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128 results on '"NICOLOSO, L."'

12. Increase of prostaglandin E2 in the reversal of fetal ductal constriction after polyphenol restriction

Author

Vian, I., primary, Zielinsky, P., additional, Zílio, A. M., additional, Schaun, M. I., additional, Brum, C., additional, Lampert, K. V., additional, De Ávila, N., additional, Baldissera, G., additional, Klanovicz, T. M., additional, Zenki, K., additional, Zurita-Peralta, J., additional, Olszewski, A., additional, Piccoli, A., additional, Nicoloso, L. H., additional, Sulis, N., additional, Van Der Sand, L., additional, and Markoski, M., additional

Published
2018
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15. A method for single nucleotide polymorphism selection for parentage assessment in goats

Author

Talenti, A, Nicolazzi, E. L., Chessa, S., Frattini, S., Moretti, R., Coizet, B., Nicoloso, L., Colli, Licia, Pagnacco, G., Stella, A., Ajmone Marsan, Paolo, Ptak, G., Crepaldi, P., Colli, Licia (ORCID:0000-0002-7221-2905), Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Talenti, A, Nicolazzi, E. L., Chessa, S., Frattini, S., Moretti, R., Coizet, B., Nicoloso, L., Colli, Licia, Pagnacco, G., Stella, A., Ajmone Marsan, Paolo, Ptak, G., Crepaldi, P., Colli, Licia (ORCID:0000-0002-7221-2905), and Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579)

Abstract

Accurate pedigrees are essential to optimize genetic improvement and conservation of animal genetic resources. In goats, the use of mating groups and kidding management procedures hamper the identification of parentage. Small panels of single nucleotide polymorphisms (SNP) have been proposed in other species to substitute microsatellites for parentage assessment. Using data from the current GoatSNP50 chip, we developed a new 3-step procedure to identify a low-density SNP panel for highly accurate parentage assessment. Methodologies for SNP selection used in other species are less suitable in the goat because of uncertainties in the genome assembly. The procedure developed in this study is based on parent-offspring identification and on estimation of Mendelian errors, followed by canonical discriminant analysis identification and stepwise regression reduction. Starting from a reference sample of 109 Alpine goats with known pedigree relationships, we first identified a panel of 200 SNP that was further reduced to 2 final panels of 130 and 114 SNP with random coincidental match inclusion of 1.51 × 10-57 and 2.94 × 10-34, respectively. In our reference data set, all panels correctly identified all parent-offspring combinations, revealing a 40% pedigree error rate in the information provided by breeders. All reference trios were confirmed by official tests based on microsatellites. Panels were also tested on Saanen and Teramana breeds. Although the testing on a larger set of breeds in the reference population is still needed to validate these results, our findings suggest that our procedure could identify SNP panels for accurate parentage assessment in goats or in other species with unreliable marker positioning.

Published
2016

16. Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers

Author

Colli, L., Joost, S., Negrini, R., Nicoloso, L., Crepaldi, P., Ajmone Marsan, P., Abo Shehada, M., Al Tarrayrah, J., Baret, P., Baumung, R., Beja Pereira, A., Bertaglia, M., Bordonaro, Salvatore, Bruford, M., Caloz, R., Canali, G., Canon, J., Cappuccio, I., Carta, A., Cicogna, M., Cortes, O., Dalamitra, S., Daniela, K., Dobi, P., Dominik, P. w, Dunner, S. p, D'Urso, G. l, Barody, El, M. A. A. x, England, P. j, Erhardt, G. u, Ertugrul, O. y, Prinzenberg, E. M., Ibeagha, Awemu, Strzelec, E., Fadlaoui, E., Fornarelli, A., Garcia, F., Georgoudis, D., Lühken, A., Giovenzana, G., Gutscher, S., Hewitt, K., Hoda, G., Brandt, A., Istvan, H., Juma, A., Jones, G., Karetsou, S., Kliambas, K., Koban, G., Kutita, E., Fesus, O., Lenstra, Johannes, Ligda, A., Lipsky, C., Luikart, S., Marie, Louise, Marilli, G., Marletta, Donata, Milanesi, E., Nijman, Isaäc, Obexer, Ruff, Papachristoforou, G., Pariset, C., Pellecchia, L., Peter, M., Perez, C., Pilla, T., D'Andrea, F., Niznikowskian, M., Roosen, R., Juttak, Scarpa, Sechi, R., Taberlet, T., Taylor, P., Togan, M., Trommetter, I., Valentini, M., Van Cann Lisette, Vlaic, M., Wiskin, A., Zundel, L., and UCL - SST/ELI/ELIA - Agronomy

