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Piacenza d'Adige, Italy

Groeneveld L.F.,Institute of Farm Animal Genetics | Lenstra J.A.,University Utrecht | Eding H.,Animal Evaluations Unit | Toro M.A.,Technical University of Madrid | And 7 more authors.
Animal Genetics | Year: 2010

Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology. © 2010 International Society for Animal Genetics. Source

Capomaccio S.,Istituto di Zootecnica | Milanesi M.,Istituto di Zootecnica | Bomba L.,Istituto di Zootecnica | Cappelli K.,University of Perugia | And 5 more authors.
Animal Genetics | Year: 2015

Summary Genome-wide association studies (GWAS) have been widely applied to disentangle the genetic basis of complex traits. In cattle breeds, classical GWAS approaches with medium-density marker panels are far from conclusive, especially for complex traits. This is due to the intrinsic limitations of GWAS and the assumptions that are made to step from the association signals to the functional variations. Here, we applied a gene-based strategy to prioritize genotype-phenotype associations found for milk production and quality traits with classical approaches in three Italian dairy cattle breeds with different sample sizes (Italian Brown n = 745; Italian Holstein n = 2058; Italian Simmental n = 477). Although classical regression on single markers revealed only a single genome-wide significant genotype-phenotype association, for Italian Holstein, the gene-based approach identified specific genes in each breed that are associated with milk physiology and mammary gland development. As no standard method has yet been established to step from variation to functional units (i.e.; genes), the strategy proposed here may contribute to revealing new genes that play significant roles in complex traits, such as those investigated here, amplifying low association signals using a gene-centric approach. © 2015 Stichting International Foundation for Animal Genetics. Source

Bomba L.,Istituto di Zootecnica | Nicolazzi E.L.,Fondazione Parco Tecnologico Padano | Milanesi M.,Istituto di Zootecnica | Negrini R.,Associazione Italiana Allevatori AIA | And 5 more authors.
Genetics Selection Evolution | Year: 2015

Background: A number of methods are available to scan a genome for selection signatures by evaluating patterns of diversity within and between breeds. Among these, "extended haplotype homozygosity" (EHH) is a reliable approach to detect genome regions under recent selective pressure. The objective of this study was to use this approach to identify regions that are under recent positive selection and shared by the most representative Italian dairy and beef cattle breeds. Results: A total of 3220 animals from Italian Holstein (2179), Italian Brown (775), Simmental (493), Marchigiana (485) and Piedmontese (379) breeds were genotyped with the Illumina BovineSNP50 BeadChip v.1. After standard quality control procedures, genotypes were phased and core haplotypes were identified. The decay of linkage disequilibrium (LD) for each core haplotype was assessed by measuring the EHH. Since accurate estimates of local recombination rates were not available, relative EHH (rEHH) was calculated for each core haplotype. Genomic regions that carry frequent core haplotypes and with significant rEHH values were considered as candidates for recent positive selection. Candidate regions were aligned across to identify signals shared by dairy or beef cattle breeds. Overall, 82 and 87 common regions were detected among dairy and beef cattle breeds, respectively. Bioinformatic analysis identified 244 and 232 genes in these common genomic regions. Gene annotation and pathway analysis showed that these genes are involved in molecular functions that are biologically related to milk or meat production. Conclusions: Our results suggest that a multi-breed approach can lead to the identification of genomic signatures in breeds of cattle that are selected for the same production goal and thus to the localisation of genomic regions of interest in dairy and beef production. © 2015 Bomba et al.; licensee BioMed Central. Source

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