http://http://dspace.unitus.it:80 The DSpace digital repository system captures, stores, indexes, preserves, and distributes digital research material. 2013-06-18T23:11:12Z http://hdl.handle.net/2067/117 Title: Assessment of population structure by single nucleotide polymorphisms (SNPs) in goat breeds. Authors: Pariset, Lorraine; Valentini, Alessio; Cappuccio, Irene Abstract: Single nucleotide polymorphisms (SNPs) may be used in biodiversity studies and commercial tasks like traceability, paternity testing and selection for suitable genotypes. Twenty-seven SNPs were characterized and genotyped on 250 individuals belonging to eight Italian goat breeds. Multilocus genotype data were used to infer population structure and assign individuals to populations. To estimate the number of groups (K) to test in population structure analysis we used likelihood values and variance of the bootstrap samples, deriving optimal K from a drop in the likelihood and a rise in the variance plots against K. Description: SNPs; Goat; Population structure 2006-03-19T23:00:00Z http://hdl.handle.net/2067/119 Title: Characterization of single nucleotide polymorphisms in sheep and their variation as evidence of selection Authors: Pariset, Lorraine; Cappuccio, Irene; Valentini, Alessio Abstract: The discovery of SNPs was performed using animals from eight European sheep breeds. Eleven SNPs were further characterized using about 1700 sheep belonging to 57 breeds. A method for the identification of loci that were likely subject to selection was applied; three of the 11 SNPs lying outside the 95% confidence region of the conditional joint distribution of FST and mean heterozygosity were identified as outliers. 2005-12-31T23:00:00Z http://hdl.handle.net/2067/118 Title: Use of microsatellites for genetic variation and inbreeding Authors: Pariset, Lorraine; Savarese, Maria Carmela; Cappuccio, Irene; Valentini, Alessio Abstract: A set of 11 polymorphic microsatellites has been used to assess the distribution of genetic variability in 17 flocks of the Sarda sheep breed in the Viterbo province, located in central Italy. The suitability of samples size and number of loci analysed were tested using a bootstrap procedure. The data obtained were used to estimate the genetic diversity within and among flocks, and to test the presence of inbreeding within flocks. To study the genetic relationship among flocks, a principal component analysis based on Nei standard distances was performed. The results of genetic analysis show a significant excess of homozygotes in some of the flocks. The use of genetic data for maximum likelihood tests of assignment is investigated in order to establish suitable breeding policies. This research represents a case study for the development of mating strategies suitable for incrementing genetic variability within flocks that can be applied in other domestic species showing similar breeding problems (goat, buffalo and small populations of cattle). 2002-12-31T23:00:00Z http://hdl.handle.net/2067/122 Title: Allele frequencies and diversity parameters of 27 single nucleotide polymorphisms within and across goat breeds Authors: Cappuccio, Irene; Pariset, Lorraine; Valentini, Alessio Abstract: Single-nucleotide polymorphisms (SNPs) are useful markers for biodiversity assessment, linkage analysis, traceability and paternity testing. To date, there are no available SNPs for goat in the NCBI dbSNP database and only a few are reported in the literature. Within the European Union Econogene project, we characterized 27 SNPs in goats using a targeted-gene approach. Polymorphisms were identified in a panel of 16 unrelated individuals belonging to eight different goat breeds selected throughout Europe. Genotypes of 30 goats from each of the eight breeds were determined for all the SNPs characterized and diversity measures were estimated. The caprine SNPs described will be a useful complement to the available genome markers. 2005-12-31T23:00:00Z http://hdl.handle.net/2067/123 Title: Convenient genotyping of six myostatin mutations causing double-muscling in cattle using a multiplex oligonucleotide ligation assay Authors: Karim, Latifa; Coppieters, Wouter; Grobet, Luc; Valentini, Alessio; Georges, Michel Abstract: We herein describe a procedure that allows for simultaneous genotyping of six loss-of-function mutations in the bovine myostatin gene associated with the double-muscling phenotype. The proposed method relies on a multiplex oligonucleotide ligation assay and detection of the fluorescently labelled products using automatic sequencers. 1999-12-31T23:00:00Z 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. 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. 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. 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. 