Whole‐genome analysis identifying candidate genes of altitude adaptive ecological thresholds in yak populations

Abstract

The domestic yak (Bos grunniens) is an iconic symbol of animal husbandry on the Qinghai-Tibet Plateau. Long-term domestication and natural selection have led to a wide distribution of yak, forming many ecological populations to adapt to the local ecological environment. High altitude is closely related to oxygen density, and it is an important environmental ecological factor for biological survival and livestock production. The aim of the present study was to perform a preliminary analysis to identify the candidate genes of altitude distribution adapted ecological thresholds in yak using next-generation sequence technology. A total of 15,762,829 SNPs were obtained from 29 yaks with high-and low-altitude distribution by genome-wide sequencing. According to the results of the selective sweep analysis with FST and ZHp, 21 candidate genes were identified. 14 genes (serine/threonine protein kinase TNNI3K, TEN1, DYM, ITPR1, ZC4H2, KNTC1, ADGRB3, CLYBL, TANGO6, ASCC3, KLHL3, PDE4D, DEPDC1B and AGBL4) were grouped into 32 Gene Ontology terms, and four genes (RPS6KA6, ITPR1, GNAO1 and PDE4D) annotated in 35 pathways, including seven environmental information processing and one environmental adaptation. Therefore, the novel candidate genes found in the current study do not only support new theories about high-altitude adaptation, but also further explain the molecular mechanisms of altitude adaptation threshold in yaks. K E Y W O R D Saltitude adaption, ecological threshold, selection signatures, yak 372 | E Et al.

Cross-Species Insights Into Genomic Adaptations to Hypoxia

“…Yaks at sea level and at altitudes of 2260−4500 m exhibit lower pulmonary artery pressures (Ishizaki et al, 2005). Genomic analysis of yaks indicates several HIF-specific mutations have occurred in high vs. low altitude populations, including to two important regulators of HIF (ADAM17 and ARG2) (Qiu et al, 2012(Qiu et al, , 2015Guang-Xin et al, 2019). Furthermore, transcriptomic analysis of yaks endemic to an altitudinal gradient demonstrated that EPAS1 expression increases with altitude (Qi et al, 2019).…”

Adaptation Mechanisms of Yak (Bos grunniens) to High-Altitude Environmental Stress

“…In the yak populations, several genes putatively associated with adaptation to life at high altitudes were identified. These genes are primarily related to physiological pathways in response to hypoxia and temperature acclimatization and modifications of the cardiovascular system and energy metabolism [13,20,56]. Endothelial PAS domain-containing protein 1 (EPAS1) is the top candidate gene encoding the hypoxia-inducible transcription factor (HIF-2α).…”

“…Camk2b, Gcnt3, Hsd17b12, Whsc1, and Glul High level of nutrition utilization in high altitudes [13] HIF1A, MMP3, ADAM17, ARG2 High-altitude adaptation [13] DEXI, DCC, and MRP4 Adaptation to high-altitude environments [14] PDE4D, RPS6KA6, ITPR1, and GNAO1 Environmental information processing and environmental adaptability [20] EPAS1 Key transcription factor that activates the expression of oxygen-regulated genes [21] ABCG8, COL4A1, LOC102287650, PDCD1, and NUP210 Adaptation to high-altitude environments [22] VEGF-A Regulation of blood vessel size [35] MMP3…”

“…Knowledge of the mechanisms underlying adaptation to various agro-ecosystems is essential for the effective management of farm animal genetic resources [7,19]. Intriguingly, multiple studies have focused on yak adaptation, allowing researchers to understand the morphological, physiological, biochemical, and genetic mechanisms of adaptation to extremely high altitudes [13,15,[20][21][22]. Although research on the adaptation mechanisms of the yak in high altitudes has increased exponentially, review studies on the comprehensive, adaptive mechanisms remain scarce.…”

Influence of Salinity Gradient Changes on Phytoplankton Growth Caused by Sluice Construction in Yongjiang River Estuary Area

“…ET can be recognized both in time series analysis and in spatial comparison of environmental gradients [20][21][22]. ET studies have become a hot issue in recent years with the development of sustainability research [23][24][25]. The threshold analysis method is popular in evaluating the nonlinear response of environment changes.…”