Animal Genetics, ICAR-IVRI, Izatnagar, Uttar Pradesh, 243122, India.
Physiology and climatology, ICAR-IVRI, Izatnagar, Uttar Pradesh, 243122, India.
Trop Anim Health Prod. 2020 Nov 19;53(1):14. doi: 10.1007/s11250-020-02440-1.
In the present investigation, differentially expressed genes (DEGs) were studied using RNA sequencing (RNA-seq) technique in porcine peripheral blood mononuclear cells (PBMC) of weaned Ghurrah and crossbred piglets at 3-month age. Transcriptomic analysis was done using three different packages, namely, EBSeq, DESeq2, and edgeR, to identify the DEGs between Ghurrah and crossbred piglets. Total 7717 DEGs were commonly identified by all three packages, out of which 4151 genes found to be up-regulated, and 3566 genes were down-regulated. Functional annotation of these DEGs indicated metabolism as the most commonly enriched category followed by the immune response. Genes related to metabolism and growth were up-regulated in crossbred piglets as compared with Ghurrah piglets, whereas immunity-related genes were up-regulated in Ghurrah piglets elucidating the disease resistance nature of this indigenous breed over crossbred counterparts. Further, eight DEGs, namely, LRP-1, ADCY4, ERRFI1, LDHD, ARG1, OASL, MGARP, and S100A8, were validated by qRT-PCR in a separate set of biological samples and found to be in concordance with RNA-seq results. Finding in the present study provides insight into genes and their molecular mechanisms governing difference in growth performance between Ghurrah and crossbred pigs.
在本研究中，使用 RNA 测序 (RNA-seq) 技术研究了断奶 Ghurrah 和杂交仔猪 3 月龄外周血单个核细胞 (PBMC) 中的差异表达基因 (DEGs)。使用三个不同的软件包（EBSeq、DESeq2 和 edgeR）进行转录组分析，以鉴定 Ghurrah 和杂交仔猪之间的 DEGs。三个软件包共鉴定出 7717 个 DEGs，其中 4151 个基因上调，3566 个基因下调。这些 DEGs 的功能注释表明，代谢是最常见的富集类别，其次是免疫反应。与 Ghurrah 仔猪相比，杂交仔猪的代谢和生长相关基因上调，而 Ghurrah 仔猪的免疫相关基因上调，这表明该本土品种比杂交品种具有更强的抗病能力。此外，通过 qRT-PCR 在另一组生物样本中验证了 8 个 DEGs（LRP-1、ADCY4、ERRFI1、LDHD、ARG1、OASL、MGARP 和 S100A8），结果与 RNA-seq 结果一致。本研究的结果为 Ghurrah 和杂交猪生长性能差异的基因及其分子机制提供了深入了解。
