Truong Anh Duc, Hong Yeojin, Ban Jihye, Park Boyeong, Hoang Thanh C, Hong Yeong H, Lillehoj Hyun S
Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea.
Animal Biosciences and Biotechnology Laboratory, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD 20705, USA.
J Poult Sci. 2017 Apr 25;54(2):121-133. doi: 10.2141/jpsa.0160053.
We identified and evaluated differentially expressed genes (DEGs) by RNA-Sequencing (RNA-Seq) in the intestinal mucosa of two Fayoumi chicken lines, M5.1 and M15.2, that are affected by necrotic enteritis (NE); these chicken lines share the same genetic background but have different major histocompatibility complexes. RNA-Seq generated over 49 and 40 million reads for lines M5.1 and M15.2, respectively. The alignment of these sequences with the genome database revealed the expression of more than 14,500 genes in two lines, among which 581, 1270, and 1140 DEGs were detected when lines M15.2 and M5.1 were compared with the control and compared between each other. The analysis of all DEGs using the gene ontology database revealed annotations for 111 biological processes, 32 cellular components, and 17 molecular functions, and KEEG pathway mapping indicated that the DEGs were primarily involved in immunity, responses to various stimuli, and signal transduction. In addition, we analyzed 183 innate immune genes that were differentially expressed in NE-induced chicken lines, including 46 CD molecular genes, 89 immune-related genes, and 13 -defensin genes with 3 lineage-specific duplications. Taken together, the transcriptional profiles showed that line M5.1 was more resistant to NE than line M15.2 and that differential gene expression patterns were associated with host genetic differences in resistance to NE. qRT-PCR and RNA-Seq analyses showed that all the genes examined had similar responses to NE (correlation coefficient R=0.84 to 0.88, <0.01) in both lines. To the best of our knowledge, this is the first study that describes NE-induced DEGs using RNA-seq in two lines with different levels of susceptibility to NE. These results will lead to increased insights on NE disease resistance mechanisms and the role of host genes in the control of the host immune response.
我们通过RNA测序（RNA-Seq）在受坏死性肠炎（NE）影响的两个法尤米鸡品系M5.1和M15.2的肠黏膜中鉴定并评估了差异表达基因（DEG）；这两个鸡品系具有相同的遗传背景，但主要组织相容性复合体不同。RNA-Seq分别为M5.1和M15.2品系生成了超过4900万和4000万条读数。这些序列与基因组数据库的比对揭示了两个品系中超过14500个基因的表达，其中当将M15.2和M5.1品系与对照进行比较以及相互比较时，分别检测到581、1270和1140个DEG。使用基因本体数据库对所有DEG进行分析，揭示了111个生物学过程、32个细胞成分和17个分子功能的注释，KEGG通路映射表明DEG主要参与免疫、对各种刺激的反应和信号转导。此外，我们分析了在NE诱导的鸡品系中差异表达的183个先天免疫基因，包括46个CD分子基因、89个免疫相关基因和13个具有3个谱系特异性重复的防御素基因。综上所述，转录谱表明M5.1品系比M15.2品系对NE更具抗性，并且差异基因表达模式与宿主对NE抗性的遗传差异相关。qRT-PCR和RNA-Seq分析表明，两个品系中所有检测的基因对NE都有相似的反应（相关系数R = 0.84至0.88，<0.01）。据我们所知，这是第一项使用RNA-seq描述在对NE易感性不同的两个品系中NE诱导的DEG的研究。这些结果将有助于深入了解NE抗病机制以及宿主基因在控制宿主免疫反应中的作用。
