzioni Alimentari (ISPA), Consiglio Nazionale delle Ricerche (CNR), SP Lecce-Monteroni, 73100, Lecce, Italy
| | - Nicola Trivellin
- Department of Industrial Engineering, University of Padua, via Venezia, 1, 35131, Padova, Italy
| | - Daniela Chirizzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, via Manfredonia 20, 71100, Foggia, Italy
| | - Annamaria Tarantini
- Istituto di Scienze delle Produzioni Alimentari (ISPA), Consiglio Nazionale delle Ricerche (CNR), SP Lecce-Monteroni, 73100, Lecce, Italy
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (Di.S.S.P.A), Università di Bari, via G. Amendola, 165/A, Bari, 70126, Italy
| | - Viviana Teresa Orlandi
- Departemnt of Biotechnologies and Life Sciences, University of Insubria, via J. H. Dunant, 3, 21100, Varese, Italy.
| | - Francesco Milano
- Istituto di Scienze delle Produzioni Alimentari (ISPA), Consiglio Nazionale delle Ricerche (CNR), SP Lecce-Monteroni, 73100, Lecce, Italy
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5
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Almasri F, Collotta D, Aimaretti E, Sus N, Aragno M, Dal Bello F, Eva C, Mastrocola R, Landberg R, Frank J, Collino M. Dietary Intake of Fructooligosaccharides Protects against Metabolic Derangements Evoked by Chronic Exposure to Fructose or Galactose in Rats. Mol Nutr Food Res 2024; 68:e2300476. [PMID: 38158337 DOI: 10.1002/mnfr.202300476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/30/2023] [Indexed: 01/03/2024]
Abstract
SCOPE Diets rich in fat and sugars evoke chronic low-grade inflammation, leading to metabolic derangements. This study investigates the impact of fructose and galactose, two commonly consumed simple sugars, on exacerbation of the harmful effects caused by high fat intake. Additionally, the potential efficacy of fructooligosaccharides (FOS), a fermentable dietary fiber, in counteracting these effects is examined. METHODS AND RESULTS Male Sprague-Dawley rats (six/group) are fed 8 weeks as follows: control 5% fat diet (CNT), 20% fat diet (FAT), FAT+10% FOS diet (FAT+FOS), FAT+25% galactose diet (FAT+GAL), FAT+GAL+10% FOS diet (FAT+GAL+FOS), FAT+25% fructose diet (FAT+FRU), FAT+FRU+10% FOS diet (FAT+FRU+FOS). The dietary manipulations tested do not affect body weight gain, blood glucose, or markers of systemic inflammation whereas significant increases in plasma concentrations of triacylglycerols, cholesterol, aspartate aminotransferase, and alanine aminotrasferase are detected in both FAT+FRU and FAT+GAL compared to CNT. In the liver and skeletal muscle, both sugars induce significant accumulation of lipids and advanced glycation end-products (AGEs). FOS supplementation prevents these impairments. CONCLUSION This study extends the understanding of the deleterious effects of a chronic intake of simple sugars and demonstrates the beneficial role of the prebiotic FOS in dampening the sugar-induced metabolic impairments by prevention of lipid and AGEs accumulation.
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Affiliation(s)
- Fidèle Almasri
- Department of Food Biofunctionality, Institute of Nutritional Sciences, University of Hohenheim, Garbenstr. 28, 70599, Stuttgart, Germany
| | - Debora Collotta
- Department of Neurosciences "Rita Levi Montalcini", University of Turin, Corso Raffaello 30, Torino, 10125, Piemonte, Italy
| | - Eleonora Aimaretti
- Department of Clinical and Biological Sciences, University of Turin, Corso Raffaello 30, Turin, 10125, Piemonte, Italy
| | - Nadine Sus
- Department of Food Biofunctionality, Institute of Nutritional Sciences, University of Hohenheim, Garbenstr. 28, 70599, Stuttgart, Germany
| | - Manuela Aragno
- Department of Clinical and Biological Sciences, University of Turin, Corso Raffaello 30, Turin, 10125, Piemonte, Italy
| | - Federica Dal Bello
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, Torino, 10126, Piemonte, Italy
| | - Carola Eva
- Department of Neurosciences "Rita Levi Montalcini", University of Turin, Corso Raffaello 30, Torino, 10125, Piemonte, Italy
| | - Raffaella Mastrocola
- Department of Clinical and Biological Sciences, University of Turin, Corso Raffaello 30, Turin, 10125, Piemonte, Italy
| | - Rikard Landberg
- Department of Life Sciences, Division of Food and Nutrition Science, Chalmers University of Technology, Gothenburg, 41296, Sweden
| | - Jan Frank
- Department of Food Biofunctionality, Institute of Nutritional Sciences, University of Hohenheim, Garbenstr. 28, 70599, Stuttgart, Germany
| | - Massimo Collino
- Department of Neurosciences "Rita Levi Montalcini", University of Turin, Corso Raffaello 30, Torino, 10125, Piemonte, Italy
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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. Ascomycetes yeasts: The hidden part of human microbiome. WIREs Mech Dis 2024:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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Cendron F, Cassandro M, Penasa M. Genome-wide investigation to assess copy number variants in the Italian local chicken population. J Anim Sci Biotechnol 2024; 15:2. [PMID: 38167097 PMCID: PMC10763469 DOI: 10.1186/s40104-023-00965-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Copy number variants (CNV) hold significant functional and evolutionary importance. Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of livestock. High-density chips have enabled the detection of CNV with increased resolution, leading to the identification of even small CNV. This study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the genome. RESULTS Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV. The majority of CNV in the investigated breeds were of types 0 and 1, and the minimum length of CNV was significantly larger than that reported in previous studies. Interestingly, a high proportion of the length of chromosome 16 was covered by copy number variation regions (CNVR), with the major histocompatibility complex being the likely cause. Among the genes identified within CNVR, only those present in at least five animals across breeds (n = 95) were discussed to reduce the focus on redundant CNV. Some of these genes have been associated to functional traits in chickens. Notably, several CNVR on different chromosomes harbor genes related to muscle development, tissue-specific biological processes, heat stress resistance, and immune response. Quantitative trait loci (QTL) were also analyzed to investigate potential overlapping with the identified CNVR: 54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size, carcass characteristics, egg production, egg components, fat deposition, and feed intake. CONCLUSIONS The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources.
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Affiliation(s)
- Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, 35020, Legnaro, PD, Italy.
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, 35020, Legnaro, PD, Italy
- Federazione Delle Associazioni Nazionali Di Razza E Specie, Via XXIV Maggio 43, 00187, Rome, Italy
| | - Mauro Penasa
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, 35020, Legnaro, PD, Italy
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Russo GL, Langellotti AL, Torrieri E, Masi P. Emerging technologies in seafood processing: An overview of innovations reshaping the aquatic food industry. Compr Rev Food Sci Food Saf 2024; 23:e13281. [PMID: 38284572 DOI: 10.1111/1541-4337.13281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/01/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024]
Abstract
Seafood processing has traditionally been challenging due to the rapid spoilage rates and quality degradation of these products. With the rise of food science and technology, novel methods are being developed to overcome these challenges and improve seafood quality, shelf life, and safety. These methods range from high-pressure processing (HPP) to edible coatings, and their exploration and application in seafood processing are of great importance. This review synthesizes the recent advancements in various emerging technologies used in the seafood industry and critically evaluates their efficacy, challenges, and potential benefits. The technologies covered include HPP, ultrasound, pulsed electric field, plasma technologies, pulsed light, low-voltage electrostatic field, ozone, vacuum cooking, purified condensed smoke, microwave heating, and edible coating. Each technology offers unique advantages and presents specific challenges; however, their successful application largely depends on the nature of the seafood product and the desired result. HPP and microwave heating show exceptional promise in terms of quality retention and shelf-life extension. Edible coatings present a multifunctional approach, offering preservation and the potential enhancement of nutritional value. The strength, weakness, opportunity, and threat (SWOT) analysis indicates that, despite the potential of these technologies, cost-effectiveness, scalability, regulatory considerations, and consumer acceptance remain crucial issues. As the seafood industry stands on the cusp of a technological revolution, understanding these nuances becomes imperative for sustainable growth. Future research should focus on technological refinements, understanding consumer perspectives, and developing regulatory frameworks to facilitate the adoption of these technologies in the seafood industry.
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Affiliation(s)
| | | | - Elena Torrieri
- CAISIAL Centre, University of Naples Federico II, Portici, Italy
- Department of Agricultural Sciences, Unit of Food Science and Technology-University of Naples Federico II, Portici, Italy
| | - Paolo Masi
- CAISIAL Centre, University of Naples Federico II, Portici, Italy
- Department of Agricultural Sciences, Unit of Food Science and Technology-University of Naples Federico II, Portici, Italy
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9
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Vanzin A, Franchin C, Arrigoni G, Battisti I, Masi A, Squartini A, Bisutti V, Giannuzzi D, Gallo L, Cecchinato A, Pegolo S. Subclinical Mastitis from Streptococcus agalactiae and Prototheca spp. Induces Changes in Milk Peptidome in Holstein Cattle. J Agric Food Chem 2023; 71:16827-16839. [PMID: 37890871 PMCID: PMC10636762 DOI: 10.1021/acs.jafc.3c03065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 10/29/2023]
Abstract
Early detection of bovine subclinical mastitis may improve treatment strategies and reduce the use of antibiotics. Herein, individual milk samples from Holstein cows affected by subclinical mastitis induced by S. agalactiae and Prototheca spp. were analyzed by untargeted and targeted mass spectrometry approaches to assess changes in their peptidome profiles and identify new potential biomarkers of the pathological condition. Results showed a higher amount of peptides in milk positive on the bacteriological examination when compared with the negative control. However, the different pathogens seemed not to trigger specific effects on the milk peptidome. The peptides that best distinguish positive from negative samples are mainly derived from the most abundant milk proteins, especially from β- and αs1-casein, but also include the antimicrobial peptide casecidin 17. These results provide new insights into the physiopathology of mastitis. Upon further validation, the panel of potential discriminant peptides could help the development of new diagnostic and therapeutic tools.
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Affiliation(s)
- Alice Vanzin
- Department
of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, Legnaro
(PD) 35020, Italy
| | - Cinzia Franchin
- Department
of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, Legnaro
(PD) 35020, Italy
| | - Giorgio Arrigoni
- Department
of Biomedical Sciences, University of Padova, via U. Bassi 58/B, Padova 35131, Italy
| | - Ilaria Battisti
- Department
of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, Legnaro
(PD) 35020, Italy
| | - Antonio Masi
- Department
of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, Legnaro
(PD) 35020, Italy
| | - Andrea Squartini
- Department
of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, Legnaro
(PD) 35020, Italy
| | - Vittoria Bisutti
- Department
of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, Legnaro
(PD) 35020, Italy
| | - Diana Giannuzzi
- Department
of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, Legnaro
(PD) 35020, Italy
| | - Luigi Gallo
- Department
of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, Legnaro
(PD) 35020, Italy
| | - Alessio Cecchinato
- Department
of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, Legnaro
(PD) 35020, Italy
| | - Sara Pegolo
- Department
of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, Legnaro
(PD) 35020, Italy
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10
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Pompili V, Mazzocchi E, Moglia A, Acquadro A, Comino C, Rotino GL, Lanteri S. Structural and expression analysis of polyphenol oxidases potentially involved in globe artichoke (C. cardunculus var. scolymus L.) tissue browning. Sci Rep 2023; 13:12288. [PMID: 37516733 PMCID: PMC10387078 DOI: 10.1038/s41598-023-38874-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 07/16/2023] [Indexed: 07/31/2023] Open
Abstract
Globe artichoke capitula are susceptible to browning due to oxidation of phenols caused by the activity of polyphenol oxidases (PPOs), this reduces their suitability for fresh or processed uses. A genome-wide analysis of the globe artichoke PPO gene family was performed. Bioinformatics analyses identified eleven PPOs and their genomic and amino acidic features were annotated. Cis-acting element analysis identified a gene regulatory and functional profile associated to plant growth and development as well as stress response. For some PPOs, phylogenetic analyses revealed a structural and functional conservation with different Asteraceae PPOs, while the allelic variants of the eleven PPOs investigated across four globe artichoke varietal types identified several SNP/Indel variants, some of which having impact on gene translation. By RTqPCR were assessed the expression patterns of PPOs in plant tissues and in vitro calli characterized by different morphologies. Heterogeneous PPO expression profiles were observed and three of them (PPO6, 7 and 11) showed a significant increase of transcripts in capitula tissues after cutting. Analogously, the same three PPOs were significantly up-regulated in calli showing a brown phenotype due to oxidation of phenols. Our results lay the foundations for a future application of gene editing aimed at disabling the three PPOs putatively involved in capitula browning.
