Truong Anh Duc, Hong Yeong Ho, Lillehoj Hyun S
Animal Biosciences and Biotechnology Laboratory, Agricultural Research Services, U. S. Department of Agriculture, Beltsville, MD 20705, USA .
Asian-Australas J Anim Sci. 2015 Oct;28(10):1496-511. doi: 10.5713/ajas.15.0143.
The study aimed to compare the necrotic enteritis (NE)-induced transcriptome differences between the spleens of Marek's disease resistant chicken line 6.3 and susceptible line 7.2 co-infected with Eimeria maxima/Clostridium perfringens using RNA-Seq. Total RNA from the spleens of two chicken lines were used to make libraries, generating 42,736,296 and 42,617,720 usable reads, which were assembled into groups of 29,897 and 29,833 mRNA genes, respectively. The transcriptome changes were investigated using the differentially expressed genes (DEGs) package, which indicated 3,255, 2,468 and 2,234 DEGs of line 6.3, line 7.2, and comparison between two lines, respectively (fold change ≥2, p<0.01). The transcription levels of 14 genes identified were further examined using qRT-PCR. The results of qRT-PCR were consistent with the RNA-seq data. All of the DEGs were analysed using gene ontology terms, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the DEGs in each term were found to be more highly expressed in line 6.3 than in line 7.2. RNA-seq analysis indicated 139 immune related genes, 44 CD molecular genes and 150 cytokines genes which were differentially expressed among chicken lines 6.3 and 7.2 (fold change ≥2, p<0.01). Novel mRNA analysis indicated 15,518 novel genes, for which the expression was shown to be higher in line 6.3 than in line 7.2 including some immune-related targets. These findings will help to understand host-pathogen interaction in the spleen and elucidate the mechanism of host genetic control of NE, and provide basis for future studies that can lead to the development of marker-based selection of highly disease-resistant chickens.
本研究旨在利用RNA测序技术比较马立克氏病抗性鸡品系6.3和易感鸡品系7.2在同时感染巨型艾美耳球虫/产气荚膜梭菌后，脾脏中坏死性肠炎（NE）诱导的转录组差异。从两个鸡品系的脾脏中提取总RNA用于构建文库，分别产生了42,736,296和42,617,720条可用读数，这些读数分别组装成29,897和29,833个mRNA基因组。使用差异表达基因（DEG）软件包研究转录组变化，结果表明品系6.3、品系7.2以及两个品系之间比较的DEG分别有3,255个、2,468个和2,234个（折叠变化≥2，p<0.01）。使用qRT-PCR进一步检测了鉴定出的14个基因的转录水平。qRT-PCR结果与RNA测序数据一致。所有DEG均使用基因本体术语、京都基因与基因组百科全书（KEGG）数据库进行分析，发现每个术语中的DEG在品系6.3中的表达均高于品系7.2。RNA测序分析表明，在鸡品系6.3和7.2之间有139个免疫相关基因、44个CD分子基因和150个细胞因子基因差异表达（折叠变化≥2，p<0.01）。新mRNA分析表明有15,518个新基因，其在品系6.3中的表达高于品系7.2，包括一些免疫相关靶点。这些发现将有助于了解脾脏中的宿主-病原体相互作用，阐明宿主对NE的遗传控制机制，并为未来能够导致开发基于标记的高抗病性鸡选择方法的研究提供基础。
