Supplementary file 8 from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.

提高单胃动物对植酸（phytates）与矿质磷（mineral phosphorus, P）的利用效率，对保护有限的矿质磷资源、缓解环境污染具有重要意义。为鉴定与磷利用（phosphorus utilization, PU）相关的通路并筛选候选基因，本研究对482只日本鹌鹑中77个和80个性状依赖性表达的微小RNA（microRNAs, miRNAs）及信使RNA（messenger RNAs, mRNAs）的基因组遗传力进行了估算，并检测了表达数量性状位点（expression quantitative trait loci, eQTL）。总计104个miRNA表达数量性状位点（microRNA expression quantitative trait loci, miR-eQTL）与单核苷酸多态性（single nucleotide polymorphisms, SNPs）标记相关（错误发现率（false discovery rate, FDR）<10%），其中包含8个微小RNA的41个eQTL。类似地，在5%的FDR阈值下共鉴定出944个mRNA表达数量性状位点（mRNA-eQTL），其中573个为36个信使RNA的顺式eQTL（cis-eQTL）。微小RNA与信使RNA的高表达遗传力与极显著的eQTL结果相契合。将同批动物的表型数据、转录组数据与微生物组数据整合后，鉴定出与PU相关的遗传调控信使RNA及微小RNA转录本（SMAD3、CAV1、ENNPP6、ATP2B4、miR-148a-3p、miR-146b-5p、miR-16-5p、miR-194、miR-215-5p、miR-199-3p、miR-1388a-3p）以及微生物（Candidatus Arthromitus、Enterococcus）。本研究结果从表达的遗传调控与遗传模式，以及与微生物组组分的关联角度，为阐明信使RNA与微小RNA在宿主肠道组织功能中的作用提供了新见解，而这些功能参与了PU及其他相关性状的调控。