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Affiliation(s)
- Valerio Pompili
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy.
| | - Elena Mazzocchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Andrea Moglia
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Cinzia Comino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy
| | | | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy.
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11
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Trinchera A, Migliore M, Warren Raffa D, Ommeslag S, Debode J, Shanmugam S, Dane S, Babry J, Kivijarvi P, Kristensen HL, Lepse L, Salo T, Campanelli G, Willekens K. Can multi-cropping affect soil microbial stoichiometry and functional diversity, decreasing potential soil-borne pathogens? A study on European organic vegetable cropping systems. Front Plant Sci 2022; 13:952910. [PMID: 36237499 PMCID: PMC9552534 DOI: 10.3389/fpls.2022.952910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Crop diversification in spatial and temporal patterns can optimize the synchronization of nutrients plant demand and availability in soils, as plant diversity and soil microbial communities are the main drivers of biogeochemical C and nutrient cycling. The introduction of multi-cropping in organic vegetable production can represent a key strategy to ensure efficient complementation mediated by soil microbiota, including beneficial mycorrhizal fungi. This study shows the effect of the introduction of multi-cropping in five European organic vegetable systems (South-West: Italy; North-West: Denmark and Belgium; North-East: Finland and Latvia) on: (i) soil physicochemical parameters; (ii) soil microbial biomass stoichiometry; (iii) crop root mycorrhization; (iv) bacterial and fungal diversity and composition in crop rhizosphere; (v) relative abundance of selected fungal pathogens species. In each site, three cropping systems were considered: (1) crop 1-monocropping; (2) crop 2-monocropping; (3) crop 1-crop 2-intercropping or strip cropping. Results showed that, just before harvest, multi-cropping can increase soil microbial biomass amount and shape microbial community toward a predominance of some bacteria or fungi phyla, in the function of soil nutrient availability. We mainly observed a selection effect of crop type on rhizosphere microbiota. Particularly, Bacteroidetes and Mortierellomycota relative abundances in rhizosphere soil resulted in suitable ecological indicators of the positive effect of plant diversity in field, the first ones attesting an improved C and P cycles in soil and the second ones a reduced soil pathogens' pressure. Plant diversity also increased the root mycorrhizal colonization between the intercropped crops that, when properly selected, can also reduce the relative abundance of potential soil-borne pathogens, with a positive effect on crop productivity in long term.
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Affiliation(s)
- Alessandra Trinchera
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Melania Migliore
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Dylan Warren Raffa
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Sarah Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | | | - Sandra Dane
- Latvian Institute of Horticulture, LatHort, Dobeles Novads, Latvia
| | | | - Pirjo Kivijarvi
- LUKE (FI) Natural Resources Institute Finland, Helsinki, Finland
| | | | - Liga Lepse
- Latvian Institute of Horticulture, LatHort, Dobeles Novads, Latvia
| | - Tapio Salo
- LUKE (FI) Natural Resources Institute Finland, Helsinki, Finland
| | - Gabriele Campanelli
- Council for Agricultural Research and Economics-Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, Italy
| | - Koen Willekens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
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12
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Bretani G, Shaaf S, Tondelli A, Cattivelli L, Delbono S, Waugh R, Thomas W, Russell J, Bull H, Igartua E, Casas AM, Gracia P, Rossi R, Schulman AH, Rossini L. Multi-environment genome -wide association mapping of culm morphology traits in barley. Front Plant Sci 2022; 13:926277. [PMID: 36212331 PMCID: PMC9539552 DOI: 10.3389/fpls.2022.926277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/28/2022] [Indexed: 06/16/2023]
Abstract
In cereals with hollow internodes, lodging resistance is influenced by morphological characteristics such as internode diameter and culm wall thickness. Despite their relevance, knowledge of the genetic control of these traits and their relationship with lodging is lacking in temperate cereals such as barley. To fill this gap, we developed an image analysis-based protocol to accurately phenotype culm diameters and culm wall thickness across 261 barley accessions. Analysis of culm trait data collected from field trials in seven different environments revealed high heritability values (>50%) for most traits except thickness and stiffness, as well as genotype-by-environment interactions. The collection was structured mainly according to row-type, which had a confounding effect on culm traits as evidenced by phenotypic correlations. Within both row-type subsets, outer diameter and section modulus showed significant negative correlations with lodging (<-0.52 and <-0.45, respectively), but no correlation with plant height, indicating the possibility of improving lodging resistance independent of plant height. Using 50k iSelect SNP genotyping data, we conducted multi-environment genome-wide association studies using mixed model approach across the whole panel and row-type subsets: we identified a total of 192 quantitative trait loci (QTLs) for the studied traits, including subpopulation-specific QTLs and 21 main effect loci for culm diameter and/or section modulus showing effects on lodging without impacting plant height. Providing insights into the genetic architecture of culm morphology in barley and the possible role of candidate genes involved in hormone and cell wall-related pathways, this work supports the potential of loci underpinning culm features to improve lodging resistance and increase barley yield stability under changing environments.
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Affiliation(s)
- Gianluca Bretani
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Salar Shaaf
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Stefano Delbono
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - William Thomas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Hazel Bull
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Ernesto Igartua
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Ana M. Casas
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Pilar Gracia
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Roberta Rossi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Alan H. Schulman
- Viikki Plant Sciences Centre, Natural Resources Institue (LUKE), HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
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13
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Beccaccioli M, Pucci N, Salustri M, Scortichini M, Zaccaria M, Momeni B, Loreti S, Reverberi M, Scala V. Fungal and bacterial oxylipins are signals for intra- and inter-cellular communication within plant disease. Front Plant Sci 2022; 13:823233. [PMID: 36186042 PMCID: PMC9524268 DOI: 10.3389/fpls.2022.823233] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Lipids are central at various stages of host-pathogen interactions in determining virulence and modulating plant defense. Free fatty acids may act as substrates for oxidizing enzymes [e.g., lipoxygenases (LOXs) and dioxygenases (DOXs)] that synthesize oxylipins. Fatty acids and oxylipins function as modulators of several pathways in cell-to-cell communication; their structural similarity among plant, fungal, and bacterial taxa suggests potential in cross-kingdom communication. We provide a prospect of the known role of fatty acids and oxylipins in fungi and bacteria during plant-pathogen interactions. In the pathogens, oxylipin-mediated signaling pathways are crucial both in development and host infection. Here, we report on case studies suggesting that oxylipins derived from oleic, linoleic, and linolenic acids are crucial in modulating the pathogenic lifestyle in the host plant. Intriguingly, overlapping (fungi-plant/bacteria-plant) results suggest that different inter-kingdom pathosystems use similar lipid signals to reshape the lifestyle of the contenders and occasionally determine the outcome of the challenge.
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Affiliation(s)
- Marzia Beccaccioli
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Nicoletta Pucci
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and the Analysis of Agricultural Economics (CREA), Rome, Italy
| | - Manuel Salustri
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Marco Scortichini
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and the Analysis of Agricultural Economics (CREA), Rome, Italy
| | - Marco Zaccaria
- Department of Biology, Boston College, Newton, MA, United States
| | - Babak Momeni
- Department of Biology, Boston College, Newton, MA, United States
| | - Stefania Loreti
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and the Analysis of Agricultural Economics (CREA), Rome, Italy
| | - Massimo Reverberi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Valeria Scala
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and the Analysis of Agricultural Economics (CREA), Rome, Italy
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14
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Benvenuti L, De Santis A, Ferrari M, Martone D, Rossi L. The carbon footprint of Italian schools meals: An optimal choice of dishes in vegan, vegetarian, and omnivorous menus. Front Nutr 2022; 9:854049. [PMID: 36118761 PMCID: PMC9470960 DOI: 10.3389/fnut.2022.854049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
This study aims to assess the carbon footprint associated with vegan, vegetarian, and omnivorous menus for primary school lunches in Italy. For this purpose, healthy and acceptable menus with minimal greenhouse gas emissions have been designed by a binary linear programming model. The results show that the adoption of a specific diet may help in reducing the carbon footprint of menus, but it is the optimal selection of dishes that ultimately makes the difference. Interestingly enough, the optimal choice of dishes and the restriction of meat consumption in omnivorous menus can lead up to a 40% emission reduction compared to the current school lunch menu of the municipality of Rome. Moreover, the optimal choice of dishes in vegan menus provides the menu with the lowest carbon footprint among all kinds of diets.
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Affiliation(s)
- Luca Benvenuti
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Alberto De Santis
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
- *Correspondence: Alberto De Santis
| | - Marika Ferrari
- CREA Council for Agricultural Research and Economics, Research Centre for Food and Nutrition, Rome, Italy
| | - Deborah Martone
- CREA Council for Agricultural Research and Economics, Research Centre for Food and Nutrition, Rome, Italy
| | - Laura Rossi
- CREA Council for Agricultural Research and Economics, Research Centre for Food and Nutrition, Rome, Italy
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15
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Di Miceli G, Iacuzzi N, Licata M, La Bella S, Tuttolomondo T, Aprile S. Growth and development of succulent mixtures for extensive green roofs in a Mediterranean climate. PLoS One 2022; 17:e0269446. [PMID: 35657910 PMCID: PMC9165813 DOI: 10.1371/journal.pone.0269446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/21/2022] [Indexed: 11/19/2022] Open
Abstract
Green roof systems, aimed at reducing anthropic impact on the environment, are considered environmental mitigation technologies and adopted by many countries across the world to strengthen urban ecosystem services. This study evaluates two mixtures of succulent: one of Crassulaceae and the other of Aizoaceae, used in the creation of a continuous and homogenous plant groundcover in Mediterranean environments. To assess the species mixtures, the parameters plant height, growth index, cover percentage and flowering were observed. Hydrological observations were also carried out to evaluate the rainfall retained by the test system in any given month. All data were subjected to analysis of variance. Growth indicators in the study showed trends characteristic of xeric plants, which tend to slow down in dry, summer climate conditions to the point of halting plant vertical growth and ground cover development completely. The Aizocaeae mix, during the initial stage, showed prevalent horizontal growth, confirmed by greater a greater growth index (13,21) and cover percentage (45%) compared to Sedum (Growth index: 3,61; Cover: 36%). In contrast, the Sedum mix recorded greater vertical growth at the beginning (Sedum mixture: 7.53 cm; Aizoaceae mixture: 6,11 cm). During the final stages of observations, however, greater vertical growth in the Aizoaceae (7,88 cm) became apparent together with a recovery in horizontal growth in the Sedum (79%), albeit not sufficient to outperform the Aizoaceae mixture (87%). Flowering in the two mixtures occurred between late spring and late summer. The Sedum mixture guaranteed a longer flowering period (130 days) compared to the Aizoaceae (93 days), with a gradual start followed by steady flower emission. Regarding rainfall water retention, a comparison of the mixtures in late winter/early spring revealed that the Sedum performed best (44.9 L m2vs 37.4 L m2), whilst the Aizoaceae outperformed the Sedum in Autumn (63 L m2vs 55 L m2), in conjunction with favorable growth rates in both species mixtures. Both mixtures demonstrated satisfying results and are considered suited to a Mediterranean environment. Furthermore, based on the different growth rates of the species in the two test mixtures, this study suggests that new combinations of Sedum and Aizoaceae together might prove more resilient in Mediterranean environments.
