http://http://dspace.unitus.it:80 The DSpace digital repository system captures, stores, indexes, preserves, and distributes digital research material. Wed, 19 Jun 2013 06:09:34 GMT 2013-06-19T06:09:34Z http://hdl.handle.net/2067/124 Title: AFLP markers for DNA fingerprinting in cattle Authors: Ajmone-Marsan, Paolo; Valentini, Alessio; Bertoni, Giuseppe Abstract: his work reports on use of the recently described amplified fragment length polymorphism (AFLP) technology for DNA fingerprinting in cattle. The AFLP technology produces molecular markers through the high-stringency polymerase chain reaction (PCR)-amplification of restriction fragments that are ligated to synthetic adapters and amplified using primers, complementary to the adapters, which carry selective nucleotides at their 3' ends. While, for plants, the double digestion of genomic DNA with EcoRI and MseI is suggested, in mammals the enzyme combination EcoRI/TaqI produces clearer and more polymorphic AFLP patterns. In a sample of 47 Italian Holstein genotypes, 16 EcoRI/TaqI primer combinations identified 248 polymorphic bands in a species known for its low level of restriction polymorphism. In spite of the low information content carried by each AFLP polymorphism (average polymorphism information content = 0·31), the number of fragments revealed by each primer combination increased significantly the level of genetic information gained in each experiment. AFLP patterns are reproducible in independent experiments and polymorphic fragments segregate in cattle families according to Mendelian rules. Tue, 31 Dec 1996 23:00:00 GMT http://hdl.handle.net/2067/124 1996-12-31T23:00:00Z http://hdl.handle.net/2067/125 Title: Signatures of selection? Patterns of microsatellite diversity on a chromosome containing a selected locus Authors: Wiener, Pamela; Burton, David; Ajmone-Marsan, Paolo; Dunner, Susana; Valentini, Alessio; Williams, John L. Abstract: This paper explores patterns of genetic diversity near a locus known to have been under selection. The myostatin gene (GDF-8) has been shown to be associated with double muscling, a phenotype selected for in a number of cattle breeds. We examined population genetic parameters for microsatellite loci at varying distances from GDF-8 in double-muscled (DM) and non-double-muscled (non-DM) cattle breeds in order to assess patterns of diversity. A theoretical analysis was also performed to predict the patterns of diversity expected under different scenarios. We found differences in the patterns of heterozygosity, allele diversity and linkage disequilibrium between DM and non-DM breeds. However, there were some exceptions to the predicted patterns. These are discussed in light of the histories of the breeds and the potential for using microsatellite diversity for mapping trait genes in livestock populations. Tue, 31 Dec 2002 23:00:00 GMT http://hdl.handle.net/2067/125 2002-12-31T23:00:00Z http://hdl.handle.net/2067/144 Title: Double muscling in Marchigiana beef breed is caused by a stop codon in the third exon of myostatin gene Authors: Marchitelli, Cinzia; Savarese, Maria Carmela; Crisà, Alessandra; Nardone, Alessandro; Ajmone-Marsan, Paolo; Valentini, Alessio Abstract: Double muscling is a partially recessive trait present in some beef breeds. It shows a high frequency in some breeds, while in others the frequency is low, and double-muscled individuals are rare. The double muscling is caused by an allelic series of mutations that cause a loss of function of the myostatin gene (GDF8). We describe here a new mutation in the myostatin gene in Marchigiana breed, a typical beef breed of Central Italy, in which rare double-muscling individuals have been described. A PCR product of the third exon was sequenced in subjects phenotypically showing double muscling, and a C > T transversion was discovered that introduces a premature stop codon. The variant found adds to the large series of mutations present in cattle, and particularly to the only two causative of double muscling in the third exon. A PCR-RFLP test is described for the rapid and effective identification of both heterozygous