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到的特征。由于野生红色丛林鸡(RJF)，鸡的主要祖先仍然存在，因此有可能进行驯化后和驯化前的基因组模式比较。这有助于识别所谓的驯化基因，这些基因在驯化过程中一直是选择性力量的主要目标。它还允许检验这样一种假设，即驯化和随后的育种导致了特定基因和途径上的负面选择的放松。为此，我们将对来自三个群体(一个蛋鸡品系，一个肉鸡品系，RJF)的30只鸡进行重新排序。四个主要目标是：(1)我们将分析人口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上的负选择被放松的证据，(3)我们将构建正选择留下的高分辨率标记图，以及(4)我们将揭示平衡选择对鸡基因组变异的影响程度。我们将与人口基因组领域的一些开创性实验室合作，采用尖端方法和广泛的模拟。其新颖性有三个方面：首先，在种群规模上对单个鸟类进行重新测序，提供了迄今为止尚未在全基因组范围内获得的每个个体的完整数据概况(例如，等位基因、基因类型和单倍型状态)。这使得基因组扫描具有最高的分辨率，并且几乎没有确证偏差，结果可以通过多种方法和/或信息源进行验证。其次，将对相当大的RJF群体进行测序，可用于验证、纠正并在必要时扩展参考序列，为未来任何基于群体的鸡基因组研究奠定基础。第三，这个项目朝着揭开鸡基因组中除正向选择(例如放松的负选择和平衡选择)之外的适应性力量留下的足迹迈出了第一步。预期的结果将极大地促进我们对适应生物学的了解，并有助于深入了解现代鸡的驯化和随后的人类驱动的品种形成的过程，作为农场动物驯化的模式。

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.