Subjects
Evolutionary Genetics, Population genetics, Q1, amplified fragment length polymorphism, computer program, Geoinformatics, Natural Selection, Amplified Fragment Length Polymorphism Analysis, media_common, Animal Management, AFLP Markers, Multidisciplinary, Natural selection, Settore AGR/17 - ZOOTECNICA GENERALE E MIGLIORAMENTO GENETICO, Spatial statistics, Geography, Goats, article, natural selection, Agriculture, GIS, Adaptation, Physiological, Spatial Autocorrelation, Europe, Phylogeography, Landscape genomics, environmental temperature, Medicine, Livestock, Identification (biology), genetic marker, altitude, Research Article, Genetic Markers, AFLP, gene locus, solar radiation, media_common.quotation_subject, Science, Genomics, precipitation, Biology, Environment, Adaptability, Asia, Western, Genetics, Animals, controlled study, Adaptation, Environmental Systems Modeling, Genetic Association Studies, Western Asian Goat Breeds, Evolutionary Biology, nonhuman, Models, Genetic, business.industry, humidity, Bayes Theorem, landscape, Biotechnology, Genetic Loci, goat breed, Earth Sciences, Amplified fragment length polymorphism, business, Animal Genetics, Population Genetics
Abstract

Background\ud During the past decades, neutral DNA markers have been extensively employed to study demography, population genetics and structure in livestock, but less interest has been devoted to the evaluation of livestock adaptive potential through the identification of genomic regions likely to be under natural selection.\ud \ud Methodology/Principal findings\ud Landscape genomics can greatly benefit the entire livestock system through the identification of genotypes better adapted to specific or extreme environmental conditions. Therefore we analyzed 101 AFLP markers in 43 European and Western Asian goat breeds both with Matsam software, based on a correlative approach (SAM), and with Mcheza and Bayescan, two FST based software able to detect markers carrying signatures of natural selection.\ud \ud Matsam identified four loci possibly under natural selection – also confirmed by FST-outlier methods – and significantly associated with environmental variables such as diurnal temperature range, frequency of precipitation, relative humidity and solar radiation.\ud \ud Conclusions/Significance\ud These results show that landscape genomics can provide useful information on the environmental factors affecting the adaptive potential of livestock living in specific climatic conditions. Besides adding conservation value to livestock genetic resources, this knowledge may lead to the development of novel molecular tools useful to preserve the adaptive potential of local breeds during genetic improvement programs, and to increase the adaptability of industrial breeds to changing environments.

Published
2013

17. Italian Goat Consortium: a first overview of genetic variability using a medium density single nucleotide polymorphism array

Author

Crepaldi, P., Bordonaro, S., Chessa, S., Coizet, B., Colli, L., Andrea, Mariasilvia D., Mazza, R., Miari, S., Murru, S., Nicoloso, L., Pagnacco, G., Ptak, G., Fabio PILLA, Sechi, T., and Valentini, A.

