Phosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota. Among the 59 bacterial genera examined, 24 showed a significant heritability (nominal p ≤ 0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host’s quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host’s quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs. Our results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host’s quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.

中文翻译：

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回肠微生物群的组成是日本鹌鹑 (Coturnix japonica) 宿主基因组与磷利用和其他效率性状之间的中介

磷是所有生物体的必需营养素，目前由于其全球稀缺性、排泄物中磷对环境的影响以及由于其以植酸盐形式储存在植物中而导致的低消化率，因此成为备受关注的焦点。在家禽中，磷的利用受回肠微生物群组成和宿主遗传的影响。在我们的研究中，我们分析了宿主遗传学对日本鹌鹑回肠微生物群组成的影响以及回肠细菌属的相对丰度与磷利用和相关数量性状的关系。使用 4k 全基因组单核苷酸多态性 (SNP) 对 758 只鹌鹑的 F2 杂交进行基因分型，并使用靶扩增子测序表征回肠微生物群的组成。估计细菌属的相对丰度的遗传力，并对可遗传的属进行宿主的数量性状基因座（QTL）连锁作图。使用结构方程模型估计细菌属和数量性状之间的表型和遗传相关性以及递归关系。基于宿主基因组和回肠微生物群组成的可遗传部分，应用基因组最佳线性无偏预测 (GBLUP) 和微生物 (M)BLUP 全基因组选择方法来评估提高磷利用率的育种可行性。在检查的 59 个细菌属中，24 个显示出显着的遗传力（标称 p ≤ 0.05），范围从 0.04 到 0.17。对于这些属，绘制了六个全基因组显着 QTL。发现了显着的递归效应，这支持了通过鹌鹑回肠中的微生物群组成对宿主数量性状的间接宿主遗传影响。交叉验证的微生物和基因组预测准确度证实了微生物组成和宿主遗传学对宿主数量性状的强烈影响，因为基于可遗传微生物群介导的性状成分的 GBLUP 准确度与基于基因组的传统 GBLUP 准确度相似范围的 SNP。我们的研究结果揭示了宿主遗传学对回肠微生物群组成的显着影响，并证实宿主遗传学和回肠微生物群的组成对宿主的数量性状有影响。这提供了基于宿主基因组和回肠微生物群组成的可遗传部分进行育种以提高磷利用的可能性。