The poultry industry occupies an important position in the provision of animal protein. Recently, next generation sequencing technology (RNA-Seq) has become available as a powerful tool to investigate transcriptional profiles for gene expression analysis of many organisms. The main use of RNA-Seq in agriculture species are focusing on finding the immune related genes or pathways by comparison of the whole transcriptome following pathogen challenge. Alternative splicing (AS) is the major fundamental mechanism generating the protein diversity and regulating the gene expression in eukaryotic organism. Identifying genes that are differentially spliced between two groups of RNAsequencing samples is interesting subject in transcriptome with next-generation sequencing technology in this study used RNA sequencing to comparison isoforms of two breeds. A total of 64,819 transcripts were identified by aligning sequence reads to genome among the evaluated isoforms for expression analysis, 310 were significantly differentially expressed between two breeds, including 251 up-regulated and 59 down-regulated. The KEGG results of up regulated isoforms showed that that no pathway was found significantly different (FDR ≤ 0.05). However, enrichment analysis suggested that seven were over-represented (P-value ≤ 0.05) within the up regulated isoforms. Only one of them functionally related to immune system, natural killer cell mediated cytotoxicity. The results showed genes which are breed-specific expression and the comparative transcriptome analysis help to understand the difference of genetic mechanism.

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