Ghosh M, Sodhi S S, Song K-D, Kim J H, Mongre R K, Sharma N, Singh N K, Kim S W, Lee H K, Jeong D K
Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, 690-756, Korea.
Anim Genet. 2015 Jun;46(3):255-64. doi: 10.1111/age.12281. Epub 2015 Mar 6.
This study was carried out with the objective to investigate the differentially expressed genes (DEGs) between Jeju native pig (JNP) and Berkshire piglets. The RNA-Seq technique was used to investigate the transcriptomes in the fat, liver and longissimus dorsi muscle from these two breeds. Paired-end reads of the sequences that passed the quality filters were aligned to the Sus scrofa genome using tophat2 (v2.0.2). In this study, 65% of muscle, 20% of fat and 54% of liver genes showed higher expression in the piglets of JNP than in Berkshire. Gene Ontology and signaling pathways showed that immune response and lipid metabolisms were commonly enriched pathways in all three tissues. It was found that the genes pertaining to body growth and immune system are significantly (P < 0.01) more highly expressed in Berkshire piglets. DEGs explored between the piglets of the two breeds might influence the identification of the genetic markers for further breed improvement programs. Our findings provide a new perspective for understanding and identifying candidate genes that are involved in various biological functions. Moreover, transcriptome analysis makes it easier to understand the differences between genetic mechanisms of breeds.
本研究旨在调查济州本地猪（JNP）和伯克希尔仔猪之间的差异表达基因（DEG）。采用RNA-Seq技术研究这两个品种仔猪的脂肪、肝脏和背最长肌的转录组。通过质量过滤的序列的双末端读段使用tophat2（v2.0.2）与猪基因组进行比对。在本研究中，65%的肌肉、20%的脂肪和54%的肝脏基因在JNP仔猪中的表达高于伯克希尔仔猪。基因本体论和信号通路显示，免疫反应和脂质代谢是所有三种组织中共同富集的通路。发现与身体生长和免疫系统相关的基因在伯克希尔仔猪中显著（P < 0.01）高表达。两个品种仔猪之间探索的差异表达基因可能会影响进一步品种改良计划的遗传标记的鉴定。我们的研究结果为理解和鉴定参与各种生物学功能的候选基因提供了新的视角。此外，转录组分析使我们更容易理解品种间遗传机制的差异。
