title: Detection of selection signatures in Piemontese and Marchigiana cattle, two breeds with similar production aptitudes but different selection histories.
abstract: BACKGROUND
  Domestication and selection are processes that alter the pattern of within- and between-population genetic variability. They can be investigated at the genomic level by tracing the so-called selection signatures. Recently, sequence polymorphisms at the genome-wide level have been investigated in a wide range of animals. A common approach to detect selection signatures is to compare breeds that have been selected for different breeding goals (i.e. dairy and beef cattle). However, genetic variations in different breeds with similar production aptitudes and similar phenotypes can be related to differences in their selection history.
  
  
  METHODS
  In this study, we investigated selection signatures between two Italian beef cattle breeds, Piemontese and Marchigiana, using genotyping data that was obtained with the Illumina BovineSNP50 BeadChip. The comparison was based on the fixation index (Fst), combined with a locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach. In addition, analyses of Fst were carried out to confirm candidate genes. In particular, data were processed using the varLD method, which compares the regional variation of linkage disequilibrium between populations.
  
  
  RESULTS
  Genome scans confirmed the presence of selective sweeps in the genomic regions that harbour candidate genes that are known to affect productive traits in cattle such as DGAT1, ABCG2, CAPN3, MSTN and FTO. In addition, several new putative candidate genes (for example ALAS1, ABCB8, ACADS and SOD1) were detected.
  
  
  CONCLUSIONS
  This study provided evidence on the different selection histories of two cattle breeds and the usefulness of genomic scans to detect selective sweeps even in cattle breeds that are bred for similar production aptitudes.
authors.affiliation: Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy. ssorbolini@uniss.it.
authors.forename: Silvia
authors.initials: S
authors.lastname: Sorbolini
authors.affiliation: Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy. gbmarras@uniss.it.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Marras
authors.affiliation: Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy. gigaspa@uniss.it.
authors.forename: Giustino
authors.initials: G
authors.lastname: Gaspa
authors.affiliation: Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy. dimauro@uniss.it.
authors.forename: Corrado
authors.initials: C
authors.lastname: Dimauro
authors.affiliation: Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy. mcellesi@uniss.it.
authors.forename: Massimo
authors.initials: M
authors.lastname: Cellesi
authors.affiliation: Dipartimento per l'Innovazione dei Sistemi Biologici Agroalimentari e Forestali DIBAF, Università della Tuscia, Viterbo, Italy. alessio@unitus.it.
authors.forename: Alessio
authors.initials: A
authors.lastname: Valentini
authors.affiliation: Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy. macciott@uniss.it.
authors.forename: Nicolò Pp
authors.initials: NP
authors.lastname: Macciotta
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D030541:Databases, Genetic; D015810:Linkage Disequilibrium; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D000068618:Selective Breeding / Q000235:genetics*