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Affiliation(s)
- Giuseppe Di Miceli
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Palermo, Italy
| | - Nicolò Iacuzzi
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Palermo, Italy
| | - Mario Licata
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Palermo, Italy
- * E-mail:
| | - Salvatore La Bella
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Palermo, Italy
| | - Teresa Tuttolomondo
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Palermo, Italy
| | - Simona Aprile
- CREA Research Centre for Plant Protection and Certification, Bagheria (PA), Italy
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16
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Oteri M, Chiofalo B, Maricchiolo G, Toscano G, Nalbone L, Lo Presti V, Di Rosa AR. Black Soldier Fly Larvae Meal in the Diet of Gilthead Sea Bream: Effect on Chemical and Microbiological Quality of Filets. Front Nutr 2022; 9:896552. [PMID: 35685870 PMCID: PMC9172839 DOI: 10.3389/fnut.2022.896552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The chemical and microbiological characteristics of filets of Spaurus aurata L. specimens fed with diets containing a Hermetia illucens meal (HIM) at the 25, 35, and 50%, as a partial replacement for fish meal (FM) were evaluated. The diets, formulated to satisfy the nutritional needs of fish, were isoenergetic (22 MJ/kg gross energy), isonitrogenous (43 g/100 g, a.f.), and isolipidic (19 g/100 g, a.f.). Seventy-two specimens were randomly killed after 186 days of growing trials. Then, the filets were analyzed for chemical profile, fatty acids, amino acids, minerals, and microbial flora. Data were subjected to statistical analysis. No significant differences were observed in chemical composition. The sum of polyunsaturated fatty acids (PUFAs) showed a similar content in the filets; eicosapentaenoic acid was similar in the filets of HIM0, HIM35%, and HIM50%, whereas docosahexaenoic acid was higher in filets of the HIM0 group. n3/n6 PUFA ratio and the sum of EPA + DHA showed a high value (p < 0.001) in filets of the group fed with FM. No significant difference was observed in thrombogenic index and hypocholesterolaemic/hypercholesterolaemic ratio in the groups; the atherogenic index showed a higher value (p = 0.001) in the HIM50% group. Indispensable amino acids showed some significant (p < 0.0001) differences in the groups; arginine and phenylalanine content was higher in the filets of fish fed with FM; isoleucine and valine content was higher in the filets of HIM50%; leucine, lysine and methionine content was lower in the filets of HIM35%; histidine content was lower in the filets of HIM25%; tryptophan content was lower in filets of the HIM50% group. EAA/NEAA ratio showed highest value in the filets of the group that received FM. The presence of HIM in the three diets kept chromium, manganese, iron, copper, zinc, and nickel levels lower than those recommended by various authorities. Ca/P ratio showed a higher level (p < 0.0001) in the group fed with FM than those fed with diets containing HIM. The insect meal in the diets did not influence the microbiological profile of fish. Use of HIM as an unconventional feed ingredient in Sparus aurata diet looks promising, although the quality of filets may be affected.
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Affiliation(s)
- Marianna Oteri
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Biagina Chiofalo
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Giulia Maricchiolo
- Institute of Biological Resources and Marine Biotechnologies, National Research Council, Messina, Italy
| | - Giovanni Toscano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Luca Nalbone
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Vittorio Lo Presti
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Ambra Rita Di Rosa
- Department of Veterinary Sciences, University of Messina, Messina, Italy
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17
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Luigi M, Manglli A, Dragone I, Antonelli MG, Contarini M, Speranza S, Bertin S, Tiberini A, Gentili A, Varvaro L, Tomassoli L, Faggioli F. Effects of Biochar on the Growth and Development of Tomato Seedlings and on the Response of Tomato Plants to the Infection of Systemic Viral Agents. Front Microbiol 2022; 13:862075. [PMID: 35615512 PMCID: PMC9125222 DOI: 10.3389/fmicb.2022.862075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Biochar is a rich carbon product obtained by pyrolysis of biomass under a limited supply of oxygen. It is composed mainly of aromatic molecules, but its agronomic value is hard to evaluate and difficult to predict due to its great variable characteristics depending on the type of starting biomass and the conditions of pyrolysis. Anyway, it could be used as soil amendment because it increases the soil fertility of acidic soils, increases the agricultural productivity, and seems to provide protection against some foliar and soilborne diseases. In this study, the effects of biochar, obtained from olive pruning, have been evaluated on tomato seedlings growth and on their response to systemic agents' infection alone or added with beneficial microorganisms (Bacillus spp. and Trichoderma spp.). First, experimental data showed that biochar seems to promote the development of the tomato seedlings, especially at concentrations ranging from 1 to 20% (w/w with peat) without showing any antimicrobial effects on the beneficial soil bacteria at the tomato rhizosphere level and even improving their growth. Thus, those concentrations were used in growing tomato plants experimentally infected with tomato spotted wilt virus (TSWV) and potato spindle tuber viroid (PSTVd). The biochar effect was estimated by evaluating three parameters, namely, symptom expression, number of infected plants, and pathogen quantification, using RT-qPCR technique and −ΔΔCt analysis. Biochar at 10–15% and when added with Trichoderma spp. showed that it reduces the replication of PSTVd and the expression of symptoms even if it was not able to block the start of infection. The results obtained on TSWV-infected plants suggested that biochar could contribute to reducing both infection rate and virus replication. For systemic viral agents, such as PSTVd and TSWV, there are no curative control methods, and therefore, the use of prevention means, as can be assumed the use biochar, for example, in the nursery specialized in horticultural crops, can be of great help. These results can be an encouraging starting point to introduce complex biochar formulates among the sustainable managing strategies of plant systemic diseases.
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Affiliation(s)
- Marta Luigi
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Ariana Manglli
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Immacolata Dragone
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | | | - Mario Contarini
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Stefano Speranza
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Sabrina Bertin
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Antonio Tiberini
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Andrea Gentili
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Leonardo Varvaro
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Laura Tomassoli
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Francesco Faggioli
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
- *Correspondence: Francesco Faggioli
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18
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Scala V, Salustri M, Loreti S, Pucci N, Cacciotti A, Tatulli G, Scortichini M, Reverberi M. Mass Spectrometry-Based Targeted Lipidomics and Supervised Machine Learning Algorithms in Detecting Disease, Cultivar, and Treatment Biomarkers in Xylella fastidiosa subsp. pauca-Infected Olive Trees. Front Plant Sci 2022; 13:833245. [PMID: 35528940 PMCID: PMC9072861 DOI: 10.3389/fpls.2022.833245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
In 2013, Xylella fastidiosa (Xf) was detected for the first time in Apulia and, subsequently, recognized as the causal agent of the olive quick decline syndrome (OQDS). To contain the disease, the olive germplasm was evaluated for resistance to Xf, identifying cultivars with different susceptibility to the pathogen. Regarding this, the resistant cultivar Leccino has generally a lower bacterial titer compared with the susceptible cultivar Ogliarola salentina. Among biomolecules, lipids could have a pivotal role in the interaction of Xf with its host. In the grapevine Pierce's disease, fatty acid molecules, the diffusible signaling factors (DSFs), act as regulators of Xf lifestyle and are crucial for its virulence. Other lipid compounds derived from fatty acid oxidation, namely, oxylipins, can affect, in vitro, biofilm formation in Xf subsp. pauca (Xfp) strain De Donno, that is, the strain causing OQDS. In this study, we combined high-performance liquid chromatography-mass spectrometry-MS-based targeted lipidomics with supervised learning algorithms (random forest, support vector machine, and neural networks) to classify olive tree samples from Salento. The dataset included samples from either OQDS-positive or OQDS-negative olive trees belonging either to cultivar Ogliarola salentina or Leccino treated or not with the zinc-copper-citric acid biocomplex Dentamet®. We built classifiers using the relative differences in lipid species able to discriminate olive tree samples, namely, (1) infected and non-infected, (2) belonging to different cultivars, and (3) treated or untreated with Dentamet®. Lipid entities emerging as predictors of the thesis are free fatty acids (C16:1, C18:1, C18:2, C18:3); the LOX-derived oxylipins 9- and 13-HPOD/TrE; the DOX-derived oxylipin 10-HPOME; and diacylglyceride DAG36:4(18:1/18:3).
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Affiliation(s)
- Valeria Scala
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Rome, Italy
| | - Manuel Salustri
- Department of Environmental Biology, Sapienza University, Rome, Italy
| | - Stefania Loreti
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Rome, Italy
| | - Nicoletta Pucci
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Rome, Italy
| | - Andrea Cacciotti
- Department of Environmental Biology, Sapienza University, Rome, Italy
| | - Giuseppe Tatulli
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Rome, Italy
| | - Marco Scortichini
- Council for Agricultural Research and Economics (CREA), Research Centre for Olive, Fruit and Citrus Crops, Rome, Italy
| | - Massimo Reverberi
- Department of Environmental Biology, Sapienza University, Rome, Italy
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Valeriano T, Fischer K, Ginaldi F, Giustarini L, Castello G, Bregaglio S. Rotten Hazelnuts Prediction via Simulation Modeling-A Case Study on the Turkish Hazelnut Sector. Front Plant Sci 2022; 13:766493. [PMID: 35444678 PMCID: PMC9014268 DOI: 10.3389/fpls.2022.766493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
The quality defects of hazelnut fruits comprise changes in morphology and taste, and their intensity mainly depends on seasonal environmental conditions. The strongest off-flavor of hazelnuts is known as rotten defect, whose candidate causal agents are a complex of fungal pathogens, with Diaporthe as the dominant genus. Timely indications on the expected incidence of rotten defect would be essential for buyers to identify areas where hazelnut quality will be superior, other than being useful for farmers to have the timely indications of the risk of pathogens infection. Here, we propose a rotten defect forecasting model, and we apply it in the seven main hazelnut producing municipalities in Turkey. We modulate plant susceptibility to fungal infection according to simulated hazelnut phenology, and we reproduce the key components of the Diaporthe spp. epidemiological cycle via a process-based simulation model. A model sensitivity analysis has been performed under contrasting weather conditions to select most relevant parameters for calibration, which relied on weekly phenological observations and the post-harvest analyses of rotten incidence in the period 2016-2019, conducted in 22 orchards. The rotten simulation model reproduced rotten incidence data in calibration and validation datasets with a mean absolute error below 1.8%. The dataset used for model validation (321 additional sampling locations) has been characterized by large variability of rotten incidence, in turn contributing to decrease the correlation between reference and simulated data (R 2 = 0.4 and 0.21 in West and East Black Sea region, respectively). This denotes the key effect of other environmental and agronomic factors on rotten incidence, which are not yet taken into account by the predictive workflow and will be considered in further improvements. When applied in spatially distributed simulations, the model differentiated the rotten incidence across municipalities, and reproduced the interannual variability of rotten incidence. Our results confirmed that the rotten defect is strictly dependent on precipitation amount and timing, and that plant susceptibility is crucial to trigger fungal infections. Future steps will envisage the application of the rotten simulation model to other hazelnut producing regions, before being operationally used for in-season forecasting activities.