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1848 Title: Comparative proteomics and transcriptomics analyses of livers from two different Bos taurus breeds: “Chianina and Holstein Friesian” Authors: Timperio, Anna Maria; D'Alessandro, Angelo; Pariset, Lorraine; D'Amici, Gian Maria; Valentini, Alessio; Zolla, Lello Abstract: The Holstein Friesian and Chianina cattle breeds are representative of extreme selection for milk and meat traits, respectively, with significant changes in metabolism resulting from human selection over the past centuries. In the present study, we wanted to assess whether selection for different purposes has had a measurable effect on liver metabolism through a comparison of the protein and gene expression profiles of the two breeds. We applied 2-DE in order to identify proteins which were differentially expressed in the livers of the two breeds and relate them to different liver functions. We expected to find that only a small number of proteins would be differentially expressed, due to the relatively short phylogenetic distance between these cattle breeds. Nonetheless, thirty nine differentially-expressed proteins were characterized between Chianina and Holstein Friesian, out of a total of 560 ± 57 spots that matched. Microarray analyses evidenced the differential expression of 167 genes (148 for the Holstein Friesian and 19 for the Chianina). Despite being closely related at the genetic level, the disparity of the proteomic and transcriptomic profiles of these two breeds allows us to perform pathway analysis thus to pinpoint proteins whose expression might render the latter capable of greater milk production, or proteins involved in altered thermoregulatory ability or hormone production. On the other hand, we found proteins and gene transcripts in Chianina, not expressed in Holstein, which, upon interaction pathway analysis, were mainly involved in anabolic pathways. In brief, our integrated study provides molecular evidences to support the physiological differences between Holstein and Chianina cattle breeds. Description: L'articolo è disponibile sul sito dell'editore http://www.sciencedirect.com/ 2008-12-31T23:00:00Z 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. 2011-04-06T22:00:00Z 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. 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1894 Title: Ancient DNA: genomic amplification of Roman and medieval bovine bones. Authors: Pariset, Lorraine; Gabbianelli, Federica; De Bernardis, Donatella; Fortunato, Michele Tommaso; Alhaique, Francesca; De Minicis, Elisabetta; Valentini, Alessio Abstract: Cattle remains (bones and teeth) of both roman and medieval age were collected in the archaeological site of Ferento (Viterbo, Italy) with the aim of extracting and characterising nucleic acids. Procedures to minimize contamination with modern DNA and to help ancient DNA (aDNA) preservation of the archaeological remains were adopted. Different techniques to extract aDNA (like Phenol/chloroform extraction) from bovine bones were tested to identify the method that applies to the peculiar characteristics of the study site. Currently, aDNA investigation is mainly based on mtDNA, due to the ease of amplification of the small and high-copied genome and to its usefulness in evolutionary studies. Preliminary amplification of both mitochondrial and nuclear aDNA fragments from samples of Roman and medieval animals were performed and partial specific sequences of mitochondrial D-loop as well as of nuclear genes were obtained. The innovative amplification of nuclear aDNA could enable the analysis of genes involved in specific animal traits, giving insights of ancient economic and cultural uses, as well as providing information on the origin of modern livestock population. 2011-04-07T22:00:00Z http://hdl.handle.net/2067/1887 Title: Comparative proteomics and transcriptomics analyses of livers from two different Bos taurus breeds: “Chianina and Holstein Friesian” Authors: Timperio, Anna Maria; D'Alessandro, Angelo; Pariset, Lorraine; D'Amici, Gian Maria; Valentini, Alessio; Zolla, Lello Abstract: The Holstein Friesian and Chianina cattle breeds are representative of extreme selection for milk and meat traits, respectively, with significant changes in metabolism resulting from human selection over the past centuries. In the present study, we wanted to assess whethe selection for different purposes has had a measurable effect on liver metabolism through a comparison of the protein and gene expression profiles of the two breeds. We applied 2-DE in order to identify proteins which were differentially expressed in the livers of the two breeds and relate them to different liver functions. We expected to find that only a small number of proteins would be differentially expressed, due to the