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Detection of selection signatures in Limousin cattle using whole-genome resequencing.
Animal Genetics ( IF 2.4 ) Pub Date : 2020-07-20 , DOI: 10.1111/age.12982
M Mariadassou 1 , Y Ramayo-Caldas 2, 3 , M Charles 2, 4 , M Féménia 2 , G Renand 2 , D Rocha 2
Affiliation  

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.

中文翻译:

使用全基因组重测序检测利穆赞牛的选择特征。

利穆赞(Limousin)是起源于法国中部的著名牛肉品种,在过去100年中经过选择性育种,以改善重要的经济性状。我们使用来自10个不相关的利穆赞牛犊的全基因组测序数据来检测多态性并鉴定选择区域。总共鉴定出13 943 766个变体。此外,在所有测序动物中,包括常报道的常染色体上的311 852个双等位基因SNP和92 229个插入缺失被固定为备选等位基因,包括先前报道的MSTN中的错义有害F94L突变。。我们使用汇总的杂合度评分进行了全基因组筛选,以发现具有过量纯合度的基因组区域,并确定了171种不同的候选选择性扫描。总共在这些区域中的57个区域中发现了68个候选基因,这表明正在选择的基因组很大一部分可能位于非编码区域,这表明大多数适应性突变可能是自然调控的。在候选的选择性扫描区域内发现了许多QTL,包括与剪切力或cas体重量相关的QTL。在推定的选择性扫描中,我们定位了基因(MSTNNCKAP5RUNX2),可能对利木赞的重要表型有所贡献。在利穆赞以前进行的全基因组选择扫描中,还发现了一些候选区域和正在选择的基因。此外,我们还可以查明可能在选择中的GRIK3RUNX2中的候选致病性调控多态性。我们的结果将有助于增进对人工选择机制和目标的了解,并将有助于解释利木赞中进行的GWAS。
更新日期:2020-09-12
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