Genome-wide association studies (GWAS) based on high throughput SNP genotyping technologies open a broad avenue for exploring genes associated with milk production traits in dairy cattle. Motivated by pinpointing novel quantitative trait nucleotide (QTN) across Bos Taurus genome, the present study is to perform GWAS to identify genes affecting milk production traits using current state-of-the-art SNP genotyping technology, i.e., the Illumina BovineSNP50 BeadChip. In the analyses, the five most commonly evaluated milk production traits are involved, including milk yield (MY), milk fat yield (FY), milk protein yield (PY), milk fat percentage (FP) and milk protein percentage (PP). Estimated breeding values (EBVs) of 2,093 daughters from 14 paternal half-sib families are considered as phenotypes within the framework of a daughter design. Association tests between each trait and the 54K SNPs are achieved via two different analysis approaches, a paternal transmission disequilibrium test (TDT)-based approach (L1-TDT) and a mixed model based regression analysis (MMRA). In total, 105 SNPs were detected to be significantly associated genome-wise with one or multiple milk production traits. Of the 105 SNPs, 38 were commonly detected by both methods, while four and 63 were solely detected by L1-TDT and MMRA, respectively. The majority (86 out of 105) of the significant SNPs is located within the reported QTL regions and some are within or close to the reported candidate genes. In particular, two SNPs, ARS-BFGL-NGS-4939 and BFGL-NGS-118998, are located close to the DGAT1 gene (160bp apart) and within the GHR gene, respectively. Our findings herein not only provide confirmatory evidences for previously findings, but also explore a suite of novel SNPs associated with milk production traits, and thus form a solid basis for eventually unraveling the causal mutations for milk production traits in dairy cattle.

Hepatitis E virus (HEV) causes both endemic and epidemic human hepatitis by fecal-oral transmission in many parts of the world. Zoonotic transmission of HEV from animals to humans has been reported. Due to the lack of an efficient cell culture system, the molecular mechanisms of HEV infection remain largely unknown. In this study, we found that HEV replication in hepatoma cells inhibited poly (

By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas and studied tissue specificity of genes in cattle. We demonstrated that tissue-specific genes significantly reflected the tissue-relevant biology, showing distinct promoter methylation and evolution patterns (e.g., brain-specific genes evolve slowest, whereas testis-specific genes evolve fastest). Through integrative analyses of those tissue-specific genes with large-scale genome-wide association studies, we detected relevant tissues/cell types and candidate genes for 45 economically important traits in cattle, including blood/immune system (e.g., CCDC88C) for male fertility, brain (e.g., TRIM46 and RAB6A) for milk production, and multiple growth-related tissues (e.g., FGF6 and CCND2) for body conformation. We validated these findings by using epigenomic data across major somatic tissues and sperm. Collectively, our findings provided novel insights into the genetic and biological mechanisms underlying complex traits in cattle, and our transcriptome atlas can serve as a primary source for biological interpretation, functional validation, studies of adaptive evolution, and genomic improvement in livestock.

Tumor initiation and growth depend on its microenvironment in which cancer-associated fibroblasts (CAFs) in tumor stroma play an important role. Prostaglandin E2 (PGE2) and interleukin (IL)-6 signal pathways are involved in the crosstalk between tumor and stromal cells. However, how PGE2-mediated signaling modulates this crosstalk remains unclear. Here, we show that microRNA (miR)-149 links PGE2 and IL-6 signaling in mediating the crosstalk between tumor cells and CAFs in gastric cancer (GC). miR-149 inhibited fibroblast activation by targeting IL-6 and miR-149 expression was substantially suppressed in the CAFs of GC. miR-149 negatively regulated CAFs and their effect on GC development both in vitro and in vivo. CAFs enhanced epithelial-to-mesenchymal transition (EMT) and the stem-like properties of GC cells in a miR-149-IL-6-dependent manner. In addition to IL-6, PGE2 receptor 2 (PTGER2/EP2) was revealed as another potential target of miR-149 in fibroblasts. Furthermore, H. pylori infection, a leading cause of human GC, was able to induce cyclooxygenase-2 (COX-2)/PGE2 signaling and to enhance PGE2 production, resulting in the hypermethylation of miR-149 in CAFs and increased IL-6 secretion. Our findings indicate that miR-149 mediates the crosstalk between tumor cells and CAFs in GC and highlight the potential of interfering miRNAs in stromal cells to improve cancer therapy.