Abstract

The Italian Goat Consortium was established from the Innovagen Project to join local efforts and resources for the genomic characterisation of Italian goat breeds. Thirteen Italian goat breeds (Valdostana, Saanen, Orobica, Bionda dell'Adamello, Val Passiria, Grigia Ciociara, Teramana, Nicastrese, Aspromontana, Girgentana, Argentata dell'Etna, Sarda and Maltese - the latter sampled in Sardinia and Sicily) for a total of 350 animals (15-32 per breed) were analysed using a medium density SNP array. Data editing was based on the following thresholds: MAF 5%; Missing animal >5%; HW within breed FDR >20%. After filtering, a total of 51,136 SNPs were retained, showing that the adopted SNP chip is highly informative for the characterization of Italian goat breeds. Population structure and breed distinctiveness were investigated with the software Admixture, that revealed the best fitting solution at K=11 partitions. The software also highlighted variable levels of admixture and an early differentiation of Val Passiria, Orobica, Valdostana, Teramana, Girgentana and Sarda breeds. Within MDS plot, some breeds are clearly appreciable as distinct: Girgentana, Teramana, Orobica and Maltese. PCA analysis revealed a gradient of diversity North (from alpine breeds) - South (to Sicilian breeds) and East (from Val Passiria breed) - West (to Valdostana breed) in the Alps. The calculation of Fis index indicated little or no inbreeding, while LD analysis in Chromosome 6 showed levels of disequilibrium much lower than cattle at short physical distance.

Published
2013

20. Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip

Author

Nicoloso, L, BOMBA, LORENZO, COLLI, LICIA, NEGRINI, RICCARDO, MILANESI, MARCO, Mazza, R, Sechi, T, Frattini, S, Talenti, A, Coizet, B, Chessa, S, Marletta, D, D’Andrea, M, Bordonaro, S, Ptak, G, Carta, A, Pagnacco, G, Valentini, A, Pilla, F, AJMONE MARSAN, PAOLO, Crepaldi, P, Nicoloso, L, BOMBA, LORENZO, COLLI, LICIA, NEGRINI, RICCARDO, MILANESI, MARCO, Mazza, R, Sechi, T, Frattini, S, Talenti, A, Coizet, B, Chessa, S, Marletta, D, D’Andrea, M, Bordonaro, S, Ptak, G, Carta, A, Pagnacco, G, Valentini, A, Pilla, F, AJMONE MARSAN, PAOLO, and Crepaldi, P

Published
2015

23. Traceability of four European Protected Geographic Indication (PGI) beef products using Single Nucleotide Polymorphisms (SNP) and bayesian statistics

Author

Negrini, R., NICOLOSO, L., Crepaldi, P., Milanesi, E., Marino, R., Perini, D., PARISET, L., Dunner, S., Levéziel, Hubert, Williams, J.L., AJMONE MARSAN, P., Unité de Génétique Moléculaire Animale (UMR GMA), Institut National de la Recherche Agronomique (INRA)-Université de Limoges (UNILIM), Unité de Génétique Moléculaire Animale (UGMA), Université de Limoges (UNILIM)-Institut National de la Recherche Agronomique (INRA), and ProdInra, Archive Ouverte

Subjects
Bovino, [SDV] Life Sciences [q-bio], TRACEABILITY, [SDV]Life Sciences [q-bio], Razza, CATTLE, Tracciabilità, Breed, SNPs
Abstract

The use of SNPs in combination with Bayesian statistics for the geographic traceability of cattle were evaluated using a dataset comprising 24 breeds from Italy,France,Spain, Denmark, the Netherlands,Switzerland and UK genotyped with 90 polymorphic markers. The percentage of correct assignment of the individuals to their Country of origin was 90%, with an average assignment probability of 93% and an average specificity of 92%. The higher value was observed for UK breeds (97% of correct assignment) while Swiss animals were the most difficult to allocate (77% of correct assignment). Tracing of Protected Geographic Indication (PGI) products, the approach correctly assigned 100% of Guaranteed Pure Highland Beef; 97% of “Vitellone dell’Appennino Centrale” breeds; 84% of Ternera de Navarra, and 80% of Boeuf de Chalosse. Methods to verify Products of Designated Origin (PDO) and Protected Geographic Indication (PGI) products will help to protect regional foods and promote the economic growth of marginal rural areas by encouraging the product on of high quality niche market foods.

