Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle
Open accessAbstract
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.
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7293 SVs in Tibetan cattle originated from yak introgression, including an upstream regulatory variant of EGLN1 and intronic deletions in PPP1R14C and NFE2L2.
“A structural variation analysis further revealed that 7293 SVs in Tibetan cattle originated from yak introgression. These variants included an upstream regulatory variant of EGLN1 and intronic deletions in PPP1R14C and NFE2L2, which are associated with angiogenesis and glucose transporter 1 upregulation, respectively [89].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [89]
The Results (‘Yak Introgression’; page not supplied) identify 7,293 SVs as possibly derived from yak, with 5,642 subsequently classified as probable introgressions. The same section reports SVs upstream of EGLN1 and intronic deletions in PPP1R14C and NFE2L2. The claim overstates the certainty of yak origin for all 7,293 and calls the EGLN1 variant regulatory, whereas the passage establishes its location upstream of the gene, not a regulatory effect. (LLM, conf=0.88)
Experimental — accuracy not yet measuredA 2 Mb heterozygous inversion and two translocations harboring KIT were associated with the gray coat phenotype in Tibetan cattle, and the inversion haplotype originated from South Asian indicine cattle.
“A 2 Mb heterozygous inversion and two translocations harboring genes including KIT were associated with the gray coat phenotype in Tibetan cattle, and the inversion haplotype segment originated from South Asian indicine cattle [89].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [89]
The Results section (“A 2-Mb Heterozygous Inversion Related to the Gray Coat Phenotype”) identifies a 2-Mb heterozygous inversion and two translocations associated with gray coat color; the region includes KIT. Its haplotype analysis suggests the inversion segment likely originated from South Asian indicine cattle, but the citing sentence states that origin as certain. (LLM, conf=0.87)
Experimental — accuracy not yet measuredStructural variation analyses identified genes involved in erythropoiesis and angiogenesis and energy metabolism in high-altitude cattle.
“Structural variation analyses further identified genes involved in erythropoiesis and angiogenesis (SSH2, VGLL4, PLCB1, HPSE2, HPSE) and energy metabolism (SORD, NDUFB6, SARDH, ADIPOQ) [89].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [89]
Precise characterization of SVs has linked a 108 bp insertion in SPN to M. tuberculosis resistance and associated specific upstream variants of EGLN1 to high-altitude adaptation.
“Furthermore, precise characterization of SVs has linked a 108 bp insertion in SPN to M. tuberculosis resistance and associated specific upstream variants of EGLN1 to high-altitude adaptation [89,101].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [89]
The Introduction mentions EGLN1 only as a candidate identified by previous SNP studies, not as a gene with upstream SVs characterized in this paper. The Results identify other SVs associated with high-altitude adaptation, but searches for SPN, a 108-bp insertion, tuberculosis resistance, and upstream EGLN1 variants found no passage addressing either specific claim. Page numbers were not available in our copy. (LLM, conf=0.76)
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Pangenome-genotyped structural variation improves molecular phenotype mapping in cattlePreprint
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Ruminant-specific retrotransposons shape regulatory evolution of bovine immunityPreprint
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Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors
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A Robertsonian Translocation and its Effect upon Fertility in Brown Swiss Cattle
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De novo genome assembly depicts the immune genomic characteristics of cattle
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Modulation of nuclear PI-PLCbeta1 during cell differentiation
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Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep
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The Good and Bad Sides of Heparanase-1 and Heparanase-2
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Genetic Origins and Adaptive Evolution of the Deng People on the Tibetan Plateau
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TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene
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Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gapsPreprint
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Crtc modulates fasting programs associated with 1-C metabolism and inhibition of insulin signaling
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Genetic assessment of BoLA-DRB3 polymorphisms by comparing Bangladesh, Ethiopian, and Korean cattle
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Cited by
Sorted by citations
Exploring the genetic footprints of high altitude adapted humans and livestock
Tiwari, M., Gujar, G., Ponsuksili, S., Shashank, C. G., Sharma, S., Sodhi, M., & Mukesh, M. (2025) · Mammalian Genome · doi:10.1007/s00335-025-10161-9 · Cited by 6 · see citing works
“Yang et al. (2021), reported that Tibetan pigs living at high altitudes possess larger, broader lungs with thicker, more extensively a de novo chromosome-level genome assembly for Tibetan cattle revealed 222,528 SVs and 259 hotspot regions (Xia et al. 2025 ).”
