Plateau Adaptation Gene Analyses Reveal Transcriptomic, Proteomic, and Dual Omics Expression in the Lung Tissues of Tibetan and Yorkshire Pigs

Peng Shang; Bo Zhang; Pan Li; Zulfiqar Ahmed; Xiaoxiang Hu; Yangzom Chamba; Hao Zhang

doi:10.3390/ani12151919

Plateau Adaptation Gene Analyses Reveal Transcriptomic, Proteomic, and Dual Omics Expression in the Lung Tissues of Tibetan and Yorkshire Pigs

Animals (Basel). 2022 Jul 27;12(15):1919. doi: 10.3390/ani12151919.

Authors

Peng Shang^{1

2}, Bo Zhang¹, Pan Li¹, Zulfiqar Ahmed³, Xiaoxiang Hu¹, Yangzom Chamba², Hao Zhang¹

Affiliations

¹ Laboratory National Engineering for Animal Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China.
² Department of animal husbandry, College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China.
³ Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot 12350, Pakistan.

Abstract

Elevated environments such as plateaus are often classified as low oxygen environments. The hypoxic adaptation mechanisms utilized by organisms in these conditions are not well understood. To address this, the differentially expressed genes (DEGs) involved in hypoxia adaptation were assessed using two pig breeds (Tibetan pig [TP] and Yorkshire sow [YY]). Genes related to lung tissue responses to hypoxia were assessed using transcriptomic (using RNA-seq) and proteomic (using iTRAQ) analysis. A total of 1021 DEGs were screened out. In the iTRAQ omics data, a total of 22,100 peptides were obtained and 4518 proteins were found after filtering. A total of 271 differentially expressed proteins [DEPs] were screened using the conditions of p < 0.05; FC ≤ 0.833; and FC ≥ 1.2. A total of 14 DEGs at the mRNA and protein levels were identified and found to be associated with regulation of the inflammatory response; blood particles; and MAPK cascade response regulation. Among the DEGs, six were associated with hypoxia adaptation function (mitochondria and glycolysis) in pigs. The results of this study identify novel candidate genes involved in porcine hypoxia adaptation mechanisms.

Keywords: Tibetan pigs; Yorkshire pigs; plateau adaptation gene; proteomic; transcriptomic.

Grants and funding

This work was supported by the Major Science and Technology Projects of the Tibet Autonomous Region (XZ202101ZD0005N), the Basic Research Funds of the China Agricultural University (2022TC002), and the National Natural Science Foundation of China (32160773).