ABSTRACT
Growth performance and meat quality are important traits for the pig industry and consumers. Adipose tissue is the main site at which fat storage and fatty acid synthesis occur. Therefore, we combined high-throughput transcriptomic sequencing in adipose and muscle tissues with the quantification of corresponding phenotypic features using seven Chinese indigenous pig breeds and one Western commercial breed (Yorkshire). We obtained data on 101 phenotypic traits, from which principal component analysis distinguished two groups: one associated with the Chinese breeds and one with Yorkshire. The numbers of differentially expressed genes between all Chinese breeds and Yorkshire were shown to be 673 and 1056 in adipose and muscle tissues, respectively. Functional enrichment analysis revealed that these genes are associated with biological functions and canonical pathways related to oxidoreductase activity, immune response, and metabolic process. Weighted gene coexpression network analysis found more coexpression modules significantly correlated with the measured phenotypic traits in adipose than in muscle, indicating that adipose regulates meat and carcass quality. Using the combination of differential expression, QTL information, gene significance, and module hub genes, we identified a large number of candidate genes potentially related to economically important traits in pig, which should help us improve meat production and quality.
Subject(s)
Adipose Tissue/metabolism , Lipid Metabolism/physiology , Muscle, Skeletal/metabolism , Adipose Tissue/growth & development , Animals , Gene Expression Profiling , Genes/genetics , Genes/physiology , Lipid Metabolism/genetics , Muscle, Skeletal/growth & development , Phenotype , Principal Component Analysis , Quantitative Trait, Heritable , Swine/genetics , Swine/metabolism , Transcriptome/genetics , Transcriptome/physiologyABSTRACT
One genome and 12 Nsp2 genes of porcine reproductive and respiratory syndrome virus (PRRSV), isolated from southwestern China during 2009-2010, were sequenced and analyzed. The whole genome comparison analysis revealed that SCwhn09CD is a North American-type PRRSV with separate 30aa deletion in Nsp2 gene, and its sequence highly identical to highly pathogenic PRRSV (HP-PRRSV) outbreak in 2006 in almost half area of China. However, an extra 7aa deletion was detected in its Nsp2 coding region. Based on the phylogenetic analysis of Nsp2 gene, all the 12 viruses were grouped into North American-type PRRSV, but two in classical-PRRSV (C-PRRSV) subcluster without typical 30aa deletion and ten in HP-PRRSV subcluster with the signature deletion. In addition, many nucleotide substitutions were found in all 12 Nsp2 genes and extra three novel deletions were identified in three out of ten HP-PRRSV. Combining the above data, it may be concluded that: (1) HP-PRRSV and C-PRRSV co-existed in the local pig farms and the majority of the viruses is HR-PRRSV, and (2) the HR-PRRSV continues to undergo its genomic divergence although it does not outbreak in large-scale in recent years. Therefore, continuous surveillance on PRRSV is necessary for the controlling of the virus in this region.
Subject(s)
Genome, Viral , Porcine respiratory and reproductive syndrome virus/genetics , Porcine respiratory and reproductive syndrome virus/isolation & purification , RNA, Viral/isolation & purification , Amino Acid Sequence , Animals , China , Cloning, Molecular , Gene Deletion , Genetic Variation , Molecular Sequence Data , Open Reading Frames , Phylogeny , RNA, Viral/genetics , Sequence Alignment , Sequence Analysis, DNA , Sus scrofa/virologyABSTRACT
Epitope-based vaccines designed to induce cellular immune response and antibody responses specific for infectious bronchitis virus (IBV) are being developed as a means for increasing vaccine potency. In this study, we selected seven epitopes from the spike (S1), spike (S2), and nucleocapsid (N) protein and constructed a multi-epitope DNA vaccine. The 7-day-old chickens were immunized intramuscularly with multi-epitope DNA vaccine encapsulated by liposome and boosted two weeks later, and were challenged by virulent IBV strain five weeks post booster. The results showed that multi-epitope DNA vaccine led to a dramatic augmentation of humoral and cellular responses, and provided up to 80.0% rate of immune protection. The novel immunogenic chimeric multi-epitope DNA vaccine revealed in this study provided a new candidate target for IBV vaccine development.