and homozygous subjects. It was applied to a larger survey carried on the same and also in two other beef breeds, Chianina and Romagnola. Further individuals carrying the new variant were found in Marchigiana, but none in the other breeds. The results may be important for a better comprehension of the role of myostatin in muscular development, for commercial use and for the inference of phylogeny of this gene. Tue, 31 Dec 2002 23:00:00 GMT http://hdl.handle.net/2067/144 2002-12-31T23:00:00Z http://hdl.handle.net/2067/1923 Title: Differentiation of European cattle by AFLP fingerprinting Authors: Negrini, Riccardo; Nijman, Isaäc J.; Milanesi, Elisabetta; Moazami-Goudarzi, Katayoun; Williams, J. L.; Erhardt, Georg; Dunner, Susana; Rodellar, Clementina; Valentini, Alessio; Bradley, Dan G.; Olsaker, Ingrid; Kantanen, Juha; Ajmone-Marsan, Paolo; Lenstra, Johannes A. Abstract: The Neolithic introduction of domestic cattle into Europe was followed by differential adaptation, selection, migration and genetic isolation, leading ultimately to the emergence of specialized breeds. We have studied the differentiation of European cattle by amplified fragment length polymorphism (AFLP) fingerprinting. Combining AFLP data sets from two laboratories yielded 81 biallelic polymorphic markers scored in 19–22 individual animals from 51 breeds. Model-based clustering differentiated Podolian cattle as well as French and Alpine breeds from other European cattle. AFLP genetic distances correlated well with microsatellite-based genetic distances calculated for the same breeds. However, the AFLP data emphasized the divergence of taurine and indicine cattle relative to the variation among European breeds and indicated an Eastern influence on Italian and Hungarian Podolian breeds. This probably reflects import from the East after the original introduction of domestic cattle into Europe. Our data suggest that Italian cattle breeds are relatively diverse at the DNA sequence level. Thu, 14 Apr 2011 22:00:00 GMT http://hdl.handle.net/2067/1923 2011-04-14T22:00:00Z http://hdl.handle.net/2067/1883 Title: Geographical patterning of sixteen goat breeds from Italy, Albani a and Greece assessed by Single Nucleotide Polymorphisms Authors: Pariset, Lorraine; Cuteri, Antonella; Ligda, Christina; Ajmone-Marsan, Paolo; Valentini, Alessio; Econogene Consortium Abstract: Background: SNP data of goats of three Mediterranean countries were used for population studies and reconstruction of geographical patterning. 496 individuals belonging to Italian, Albanian and Greek breeds were genotyped to assess the basic population parameters. Results: A total of 26 SNPs were used, for a total of 12,896 genotypes assayed. Statistical analysis revealed that breeds are not so similar in terms of genetic variability, as reported in studies performed using different markers. The Mantel test showed a strongly significant correlation between genetic and geographic distance. Also, PCA analysis revealed that breeds are grouped according to geographical origin, with the exception of the Greek Skopelos breed. Conclusion: Our data point out that the use of SNP markers to analyze a wider breed sample could help in understanding the recent evolutionary history of domestic goats. We found correlation between genetic diversity and geographic distance. Also PCA analysis shows that the breeds are well differentiated, with good correspondence to geographical locations, thus confirming the correlation between geographical and genetic distances. This suggests that migration history of the species played a pivotal role in the present-day structure of the breeds and a scenario in which coastal routes were easier for migrating in comparison with inland routes. A westward coastal route to Italy through Greece could have led to gene flow along the Northern Mediterranean. Tue, 05 Apr 2011 22:00:00 GMT http://hdl.handle.net/2067/1883 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1882 Title: Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean Authors: Pariset, Lorraine; Joost, Stéphane; Ajmone-Marsan, Paolo; Valentini, Alessio; Econogene