relatively short phylogenetic distance between these cattle breeds. Nonetheless, thirty nine differentially expressed proteins were characterized between Chianina and Holstein Friesian, out of a total of 560 ± 57 spots that matched. Microarray analyses evidenced the differential expression of 167 genes (148 for the Holstein Friesian and 19 for the Chianina). Despite being closely related at the genetic level, the disparity of the proteomic and transcriptomic profiles of these two breeds allows us to perform pathway analysis thus to pinpoint proteins whose expression might render the latter capable of greater milk production, or proteins involved in altered thermoregulatory ability or hormone production. On the other hand, we found proteins and gene transcripts in Chianina, not expressed in Holstein, which, upon interaction pathway analysis, were mainly involved in anabolic pathways. In brief, our integrated study provides molecular evidences to support the physiological differences between Holstein and Chianina cattle breeds. 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1877 Title: Telomere length diversity in cattle breeds Authors: Tilesi, Francesca; Di Domenico, Enea Gino; Pariset, Lorraine; Bosco, Luigi; Willems, Daniela; Valentini, Alessio; Ascenzioni, Fiorentina Abstract: Telomeres are specialized nucleoprotein structures that have two important functions: (i) protection of the chromosomal ends from deleterious events such as chromosome fusion and degradation; (ii) counteraction of the “end replication problem” by allowing telomerase-dependent or, more rarely, telomerase-independent telomere elongation. The DNA sequences underlying these activities are short simple tandem repeats, which in vertebrate consist of a variable number of TTAGGG. Telomeres dysfunction may be caused either by the absence of telomerase activity or by mutations in telomeric proteins nvolved in telomere length and structure regulation. Additionally,increasing experimental evidence suggests that telomeres take part in the complex network regulating cell roliferation. Accordingly, telomeres are involved in biological process such as aging and tumor progression. In this study we determined the telomere length in two bovine Italian cattle breeds, Chianina and Maremmana, which are characterized by high longevity and range breeding. In order to account for possible variation among different tissues, we have determined telomere length in different organs such as spleen,lung and liver. Overall, the median telomere length was significant lower in Chianina (11 ± 0.69 kb) than in Maremmana (12.05 ± 1.57 kb). Moreover, telomere length variation among individuals was very low in Chianina but rather high in Maremmana. These data suggest that telomere length is influenced by the breeds. This hypothesis is confirmed by the different history of these Italian breeds. Indeed, Chianina has a long history and its size was maintained by the Breeders Association without necessity to crossbreed with other breeds, whereas the population of Maremmana underwent a dramatic shrinkage in the recent past. Therefore, breeders have crossed Maremmana with other breeds, like Charolais, and have relaxed the rules for the inclusion in the herd book. 2011-04-04T22:00:00Z 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. 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1878 Title: Not working on mice or humans Authors: Pariset, Lorraine; Bueno, Susana; Bongiorni, Silvia; Valentini, Alessio Abstract: Microarrays technology is fast devel- oping and its application is expanding from Homo sapiens to a wide number of species where enough information on sequences and annotations are available. The number of species for which a dedicated platform exists is not high. The Expressed Sequence Tags (ESTs) databases represent a collection of anonymous sequences that can be used to build species spe- cific microarrays for species whose genome sequences are largely un- known. 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1880 Title: Comparison of Milk Fat Globule Membrane (MFGM) Proteins of Chianina and Holstein Cattle Breed Milk Samples Through Proteomics Methods Authors: Murgiano, Leonardo; Timperio, Anna Maria; Zolla, Lello; Bongiorni, Silvia; Valentini, Alessio; Pariset, Lorraine Abstract: Identification of proteins involved in milk production is important to understand the biology of lactation. Many studies have advanced the understanding of mammary function and milk secretion, but the critical molecular mechanisms implicated in milk fat secretion is still incomplete. Milk Fat Globules are secreted from the apical surface of the mammary cells, surrounded by a thin membrane bilayer, the Milk Fat Globule Membrane (MFGM), formed by proteins which have been suggested to be holesterolemia-lowering