Whole-genome resequencing reveals loci under selection during chicken domestication
Whole-genome resequencing reveals loci under selection during chicken domestication
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DOI：
10.1038/nature08832
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发表时间：
2010-03-25
期刊：
影响因子：
64.8
通讯作者：
Andersson, Leif
中科院分区：
文献类型：
--
作者：
Rubin, Carl-Johan;Zody, Michael C.;Andersson, Leif
家畜是表型进化遗传研究的绝佳模型（1 - 3）。它们已经进化出对新环境——农场的遗传适应性，并且受到了人类强烈的定向选择，导致在形态、生理和行为方面出现了显著的表型变化。确定这些发展背后的遗传变化为遗传变异塑造表型多样性的一般机制提供了新的见解。在此，我们描述了利用大规模平行测序来识别有利等位基因的选择性清除以及在鸡（家鸡）驯化及其随后分化为肉鸡（用于产肉）和蛋鸡（用于产蛋）过程中起重要作用的候选突变。我们使用代表8种不同家鸡群体以及红原鸡（家鸡的主要野生祖先）的基因组DNA池，对鸡的基因组进行了44.5倍的覆盖测序（4）。我们报道了超过700万个单核苷酸多态性、近1300个缺失以及一些假定的选择性清除。在所有家鸡中发现的最显著的选择性清除之一发生在促甲状腺激素受体（TSHR）基因座，该基因座在脊椎动物的代谢调节和繁殖的光周期控制中起着关键作用。在肉鸡中检测到的一些选择性清除与生长、食欲和代谢调节相关的基因重叠。我们几乎没有发现功能缺失突变的选择在鸡驯化中起重要作用的证据，但我们检测到两个编码序列中的缺失，我们认为它们在功能上是重要的。这项研究直接应用于动物育种，并提高了家鸡作为生物医学研究模式生物的重要性。
Domestic animals are excellent models for genetic studies of phenotypic evolution(1-3). They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor(4). We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.