Zhou, Z., Cai, D., Zhao, C., Zhang, S., Li, J., Zhang, Z., Kong, S., Yang, X., Zhou, X., Bordbar, F., et al. (2026) · Advanced Science · doi:10.1002/advs.202520068 · Cited by 3 · see citing works
Population-scale long-read DNA sequencing: peering under the hood of the new evolutionary genomics
Edwards, S. V., & Li, H. (2026) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2025.2899 · Cited by 3 · see citing works
The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution
Liu, Y., Dao, W., Gao, R., Fan, X., Yang, R., & Miao, Y. (2026) · Animals · doi:10.3390/ani16050776 · Cited by 1 · see citing works
“Structural variation analyses further identified genes involved in erythropoiesis and angiogenesis ( SSH2 , VGLL4 , PLCB1 , HPSE2 , HPSE ) and energy metabolism ( SORD , NDUFB6 , SARDH , ADIPOQ ) [89].”
InfluentialGe, F., Guo, Y., Xu, L., Low, W. Y., Ma, H., Li, Q., Wang, Z., Zhu, B., Xu, L., Gao, X., et al. (2025) · DNA Research · doi:10.1093/dnares/dsaf034 · Cited by 1 · see citing works
“12 18 To overcome this limitation, high-quality, breed-specific genome assemblies have been generated, including Simmental, 19 Angus and Brahman, 20 Mongolian cattle and Hainan cattle, 21 and Tibetan cattle.”
Genetic Diversity, Adaptation, Wild Introgression, and Coat Color Mutation of Golden Yak
Yan, H., Chen, J., Lei, C., Zhang, F., He, S., Song, W., Ma, H., Li, S., Li, G., Yongcuo, L., et al. (2026) · Animal Research and One Health · doi:10.1002/aro2.70049 · Cited by 1 · see citing works
Alberts, D., van Marle-Köster, E., Joubert, F., & Berry, D. P. (2026) · Frontiers in Genetics · doi:10.3389/fgene.2026.1717538 · Cited by 1 · see citing works
“Similarly, the TRGC3 gene, located near 4: 82,720,073 in both the Afrikaner and Bonsmara breeds, has been associated with immunity in Tibetan cattle (Xia et al., 2025).”
Zhang, Y., Liu, X., Liu, J., Fu, T., Huang, H., Han, M., Liang, D., & Gao, T. (2025) · Animals · doi:10.3390/ani15203033 · Cited by 1 · see citing works
“…methodologies, this approach has been successfully deployed in model systems ranging from thermotoler-ance adaptation in Chinese cattle to high-altitude acclimatization in Tibetan cattle [11,12], demonstrating that environmental adaptation phenotypes exhibit definable genomic foot-prints.”
Structure and genomic organization of the human DUX4 homologue bovine DUXCPreprint
Yaşar, B., Org, T., Ivask, M., Gamze, Y., Boskovic, N., Jaakma, Ü., Kere, J., Kurg, A., & Katayama, S. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.05.709741
ZHANG, X., Zihuan, D. U., & Gao, S. (2026) · China basic science · doi:10.3724/cbs.202601001
Genome-wide variation landscape reveals temperature adaptation in Chinese indigenous cattle
Zhao, C., Teng, J., Chen, Y., Yang, C., Zhang, X., Ning, C., Wang, H., Yang, Q., Lv, W., Wang, D., et al. (2026) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-026-01451-6
“Some previous studies investigated the distribution of SVs in the genomes of cattle [30, 31] and found significant associations between SVs and some phenotypes [32, 33].”