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Affiliation(s)
- Taynara Valeriano
- Council for Agricultural Research and Economics (CREA), Research Centre for Agriculture and Environment, Bologna, Italy
- Ferrero Hazelnut Company, Ferrero Trading Lux S.A., Senningerberg, Luxembourg
| | - Kim Fischer
- Ferrero Hazelnut Company, Ferrero Trading Lux S.A., Senningerberg, Luxembourg
| | - Fabrizio Ginaldi
- Council for Agricultural Research and Economics (CREA), Research Centre for Agriculture and Environment, Bologna, Italy
| | | | | | - Simone Bregaglio
- Council for Agricultural Research and Economics (CREA), Research Centre for Agriculture and Environment, Bologna, Italy
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20
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Navarro A, Nicastro N, Costa C, Pentangelo A, Cardarelli M, Ortenzi L, Pallottino F, Cardi T, Pane C. Sorting biotic and abiotic stresses on wild rocket by leaf-image hyperspectral data mining with an artificial intelligence model. Plant Methods 2022; 18:45. [PMID: 35366940 PMCID: PMC8977030 DOI: 10.1186/s13007-022-00880-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/19/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Wild rocket (Diplotaxis tenuifolia) is prone to soil-borne stresses under intensive cultivation systems devoted to ready-to-eat salad chain, increasing needs for external inputs. Early detection of the abiotic and biotic stresses by using digital reflectance-based probes may allow optimization and enhance performances of the mitigation strategies. METHODS Hyperspectral image analysis was applied to D. tenuifolia potted plants subjected, in a greenhouse experiment, to five treatments for one week: a control treatment watered to 100% water holding capacity, two biotic stresses: Fusarium wilting and Rhizoctonia rotting, and two abiotic stresses: water deficit and salinity. Leaf hyperspectral fingerprints were submitted to an artificial intelligence pipeline for training and validating image-based classification models able to work in the stress range. Spectral investigation was corroborated by pertaining physiological parameters. RESULTS Water status was mainly affected by water deficit treatment, followed by fungal diseases, while salinity did not change water relations of wild rocket plants compared to control treatment. Biotic stresses triggered discoloration in plants just in a week after application of the treatments, as evidenced by the colour space coordinates and pigment contents values. Some vegetation indices, calculated on the bases of the reflectance data, targeted on plant vitality and chlorophyll content, healthiness, and carotenoid content, agreed with the patterns of variations observed for the physiological parameters. Artificial neural network helped selection of VIS (492-504, 540-568 and 712-720 nm) and NIR (855, 900-908 and 970 nm) bands, whose read reflectance contributed to discriminate stresses by imaging. CONCLUSIONS This study provided significative spectral information linked to the assessed stresses, allowing the identification of narrowed spectral regions and single wavelengths due to changes in photosynthetically active pigments and in water status revealing the etiological cause.
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Affiliation(s)
- Alejandra Navarro
- Council for Agricultural Research and Economics (CREA), Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098, Pontecagnano Faiano, Italy.
| | - Nicola Nicastro
- Council for Agricultural Research and Economics (CREA), Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098, Pontecagnano Faiano, Italy
| | - Corrado Costa
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria (CREA) - Centro di Ricerca Ingegneria e Trasformazioni Agroalimentari, Via della Pascolare 16, 00015, Monterotondo, Italy
| | - Alfonso Pentangelo
- Council for Agricultural Research and Economics (CREA), Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098, Pontecagnano Faiano, Italy
| | - Mariateresa Cardarelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098, Pontecagnano Faiano, Italy
| | - Luciano Ortenzi
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria (CREA) - Centro di Ricerca Ingegneria e Trasformazioni Agroalimentari, Via della Pascolare 16, 00015, Monterotondo, Italy
| | - Federico Pallottino
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria (CREA) - Centro di Ricerca Ingegneria e Trasformazioni Agroalimentari, Via della Pascolare 16, 00015, Monterotondo, Italy
| | - Teodoro Cardi
- Council for Agricultural Research and Economics (CREA), Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098, Pontecagnano Faiano, Italy
| | - Catello Pane
- Council for Agricultural Research and Economics (CREA), Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098, Pontecagnano Faiano, Italy
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21
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Rippa M, Battaglia V, Cermola M, Sicignano M, Lahoz E, Mormile P. Monitoring of the copper persistence on plant leaves using pulsed thermography. Environ Monit Assess 2022; 194:160. [PMID: 35137266 PMCID: PMC8825608 DOI: 10.1007/s10661-022-09807-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/22/2022] [Indexed: 05/14/2023]
Abstract
Copper-based fungicides are largely used in agriculture in the control of a wide range of plant diseases. Applied on plants, they remain deposited on leaf surfaces and are not absorbed into plant tissues. Because of accumulation problems and their ecotoxicological profiles in the soil, their use needs to be monitored and controlled, also by using modern technologies to better optimize the efficacy rendering minimum the amount of copper per season used. In this work, we test a novel approach based on pulsed thermography to evaluate the persistence of the copper on plant leaves so that the time between two applications should be the minimum needs. We monitored the thermal response observed on different treatments of both grapevine and tobacco plants over a 3-week period. Our experimental results demonstrate that the new methodological approach based on pulsed thermography can be an effective tool to evaluate in real time the presence of copper on differently treated plants allowing a tentative quantification and, therefore, to optimize its use in the agricultural practices, according also to the European Regulation n. 1107/2009.
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Affiliation(s)
- Massimo Rippa
- Institute of Applied Sciences and Intelligent Systems "E. Caianiello" of CNR, via Campi Flegrei, 34, Pozzuoli (Na), 80072, Italy.
| | - Valerio Battaglia
- CREA - Research Centre for Cereal and Industrial Crops, via Torrino, 2, Caserta, 81100, Italy
| | - Michele Cermola
- CREA - Research Centre for Cereal and Industrial Crops, via Torrino, 2, Caserta, 81100, Italy
| | - Mariarosaria Sicignano
- CREA - Research Centre for Cereal and Industrial Crops, via Torrino, 2, Caserta, 81100, Italy
| | - Ernesto Lahoz
- CREA - Research Centre for Cereal and Industrial Crops, via Torrino, 2, Caserta, 81100, Italy
| | - Pasquale Mormile
- Institute of Applied Sciences and Intelligent Systems "E. Caianiello" of CNR, via Campi Flegrei, 34, Pozzuoli (Na), 80072, Italy
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22
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Grant F, Rossi L. The Italian Observatory on Food Surplus, Recovery, and Waste: The Development Process and Future Achievements. Front Nutr 2022; 8:787982. [PMID: 35155514 PMCID: PMC8829391 DOI: 10.3389/fnut.2021.787982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/29/2021] [Indexed: 12/22/2022] Open
Abstract
Food loss and waste (FLW) is an environmental, social, and economic problem. Countries all around the world are looking for efficient strategies to prevent and reduce FLW, as recommended by target 12.3 of the Sustainable Development Goals (SDGs) of the United Nations. The European Union (EU) is strongly committed to helping solve the FLW issue, setting up the Platform on Food Losses and Food Waste, and adopting the Farm to Fork Strategy. Italy has also adopted a consolidated approach toward this issue, in particular through the redistribution of food surplus to those in need, a policy that was instituted with the Gadda Law 166/2016. Importantly, this normative framework also provided for the establishment of the National Observatory on Food Surplus, Recovery, and Waste [Osservatorio sulle Eccedenze, i Recuperi e gli Sprechi Alimentari (OERSA)]. This article describes the creation and development of the OERSA, as the technical entity supporting national FLW policies. One of the first actions taken by the OERSA was that of mapping the FLW initiatives that were being implemented along the entire food supply chain in Italy. This gave the OERSA a solid foundation on which to begin working on two different fronts: (1) Collecting data regarding the primary production sector and at the consumer level and (2) Establishing educational programs and awareness campaigns. The data collected by the OERSA highlight that, although several actors of the Italian supply chain are already conscious of the causes of FLW, new strategies that focus on innovation and cooperation should be encouraged.
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23
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Fusco V, Pasciuta V, Lumia V, Matere A, Battaglia V, Bertinelli G, Sansone D, Brunetti A, Pilotti M. Root and stem rot, and wilting of olive tree caused by Dematophora necatrix and associated with Emmia lacerata in Central Italy. Eur J Plant Pathol 2022; 163:71-96. [PMID: 35095205 PMCID: PMC8783780 DOI: 10.1007/s10658-022-02458-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/31/2021] [Indexed: 05/14/2023]
Abstract
UNLABELLED Lethal wilting was observed on young olive trees cv Favolosa in a grove in central Italy. White mycelial strands wrapped the basal portion of the stems that had been buried during planting. The bark was rotted and the xylem was discoloured. A fungal morphotype was strictly associated with symptomatic plants and identified as Dematophora (ex Rosellinia) necatrix. Pathogenicity tests on cvs Favolosa, Leccino and Ogliarola demonstrated that D. necatrix was the causal agent of the disease. Our investigations revealed that infections occurring during autumn and winter greatly favour the disease. By applying a marcottage to the inoculation point, we accelerated the course of the disease and mimicked the lethal outcome observed in the field. In in vitro tests, seven systemic (potential) fungicides strongly inhibited D. necatrix. Dentamet, Al-phosphite and Thiophanate methyl were selected to be tested in planta with a curative and preventive modality. Only Thiophanate methyl, in preventive modality, fully protected the plants from disease progression throughout the observation period. An additional fungal species was strictly associated with both diseased and apparently healthy plants. Morphological and molecular features identified the fungus as Emmia lacerata, a polypore species within the Irpicaceae, which is the agent of white rot on dead woody substrates. To our knowledge, this is the first time that E. lacerata has been reported in Italy and worldwide on olive trees. Inoculation of ‛Favolosa' trees revealed that it colonizes the xylem without causing visible alterations. The possible role of E. lacerata in the olive tree-D. necatrix pathosystem is discussed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10658-022-02458-1.
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Affiliation(s)
- Valeria Fusco
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Vittorio Pasciuta
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Valentina Lumia
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Antonio Matere
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Valerio Battaglia
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Giorgia Bertinelli
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Domenico Sansone
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Angela Brunetti
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Massimo Pilotti
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
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Zago M, Rossetti L, Bardelli T, Carminati D, Nazzicari N, Giraffa G. Bacterial Community of Grana Padano PDO Cheese and Generical Hard Cheeses: DNA Metabarcoding and DNA Metafingerprinting Analysis to Assess Similarities and Differences. Foods 2021; 10:1826. [PMID: 34441603 PMCID: PMC8392751 DOI: 10.3390/foods10081826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
The microbiota of Protected Designation of Origin (PDO) cheeses plays an essential role in defining their quality and typicity and could be applied to protect these products from counterfeiting. To study the possible role of cheese microbiota in distinguishing Grana Padano (GP) cheese from generical hard cheeses (HC), the microbial structure of 119 GP cheese samples was studied by DNA metabarcoding and DNA metafingerprinting and compared with 49 samples of generical hard cheeses taken from retail. DNA metabarcoding highlighted the presence, as dominant taxa, of Lacticaseibacillus rhamnosus, Lactobacillus helveticus, Streptococcus thermophilus, Limosilactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus spp., and Lactococcus spp. in both GP cheese and HC. Differential multivariate statistical analysis of metataxonomic and metafingerprinting data highlighted significant differences in the Shannon index, bacterial composition, and species abundance within both dominant and subdominant taxa between the two cheese groups. A supervised Neural Network (NN) classification tool, trained by metagenotypic data, was implemented, allowing to correctly classify GP cheese and HC samples. Further implementation and validation to increase the robustness and improve the predictive capacity of the NN classifier will be needed. Nonetheless, the proposed tool opens interesting perspectives in helping protection and valorization of GP and other PDO cheeses.
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Affiliation(s)
- Miriam Zago
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Lia Rossetti
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Tommaso Bardelli
- Research Centre for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, 26900 Lodi, Italy;
| | - Domenico Carminati
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Nelson Nazzicari
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Giorgio Giraffa
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
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25
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Veneziani G, Nucciarelli D, Taticchi A, Esposto S, Selvaggini R, Tomasone R, Pagano M, Servili M. Application of Low Temperature during the Malaxation Phase of Virgin Olive Oil Mechanical Extraction Processes of Three Different Italian Cultivars. Foods 2021; 10:1578. [PMID: 34359448 PMCID: PMC8304241 DOI: 10.3390/foods10071578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/25/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
The malaxation step, one of the most important phases of the virgin olive oil (VOO) mechanical extraction process involved in the development of the main quality characteristics of the final product, was carried out at a low temperature (18 °C). The rapid control of malaxer temperature was handled with the same chiller as that of the heat exchanger used in a semi-industrial extraction plant. Low temperature was used during the full olive paste kneading process and also for half of this process, which showed that there was a significant impact on the phenolic and volatile contents of VOO. Trials were conducted on three different cultivars (Canino, Moraiolo and Peranzana), and their phenolic and volatile concentrations showed different quantitative and qualitative effects due to the prolonged use of low temperature after the crushing phase, as a function of the different genetic origins of the olives. The process of phenolic compound solubilization into the oily phase was negatively influenced by the use of low temperature during the entire malaxation period for all the cultivars, whereas the volatile fraction showed an improvement in VOO flavor mainly due to the oil extracted from Canino olives.