factors, inhibitors of cancer cell growth, vitamin binders, bactericidal, suppressors of multiple sclerosis. Using a proteomic approach, we compared MFGM from milk samples of individuals belonging to two different cattle breeds, Chianina and Holstein,representative of selection for milk and meat traits, respectively. We were able to isolate some of the major MFGM proteins in the examined samples and to identify differences between the protein fractions of the two breeds. We detected differences in the amount of proteins linked to mammary gland development and lipid droplets formation, as well as host defence mechanisms. We have shown that proteomics is a suitable, unbiased method for the study of milk fractions proteins and a powerful tool in nutritional genomics. 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1884 Title: Exploring polymorphisms and effects of candidate genes on milk fat quality in dairy sheep Authors: Crisà, Alessandra; Marchitelli, Cinzia; Pariset, Lorraine; Contarini, Giovanna; Signorelli, Federica; Napolitano, Francesco; Catillo, Gennaro; Valentini, Alessio; Moioli, Bianca Abstract: Aim of the present study was to investigate the genetic control of the fatty acid (FA) composition in milk from three breeds of sheep: Altamurana, Gentile di Puglia and Sarda. SNP within genes, encoding enzymes putatively involved in the synthesis and metabolism of milk fat, were selected for analysis, and the allele substitution effects were determined for 16 genes, that were polymorphic in the three sheep breeds, upon the milk fat composition. Four genes (alpha-1-antichymotrypsin-2; diacylglycerol O-acyltransferase homolog-2; propionyl Coenzyme A carboxylase, beta polypeptide; insulin-like growth factor-I) play a role in the desaturation of stearic FA into polyunsaturated fatty acids (PUFA). Furthermore, two genes (growth hormone receptor and zona pellucida glycoprotein-2) affect the variability of the total fat content, in addition to the butyric and stearic FA profile, and that the fatty acid synthetase gene has an influence on the medium-chain FA. Milk FA profiles play an important role in dairy sheep farming because they have a large effect on cheese characteristics and also because sheep milk may be marketed as a source of nutraceuticals as it contains higher levels of CLA than milk from other ruminants. The current study evaluated the global effects of a large number of SNP and haplotypes on traits that are not commonly investigated in sheep but that are potentially very useful for improving milk quality. 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1888 Title: Microarrays and high throughput transcriptomic analysis for species with limited knowledge of genomic sequences F transcriptomic analysis for species with OO limited knowledge of genomic sequences Authors: Pariset, Lorraine; Chillemi, Giovanni; Bongiorni, Silvia; Spica, Vincenzo Romano; Valentini, Alessio Abstract: Microarrays produce a measurement of gene expression based on the relative measures of dye intensities that correspond to the amount of target RNA. This technology is fast developing and its application is expanding from Homo sapiens to a wide number of species, where enough information on sequences and annotations exist. Anyway, the number of species for which a dedicated platform exists is not many. The use of heterologous array hybridization, screening for gene expression in one species using an array developed for another species, is still quite frequent, even though cross-species microarray hybridization has raised many arguments. Some methods which are high throughput and do not rely on knowledge of the DNA/RNA sequence exist, namely serial analysis of gene expression (SAGE), Massively Parallel Signature Sequencing (MPSS) and deep sequencing of full transcriptome. Although very powerful methods, particularly the last one, they are still quite costly and cumbersome. In some species where genome sequences are largely unknown, several anonymous sequences are deposited in gene banks as a result of Expressed Sequence Tags (ESTs) sequencing projects. The ESTs databases represent a valuable knowledge that can be exploited with some bioinformatic effort to build species-specific microarrays. We present here a method of high-density in situ synthesized microarrays starting from available EST sequences in, Ovis aries. Our data indicate that the method is very efficient and can be easily extended to other species of which genetic sequences are present in public databases, but neglected so far with advanced devices like microarrays. As a perspective, the approach can be applied also to species of which no sequences are available to date, thanks to high-throughput deep sequencing methods. 