Supplementary tables and figures for "Integrated multi-RNA genomic analyses reveal candidate regulatory variants underlying bovine subclinical mastitis"

作者：Eveline Mengwi Ibeagha-Awemu, X F Zhao, mengqi wang, Faith Omonijo, Mario Laterrière, David Gagné · 发表于：Figshare · 年份：2026 · DOI：10.6084/m9.figshare.32682507.v1 · 研究领域：Biology、Genetics、Computational biology

This study characterize the regulatory architecture underlying bovine subclinical mastitis (S. aureus and S. chromogenes), SNP discovery, functional annotation, expression quantitative trait loci (eQTL), quantitative trait loci (QTL), multi-RNA hotspot analyses, and miRNA target-rewiring analyses. A total of 111,657 mRNA-, 6,191 lncRNA-, 225 snoRNA-, and 28 miRNA-associated SNPs and INDELs were identified.SC-associated variants - milk yield, clinical mastitis, body weight, and reproductive traits.SA-associated variants - milk production, udder conformation, fertility, and somatic cell score traitsMulti-RNA analyses identified overlapping regulatory SNPs shared among mRNAs, lncRNAs, snoRNAs, and miRNAs - associated with immune-related genes including CD37, DOCK2, PIK3CD, STAT2, PRKCB, IL2RA, FCGR3A, and CXCL8 and were enriched in NF-κB, Toll-like receptor, TNF, chemokine, cytokine–cytokine receptor interaction, and Staphylococcus aureus infection pathways.Chromosomal hotspot - CHR 23, 18, 11, 7, and 5 that were enriched for mastitis-, production-, and reproduction-related QTLsSNPs within mature miRNAs generated extensive target-network rewiring, with bta-miR-24-3p, bta-miR-2313, and bta-miR-1291 exhibiting the largest regulatory changes. Target loss in bta-miR-1291 and bta-miR-24-3p affected CATHL2, CATHL3, CATHL4, C1QB and C1S, linking these miRNAs to Staphylococcus aureus infection pathway.Target gain in bta0miR-24-3p and bta-miR-2313 support cellular adaptation, metabolic r...