Selection Signatures Analysis Reveals Genes Associated with High-Altitude Adaptation in Tibetan Goats from Nagqu, Tibet

Abstract

Tibetan goat is an ancient breed, which inhabits the adverse conditions of the plateaus in China. To investigate the role of selection in shaping its genomes, we genotyped Tibetan goats (Nagqu Prefecture, above 4500 m) and three lowland populations (Xinjiang goats, Taihang goats and Huanghuai goats). The result of PCA, neighbor-joining (N-J) tree and model-based clustering showed that the genetic structure between the Tibetan goat and the three lowland populations has significant difference. As demonstrated by the di statistic, we found that some genes were related to the high-altitude adaptation of Tibetan goats. Functional analysis revealed that these genes were enriched in the VEGF (vascular endothelial growth factor) signaling pathway and melanoma, suggesting that nine genes (FGF2, EGFR, AKT1, PTEN, MITF, ENPEP, SIRT6, KDR, and CDC42) might have important roles in the high-altitude adaptation of Nagqu Tibetan goats. We also found that the LEPR gene was under the strongest selection (di value = 16.70), and it could induce upregulation of the hypoxic ventilatory response. In addition, five genes (LEPR, LDB1, EGFR, NOX4 and FGF2) with high di values were analyzed using q-PCR. Among them, we found that LEPR, LDB1 and FGF2 exhibited higher expression in the lungs of the Tibetan goats; LEPR, EGFR and LDB1 exhibited higher expression in the hearts of the Huanghuai goat. Our results suggest that LEPR, LDB1, EGFR and FGF2 genes may be related to the high-altitude adaptation of the goats. These findings improve our understanding of the selection of the high-altitude adaptability of the Nagqu Tibetan goats and provide new theoretical knowledge for the conservation and utilization of germplasm resources.

Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya

“…This biological pathway is vital in goat breeds in Kenya to maintain adequate energy production and activity in their harsh environment, especially during the lactation period. The LEPR gene is also related to hypoxic in Tibetan goats ( Jin et al, 2020 ) and reproductive and fatness traits in goats and sheep ( Alim et al, 2019 ; Gunawan et al, 2019 ). The parathyroid hormone synthesis, secretion, and action of the KEGG pathway is associated with GNAI2 , PDE4B , and RHOA genes identified in this study.…”

Whole-Genome Analysis Deciphers Population Structure and Genetic Introgression Among Bovine Species

“…Among CDC42 related to the morphology, adhesion, migration, and erythropoiesis of hematopoietic stem cells ( Wang et al, 2006 ; Yang et al, 2007 ), this gene can mediate bmp-induced sprouting angiogenesis ( Wakayama et al, 2015 ). CDC42 was under positive selection and enriched with vascular endothelial growth factor (VEGF) for Tibetan goats ( Jin et al, 2020 ). SLC39A2 and SLC9A6 genes were related to heart functions ( Du et al, 2019 ), which have also been reported in Yunnan golden monkeys ( Zhou et al, 2016 ).…”

Oar-miR-432 Regulates Fat Differentiation and Promotes the Expression of BMP2 in Ovine Preadipocytes

“…TRIzol was used to extract total RNA. Reverse transcription and RT-qPCR reaction were descripted by Jin et al (2020 ) with β-actin as the housekeeping gene. The stem-loop method was used to synthesize cDNA from miRNAs and miRNA Design V1.01 ( https://www.vazyme.com/ ) was used to design the primers.…”

“…The primer information is listed in Supplementary Table S1 . The ANOVA program in SPSS version 19.0 was used for statistical analysis ( Jin et al, 2020 ) and considered statistically significant at p-value < 0.05 . GraphPad Prism software (San Diego, CA, United States) was used to draw plots.…”