Assessing selection signatures within and between selected lines of dual‐purpose black and white and German Holstein cattle

Abstract

SummaryThe aim of this study was to detect selection signatures considering cows from the German Holstein (GH) and the local dual‐purpose black and white (DSN) population, as well as from generated sub‐populations. The 4654 GH and 261 DSN cows were genotyped with the BovineSNP50 Genotyping BeadChip. The geographical herd location was used as an environmental descriptor to create the East‐DSN and West‐DSN sub‐populations. In addition, two further sub‐populations of GH cows were generated, using the extreme values for solutions of residual effects of cows for the claw disorder dermatitis digitalis. These groups represented the most susceptible and most resistant cows. We used cross‐population extended haplotype homozygosity methodology (XP‐EHH) to identify the most recent selection signatures. Furthermore, we calculated Wright’s fixation index (FST). Chromosomal segments for the top 0.1 percentile of negative or positive XP‐EHH scores were studied in detail. For gene annotations, we used the Ensembl database and we considered a window of 250 kbp downstream and upstream of each core SNP corresponding to peaks of XP‐EHH. In addition, functional interactions among potential candidate genes were inferred via gene network analyses. The most outstanding XP‐EHH score was on chromosome 12 (at 77.34 Mb) for DSN and on chromosome 20 (at 36.29–38.42 Mb) for GH. Selection signature locations harbored QTL for several economically important milk and meat quality traits, reflecting the different breeding goals for GH and DSN. The average FST value between GH and DSN was quite low (0.068), indicating shared founders. For group stratifications according to cow health, several identified potential candidate genes influence disease resistance, especially to dermatitis digitalis.

Food Resources Biodiversity: The Case of Local Cattle in Slovakia

“…The strong impact of selection on the genomic region related to carcass traits in beef cattle was also reported by Moravčíková et al [88], Jahuey-Martínez et al [89] or Paim et al [90]. In dairy cattle, the most significant selection signatures were found mainly on chromosome 6 that is strongly connected to milk production and composition [91,92]. The functional analyses of known and novel genetic variants continuously improve the knowledge of genetic control of these complex traits that are usually affected by several genes or quantitative trait loci.…”

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

“…Our approach to detect a strong signal of homozygosity considering temporal subpopulations within the same breed is similar to the one applied by Naderi et al (2020 ), who contrasted the current German Holstein to one of its recent ancestors, the local dual-purpose German black pied cattle (DSN). In addition, we aimed to reduce the bias due to the uncertainty of the ancestral base population and applied the XP-EHH method to detect complete sweeps in contrast to the Integrated Haplotype Score (IHS) approach ( Qanbari and Simianer, 2014 ).…”

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

“…For these loci, we then considered a ±250 kbp region as also putatively under selection. The choice of this window size was based on the knowledge that the extent of linkage disequilibrium among markers in the cattle genome does not significantly exceed 500 kbp [34] and was corroborated by a common usage in published selection signature studies in cattle [35][36][37].…”