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Affiliation(s)
- Gianluca Veneziani
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Via S. Costanzo, 06126 Perugia, Italy; (G.V.); (D.N.); (A.T.); (R.S.); (M.S.)
| | - Davide Nucciarelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Via S. Costanzo, 06126 Perugia, Italy; (G.V.); (D.N.); (A.T.); (R.S.); (M.S.)
| | - Agnese Taticchi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Via S. Costanzo, 06126 Perugia, Italy; (G.V.); (D.N.); (A.T.); (R.S.); (M.S.)
| | - Sonia Esposto
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Via S. Costanzo, 06126 Perugia, Italy; (G.V.); (D.N.); (A.T.); (R.S.); (M.S.)
| | - Roberto Selvaggini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Via S. Costanzo, 06126 Perugia, Italy; (G.V.); (D.N.); (A.T.); (R.S.); (M.S.)
| | - Roberto Tomasone
- Council for Agricultural Research and Economics Research, Centre for Engineering and Agro-Food Processing, 00015 Monterotondo, Italy; (R.T.); (M.P.)
| | - Mauro Pagano
- Council for Agricultural Research and Economics Research, Centre for Engineering and Agro-Food Processing, 00015 Monterotondo, Italy; (R.T.); (M.P.)
| | - Maurizio Servili
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Via S. Costanzo, 06126 Perugia, Italy; (G.V.); (D.N.); (A.T.); (R.S.); (M.S.)
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Pieracci Y, Ascrizzi R, Terreni V, Pistelli L, Flamini G, Bassolino L, Fulvio F, Montanari M, Paris R. Essential Oil of Cannabis sativa L: Comparison of Yield and Chemical Composition of 11 Hemp Genotypes. Molecules 2021; 26:4080. [PMID: 34279420 PMCID: PMC8271456 DOI: 10.3390/molecules26134080] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 01/11/2023] Open
Abstract
Cannabis sativa L. is an annual species cultivated since antiquity for different purposes. While, in the past, hemp inflorescences were considered crop residues, at present, they are regarded as valuable raw materials with different applications, among which extraction of the essential oil (EO) has gained increasing interest in many fields. The aim of the present study is the evaluation of the yield and the chemical composition of the EO obtained by hydrodistillation from eleven hemp genotypes, cultivated in the same location for two consecutive growing seasons. The composition of the EOs was analyzed by GC-MS, and then subjected to multivariate statistical analysis. Sesquiterpenes represented the main class of compounds in all the EOs, both in their hydrocarbon and oxygenated forms, with relative abundances ranging from 47.1 to 78.5%; the only exception was the Felina 32 sample collected in 2019, in which cannabinoids predominated. Cannabinoids were the second most abundant class of compounds, of which cannabidiol was the main one, with relative abundances between 11.8 and 51.5%. The statistical distribution of the samples, performed on the complete chemical composition of the EOs, evidenced a partition based on the year of cultivation, rather than on the genotype, with the exception of Uso-31. Regarding the extraction yield, a significant variation was evidenced among both the genotypes and the years of cultivation.
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Affiliation(s)
- Ylenia Pieracci
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Roberta Ascrizzi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Valentina Terreni
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Luisa Pistelli
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Interdepartmental Research Center "Nutraceuticals and Food for Health" (NUTRAFOOD), University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Guido Flamini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Interdepartmental Research Center "Nutraceuticals and Food for Health" (NUTRAFOOD), University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Laura Bassolino
- CREA-Research Center for Cereal and Industrial Crops, Via di Corticella 133, 40128 Bologna, Italy
| | - Flavia Fulvio
- CREA-Research Center for Cereal and Industrial Crops, Via di Corticella 133, 40128 Bologna, Italy
- Department of Sciences of Agriculture, Food Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Massimo Montanari
- CREA-Research Center for Cereal and Industrial Crops, Via di Corticella 133, 40128 Bologna, Italy
| | - Roberta Paris
- CREA-Research Center for Cereal and Industrial Crops, Via di Corticella 133, 40128 Bologna, Italy
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Picchi V, Gobbi S, Fattizzo M, Zefelippo M, Faoro F. Chitosan Nanoparticles Loaded with N-Acetyl Cysteine to Mitigate Ozone and Other Possible Oxidative Stresses in Durum Wheat. Plants (Basel) 2021; 10:691. [PMID: 33918532 PMCID: PMC8065401 DOI: 10.3390/plants10040691] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/01/2021] [Accepted: 04/01/2021] [Indexed: 01/16/2023]
Abstract
Modern durum wheat cultivars are more prone to ozone stress because of their high photosynthetic efficiency and leaf gas exchanges that cause a greater pollutant uptake. This, in turn, generates an increased reactive oxygen species (ROS) production that is a challenge to control by the antioxidant system of the plant, therefore affecting final yield, with a reduction up to 25%. With the aim of mitigating oxidative stress in wheat, we used chitosan nanoparticles (CHT-NPs) either unloaded or loaded with the antioxidant compound N-acetyl cysteine (NAC), on plants grown either in a greenhouse or in an open field. NAC-loaded NPs were prepared by adding 0.5 mg/mL NAC to the CHT solution before ionotropic gelation with tripolyphosphate (TTP). Greenhouse experiments evidenced that CHT-NPs and CHT-NPs-NAC were able to increase the level of the leaf antioxidant pool, particularly ascorbic acid (AsA) content. However, the results of field trials, while confirming the increase in the AsA level, at least in the first phenological stages, were less conclusive. The presence of NAC did not appear to significantly affect the leaf antioxidant pool, although the grain yield was slightly higher in NAC-treated parcels. Furthermore, both NAC-loaded and -unloaded CHT-NPs partially reduced the symptom severity and increased the weight of 1000 seeds, thus showing a moderate mitigation of ozone injury.
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Affiliation(s)
- Valentina Picchi
- CREA Research Centre for Engineering and Agro-Food Processing, Via G. Venezian 26, 20133 Milan, Italy
| | - Serena Gobbi
- Department of Agricultural and Environmental Sciences, University of Milano, Via Celoria 2, 20133 Milano, Italy; (S.G.); (M.F.)
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Via Celoria 2, 20133 Milano, Italy
| | - Matteo Fattizzo
- Department of Agricultural and Environmental Sciences, University of Milano, Via Celoria 2, 20133 Milano, Italy; (S.G.); (M.F.)
| | - Mario Zefelippo
- Agronomist and Agricultural Consultant, Via S. Francesco D’Assisi 7/A, 27058 Voghera, Italy;
| | - Franco Faoro
- Department of Agricultural and Environmental Sciences, University of Milano, Via Celoria 2, 20133 Milano, Italy; (S.G.); (M.F.)
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Nanetti A, Ellis JD, Cardaio I, Cilia G. Detection of Lotmaria passim, Crithidia mellificae and Replicative Forms of Deformed Wing Virus and Kashmir Bee Virus in the Small Hive Beetle ( Aethina tumida). Pathogens 2021; 10:372. [PMID: 33808848 PMCID: PMC8003614 DOI: 10.3390/pathogens10030372] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022] Open
Abstract
Knowledge regarding the honey bee pathogens borne by invasive bee pests remains scarce. This investigation aimed to assess the presence in Aethina tumida (small hive beetle, SHB) adults of honey bee pathogens belonging to the following groups: (i) bacteria (Paenibacillus larvae and Melissococcus plutonius), (ii) trypanosomatids (Lotmaria passim and Crithidia mellificae), and (iii) viruses (black queen cell virus, Kashmir bee virus, deformed wing virus, slow paralysis virus, sacbrood virus, Israeli acute paralysis virus, acute bee paralysis virus, chronic bee paralysis virus). Specimens were collected from free-flying colonies in Gainesville (Florida, USA) in summer 2017. The results of the molecular analysis show the presence of L. passim, C. mellificae, and replicative forms of deformed wing virus (DWV) and Kashmir bee virus (KBV). Replicative forms of KBV have not previously been reported. These results support the hypothesis of pathogen spillover between managed honey bees and the SHB, and these dynamics require further investigation.
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Affiliation(s)
- Antonio Nanetti
- CREA Research Centre for Agriculture and Environment, Via di Saliceto 80, 40128 Bologna, Italy; (A.N.); (I.C.)
| | - James D. Ellis
- Entomology and Nematology Department, University of Florida, 1881 Natural Area Dr., P.O. Box 110620, Gainesville, FL 32607-0620, USA;
| | - Ilaria Cardaio
- CREA Research Centre for Agriculture and Environment, Via di Saliceto 80, 40128 Bologna, Italy; (A.N.); (I.C.)
| | - Giovanni Cilia
- CREA Research Centre for Agriculture and Environment, Via di Saliceto 80, 40128 Bologna, Italy; (A.N.); (I.C.)
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Santoro A, Zhao J, Wu L, Carru C, Biagi E, Franceschi C. Microbiomes other than the gut: inflammaging and age-related diseases. Semin Immunopathol 2020; 42:589-605. [PMID: 32997224 PMCID: PMC7666274 DOI: 10.1007/s00281-020-00814-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022]
Abstract
During the course of evolution, bacteria have developed an intimate relationship with humans colonizing specific body sites at the interface with the body exterior and invaginations such as nose, mouth, lung, gut, vagina, genito-urinary tract, and skin and thus constituting an integrated meta-organism. The final result has been a mutual adaptation and functional integration which confers significant advantages to humans and bacteria. The immune system of the host co-evolved with the microbiota to develop complex mechanisms to recognize and destroy invading microbes, while preserving its own bacteria. Composition and diversity of the microbiota change according to development and aging and contribute to humans' health and fitness by modulating the immune system response and inflammaging and vice versa. In the last decades, we experienced an explosion of studies on the role of gut microbiota in aging, age-related diseases, and longevity; however, less reports are present on the role of the microbiota at different body sites. In this review, we describe the key steps of the co-evolution between Homo sapiens and microbiome and how this adaptation can impact on immunosenescence and inflammaging. We briefly summarized the role of gut microbiota in aging and longevity while bringing out the involvement of the other microbiota.
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Affiliation(s)
- Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Bologna, Italy.
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, 72703, USA
| | - Lu Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ciriaco Carru
- Department of Biomedical Sciences, University Hospital (AOU) - University of Sassari, Sassari, Italy
| | - Elena Biagi
- Department of Pharmacy and Biotechnology (FABIT), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
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Cendron F, Perini F, Mastrangelo S, Tolone M, Criscione A, Bordonaro S, Iaffaldano N, Castellini C, Marzoni M, Buccioni A, Soglia D, Schiavone A, Cerolini S, Lasagna E, Cassandro M. Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds. Animals (Basel) 2020; 10:E1441. [PMID: 32824706 PMCID: PMC7460279 DOI: 10.3390/ani10081441] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 01/06/2023] Open
Abstract
The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.
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Affiliation(s)
- Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell’Università, 16, 35020 Legnaro, Italy; (F.C.); (M.C.)
| | - Francesco Perini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.P.); (C.C.)
