http://http://dspace.unitus.it:80 The DSpace digital repository system captures, stores, indexes, preserves, and distributes digital research material. Sun, 19 May 2013 18:58:29 GMT 2013-05-19T18:58:29Z 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/2067/1885 Title: Polymorphisms within the Toll-Like Receptor (TLR)-2, -4, and -6 Genes in Cattle Authors: Mariotti, Marco; Williams, John L.; Dunner, Susana; Valentini, Alessio; Pariset, Lorraine Abstract: In mammals, members of the TLR gene family play a primary role in the recognition of pathogen-associated molecular patterns from bacteria, viruses, protozoa and fungi. Recently, cattle TLR genes have been mapped to chromosomes using a radiation hybrid panel. Nucleotide sequences of bovine TLR2, TLR4 and TLR6 genes were screened to identify novel SNPs that can be used in studies of cattle resistance to diseases. In total, 8 SNPs were identified and were submitted to the NCBI dbSNP database. The frequencies of the SNPs were assessed in 16 different bovine European cattle breeds and a phylogenetic analysis carried out to describe the relationships between the breeds. Even if from our analysis the SNPs do not appear located in loci under selection, a deviation of three SNPs from Hardy Weinberg equilibrium was observed, and we hypothesize that some of the polymorphisms may be fixated since many generations. The described variations in immune function related genes will contribute to research on disease response in cattle. In fact, the SNPs can be used in association studies between polymorphisms and cattle resistance to diseases. Tue, 05 Apr 2011 22:00:00 GMT http://hdl.handle.net/2067/1885 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1890 Title: Relationships of Podolic cattle breeds assessed by single nucleotide polymorphisms (SNPs) genotyping Authors: Pariset, Lorraine; Mariotti, Marco; Nardone, Alessandro; Soysal, M. Ihsan; Ozkan, Emel; Williams, J. L.; Dunner, Susana; Leveziel, Hubert; Maróti-Agóts, Ákos; Bodò, I.; Valentini, Alessio Abstract: Italian Maremmana, Turkish Grey and Hungarian Grey breeds belong to the same Podolic group of cattle, have a similar conformation and recently experienced a similar demographic reduction. The aim of this study was to assess the relationship among the analysed Podolic breeds and to verify whether their genetic state reflects their history. To do so, approximately 100 single nucleotide polymorphisms (SNPs) were genotyped on individuals belonging to these breeds and compared to genotypes of individuals of two Italian beef breeds, Marchigiana and Piemontese, which underwent different selection and migration histories. Population genetic parameters such as allelic frequencies and heterozygosity values were assessed, genetic distances calculated and assignment test performed to evaluate the possibility of recent admixture between the populations. The data show that the physical similarity among the Podolic breeds examined, and particularly between Hungarian Grey and Maremmana cattle that experienced admixture in the recent past, is mainly morphological. The assignment of individuals from genotype data was achieved using Bayesian inference, confirming that the set of chosen SNPs is able to distinguish among the breeds and that the breeds are genetically distinct. Individuals of Turkish Grey breed were clearly assigned to their breed of origin for all clustering alternatives, showing that this breed can be differentiated from the others on the basis of the allelic frequencies. Remarkably, in the Turkish Grey there were differences observed between the population of Enez district, where in situ conservation studies are practised, and that of Bandirma district of Balikesir, where ex situ conservation studies are practised out of the original raising area. In conclusion, this study demonstrates that molecular data could be used to reveal an unbiased view of past events and provide the basis for a rational exploitation of livestock, suggesting appropriate cross-breeding plans based on genetic distance or breeding strategies that include the population structure. Wed, 06 Apr 2011 22:00:00 GMT http://hdl.handle.net/2067/1890 2011-04-06T22:00:00Z 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 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/2067/1923 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