Published
2008

25. Recent advance in DNA-based traceability and authentication of livestock meat PDO and PGI products

Author

Nicoloso, L, Crepaldi, P, Mazza, R, Ajmone Marsan, Paolo, Negrini, Riccardo, Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Negrini, Riccardo (ORCID:0000-0002-8735-0286), Nicoloso, L, Crepaldi, P, Mazza, R, Ajmone Marsan, Paolo, Negrini, Riccardo, Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), and Negrini, Riccardo (ORCID:0000-0002-8735-0286)

Abstract

This review updates the available molecular techniques and technologies and discusses how they can be used for traceability, food control and enforcement activities. The review also provides examples on how molecular techniques succeeded to trace back unknowns to their breeds of origin, to fingerprint single individuals and to generate evidence in court cases. The examples demonstrate the potential of the DNA based traceability techniques and explore possibilities for translating the next generation genomics tools into a food and feed control and enforcement framework.

Published
2013

26. On the way to functional agro biodiversity: coat colour gene variability in goats

Author

Nicoloso, L, Negrini, Riccardo, Ajmone Marsan, Paolo, Crepaldi, P., Negrini, Riccardo (ORCID:0000-0002-8735-0286), Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Nicoloso, L, Negrini, Riccardo, Ajmone Marsan, Paolo, Crepaldi, P., Negrini, Riccardo (ORCID:0000-0002-8735-0286), and Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579)

Abstract

Functional agro biodiversity defines the exploitation of biodiversity to provide ecosystem services, support sustainable agricultural production and benefit the regional and global environment and the public at large (ELN-FAB, 2009; www.eln_fab.eu). Tracking of animal products back to the breed of origin based on their genetic make-up undoubtedly falls in this category. The aim of this paper was to identify and validate a set of single nucleotide polymorphisms (SNPs) in goat coat colour genes, most of which have not been investigated before, to trace five goat populations of the Italian Alps and their product. Several regions of 28 genes influencing coat colour pathways were amplified in eight animals (two per breed). Sequence comparison revealed 48 SNPs and three INDEL (INsertion DELetion). No breed-specific alleles were detected; however, several SNPs showed an uneven frequency distribution between breeds. In BIO, the genotype frequency distribution of a non-synonymous SNP suggested a possible role of TYRP1 in brown eumelanic goat coat colour. A total of 29 independent SNPs in 20 genes were selected and used to allocate 159 minimally related goat samples using STRUCTURE 2.2 and GeneClass 2 software. STRUCTURE 2.2 assigns 99% of individuals to the correct breed considering the prior information on putative breed of origin for each sample and 81% using only the genotypic data. The three algorithms available in GeneClass 2 performed with nearly equal efficiency, with 86% and 87% correct allocations. All the methods yielded an average probability of assignment >0.92 and a specificity index >0.86. Despite their coat colour variability, individuals belonging to ORO were fully assigned, showing that, in the absence of a breed-specific allele tied to coat colour, the best assignment resulted for the most genetically distinct breed. The lowest rate of correct assignment was observed in Verzaschese (73%), not ascertained in the breed panel used in the SNP discovery phase.

Published
2012

27. Genome‐wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds

Author

Ciani, E., primary, Crepaldi, P., additional, Nicoloso, L., additional, Lasagna, E., additional, Sarti, F. M., additional, Moioli, B., additional, Napolitano, F., additional, Carta, A., additional, Usai, G., additional, D'Andrea, M., additional, Marletta, D., additional, Ciampolini, R., additional, Riggio, V., additional, Occidente, M., additional, Matassino, D., additional, Kompan, D., additional, Modesto, P., additional, Macciotta, N., additional, Ajmone‐Marsan, P., additional, and Pilla, F., additional

Published
2013
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28. OC08.02: Experimental assessment of ductus arteriosus flow, oxidative stress and polyphenol excretion after maternal polyphenol‐rich diet in late pregnancy

Author

Zielinsky, P., primary, Bubols, G., additional, Piccoli, A., additional, Vian, I., additional, Nicoloso, L. H., additional, Zilio, A., additional, Charão, M., additional, Pizzato, P., additional, Lopes, M., additional, Busato, S., additional, Barbisan, C., additional, Alievi, M., additional, Barra, M., additional, and Garcia, S. C., additional

