Analysis of selection signatures in the beef cattle genome

Abstract

This study aimed to evaluate the impact of selection on the genome structure of beef cattle through identification of selection signatures reflecting the breeding standard of each breed and to discover potential functional genetic variants to improve performance traits. Genotyping data of six beef breeds (Aberdeen Angus, Hereford, Limousin, Charolais, Piedmontese and Romagnola) were used to perform genome-wide scans for selection signatures. The approaches applied were based on an assumption that selection leads to linkage disequilibrium or to a decrease of genetic variability in genomic regions containing genotypes connected with favourable phenotypes. Thus, the selection signatures were analysed based on Wright’s F<sub>ST</sub> index, distribution of runs of homozygosity segments in the beef genome and determination of linkage disequilibrium variability between breeds. The number and length of detected selection signals were different depending on the breeds and methodological approaches. As expected due to the breeding goals of analysed breeds, common signals were located on autosomes 2, 6, 7, 13 and 20 close to the genes associated with coat colour (KIT, KDR), muscle development (GDF9, GHRH, GHR), double muscling (MSTN), meat tenderness (CAST) and intramuscular fat content (SCD). But, across the genomes of analysed breeds, unique selection signals were found as well. The subsequent analysis of those single nucleotide polymorphism markers can be beneficial for the genetic progress of studied breeds in future.

Food Resources Biodiversity: The Case of Local Cattle in Slovakia

“…Obtained results confirmed the tested assumption that the different production type of analysed breeds could cause an increase in the frequency of specific alleles (haplotypes) responsible for desired phenotypic traits. 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].…”

Genome-wide characterisation of regions under intense selection based on runs of homozygosity in Charolais cattle

“…Compared to our resultsSzmatoła et al (2019) reported five affected by directional selection regions for Charolais cattle and they observed two regions in approximately the same position (BTA5 53.26 -62.18 Mb and BTA7 28.18 -31.97 Mb) Mészáros et al (2015). identified the strongest selection signal in the position from 36 to 41 Mb for Tyrol Grey on BTA6 Moravčíková et al (2019). reported three genomic regions under intense selection on BTA2, 5 and 8 for Charolais cattle and compared to our results, we found the same genomic region affected by selection on chromosome 5 (56.38 -61.73 Mb).…”

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

“…The SCIN gene, also mapped in the region, is involved in residual feed intake in cattle ( Salleh et al, 2017 ). The remaining regions under selection in Adm_cur spanned other candidate genes including ANKRD52 , RNF41 , and MYL6 associated with height and carcass traits ( Cai et al, 2019 ; Moravčíková et al, 2019 ; Feitosa et al, 2021 ), and COQ10A and RNF41 related to milk trait and calf mortality ( Lázaro et al, 2021 ; Marín-Garzón et al, 2021 ). In addition, the SARNP gene is related to animal reproduction ( Labrecque et al, 2014 ), while the DNAJC14 is involved in heat stress ( Bahbahani et al, 2015 ; Rehman et al, 2020 ).…”