Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Wanju, 55365, Korea.
Poultry Reasearch Institute, National Institute of Animal Science, RDA, Pyeonchang, 25342, Korea.
Sci Rep. 2020 Nov 6;10(1):19288. doi: 10.1038/s41598-020-76234-8.
Transcriptome expression reflects genetic response in diverse conditions. In this study, RNA sequencing was utilized to profile multiple tissues such as liver, breast, caecum, and gizzard of Korean commercial chicken raised in Korea and Kyrgyzstan. We analyzed ten samples per tissue from each location to identify candidate genes which are involved in the adaptation of Korean commercial chicken to Kyrgyzstan. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, we found 315, 196, 167 and 198 genes in liver, breast, cecum, and gizzard respectively as differentially expressed between the two locations. GO enrichment analysis showed that these genes were highly enriched for cellular and metabolic processes, catalytic activity, and biological regulations. Similarly, KEGG pathways analysis indicated metabolic, PPAR signaling, FoxO, glycolysis/gluconeogenesis, biosynthesis, MAPK signaling, CAMs, citrate cycles pathways were differentially enriched. Enriched genes like TSKU, VTG1, SGK, CDK2 etc. in these pathways might be involved in acclimation of organisms into diverse climatic conditions. The qRT-PCR result also corroborated the RNA-Seq findings with R of 0.76, 0.80, 0.81, and 0.93 for liver, breast, caecum, and gizzard respectively. Our findings can improve the understanding of environmental acclimation process in chicken.
转录组表达反映了不同条件下的遗传反应。在这项研究中，我们利用 RNA 测序技术对来自韩国和吉尔吉斯斯坦的韩国商业鸡的多种组织（如肝脏、乳房、盲肠和肌胃）进行了分析。我们对每个组织的每个位置分析了 10 个样本，以确定参与韩国商业鸡适应吉尔吉斯斯坦的候选基因。在错误发现率（FDR）<0.05 和倍数变化（FC）>2 的条件下，我们在肝脏、乳房、盲肠和肌胃中分别发现了 315、196、167 和 198 个差异表达基因。GO 富集分析表明，这些基因在细胞和代谢过程、催化活性和生物调节中高度富集。同样，KEGG 途径分析表明，代谢、PPAR 信号、FoxO、糖酵解/糖异生、生物合成、MAPK 信号、CAMs、柠檬酸循环途径存在差异富集。这些途径中丰富的基因，如 TSKU、VTG1、SGK、CDK2 等，可能参与了生物体对不同气候条件的适应。qRT-PCR 结果也与 RNA-Seq 结果相吻合，肝脏、乳房、盲肠和肌胃的 R 值分别为 0.76、0.80、0.81 和 0.93。我们的研究结果可以提高对鸡环境适应过程的理解。