Fu, Y., Zhao, J., Yu, Y., Yue, B., Wang, H., Zhang, M., Peng, W., Shu, S., Wang, G., Zhong, J., et al. (2026) · BMC Genomics · doi:10.1186/s12864-026-13160-5
“A 1–2 Mb heterozygous inversion and two translocations on chromosome 6 may affect grey pigmentation by regulating KIT , thereby suggesting a role in evolutionary adaptation [47].”
Wei, Y., Tan, S., Chen, N., Luo, X., Zhang, L., Luo, W., khan, N., Jafari, H., Jin, J., Li, Y., et al. (2026) · Research Square · doi:10.21203/rs.3.rs-10520900/v1
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“Moreover, structural variations and introgression from wild relatives have been proposed as important sources of genetic variation facilitating rapid adaptation of domestic animals to high-altitude environments [17,18].”
- Authors
- Xia, X., Wang, F., Luo, X., Li, S., Lyu, Y., Zheng, Y., Ma, Z., Qu, K., Song, R., Liu, J., Zhang, J., Wangdui, B., Zhuzha, B., Quji, S., Zhao, L., Wangmu, S., Luobu, C., Cangjue, N., Luosang, D., Sizhu, S., Cheng, H., Li, R., Wu, Z., Dang, R., Huang, Y., Lan, X., Xu, L., Hu, H., Low, W., Zheng, Z., Wang, Y., Gao, Y., Deng, L., Lenstra, J. A., Han, J., Yang, X., Lyu, W., Huang, B., Lei, C., & Chen, N.
- Affiliations
- Northwest A&F University (CN)
- Qinghai University (CN)
- Jilin Agricultural University (CN)
- Chuxiong Normal University (CN)
- Animal Disease Prevention and Control Centre of Yushu Tibetan Autonomous Prefecture Yushu 810099 China
- Yunnan Academy of Grassland and Animal Science Kunming 650500 China
- Tibet Academy of Agricultural and Animal Husbandry Sciences (CN)
- Institute of Animal Husbandry and Veterinary Science Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa 850030 China
- Animal Science College Tibet Agriculture and Animal Husbandry University Nyingchi 860000 China
- Shandong Academy of Agricultural Sciences (CN)
- Southwest University (CN)
- Rice Research Institute (CN)
- The Davies Research Centre School of Animal and Veterinary Sciences University of Adelaide Roseworthy SA 5371 Australia
- Jingchu University of Technology (CN)
- Utrecht University (NL)
- Luoyang Normal University (CN)
- Key Laboratory of Animal Production Product Quality and Security Ministry of Education College of Animal Science and Technology Jilin Agricultural University Changchun 130118 China
- Corresponding author
- Huang, Bizhi
- Lei, Chuzhao
- Chen, Ningbo
- ORCID
- Venue
- Advanced Science
- Publisher
- Wiley
- Published
- 2025-06-05
- Volume
- 12
- Issue
- 31
- Pages
- e03258-e03258
- ISSN
- 2198-3844 (ISSN-L)
- PMC
- PMC12376619
- OpenAlex
- W4411065279
- Cited by
- 14
- References
- 137
- Citations by year
- 2026: 11 · 2025: 3
- FWCI
- 8.23
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Advanced Science (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- National Key Research and Development Program of China (2021YFF1001000, 2021YFD1200400)
- National Natural Science Foundation of China (32372854, 32341054, 32102523, 32260823)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- structural variants, Tibetan Plateau, high-altitude adaptation, coat color, GNPAT, EGLN1, KIT, heterozygous inversions, translocation, chromosome 6, de novo genome assembly, positive selection, hypoxia, erythropoiesis, peroxisomal metabolism, energy metabolism, angiogenesis
- MeSH terms
- Acclimatization, Adaptation, Physiological, Altitude, Animals, Cattle, Tibet
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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