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest sciences, University of Palermo, Viale delle Scienze, Ed. 4, 90128 Palermo, Italy; (S.M.); (M.T.)
| | - Marco Tolone
- Department of Agricultural, Food and Forest sciences, University of Palermo, Viale delle Scienze, Ed. 4, 90128 Palermo, Italy; (S.M.); (M.T.)
| | - Andrea Criscione
- Department of Agronomy, Food, and Environment, University of Catania, Via Valdisavoia, 5, 95100 Catania, Italy; (A.C.); (S.B.)
| | - Salvatore Bordonaro
- Department of Agronomy, Food, and Environment, University of Catania, Via Valdisavoia, 5, 95100 Catania, Italy; (A.C.); (S.B.)
| | - Nicolaia Iaffaldano
- Department of Agricultural, Environment and Food, University of Molise, Via De Sanctis s/n, 86100 Campobasso, Italy;
| | - Cesare Castellini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.P.); (C.C.)
| | - Margherita Marzoni
- Department of Veterinary Science, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy;
| | - Arianna Buccioni
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, Via di San Bonaventura, 50145 Firenze, Italy;
| | - Dominga Soglia
- Department of Veterinary Science, University of Torino, Largo Paolo Braccini, 2, 10095 Grugliasco, Italy; (D.S.); (A.S.)
| | - Achille Schiavone
- Department of Veterinary Science, University of Torino, Largo Paolo Braccini, 2, 10095 Grugliasco, Italy; (D.S.); (A.S.)
| | - Silvia Cerolini
- Department of Veterinary Science, University of Milano, Via Trentacoste, 2, 20134 Milano, Italy;
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.P.); (C.C.)
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell’Università, 16, 35020 Legnaro, Italy; (F.C.); (M.C.)
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Cintio M, Polacchini G, Scarsella E, Montanari T, Stefanon B, Colitti M. MicroRNA Milk Exosomes: From Cellular Regulator to Genomic Marker. Animals (Basel) 2020; 10:E1126. [PMID: 32630756 PMCID: PMC7401532 DOI: 10.3390/ani10071126] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
Recent advances in ruminants' milk-derived exosomes (EXO) have indicated a role of microRNAs (miRNAs) in cell-to-cell communication in dairy ruminants. The miRNAs EXO retain peculiar mechanisms of uptake from recipient cells, which enables the selective delivery of cargos, with a specific regulation of target genes. Although many studies have been published on the miRNAs contained in milk, less information is available on the role of miRNAs EXO, which are considered stable over time and resistant to digestion and milk processing. Several miRNAs EXO have been implicated in the cellular signaling pathway, as in the regulation of immune response. Moreover, they exert epigenetic control, as extenuating the expression of DNA methyltransferase 1. However, the study of miRNAs EXO is still challenging due to the difficulty of isolating EXO. In fact, there are not agreed protocols, and different methods, often time-consuming, are used, making it difficult to routinely process a large number of samples. The regulation of cell functions in mammary glands by miRNAs EXO, and their applications as genomic markers in livestock, is presented.
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Affiliation(s)
| | | | | | | | - Bruno Stefanon
- Department of Agriculture, Food, Environmental and Animal Science, University of Udine, 33100 Udine, Italy; (M.C.); (G.P.); (E.S.); (T.M.); (M.C.)
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Fontana A, Soldano M, Bellassi P, Fabbri C, Gallucci F, Morelli L, Cappa F. Dynamics of Clostridium genus and hard-cheese spoiling Clostridium species in anaerobic digesters treating agricultural biomass. AMB Express 2020; 10:102. [PMID: 32488433 PMCID: PMC7266885 DOI: 10.1186/s13568-020-01040-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/26/2020] [Indexed: 11/29/2022] Open
Abstract
Biogas plants are a widespread renewable energy technology. However, the use of digestate for agronomic purposes has often been a matter of concern. It is controversial whether biogas plants might harbor some pathogenic clostridial species, which represent a biological risk. Moreover, the inhabitance of Clostridium hard-cheese spoiling species in anaerobic digesters can be problematic for hard-cheese manufacturing industries, due to the issue of cheese blowing defects. This study investigated the effect of mesophilic anaerobic digestion processes on the Clostridium consortia distribution over time. Specifically, three lab-scale CSTRs treating agricultural biomass were characterized by considering both the whole microbial community and the cultivable clostridial spores. It is assessed an overall reduction of the Clostridium genus during the anaerobic digestion process. Moreover, it was evidenced a slight, but steady decrease of the cultivable clostridial spores, mainly represented by two pathogenic species, C. perfringens and C. bifermentans, and one hard-cheese spoiling species, C. butyricum. Thus, it is revealed an overall reduction of the clostridial population abundance after the mesophilic anaerobic digestion treatment of agricultural biomass.
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Affiliation(s)
- Alessandra Fontana
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy.
| | - Mariangela Soldano
- Centro Ricerche Produzioni Animali - C.R.P.A. S.p.A., Viale Timavo, 43/2, 42121, Reggio Emilia, Italy
| | - Paolo Bellassi
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy
| | - Claudio Fabbri
- Centro Ricerche Produzioni Animali - C.R.P.A. S.p.A., Viale Timavo, 43/2, 42121, Reggio Emilia, Italy
| | - Francesco Gallucci
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - CREA, Via della Pascolare, 16, Monterotondo, 00015, Rome, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy
- Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Via Milano, 24, 26100, Cremona, Italy
| | - Fabrizio Cappa
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy
- Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Via Milano, 24, 26100, Cremona, Italy
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Ciaccia C, Armengot Martinez L, Testani E, Leteo F, Campanelli G, Trinchera A. Weed Functional Diversity as Affected by Agroecological Service Crops and No-Till in a Mediterranean Organic Vegetable System. Plants (Basel) 2020; 9:E689. [PMID: 32481720 PMCID: PMC7356168 DOI: 10.3390/plants9060689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 11/16/2022]
Abstract
This paper explores the effect of agroecological service crops (ASCs), i.e., crops included in the crop rotation for their ecosystem services, terminated with an in-line tillage roller crimper (ILRC) on weed community composition and their functional traits in comparison to a tilled control without ASC. A two-year study was performed in a long-term experiment with vegetables under organic management. Four different cereal crops were introduced as ASCs. Weed abundance and richness and the functional traits were assessed at three different stages, i.e., before and after ASC termination and before harvest of the following crop, melon. All the ASCs showed strong weed suppression, with few differences between the cereals tested. Weed communities with ASCs had later flowering onset and wider flowering span compared to the control, which positively affects weed dispersal and attraction of beneficial insects. However, weed communities with ASCs had higher values for traits related to competition (specific leaf area, seed weight and more perennials). A trade-off between weed suppression and selection of more competitive weed communities by the introduction of ASCs managed with the ILRC should be evaluated in the long-run. The use of the ILRC alternating with other soil management practices seems the more effective strategy to benefit from the minimal soil tillage while avoiding the selection of disservice-related traits in the weed community.
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Affiliation(s)
- Corrado Ciaccia
- Council for Agricultural Research and Economics (CREA), Research Centre for Agriculture and Environment, Via della Navicella, 2, 00184 Roma, Italy; (E.T.); (A.T.)
| | - Laura Armengot Martinez
- Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, Postfach 219, 5070 Frick, Switzerland;
| | - Elena Testani
- Council for Agricultural Research and Economics (CREA), Research Centre for Agriculture and Environment, Via della Navicella, 2, 00184 Roma, Italy; (E.T.); (A.T.)
| | - Fabrizio Leteo
- Council for Agricultural Research and Economics (CREA), Research Centre for Vegetable and Ornamental Crops, Via Salaria 1, 63030 Monsampolo del Tronto, Italy; (F.L.); (G.C.)
| | - Gabriele Campanelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Vegetable and Ornamental Crops, Via Salaria 1, 63030 Monsampolo del Tronto, Italy; (F.L.); (G.C.)
| | - Alessandra Trinchera
- Council for Agricultural Research and Economics (CREA), Research Centre for Agriculture and Environment, Via della Navicella, 2, 00184 Roma, Italy; (E.T.); (A.T.)
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Scala V, Pucci N, Salustri M, Modesti V, L’Aurora A, Scortichini M, Zaccaria M, Momeni B, Reverberi M, Loreti S. Xylella fastidiosa subsp. pauca and olive produced lipids moderate the switch adhesive versus non-adhesive state and viceversa. PLoS One 2020; 15:e0233013. [PMID: 32413086 PMCID: PMC7228078 DOI: 10.1371/journal.pone.0233013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/26/2020] [Indexed: 12/14/2022] Open
Abstract
Global trade and climate change are re-shaping the distribution map of pandemic pathogens. One major emerging concern is Xylella fastidiosa, a tropical bacterium recently introduced into Europe from America. In last decades, X. fastidiosa was detected in several European countries. X. fastidiosa is an insect vector-transmitted bacterial plant pathogen associated with severe diseases in a wide range of hosts. X. fastidiosa through a tight coordination of the adherent biofilm and the planktonic states, invades the host systemically. The planktonic phase is correlated to low cell density and vessel colonization. Increase in cell density triggers a quorum sensing system based on mixture of cis 2-enoic fatty acids-diffusible signalling factors (DSF) that promote stickiness and biofilm. The lipidome profile of Olea europaea L. (cv. Ogliarola salentina) samples, collected in groves located in infected zones and uninfected zones was performed. The untargeted analysis of the lipid profiles of Olive Quick Decline Syndrome (OQDS) positive (+) and negative (-) plants showed a clustering of OQDS+ plants apart from OQDS-. The targeted lipids profile of plants OQDS+ and OQDS- identified a shortlist of 10 lipids that increase their amount in OQDS+ and X. fastidiosa positive olive trees. These lipid entities, provided to X. fastidiosa subsp. pauca pure culture, impact on the dual phase, e.g. planktonic ↔ biofilm. This study provides novel insights on OQDS lipid hallmarks and on molecules that might modulate biofilm phase in X. fastidiosa subsp. pauca.
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Affiliation(s)
- Valeria Scala
- Council for Agricultural research and Economics (CREA), Research Centre for Plant Protection and Certification, Roma, Italy
| | - Nicoletta Pucci
- Council for Agricultural research and Economics (CREA), Research Centre for Plant Protection and Certification, Roma, Italy
| | - Manuel Salustri
- Dept. of Environmental Biology, Sapienza University, Roma, Italy
| | - Vanessa Modesti
- Council for Agricultural research and Economics (CREA), Research Centre for Plant Protection and Certification, Roma, Italy
| | - Alessia L’Aurora
- Council for Agricultural research and Economics (CREA), Research Centre for Plant Protection and Certification, Roma, Italy
| | - Marco Scortichini
- Council for Agricultural research and Economics (CREA), Research Centre for Olive, Fruit Trees and Citrus, Roma, Italy
| | - Marco Zaccaria
- Department of Biology, Boston College, Chestnut Hill, MA, United States of America
| | - Babak Momeni
- Department of Biology, Boston College, Chestnut Hill, MA, United States of America
| | | | - Stefania Loreti
- Council for Agricultural research and Economics (CREA), Research Centre for Plant Protection and Certification, Roma, Italy
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Annicchiarico P, Nazzicari N, Laouar M, Thami-Alami I, Romani M, Pecetti L. Development and Proof-of-Concept Application of Genome-Enabled Selection for Pea Grain Yield under Severe Terminal Drought. Int J Mol Sci 2020; 21:E2414. [PMID: 32244428 PMCID: PMC7177262 DOI: 10.3390/ijms21072414] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/27/2020] [Accepted: 03/27/2020] [Indexed: 11/16/2022] Open
Abstract
Terminal drought is the main stress limiting pea (Pisum sativum L.) grain yield in Mediterranean environments. This study aimed to investigate genotype × environment (GE) interaction patterns, define a genomic selection (GS) model for yield under severe drought based on single nucleotide polymorphism (SNP) markers from genotyping-by-sequencing, and compare GS with phenotypic selection (PS) and marker-assisted selection (MAS). Some 288 lines belonging to three connected RIL populations were evaluated in a managed-stress (MS) environment of Northern Italy, Marchouch (Morocco), and Alger (Algeria). Intra-environment, cross-environment, and cross-population predictive ability were assessed by Ridge Regression best linear unbiased prediction (rrBLUP) and Bayesian Lasso models. GE interaction was particularly large across moderate-stress and severe-stress environments. In proof-of-concept experiments performed in a MS environment, GS models constructed from MS environment and Marchouch data applied to independent material separated top-performing lines from mid- and bottom-performing ones, and produced actual yield gains similar to PS. The latter result would imply somewhat greater GS efficiency when considering same selection costs, in partial agreement with predicted efficiency results. GS, which exploited drought escape and intrinsic drought tolerance, exhibited 18% greater selection efficiency than MAS (albeit with non-significant difference between selections) and moderate to high cross-population predictive ability. GS can be cost-efficient to raise yields under severe drought.