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1889 Title: A Tool for Sheep Product Quality: Custom Microarrays from Public Databases Authors: Bongiorni, Silvia; Chillemi, Giovanni; Prosperini, Gianluca; Bueno, Susana; Valentini, Alessio; Pariset, Lorraine Abstract: Milk and dairy products are an essential food and an economic resource in many countries. Milk component synthesis and secretion by the mammary gland involve expression of a large number of genes whose nutritional regulation remains poorly defined. The purpose of this study was to gain an understanding of the genomic influence on milk quality and synthesis by comparing two sheep breeds with different milking attitude (Sarda and Gentile di Puglia) using sheep-specific microarray technology. From sheep ESTs deposited at NCBI, we have generated the first annotated microarray developed for sheep with a coverage of most of the genome. 2011-04-05T22:00:00Z http://hdl.handle.net/2067/1895 Title: Genetic variation and relationships among Turkish water buffalo populations Authors: Gargani, Maria; Pariset, Lorraine; Soysal, M. Ihsan; Ozkan, Emel; Valentini, Alessio Abstract: The genetic variation and relationships among six Turkish water buffalo populations,typical of different regions was assessed using a set of twenty-six heterologous (bovine) microsatellite markers. Between 7 and 17 different alleles were identified per microsatellite in a total of 254 alleles. The average number of alleles across all loci in all the analyzed populations was found to be 12.57. The expected mean heterozygosity (HE) per population was between 0.5 and 0.58. Significant departures from Hardy-Weinberg equilibrium were observed for 44 locus-population combinations. Population differentiation was analyzed by estimation of the FST index (values ranging from 0.053 to 0.123) among populations. In the PCA analysis the Merzifon population showed the highest differentiation compared to the others. Also some individuals of the Danamandira population appeared clearly separated. Instead Afyon, Coskun, Pazar and Thural populations represented one single cluster. The assignment of individuals to their source populations, performed using the Bayesian clustering approach implemented in STRUCTURE 2.2 software, has evidenced a high differentiation of Merzifon and Danamandira populations as well. The results of this study could be useful for the development of conservation strategies of the Turkish buffalo. 2011-04-07T22:00:00Z 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. 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. 2011-04-14T22:00:00Z http://hdl.handle.net/2067/1924 Title: European cattle breed cluster accordingly to their meat quality parameters Authors: Valentini, Alessio; Nardone, Alessandro; Crisà, Alessandra; Marchitelli, Cinzia; Failla, Sebastiana; Gigli, S.; Albertí, Pere; Sañudo, Carlos; Nutte, G.; Ertbjerg, Per; Hocquette, Jean Francois; Williams, J. L. Abstract: The concept of breed is rather questionable and it’s used more as a tool for “labelling” production systems than as a biological category. Here, production system is intended as a whole set of animal units, techniques, breeding schemes, marketing, etc. However, man has demonstrated to be very quick in capturing and disseminating good characteristics whence they appear in a breed by mutation or by selection. Therefore, it might be expected that breeds, nevertheless of recent origin, could bear distinguished productive characteristics. Due to the quan- titative nature of them, more characteristics should be measured in order to obtain a clear and statistically significant distinction. We have measured several meat characteristics in 15 European breeds (30 individuals for each breed), mostly with beef attitude, reared in similar conditions. This was accomplished to better reveal the genetic background of breeds. A canonical discriminant analysis showed a clear distinction among breeds. In particular lipid composition of meat was able to assign individuals to breeds with 57% and 63% of individuals correctly classified respectively for neutral and phospholipids. The classification is generally good for all breeds except for the Spanish ones,indicating probably some crossing in the past for these breeds. Neutral lipids can classify double muscled breeds with high precision (84% and 95% in Asturiana de los Valles and Piedmontese respectively). Tenderness related measures (collagen, µ-calpain, m-calpain, calpastatin, MFI) poorly assign indi- viduals to breeds (average 22%). The good classification of individuals to breeds for lipid composition suggests distinctive genetic features and encourages to look further to genetic determination of fat composition in the meat, as well as to exploit particular breeds to obtain products suitable for categories of consumers needing/searching for special components in their diet. 2011-04-14T22:00:00Z