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

Abstract

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 two approaches in VPR, VPN and VCA, respectively. Most of these candidate regions were population-specific but we found one common genomic region spanning 2.38 Mb on BTA06 which either overlaps or is located close to runs of homozygosity islands detected in the three populations. This region included inter alia two well-known genes: KDR, a well-established coat colour gene, and CLOCK, which plays a central role in positive regulation of inflammatory response and in the regulation of the mammalian circadian rhythm. The other candidate regions identified harboured genes associated mainly with milk and meat traits as well as genes involved in immune response/inflammation or associated with behavioural traits. This last category of genes was mainly identified in VCA, which is selected for fighting ability. Overall, our results provide, for the first time, a glimpse into regions of the genome targeted by selection in Valdostana cattle. Finally, this study illustrates the relevance of using multiple complementary approaches to identify genomic regions putatively under selection in livestock.

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

“…In total, we highlight the presence of 36 different genomic regions putatively under selection using the first type of approaches ( iHS, Rsb and XP-EHH ) and 92 outlier SNPs using Bayescan. Consistently with previous observations 19 , we observe little overlap between results obtained from each of the two types of approaches. Given that Bayescan assumes that the gene frequencies under any neutrally structured population model can be approximated by a multinomial Dirichlet distribution 20 which would not be appropriate in a hierarchical population structure 21 (as is the case for our North African sample), the 92 identified SNPs should be considered cautiously.…”

Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color

“…All extant domestic cattle belong to two major lineages, Bos taurus taurus and Bos taurus indicus, derived from independent domestications. However, current cattle biodiversity is not only the result of genetic drift and natural and artificial selection, but also of putative introgression and admixture events between the two cattle lineages, which occurred in almost all continents, giving rise to more than 1100 recognized breeds [17][18][19][20][21]. Such a tremendous diversity is emphasized by a vast array of phenotypic traits such as coat color, body size, behavior, and production traits [22].…”

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

“…In livestock species, domestication followed by breed formation and the subsequent artificial selection for economic and morphological traits have shaped genomic variation, driving the formation of detectable signatures on the genome of these populations (e.g., Stella et al, 2010 ; Qanbari et al, 2011 ; Rothammer et al, 2013 ; Signer-Hasler et al, 2017 ; Mastrangelo et al, 2020a ). With more than 30 officially recognized local cattle breeds, Italy can be considered as one of the most important hotspots of cattle diversity ( Mastrangelo et al, 2018 ).…”