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Affiliation(s)
- Paolo Annicchiarico
- Council for Agricultural Research and Economics (CREA), Research Centre for Animal Production and Aquaculture, viale Piacenza 29, 26900 Lodi, Italy; (N.N.); (M.R.); (L.P.)
| | - Nelson Nazzicari
- Council for Agricultural Research and Economics (CREA), Research Centre for Animal Production and Aquaculture, viale Piacenza 29, 26900 Lodi, Italy; (N.N.); (M.R.); (L.P.)
| | - Meriem Laouar
- Ecole Nationale Supérieure Agronomique (ENSA), Laboratoire d’Amélioration Intégrative des Productions Végétales (C2711100), Rue Hassen Badi, El Harrach, Alger DZ16200, Algeria;
| | - Imane Thami-Alami
- Institut National de la Recherche Agronomique (INRA), Centre Régional de Rabat, Av. de la Victoire, Rabat BP 415, Morocco;
| | - Massimo Romani
- Council for Agricultural Research and Economics (CREA), Research Centre for Animal Production and Aquaculture, viale Piacenza 29, 26900 Lodi, Italy; (N.N.); (M.R.); (L.P.)
| | - Luciano Pecetti
- Council for Agricultural Research and Economics (CREA), Research Centre for Animal Production and Aquaculture, viale Piacenza 29, 26900 Lodi, Italy; (N.N.); (M.R.); (L.P.)
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Abstract
BACKGROUND A thorough verification of the ability of genomic selection (GS) to predict estimated breeding values for pea (Pisum sativum L.) grain yield is pending. Prediction for different environments (inter-environment prediction) has key importance when breeding for target environments featuring high genotype × environment interaction (GEI). The interest of GS would increase if it could display acceptable prediction accuracies in different environments also for germplasm that was not used in model training (inter-population prediction). RESULTS Some 306 genotypes belonging to three connected RIL populations derived from paired crosses between elite cultivars were genotyped through genotyping-by-sequencing and phenotyped for grain yield, onset of flowering, lodging susceptibility, seed weight and winter plant survival in three autumn-sown environments of northern or central Italy. The large GEI for grain yield and its pattern (implying larger variation across years than sites mainly due to year-to-year variability for low winter temperatures) encouraged the breeding for wide adaptation. Wider within-population than between-population variation was observed for nearly all traits, supporting GS application to many lines of relatively few elite RIL populations. Bayesian Lasso without structure imputation and 1% maximum genotype missing rate (including 6058 polymorphic SNP markers) was selected for GS modelling after assessing different GS models and data configurations. On average, inter-environment predictive ability using intra-population predictions reached 0.30 for yield, 0.65 for onset of flowering, 0.64 for seed weight, and 0.28 for lodging susceptibility. Using inter-population instead of intra-population predictions reduced the inter-environment predictive ability to 0.19 for grain yield, 0.40 for onset of flowering, 0.28 for seed weight, and 0.22 for lodging susceptibility. A comparison of GS vs phenotypic selection (PS) based on predicted genetic gains per unit time for same selection costs suggested greater efficiency of GS for all traits under various selection scenarios. For yield, the advantage in predicted efficiency of GS over PS was at least 80% using intra-population predictions and 20% using inter-population predictions. A genome-wide association study confirmed the highly polygenic control of most traits. CONCLUSIONS Genome-enabled predictions can increase the efficiency of pea line selection for wide adaptation to Italian environments relative to phenotypic selection.
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Affiliation(s)
- Paolo Annicchiarico
- Council for Agricultural Research and Economics (CREA), Research Center for Animal Production and Aquaculture, viale Piacenza 29, 26900 Lodi, Italy
| | - Nelson Nazzicari
- Council for Agricultural Research and Economics (CREA), Research Center for Animal Production and Aquaculture, viale Piacenza 29, 26900 Lodi, Italy
| | - Luciano Pecetti
- Council for Agricultural Research and Economics (CREA), Research Center for Animal Production and Aquaculture, viale Piacenza 29, 26900 Lodi, Italy
| | - Massimo Romani
- Council for Agricultural Research and Economics (CREA), Research Center for Animal Production and Aquaculture, viale Piacenza 29, 26900 Lodi, Italy
| | - Luigi Russi
- Department of Agricultural, Food and Environmental Science, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
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Michelotti V, Lamontanara A, Buriani G, Orrù L, Cellini A, Donati I, Vanneste JL, Cattivelli L, Tacconi G, Spinelli F. Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl. BMC Genomics 2018; 19:585. [PMID: 30081820 PMCID: PMC6090863 DOI: 10.1186/s12864-018-4967-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since 2007, bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) has become a pandemic disease leading to important economic losses in every country where kiwifruit is widely cultivated. Options for controlling this disease are very limited and rely primarily on the use of bactericidal compounds, such as copper, and resistance inducers. Among the latter, the most widely studied is acibenzolar-S-methyl. To elucidate the early molecular reaction of kiwifruit plants (Actinidia chinensis var. chinensis) to Psa infection and acibenzolar-S-methyl treatment, a RNA seq analysis was performed at different phases of the infection process, from the epiphytic phase to the endophytic invasion on acibenzolar-S-methyl treated and on non-treated plants. The infection process was monitored in vivo by confocal laser scanning microscopy. RESULTS De novo assembly of kiwifruit transcriptome revealed a total of 39,607 transcripts, of which 3360 were differentially expressed during the infection process, primarily 3 h post inoculation. The study revealed the coordinated changes of important gene functional categories such as signaling, hormonal balance and transcriptional regulation. Among the transcription factor families, AP2/ERF, MYB, Myc, bHLH, GATA, NAC, WRKY and GRAS were found differentially expressed in response to Psa infection and acibenzolar-S-methyl treatment. Finally, in plants treated with acibenzolar-S-methyl, a number of gene functions related to plant resistance, such as PR proteins, were modulated, suggesting the set-up of a more effective defense response against the pathogen. Weighted-gene coexpression network analysis confirmed these results. CONCLUSIONS Our work provides an in-depth description of the plant molecular reactions to Psa, it highlights the metabolic pathway related to acibenzolar-S-methyl-induced resistance and it contributes to the development of effective control strategies in open field.
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Affiliation(s)
- Vania Michelotti
- Council for agriculture research and economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, CAP, 29017 Fiorenzuola d’Arda, Piacenza Italy
| | - Antonella Lamontanara
- Council for agriculture research and economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, CAP, 29017 Fiorenzuola d’Arda, Piacenza Italy
| | - Giampaolo Buriani
- Department of Agricultural Sciences Alma Mater Studiorum, University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | - Luigi Orrù
- Council for agriculture research and economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, CAP, 29017 Fiorenzuola d’Arda, Piacenza Italy
| | - Antonio Cellini
- Department of Agricultural Sciences Alma Mater Studiorum, University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | - Irene Donati
- Department of Agricultural Sciences Alma Mater Studiorum, University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | - Joel L. Vanneste
- The New Zealand Institute for Plant & Food Research Ltd, Ruakura Research Centre, Bisley Road, Ruakura, Private Bag 3123, Hamilton, 3240 New Zealand
| | - Luigi Cattivelli
- Council for agriculture research and economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, CAP, 29017 Fiorenzuola d’Arda, Piacenza Italy
| | - Gianni Tacconi
- Council for agriculture research and economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, CAP, 29017 Fiorenzuola d’Arda, Piacenza Italy
| | - Francesco Spinelli
- Department of Agricultural Sciences Alma Mater Studiorum, University of Bologna, viale Fanin 46, 40127 Bologna, Italy
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Dragsted LO, Gao Q, Scalbert A, Vergères G, Kolehmainen M, Manach C, Brennan L, Afman LA, Wishart DS, Andres Lacueva C, Garcia-Aloy M, Verhagen H, Feskens EJM, Praticò G. Validation of biomarkers of food intake-critical assessment of candidate biomarkers. Genes Nutr 2018; 13:14. [PMID: 29861790 PMCID: PMC5975465 DOI: 10.1186/s12263-018-0603-9] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 04/19/2018] [Indexed: 12/12/2022]
Abstract
Biomarkers of food intake (BFIs) are a promising tool for limiting misclassification in nutrition research where more subjective dietary assessment instruments are used. They may also be used to assess compliance to dietary guidelines or to a dietary intervention. Biomarkers therefore hold promise for direct and objective measurement of food intake. However, the number of comprehensively validated biomarkers of food intake is limited to just a few. Many new candidate biomarkers emerge from metabolic profiling studies and from advances in food chemistry. Furthermore, candidate food intake biomarkers may also be identified based on extensive literature reviews such as described in the guidelines for Biomarker of Food Intake Reviews (BFIRev). To systematically and critically assess the validity of candidate biomarkers of food intake, it is necessary to outline and streamline an optimal and reproducible validation process. A consensus-based procedure was used to provide and evaluate a set of the most important criteria for systematic validation of BFIs. As a result, a validation procedure was developed including eight criteria, plausibility, dose-response, time-response, robustness, reliability, stability, analytical performance, and inter-laboratory reproducibility. The validation has a dual purpose: (1) to estimate the current level of validation of candidate biomarkers of food intake based on an objective and systematic approach and (2) to pinpoint which additional studies are needed to provide full validation of each candidate biomarker of food intake. This position paper on biomarker of food intake validation outlines the second step of the BFIRev procedure but may also be used as such for validation of new candidate biomarkers identified, e.g., in food metabolomic studies.
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Affiliation(s)
- L. O. Dragsted
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Q. Gao
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - A. Scalbert
- International Agency for Research on Cancer (IARC), Nutrition and Metabolism Section, Biomarkers Group, Lyon, France
| | - G. Vergères
- Agroscope, Federal Office of Agriculture, Berne, Switzerland
| | | | - C. Manach
- INRA, Human Nutrition Unit, Université Clermont Auvergne, F63000 Clermont-Ferrand, France
| | - L. Brennan
- UCD Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - L. A. Afman
- Division of Human Nutrition, Wageningen University and Research, Wageningen, The Netherlands
| | - D. S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - C. Andres Lacueva
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Sciences and Gastronomy, University of Barcelona, Barcelona, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
| | - M. Garcia-Aloy
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Sciences and Gastronomy, University of Barcelona, Barcelona, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
| | - H. Verhagen
- European Food Safety Authority (EFSA), Parma, Italy
- University of Ulster, Coleraine, NIR UK
| | - E. J. M. Feskens
- Division of Human Nutrition, Wageningen University and Research, Wageningen, The Netherlands
| | - G. Praticò
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
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Pizzolotto R, Mazzei A, Bonacci T, Scalercio S, Iannotta N, Brandmayr P. Ground beetles in Mediterranean olive agroecosystems: Their significance and functional role as bioindicators (Coleoptera, Carabidae). PLoS One 2018; 13:e0194551. [PMID: 29558493 PMCID: PMC5860759 DOI: 10.1371/journal.pone.0194551] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 03/06/2018] [Indexed: 11/18/2022] Open
Abstract
The impact of agricultural practices and soil management on the communities of arthropods living in the agricultural landscape is acknowledged as a critical issue by the literature, and it needs to be better investigated to improve the ecological sustainability of agriculture. In the present study, we aimed to study how soil management affect carabid species distribution in one of the most typical agroecosystem of the Mediterranean region, i.e. the olive grove. In South Italy olive plantations feature different types of soil management, from tillage to half- or full-cover cropping. Species distribution has been examined for a total of 10,189 individuals and 62 species collected from 17 sites. Notably from our analysis we have observed that three factors (climax vegetation, soil features and soil management) explained half of the data variability. The composition of species groupings mirrors both bioclimatic conditions (climax vegetation) and soil features, especially watering, while soil management affects the species distribution, with different intensity from site to site. Eleven species have been recognized as the most abundant in the different facets of the studied olive groves and consequently designated as characteristics of the olive agroecosystem. The species traits of the sampled species have been weighted for a compelling evaluation of the effects of agricultural management on biodiversity, showing uniform traits distribution when coping with the ecological factors that characterize the different plantation facets. We have found that carabid beetles can be used as model organisms for studying the effects of agricultural practices. Our study suggests that the interaction of man-induced trasformation with the natural background of the olive agroecosystem may be difficult to disentangle, so that such complexity must be taken into account when carabid beetles are expected to provide an ecosystem service for good agricultural practices.
