Sequence-based Analysis of Selection during Domestication and Improvement of Chicken

鸡驯化和改良过程中基于序列的选择分析

• 批准号: 254651688
• 负责人: Dr. Saber Qanbari
• 金额: --
• 依托单位: Institut für Nutztiergenetik
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2014
• 资助国家: 德国
• 起止时间: 2013-12-31 至 2017-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/254651688?language=en
• 关键词: Sequence; based; Analysis; Selection; during

Domestication followed by breed formation and massive selection has likely left detectable signatures in the genome of modern chickens. Since the wild Red Jungle Fowl (RJF, Gallus gallus gallus), the primary progenitor of chicken is still available, a post versus pre-domestication comparison of genomic patterns is possible. This facilitates identifying so-called domestication genes that have been primary targets of selective forces during domestication. It also allows testing the hypothesis that domestication and subsequent breeding has led to relaxation of negative selection on particular genes and pathways. To this purpose, we will re-sequence 30 birds from three populations (one layer line, one broiler line, RJF), respectively. Four major objectives are addressed: (1) we will analyze the genome-wide pattern of demographic history to infer major evolutionary switches, (2) we will test for evidence of cases where negative selection on functional processes has been relaxed during domestication or formation of breeding lines (3) we will construct a high-resolution map of signatures left by positive selection, and (4) we will unravel the extent to which balancing selection has influenced chicken genome variability. We will employ cutting edge methodologies and extensive simulations in collaboration with some pioneering labs in the field of population genomics. The novelties are three fold: First, re-sequencing individual birds on a population scale provides the full data profile of each individual (e.g., allelic, genotypic and haplotypic states) that were not available genome-wide so far. This allows genomic scans with highest resolution and fairly free of ascertainment bias, and results can be validated across multiple methods and/or sources of information. Second, a sizable population of RJF will be sequenced that can be used to verify, correct and where necessary extend the reference sequence, improving the basis for any future population based studies of chicken genome. Third, this project takes first steps towards unraveling footprints left by adaptive forces other than positive selection (e.g. relaxed negative and balancing selection) in the chicken genome. The expected results will substantially advance our knowledge of adaptive biology and will contribute to an in-depth understanding of the processes underlying domestication and subsequent human-driven breed formation of modern chickens as a model for farm animal domestication.

驯化之后的品种形成和大规模选择可能会在现代鸡的基因组中留下可检测的标记。由于野生红原鸡（RJF，原鸡），鸡的主要祖先仍然可用，驯化后与驯化前的基因组模式比较是可能的。这有助于识别所谓的驯化基因，这些基因是驯化过程中选择力的主要目标。它也允许测试的假设，驯化和随后的育种导致放松消极选择特定的基因和途径。为此，我们将分别对来自三个群体（一个蛋鸡系，一个肉鸡系，RJF）的30只鸡进行重新测序。涉及四个主要目标：（1）我们将分析人口统计学历史的全基因组模式，以推断主要的进化开关，（2）我们将测试在驯化或育种系形成过程中功能过程的负选择已经放松的情况下的证据，（3）我们将构建正选择留下的签名的高分辨率地图，以及（4）我们将揭示平衡选择对鸡基因组变异性的影响程度。我们将采用尖端的方法和广泛的模拟与一些先锋实验室在人口基因组学领域的合作。新颖性有三个方面：首先，在种群规模上对个体鸟类重新测序提供了每个个体的完整数据概况（例如，等位基因、基因型和单倍型状态），其迄今为止在全基因组范围内不可用。这使得基因组扫描具有最高的分辨率和相当自由的确定偏差，结果可以通过多种方法和/或信息来源进行验证。其次，将对相当大的RJF群体进行测序，以用于验证、校正和必要时扩展参考序列，从而为未来任何基于群体的鸡基因组研究奠定基础。第三，该项目迈出了第一步，揭开了鸡基因组中除了正选择（例如放松的负选择和平衡选择）之外的适应力留下的足迹。预期的结果将大大推进我们的适应性生物学知识，并将有助于深入了解驯化和随后的人类驱动的现代鸡作为农场动物驯化模式的品种形成的过程。