Background Porcine epidemic diarrhea virus (PEDV) is a causative agent of serious viral enteric disease in suckling pigs. Such diseases cause considerable economic losses in the global swine industry. Enhancing our knowledge of PEDV-induced transcriptomic responses in host cells is imperative to understanding the molecular mechanisms involved in the immune response. Here, we analyzed the transcriptomic profile of intestinal porcine epithelial cell line J2 (IPEC-J2) after infection with a classical strain of PEDV to explore the host response. Results In total, 854 genes were significantly differentially expressed after PEDV infection, including 716 upregulated and 138 downregulated genes. Functional annotation analysis revealed that the differentially expressed genes were mainly enriched in the influenza A, TNF signaling, inflammatory response, cytokine receptor interaction, and other immune-related pathways. Next, the putative promoter regions of the 854 differentially expressed genes were examined for the presence of transcription factor binding sites using the MEME tool. As a result, 504 sequences (59.02%) were identified as possessing at least one binding site of signal transducer and activator of transcription (STAT), and five STAT transcription factors were significantly induced by PEDV infection. Furthermore, we revealed the regulatory network induced by STAT members in the process of PEDV infection. Conclusion Our transcriptomic analysis described the host genetic response to PEDV infection in detail in IPEC-J2 cells, and suggested that STAT transcription factors may serve as key regulators in the response to PEDV infection. These results further our understanding of the pathogenesis of PEDV.

Structural variants (SVs) represent essential forms of genetic variation, and they are associated with various phenotypic traits in a wide range of important livestock species. However, the distribution of SVs in the pig genome has not been fully characterized, and the function of SVs in the economic traits of pig has rarely been studied, especially for most domestic pig breeds. Meishan pig is one of the most famous Chinese domestic pig breeds, with excellent reproductive performance. Here, to explore the genome characters of Meishan pig, we construct an SV map of porcine using whole-genome sequencing data and report 33,698 SVs in 305 individuals of 55 globally distributed pig breeds. We perform selective signature analysis using these SVs, and a number of candidate variants are successfully identified. Especially for the Meishan pig, 64 novel significant selection regions are detected in its genome. A 140-bp deletion in the Indoleamine 2,3-Dioxygenase 2 (IDO2) gene, is shown to be associated with reproduction traits in Meishan pig. In addition, we detect two duplications only existing in Meishan pig. Moreover, the two duplications are separately located in cytochrome P450 family 2 subfamily J member 2 (CYP2J2) gene and phospholipase A2 group IVA (PLA2G4A) gene, which are related to the reproduction trait. Our study provides new insights into the role of selection in SVs' evolution and how SVs contribute to phenotypic variation in pigs.

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ABSTRACT. Wheat WAG-1 is a C-class MADS-box gene, which is orthologous to AGAMOUS in Arabidopsis. In this study, we report the cloning, characterization, and expression patterns of WAG-1 in the pistillody mutant HTS-1 and its sib-line CSTP. The cDNA of WAG-1 was found to be 765 bp in length, which was equal to the length of its open reading frame, encoding 254 amino acids. The location of WAG-1 revealed that it has three homologous genes from the short arm of chromosome 1A, 1B, and 1D. Their genomic sequences were determined to be 5864, 6454, and 6447 bp long, respectively, and possessed seven exons and six introns. Young spikes from HTS-1 contained higher levels of WAG-1 transcript than did those from CSTP, and the transcript levels in the young spikes (7-10 mm in length) of HTS-1 increased 3.3-fold relative to those of the CSTP line. The transcript level in the pistil and pistil-like stamens of HTS-1 was over 2-fold higher than that in the 12456 Q.H. Wang et al. ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 12455-12465 (2015) stamens of CSTP, and expression in the pistil-like stamens of HTS-1 was slightly higher than that in its pistils. These data provide a basis for future research into the function of WAG-1, and offer further insight into the molecular mechanism of the pistillody mutation in common wheat.

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