2020
DOI: 10.1111/age.12982
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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 re… Show more

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Cited by 11 publications
(6 citation statements)
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“…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 ].…”
Section: Discussionsupporting
confidence: 51%
See 1 more Smart Citation
“…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 ].…”
Section: Discussionsupporting
confidence: 51%
“…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.…”
Section: Discussionsupporting
confidence: 51%
“…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 ].…”
Section: Discussionmentioning
confidence: 99%
“…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).…”
Section: Introductionmentioning
confidence: 99%