Consortium Abstract: Background: In this study we compare outlier loci detected using a FST based method with those identified by a recently described method based on spatial analysis (SAM). We tested a panel of single nucleotide polymorphisms (SNPs) previously genotyped in individuals of goat breeds of southern areas of the Mediterranean basin (Italy, Greece and Albania). We evaluate how the SAM method performs with SNPs, which are increasingly employed due to their high number, low cost and easy of scoring. Results: The combined use of the two outlier detection approaches, never tested before using SNP polymorphisms, resulted in the identification of the same three loci involved in milk and meat quality data by using the two methods, while the FST based method identified 3 more loci as under selection sweep in the breeds examined. Conclusion: Data appear congruent by using the two methods for FST values exceeding the 99% confidence limits. The methods of FST and SAM can independently detect signatures of selection and therefore can reduce the probability of finding false positives if employed together. The outlier loci identified in this study could indicate adaptive variation in the analysed species, characterized by a large range of climatic conditions in the rearing areas and by a history of intense trade, that implies plasticity in adapting to new environments. Tue, 05 Apr 2011 22:00:00 GMT http://hdl.handle.net/2067/1882 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1922 Title: Large-Scale Mitochondrial DNA Analysis of the Domestic Goat Reveals Six Haplogroups with High Diversity Authors: Naderi, Saeid; Rezaei, Hamid-Reza; Taberlet, Pierre; Zundel, Stéphanie; Rafat, Seyed-Abbas; Naghash, Hamid-Reza; El- Barody, Mohamed A. A.; Ertugrul, Okan; Pompanon, François; Abo-Shehada, Mahamoud; Ajmone-Marsan, Paolo; Al Tarrayrah, Jamil; Baret, Philippe; Baumung, Roswitha; Beja-Pereira, Albano; Bertaglia, Marco; Bordonaro, Salvatore; Bruford, Mike; Caloz, Régis; Canali, Gabriele; Canon, Javier; Cappuccio, Irene; Carta, Antonello; Cicogna, Mario; Cortes, Oscar; Crepaldi, Paola; Dalamitra, Stella; Daniela, Krugmann; Dobi, Petrit; Dominik, Popielarczyk; Dunner, Susana; D'Urso, Giuseppe; England, Phillip; Erhardt, Georg; Prinzenberg, Eva-Maria; Ibeagha-Awemu, Eveline; Strzelec, Ewa; Fadlaoui, Aziz; Fornarelli, Francesca; Garcia, David; Georgoudis, Andreas; Lühken, Gesine; Giovenzana, Stefano; Gutscher, Katja; Hewitt, Godfrey; Hoda, Anila; Brandt, Horst; Istvan, Anton; Juma, Gabriela; Joost, Stéphane; Jones, Sam; Karetsou, Katerina; Kliambas, Georgios; Koban, Evren; Kutita, Olga; Fesus, Lazlo; Lenstra, Johannes A.; Ligda, Christina; Lipsky, Shirin; Luikart, Gordon; Glowatzki, Marie-Louise; Marilli, Marta; Marletta, Donata; Milanesi, Elisabetta; Negrini, Riccardo; Nijman, Isaäc J.; Obexer-Ruff, Gabriela; Papachristoforou, Christos; Pariset, Lorraine; Pellecchia, Marco; Peter, Christina; Perez, Trinidad; Pilla, Fabio; D'Andrea, Mariasilvia; Niznikowski, Roman; Roosen, Jutta; Scarpa, Riccardo; Sechi, Tiziana; Taylor, Martin; Togan, Inci; Trommetter, Michel; Valentini, Alessio; Van Cann, Lisette M.; Vlaic, Augustin; Wiskin, Louise; Zundel, Stéphanie Abstract: From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species. Methodology/Principal Findings. The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HV segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals Conclusions/Significance. We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species. Wed, 13 Apr 2011 22:00:00 GMT http://hdl.handle.net/2067/1922 2011-04-13T22:00:00Z http://hdl.handle.net/2067/1910 Title: TRACEABILITY OF FOUR EUROPEAN PROTECTED GEOGRAPHIC INDICATION (PGI) BEEF PRODUCTS USING SINGLE NUCLEOTIDE POLYMORPHISMS (SNP) AND BAYESIAN STATISTICS Authors: Negrini, Riccardo; Nicoloso, Letizia Grazia Maria; Crepaldi, Paola; Milanesi, Elisabetta; Colli, L.; Chegdani, F.; Pariset, Lorraine; Dunner, Susana; Leveziel, Hubert; Williams, J. L.; Ajmone-Marsan, Paolo 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. Tue, 12 Apr 2011 22:00:00 GMT http://hdl.handle.net/2067/1910 2011-04-12T22:00:00Z