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

驯化之后的品种形成和大规模选择可能在现代鸡的基因组中留下了可检测的特征。由于鸡的主要祖先野生红丛林鸡（RJF, Gallus Gallus Gallus）仍然可用，因此可以对驯化后与驯化前的基因组模式进行比较。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。它还允许测试驯化和随后的繁殖导致特定基因和途径上的负选择放松的假设。为此，我们将分别对3个种群（1个蛋鸡系、1个肉鸡系、RJF）的30只鸡进行重新测序。研究的四个主要目标是：(1)我们将分析人口统计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形成育种系期间功能过程中的负选择被放松的情况的证据；(3)我们将构建正选择留下的特征的高分辨率地图；(4)我们将揭示平衡选择对鸡基因组变异性的影响程度。我们将采用最先进的方法，并与人口基因组学领域的一些先驱实验室合作进行广泛的模拟。其新颖之处在于三个方面：首先，在种群规模上对单个鸟类进行重新测序，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），这是迄今为止无法在全基因组范围内获得的。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，结果可以跨多种方法和/或信息来源进行验证。其次，将对相当数量的RJF种群进行测序，可用于验证、校正并在必要时扩展参考序列，为未来任何基于种群的鸡基因组研究奠定基础。第三，该项目为解开鸡基因组中除积极选择（如放松的消极选择和平衡选择）之外的适应性力量留下的足迹迈出了第一步。预期的结果将大大提高我们对适应性生物学的认识，并将有助于深入了解驯化和随后人类驱动的现代鸡品种形成的过程，作为农场动物驯化的模型。

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.