biostudies-literatureXia XPostdoctoral Research Project Funding of Shaanxi ProvinceProgram of Yunling Scholar and Yunling Cattle Special Program of Yunnan Joint Laboratory of Seeds and Seeding IndustryChina Agriculture Research System of MOF and MARAYunnan Expert WorkstationsOpen Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai UniversityNational Natural Science Foundation of ChinaChuxiong Science and Technology Leading TalentsNational Key Research and Development Program of ChinaConstruction of Yunling Cattle Technology Innovation Center and Industrialization of AchievementsPostdoctoral Fellowship Program of CPSFKey Research and Development Program of Xizang Autonomous Region of Chinae03258https://www.ebi.ac.uk/biostudies/studies/S-EPMC12376619biostudies-literatureUnknown12(31)Structural variations (SVs) play crucial roles in the evolutionary adaptation of domesticated animals to natural and human-controlled environments, but SVs have not been explored in Tibetan cattle, which recently migrated and rapidly adapted to the high altitudes of the Qinghai-Tibetan Plateau (QTP). In this study, a de novo chromosome-level genome assembly for Tibetan cattle is constructed. It is found that using a lineage-specific reference genome significantly increased variant detection accuracy and completeness. Analysis of long-read sequencing data from 36 high-altitude QTP and 48 low-altitude cattle identified 222 528 SVs and 259 SV hotspot regions. Positively selected SVs in high-altitude cattle are related to energy metabolism erythropoiesis and angiogenesis, and peroxisomal metabolism. A 102-bp intronic deletion in GNPAT likely upregulated its expression. It is distinguished 7293 SVs that may be introgressed from yak, including variants upstream of the hypoxia-inducing gene EGLN1. Finally, a ≈2-Mb heterozygous inversion and two translocations on chromosome 6 are likely associated with the cattle gray coat via regulatory effects on the KIT gene. The results confirm the importance of SVs in evolutionary adaptation and the contribution yak-introgressed SVs to the rapid acclimatization of QTP cattle.Advanced science (Weinheim, Baden-Wurttemberg, Germany)Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle.PMC123766192019ZG007CARS-37CXKJLJRC2023-07321025232024-KF-0232341054323728542021YFD12004002023BSHEDZZ132XZ202301ZY0008NGZC202321492021YFF100100032260823202305AF150156202205AR070001Liu JLuosang DZhang JLyu YLow WWang FQu KMa ZDeng LLei CZhuzha BWu ZLenstra JAZhao LSong RLuobu CDang RWang YCheng HHuang BXu LXia XZheng ZChen NZheng YWangmu SCangjue NWangdui BLi RQuji SLan XYang XLi SHuang YHu HGao YLyu WLuo XHan JSizhu SfalseStructural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle.Structural variations (SVs) play crucial roles in the evolutionary adaptation of domesticated animals to natural and human-controlled environments, but SVs have not been explored in Tibetan cattle, which recently migrated and rapidly adapted to the high altitudes of the Qinghai-Tibetan Plateau (QTP). In this study, a de novo chromosome-level genome assembly for Tibetan cattle is constructed. It is found that using a lineage-specific reference genome significantly increased variant detection accuracy and completeness. Analysis of long-read sequencing data from 36 high-altitude QTP and 48 low-altitude cattle identified 222 528 SVs and 259 SV hotspot regions. Positively selected SVs in high-altitude cattle are related to energy metabolism erythropoiesis and angiogenesis, and peroxisomal metabolism. A 102-bp intronic deletion in GNPAT likely upregulated its expression. It is distinguished 7293 SVs that may be introgressed from yak, including variants upstream of the hypoxia-inducing gene EGLN1. Finally, a ≈2-Mb heterozygous inversion and two translocations on chromosome 6 are likely associated with the cattle gray coat via regulatory effects on the KIT gene. The results confirm the importance of SVs in evolutionary adaptation and the contribution yak-introgressed SVs to the rapid acclimatization of QTP cattle.2025-01-01T00:00:00Z2025 Aug2026-05-09T19:14:29.78Z2026-04-08T01:10:45.375ZS-EPMC123766194047071810.1002/advs.202503258