Genome-wide detection of signatures of selection in three Valdostana cattle populations

International audience; The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (F-ST) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least tw…

Genomic characterization of Algerian Guelmoise cattle and their genetic relationship with other North African populations inferred from SNP genotyping arrays

International audience; Understanding between and within-breeds genetic variability is essential in the choice of conservation management decisions for threatened populations. In this study we assessed the genetic diversity of the Algerian Guelmoise cattle (GUE) by analyzing data on 24 GUE individuals genotyped for the Illumina BovineSNP50 BeadChipv2. We also provided a detailed description of the population structure of GUE using comparisons with 23 worldwide cattle populations, selected as being representative of African, South European and indicine populations, in addition to four North African populations. We show that GUE is an admixed population which has strong genetic similarity to …

Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses …

QTL associated to bacterial cold water disease in rainbow trout

Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity in local North African cattle

International audience; Natural-driven selection is supposed to have left detectable signatures on the genome of North African cattle which are often characterized by the fixation of genetic variants associated with traits under selection pressure and/or an outstanding genetic differentiation with other populations at particular loci. Here, we investigate the population genetic structure and we provide a first outline of potential selection signatures in North African cattle using single nucleotide polymorphism genotyping data. After comparing our data to African, European and indicine cattle populations, we identified 36 genomic regions using three extended haplotype homozygosity statistic…