Detection of genomic signatures of recent selection in commercial broiler chickens.
Detection of genomic signatures of recent selection in commercial broiler chickens.
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DOI：
10.1186/s12863-016-0430-1
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发表时间：
2016-08-26
期刊：
影响因子：
2.9
通讯作者：
Abasht B
中科院分区：
文献类型：
--
作者：
Fu W;Lee WR;Abasht B
最近选择的基因组签名的鉴定可能有助于揭示因果多态性控制性状相关的近几十年的选择性育种的牲畜。在这项研究中，我们的目的是检测标记的最近选择商品肉鸡基因型信息的单核苷酸多态性（SNPs）。使用60 K SNP Illumina iSelect鸡阵列对来自五个商业纯种系（包括三个肉鸡父系（雄性）系和两个肉鸡母系（雌性）系）的总共565只鸡进行基因分型。为了检测最近选择的基因组特征，我们采用了两种基于群体比较的方法，即跨群体扩展单倍型纯合性（XP-EHH）和跨群体复合似然比（XP-EHH），并进一步分析结果，以发现多个纯种品系中最近选择的基因组区域。通过XP-EHH和XP-RFLP方法结果的一致性，在每个品系中总共检测到321个候选选择区域，跨越约1.45%的鸡基因组。为了尽量减少由于遗传漂变而导致的错误发现，在研究中，只有42个由2个或更多个纯种系共享的候选选择区域被认为是高置信度选择区域。在这42个区域中，20个区域为50 kb或更小，而4个区域大于0.5 Mb。在42个区域中共发现91个基因，其中19个区域仅包含1个或2个基因，9个区域位于基因沙漠。我们的研究结果提供了一个全基因组扫描最近的选择签名在五个纯种系的商业肉鸡。我们在多个品系中发现了几个用于最近选择的候选基因，如SOX 6（性别决定区Y盒6）和cTR（甲状腺激素受体β）。由于这些基因在鸡的生长、发育和繁殖中起着重要作用，它们可能是最近才被选择的。此外，我们的研究结果表明，在一些候选地区，相同或相反的等位基因已在多个行最近的选择。大多数候选基因的选择区域是新的，因此，他们应该是巨大的兴趣，为未来的研究到性状的遗传结构相关的现代肉鸡育种。本文的在线版本（doi：10.1186/s12863-016-0430-1）包含补充材料，可供授权用户使用。
Identification of the genomic signatures of recent selection may help uncover causal polymorphisms controlling traits relevant to recent decades of selective breeding in livestock. In this study, we aimed at detecting signatures of recent selection in commercial broiler chickens using genotype information from single nucleotide polymorphisms (SNPs). A total of 565 chickens from five commercial purebred lines, including three broiler sire (male) lines and two broiler dam (female) lines, were genotyped using the 60K SNP Illumina iSelect chicken array. To detect genomic signatures of recent selection, we applied two methods based on population comparison, cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio (XP-CLR), and further analyzed the results to find genomic regions under recent selection in multiple purebred lines. A total of 321 candidate selection regions spanning approximately 1.45 % of the chicken genome in each line were detected by consensus of results of both XP-EHH and XP-CLR methods. To minimize false discovery due to genetic drift, only 42 of the candidate selection regions that were shared by 2 or more purebred lines were considered as high-confidence selection regions in the study. Of these 42 regions, 20 were 50 kb or less while 4 regions were larger than 0.5 Mb. In total, 91 genes could be found in the 42 regions, among which 19 regions contained only 1 or 2 genes, and 9 regions were located at gene deserts. Our results provide a genome-wide scan of recent selection signatures in five purebred lines of commercial broiler chickens. We found several candidate genes for recent selection in multiple lines, such as SOX6 (Sex Determining Region Y-Box 6) and cTR (Thyroid hormone receptor beta). These genes may have been under recent selection due to their essential roles in growth, development and reproduction in chickens. Furthermore, our results suggest that in some candidate regions, the same or opposite alleles have been under recent selection in multiple lines. Most of the candidate genes in the selection regions are novel, and as such they should be of great interest for future research into the genetic architecture of traits relevant to modern broiler breeding. The online version of this article (doi:10.1186/s12863-016-0430-1) contains supplementary material, which is available to authorized users.
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