Published
2012
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39. OP18.03: Experimental study of the role of maternal consumption of green tea, mate tea and grape juice on fetal ductal constriction

Author

Zielinsky, P., primary, Manica, J. L., additional, Piccoli Jr, A., additional, Areias, J. C. N., additional, Nicoloso, L. H., additional, Menezes, H. S., additional, Frajndlich, R., additional, Busato, A. K., additional, Petracco, R., additional, Hagemann, L., additional, Moraes, M. R., additional, Silva, J., additional, Alievi, M., additional, Centeno, P., additional, and Barra, M., additional

Published
2007
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41. OC97: Ductal flow dynamics and right ventricular size are influenced by maternal ingestion of polyphenol-rich common beverages in normal pregnancies

Author

Zielinsky, P., primary, Manica, J. L., additional, Piccoli Jr, A., additional, Nicoloso, L. H., additional, Frajndlich, R., additional, Menezes, H. S., additional, Busato, A. K., additional, Hagemann, L., additional, Moraes, M. R., additional, Silva, J., additional, Behrens, T., additional, Huber, J., additional, and Brandão-da-Silva, M., additional

Published
2007
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48. Breed assignment of Italian cattle using biallelic AFLP® markers.

Author

Negrini, R., Milanesi, E., Colli, L., Pellecchia, M., Nicoloso, L., Crepaldi, P., Lenstra, J. A., and Ajmone-Marsan, P.

Subjects
CATTLE, ANIMAL products, ANIMAL breeds, FOOD safety, GENETIC polymorphisms, BAYESIAN analysis
Abstract

The verification of the breed origin of animal products is relevant for food safety and authenticity. We assessed the suitability of AFLP molecular markers in the assignment of cattle individuals to their breed of origin. Three hundred and ninety-six animals belonging to 16 cattle breeds genotyped with 141 AFLP markers were used as reference data set. Assignment was performed with likelihood (aflpop) and Bayesian (structure) methods. The Bayesian approach was superior to the likelihood algorithm with respect to (i) the correct assignment of simulated individuals to their breed of origin (93% vs. 81% respectively), (ii) the correct assignment of 44 sampled Romagnola animals (91% vs. 45% respectively) and (iii) the correct classification of animals belonging to a breed that was not included within the reference dataset. Thus, AFLP profiling in combination with the Bayesian approach seems a useful tool for breed assignment. [ABSTRACT FROM AUTHOR]

Published
2007
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50. Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers

Author

Colli, L., Joost, S., Negrini, R., Nicoloso, L., Crepaldi, P., Ajmone Marsan, P., Abo Shehada, M., Al Tarrayrah, J., Baret, P., Baumung, R., Beja Pereira, A., Bertaglia, M., Bordonaro, S., Bruford, M., Caloz, R., Canali, G., Canon, J., Cappuccio, I., Carta, A., Cicogna, M., Cortes, O., Dalamitra, S., Daniela, K., Dobi, P., Dominik, P., Dunner, S., D Urso, G., El Barody, M. A. A., England, P., Erhardt, G., Ertugrul, O., Prinzenberg, E. M., Ibeagha Awemu, E., Strzelec, E., Fadlaoui, A., Fornarelli, F., Garcia, D., Georgoudis, A., Lühken, G., Giovenzana, S., Gutscher, K., Hewitt, G., Hoda, A., Brandt, H., Istvan, A., Juma, G., Jones, S., Karetsou, K., Kliambas, G., Koban, E., Kutita, O., Fesus, L., Lenstra Johannes, A., Ligda, C., Lipsky, S., Luikart, G., Marie Louise, G., Marilli, M., Marletta, D., Milanesi, E., Nijman Isaäc, J., Obexer Ruff, G., Papachristoforou, C., Pariset, L., Pellecchia, M., Peter, C., Perez, T., Fabio PILLA, Andrea, Mariasilvia D., Niznikowskian Roosen, R., Juttak Scarpa, R., Sechi, T., Taberlet, P., Taylor, M., Togan, I., Trommetter, M., Valentini, A., Cann Lisette, M., Vlaic, A., Wiskin, L., and Zundel, S.

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