Detection of selection signatures in Limousin cattle using whole‐genome resequencing

Abstract

Summary Limousin, a renowned beef breed originating from central France, has been selectively bred over the last 100 years to improve economically important traits. We used whole‐genome sequencing data from 10 unrelated Limousin bull calves to detect polymorphisms and identify regions under selection. A total of 13 943 766 variants were identified. Moreover, 311 852 bi‐allelic SNPs and 92 229 indels located on autosomes were fixed for the alternative allele in all sequenced animals, including the previously reported missense deleterious F94L mutation in MSTN. We performed a whole‐genome screen to discover genomic regions with excess homozygosity, using the pooled heterozygosity score and identified 171 different candidate selective sweeps. In total, 68 candidate genes were found in only 57 of these regions, indicating that a large fraction of the genome under selection might lie in non‐coding regions and suggesting that a majority of adaptive mutations might be regulatory in nature. Many QTL were found within candidate selective sweep regions, including QTL associated with shear force or carcass weight. Among the putative selective sweeps, we located genes (MSTN, NCKAP5, RUNX2) that potentially contribute to important phenotypes in Limousin. Several candidate regions and genes under selection were also found in previous genome‐wide selection scans performed in Limousin. In addition, we were able to pinpoint candidate causative regulatory polymorphisms in GRIK3 and RUNX2 that might have been under selection. Our results will contribute to improved understanding of the mechanisms and targets of artificial selection and will facilitate the interpretation of GWASs performed in Limousin.

Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds

“…We sequenced genomes of 30 individuals representing six Swedish native cattle breeds, with medium to high coverage (14x—45x) to assess the genetic diversity of these native breeds in more detail compared with previous SNP-based studies [ 3 , 4 , 8 ]. The average nucleotide diversity (π = 1.6 × 10 –3 ) is on par with that reported for other native European breeds [ 20 , 30 , 31 ]. However, we were able to identify a higher number, about 22.5 million variants in 30 samples, compared to about 14–7.5 million variants identified in about 10–50 samples in other European breeds [ 20 , 30 , 31 ].…”

“…The average nucleotide diversity (π = 1.6 × 10 –3 ) is on par with that reported for other native European breeds [ 20 , 30 , 31 ]. However, we were able to identify a higher number, about 22.5 million variants in 30 samples, compared to about 14–7.5 million variants identified in about 10–50 samples in other European breeds [ 20 , 30 , 31 ]. The high number of identified variants despite the small population sizes of the native Swedish breeds is an important result that shows that these breeds harbour a lot of genetic diversity that could be very importnat for future cattle breeding.…”

Whole-genome sequencing reveals genomic diversity and selection signatures in Xia’nan cattle

“…The copy number of this gene was found to be related to the growth traits of beef cattle [ 24 ]. NCK-associated protein 5 ( NCKAP5 ) was found to be potentially associated with important phenotypes in Limousin cattle [ 25 ]. CREB-regulated transcription coactivator 1 ( CRTC1 ) and Heat shock protein 12 A ( HSPA12A ) can respectively regulate adipocyte differentiation and fat metabolism through the PPARγ pathway [ 26 , 27 ].…”

Whole-genome selective scans detect genes associated with important phenotypic traits in goat (Capra hircus)

“…Goats have formed a wealth of breed resources adapted to different natural environments and human needs in the past 10,000 years (Pereira and Amorim, 2010;Zheng et al, 2020), exhibited specialized phenotypes (e.g., coat color, horn, ear), and provided diverse productions (e.g., milk, fiber) (Skapetas and Bampidis, 2016). For the animals, those traits selected in a specific direction may be imprinted obvious characteristics in the genome (Grossman et al, 2010;Li et al, 2020;Mariadassou et al, 2020;LI et al, 2022;Seo et al, 2022).…”