Functional signals and hologenomic selection for P utilisation and related efficiency traits in two contrasting high-yielding laying hen strains

在最近的一项研究中，我们进行了数量遗传分析的磷（P）利用的F2杂交实验设计组成的约900日本鹌鹑。我们估计狭义遗传率为14%。用4K SNP标记对个体进行基因分型，并收集来自回肠的管腔样品用于微生物群分析。本项目的总体目标是更好地了解研究设计中观察到的P利用率，考虑鹌鹑遗传学，鹌鹑回肠微生物群以及这两个组成部分之间的相互作用。具体而言，我们的目标是测试以下假设。(i)鹌鹑磷利用率的变异是一个可遗传的性状，受数量少、效应大的QTL控制。(ii)磷利用率的变化部分是由鹌鹑回肠中的微生物群落驱动的。(iii)回肠中的微生物群落是可遗传的宿主性状，其可用于培育具有改善的P利用的个体。这些假设将通过使用基因组和微生物混合线性模型进行分析，其中包括QTL连锁和关联作图，基因组和微生物方差分量估计，以及微生物对磷利用的预测。将使用16S rRNA扩增子测序技术分析微生物群。结果将被解释为通过靶向育种提高家禽的P利用率，靶向育种作用于宿主的观察到的P利用率水平，或作用于宿主微生物组，以选择关于P利用率的优化微生物群，或作用于两者。将在另一个研究股项目中进行更广泛的解释，其中使用生物信息学工具，并考虑到该研究股其他项目的结果。

In a recent study, we conducted quantitative-genetic analyses of Phosphor (P) utilization in an F2 cross experimental design consisting of about 900 Japanese quails. We estimated a narrow sense heritability of 14 percent. The individuals were genotyped with 4K SNP markers and lumen samples from the ileum were collected for microbiota analyses. The overall aim of the present project is to obtain a better understanding of the P utilization observed in the study design considering the quail genetics, the quail ileum microbiota and the interplay between these two components. In particular, we aim to test the following hypotheses. (i) Variation of P utilization in quails is a heritable trait, which is controlled by few quail QTL with large effects. (ii) Variation of P utilization is partly driven by the microbial community in the ileum of the quail. (iii) The microbial community in the ileum is a heritable host trait that can be used for breeding individuals with improved P utilization. These hypotheses will be analyzed by using genomic and microbial mixed linear models, which include QTL linkage and association mapping, genomic and microbial variance component estimation, and microbial prediction of P-Utilization. The microbiota will be analyzed using 16S rRNA amplicon sequencing technology. The results will be interpreted with respect to improve P utilization in poultry by targeted breeding, which acts either on the level of the observed P utilization of the host, or on the host microbiome in order to select for an optimized microbiota with respect to P utilization, or on both. A wider interpretation, which uses bioinformatics tools and considers the results from other projects of this Research Unit into account, will be done in another Research Unit project.