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Affiliation(s)
- Roberto Pizzolotto
- Dipartimento B.E.S.T., Università della Calabria, Rende, Cosenza, Italy
- * E-mail:
| | - Antonio Mazzei
- Dipartimento B.E.S.T., Università della Calabria, Rende, Cosenza, Italy
| | - Teresa Bonacci
- Dipartimento B.E.S.T., Università della Calabria, Rende, Cosenza, Italy
| | | | - Nino Iannotta
- ex C.R.E.A. Centro di Ricerca per l’Olivicoltura e l’Industria Olearia, Rende, Cosenza, Italy
| | - Pietro Brandmayr
- Dipartimento B.E.S.T., Università della Calabria, Rende, Cosenza, Italy
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40
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Gao Q, Praticò G, Scalbert A, Vergères G, Kolehmainen M, Manach C, Brennan L, Afman LA, Wishart DS, Andres-Lacueva C, Garcia-Aloy M, Verhagen H, Feskens EJM, Dragsted LO. A scheme for a flexible classification of dietary and health biomarkers. Genes Nutr 2017; 12:34. [PMID: 29255495 PMCID: PMC5728065 DOI: 10.1186/s12263-017-0587-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/14/2017] [Indexed: 01/05/2023]
Abstract
Biomarkers are an efficient means to examine intakes or exposures and their biological effects and to assess system susceptibility. Aided by novel profiling technologies, the biomarker research field is undergoing rapid development and new putative biomarkers are continuously emerging in the scientific literature. However, the existing concepts for classification of biomarkers in the dietary and health area may be ambiguous, leading to uncertainty about their application. In order to better understand the potential of biomarkers and to communicate their use and application, it is imperative to have a solid scheme for biomarker classification that will provide a well-defined ontology for the field. In this manuscript, we provide an improved scheme for biomarker classification based on their intended use rather than the technology or outcomes (six subclasses are suggested: food compound intake biomarkers (FCIBs), food or food component intake biomarkers (FIBs), dietary pattern biomarkers (DPBs), food compound status biomarkers (FCSBs), effect biomarkers, physiological or health state biomarkers). The application of this scheme is described in detail for the dietary and health area and is compared with previous biomarker classification for this field of research.
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Affiliation(s)
- Qian Gao
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Giulia Praticò
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Augustin Scalbert
- Biomarkers Group, Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC), Lyon, France
| | - Guy Vergères
- Agroscope, Federal Office of Agriculture, Berne, Switzerland
| | | | - Claudine Manach
- INRA, Human Nutrition Unit, Université Clermont Auvergne, INRA, F63000 Clermont-Ferrand, France
| | - Lorraine Brennan
- UCD Institute of Food & Health, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Lydia A. Afman
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Cristina Andres-Lacueva
- Biomarkers and Nutrimetabolomic Laboratory, Department of Nutrition, Food Sciences and Gastronomy, University of Barcelona, Barcelona, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
| | - Mar Garcia-Aloy
- Biomarkers and Nutrimetabolomic Laboratory, Department of Nutrition, Food Sciences and Gastronomy, University of Barcelona, Barcelona, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
| | - Hans Verhagen
- European Food Safety Authority (EFSA), Parma, Italy
- University of Ulster, Coleraine, Northern Ireland UK
| | - Edith J. M. Feskens
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
| | - Lars O. Dragsted
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
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Bovo S, Mazzoni G, Ribani A, Utzeri VJ, Bertolini F, Schiavo G, Fontanesi L. A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections. PLoS One 2017; 12:e0179462. [PMID: 28662150 PMCID: PMC5491021 DOI: 10.1371/journal.pone.0179462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/29/2017] [Indexed: 12/14/2022] Open
Abstract
Shot-gun next generation sequencing (NGS) on whole DNA extracted from specimens collected from mammals often produces reads that are not mapped (i.e. unmapped reads) on the host reference genome and that are usually discarded as by-products of the experiments. In this study, we mined Ion Torrent reads obtained by sequencing DNA isolated from archived blood samples collected from 100 performance tested Italian Large White pigs. Two reduced representation libraries were prepared from two DNA pools constructed each from 50 equimolar DNA samples. Bioinformatic analyses were carried out to mine unmapped reads on the reference pig genome that were obtained from the two NGS datasets. In silico analyses included read mapping and sequence assembly approaches for a viral metagenomic analysis using the NCBI Viral Genome Resource. Our approach identified sequences matching several viruses of the Parvoviridae family: porcine parvovirus 2 (PPV2), PPV4, PPV5 and PPV6 and porcine bocavirus 1-H18 isolate (PBoV1-H18). The presence of these viruses was confirmed by PCR and Sanger sequencing of individual DNA samples. PPV2, PPV4, PPV5, PPV6 and PBoV1-H18 were all identified in samples collected in 1998-2007, 1998-2000, 1997-2000, 1998-2004 and 2003, respectively. For most of these viruses (PPV4, PPV5, PPV6 and PBoV1-H18) previous studies reported their first occurrence much later (from 5 to more than 10 years) than our identification period and in different geographic areas. Our study provided a retrospective evaluation of apparently asymptomatic parvovirus infected pigs providing information that could be important to define occurrence and prevalence of different parvoviruses in South Europe. This study demonstrated the potential of mining NGS datasets non-originally derived by metagenomics experiments for viral metagenomics analyses in a livestock species.
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Affiliation(s)
- Samuele Bovo
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Biocomputing Group, University of Bologna, Bologna, Italy
| | - Gianluca Mazzoni
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anisa Ribani
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
| | - Valerio Joe Utzeri
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- Department of Animal Science, Iowa State University, Iowa, United States of America
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- * E-mail:
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Tumino G, Voorrips RE, Rizza F, Badeck FW, Morcia C, Ghizzoni R, Germeier CU, Paulo MJ, Terzi V, Smulders MJM. Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios. Theor Appl Genet 2016; 129:1711-24. [PMID: 27318699 PMCID: PMC4983288 DOI: 10.1007/s00122-016-2734-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 05/21/2016] [Indexed: 05/19/2023]
Abstract
Infinium SNP data analysed as continuous intensity ratios enabled associating genotypic and phenotypic data from heterogeneous oat samples, showing that association mapping for frost tolerance is a feasible option. Oat is sensitive to freezing temperatures, which restricts the cultivation of fall-sown or winter oats to regions with milder winters. Fall-sown oats have a longer growth cycle, mature earlier, and have a higher productivity than spring-sown oats, therefore improving frost tolerance is an important goal in oat breeding. Our aim was to test the effectiveness of a Genome-Wide Association Study (GWAS) for mapping QTLs related to frost tolerance, using an approach that tolerates continuously distributed signals from SNPs in bulked samples from heterogeneous accessions. A collection of 138 European oat accessions, including landraces, old and modern varieties from 27 countries was genotyped using the Infinium 6K SNP array. The SNP data were analyzed as continuous intensity ratios, rather than converting them into discrete values by genotype calling. PCA and Ward's clustering of genetic similarities revealed the presence of two main groups of accessions, which roughly corresponded to Continental Europe and Mediterranean/Atlantic Europe, although a total of eight subgroups can be distinguished. The accessions were phenotyped for frost tolerance under controlled conditions by measuring fluorescence quantum yield of photosystem II after a freezing stress. GWAS were performed by a linear mixed model approach, comparing different corrections for population structure. All models detected three robust QTLs, two of which co-mapped with QTLs identified earlier in bi-parental mapping populations. The approach used in the present work shows that SNP array data of heterogeneous hexaploid oat samples can be successfully used to determine genetic similarities and to map associations to quantitative phenotypic traits.
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Affiliation(s)
- Giorgio Tumino
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands.
| | - Roeland E Voorrips
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Fulvia Rizza
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Franz W Badeck
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Caterina Morcia
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Roberta Ghizzoni
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Christoph U Germeier
- Julius Kühn Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, 06484, Quedlinburg, Germany
| | - Maria-João Paulo
- Biometris, Wageningen UR, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Valeria Terzi
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Marinus J M Smulders
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
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Porrini C, Mutinelli F, Bortolotti L, Granato A, Laurenson L, Roberts K, Gallina A, Silvester N, Medrzycki P, Renzi T, Sgolastra F, Lodesani M. The Status of Honey Bee Health in Italy: Results from the Nationwide Bee Monitoring Network. PLoS One 2016; 11:e0155411. [PMID: 27182604 PMCID: PMC4868308 DOI: 10.1371/journal.pone.0155411] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 04/28/2016] [Indexed: 11/19/2022] Open
Abstract
In Italy a nation-wide monitoring network was established in 2009 in response to significant honey bee colony mortality reported during 2008. The network comprised of approximately 100 apiaries located across Italy. Colonies were sampled four times per year, in order to assess the health status and to collect samples for pathogen, chemical and pollen analyses. The prevalence of Nosema ceranae ranged, on average, from 47-69% in 2009 and from 30-60% in 2010, with strong seasonal variation. Virus prevalence was higher in 2010 than in 2009. The most widespread viruses were BQCV, DWV and SBV. The most frequent pesticides in all hive contents were organophosphates and pyrethroids such as coumaphos and tau-fluvalinate. Beeswax was the most frequently contaminated hive product, with 40% of samples positive and 13% having multiple residues, while 27% of bee-bread and 12% of honey bee samples were contaminated. Colony losses in 2009/10 were on average 19%, with no major differences between regions of Italy. In 2009, the presence of DWV in autumn was positively correlated with colony losses. Similarly, hive mortality was higher in BQCV infected colonies in the first and second visits of the year. In 2010, colony losses were significantly related to the presence of pesticides in honey bees during the second sampling period. Honey bee exposure to poisons in spring could have a negative impact at the colony level, contributing to increase colony mortality during the beekeeping season. In both 2009 and 2010, colony mortality rates were positively related to the percentage of agricultural land surrounding apiaries, supporting the importance of land use for honey bee health.
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Affiliation(s)
- Claudio Porrini
- Dipartimento di Scienze Agrarie (DipSA), Università di Bologna, Bologna, Italy
| | - Franco Mutinelli
- Istituto Zooprofilattico Sperimentale delle Venezie, NRL for beekeeping, Legnaro (Padova), Italy
| | - Laura Bortolotti
- CRA-API, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Bologna, Italy
| | - Anna Granato
- Istituto Zooprofilattico Sperimentale delle Venezie, NRL for beekeeping, Legnaro (Padova), Italy
| | | | | | - Albino Gallina
- Istituto Zooprofilattico Sperimentale delle Venezie, NRL for beekeeping, Legnaro (Padova), Italy
| | - Nicholas Silvester
- Istituto Zooprofilattico Sperimentale delle Venezie, NRL for beekeeping, Legnaro (Padova), Italy
| | - Piotr Medrzycki
- CRA-API, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Bologna, Italy
| | - Teresa Renzi
- Dipartimento di Scienze Agrarie (DipSA), Università di Bologna, Bologna, Italy
| | - Fabio Sgolastra
- Dipartimento di Scienze Agrarie (DipSA), Università di Bologna, Bologna, Italy
| | - Marco Lodesani
- CRA-API, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Bologna, Italy
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