A comparative functional genomic approach to unravel the genetic and genomic architecture of tail length in pigs and sheep based on a unified selection experiment design

本研究的主要目的是分析猪和羊这两个畜种的尾长的遗传和基因组结构。结果对于评估短尾的繁殖潜力，作为常规尾巴停靠做法的替代方案，以及避免尾巴咬伤、尾部损伤和与卫生有关的尾部疾病至关重要。我们在猪和羊中的资源模型群体的初步结果表明，尽管在其他动物物种中报道了额外的单基因机制，但该性状具有一般的数量多基因结构。因此，我们将在这两个物种中建立统一的选择和交配实验，结合先进的表型分析方案，以揭示该性状假定的一般数量基础，并使用功能比较基因组学方法识别跨物种的潜在单基因变异。因此，我们的目标是利用全基因组重测序来识别保守的和物种特有的因果变异和参与性状形成的QTL。最终，我们打算推断导致不同物种的尾巴长度、尾巴异常和尾巴损伤的基因组机制。目前的研究为正在进行的研究提供了巨大的潜力，即开发直接的基因测试(针对尾巴异常，包括完全尾巴丢失)和/或对尾巴长度的基因组育种价值估计，也适用于其他物种。预期的发现可能有助于通过繁殖来持续改善这两个牲畜物种的动物福利。然而，潜在的多效性效应对其他育种目标性状的负面影响需要得到解决。因此，表型和遗传与重要的经济性能以及功能性状的相关性将在增强的数量遗传框架(即结构方程模型)中得到推断。

The main objective is to analyze the genetic and genomic architecture of tail length in the livestock species pig and sheep. Results are imperative to assess the breeding potential on short tails, as an alternative for routine tail docking practices, and to avoid tail biting, tail lesions and hygiene related tail diseases. Preliminarily results from our own resource model populations in pig and sheep indicate a general quantitative polygenic structure of the trait, despite additional monogenic mechanisms as reported in other animal species. Consequently, we will establish a unified selection and mating experiment in both species, combined with an advanced phenotyping protocol to unravel the postulated general quantitative basis of the trait, as well as to identify potential monogenic variants across species using a functional comparative genomics approach. Hence, we aim to identify conserved and species-specific causal variants and QTL involved in the formation of the trait using whole genome resequencing. Ultimately, we intend to infer genomic mechanisms contributing to tail length, tail abnormalities and tail lesions across species. The current study offers great potential for ongoing research, i.e., for the development of a direct gene tests (for tail abnormalities including completely tail losses) and/or genomic breeding value estimations for tail length, also in other species. The expected findings could contribute to a sustainable animal welfare improvement for both livestock species through breeding. However, potential pleiotropic effects negatively affecting other breeding goal traits need to be addressed. Therefore, phenotypic and genetic correlations with economically important performance as well as functional traits will be inferred in an enhanced quantitative genetic framework (i.e., structural equation modelling).