Structural Variation and Introgression from Wild Populations in East Asian Cattle Genomes Confer Adaptation to Local Environment
Open accessAbstract
BACKGROUND: Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle. RESULTS: In this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a "north-south" gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle. CONCLUSIONS: Our findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance.
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This insertion correlates with an increased number of O-linked glycosylation sites and confers resistance to M. tuberculosis in Hainan cattle.
“This insertion correlates with an increased number of O-linked glycosylation sites and confers resistance to M. tuberculosis in Hainan cattle [101].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [101]
The Results section identifies the 108-bp SPN insertion in Hainan cattle and reports altered M. tuberculosis uptake in transfected macrophage cells. The Discussion hypothesizes that the insertion increases O-linked glycosylation sites and may lower susceptibility to bovine tuberculosis; it does not establish that the insertion confers resistance to M. tuberculosis in Hainan cattle. (LLM, conf=0.90)
Experimental — accuracy not yet measuredSpecific SVs in CRNN, SBSN and SPINK5 were identified in Hainan and Mongolian cattle, affecting skin barrier function and heat adaptation.
“Specific SVs in CRNN, SBSN and SPINK5 were also identified in Hainan and Mongolian cattle, affecting skin barrier function and heat adaptation (hair follicle density, sweat gland area) [101].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [101]
The Results section identifies differentiated SVs in CRNN, SBSN and SPINK5 and links those genes to epidermal differentiation or skin barrier function. The Discussion says the SVs may reflect differences in environmental adaptation, citing hair follicle density and sweat gland area, but does not establish that the SVs affect those traits or heat adaptation. (LLM, conf=0.88)
Experimental — accuracy not yet measuredPrecise 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 [101]
The Results section (‘Function of an insertion in the exon of SPN gene for binding of Mycobacterium tuberculosis’; page unavailable) identifies the 108-bp SPN insertion and reports increased bacterial uptake in a macrophage experiment. The Discussion (page unavailable) presents reduced tuberculosis susceptibility as a hypothesis, not an established resistance effect. No passage found links upstream EGLN1 variants to high-altitude adaptation (searched: ‘EGLN1 upstream variants high-altitude adaptation’ and ‘high altitude EGLN1’). (LLM, conf=0.86)
Experimental — accuracy not yet measuredA 108 bp insertion in SPN generates an additional 36-amino-acid repeat sequence within the extracellular domain of CD43.
“For example, a 108 bp insertion (INS) in SPN generates an additional 36-amino-acid repeat sequence within the extracellular domain of CD43 [101].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [101]
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References 87 · Cited by 53
Research works printed but not linked: 3
- [86]Xia X. Bos indicus breed: Hainan genome sequencing. Datasets. Sequence Read Archive. 2023. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA810280.
- [87]Xia X. Bos taurus breed: Mongolian genome sequencing. Datasets. Sequence Read Archive. 2023. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA810300.
- [88]Xia X. The Nanopore, Illumina HiSeq, and Hi-C data for structural variation study in East Asian cattle. Datasets. Sequence Read Archive. 2023. https://www.ncbi.nlm.nih.gov/sra/PRJNA823479.
- Authors
- Xia, X., Zhang, F., Li, S., Luo, X., Peng, L., Dong, Z., Pausch, H., Leonard, A. S., Crysnanto, D., Wang, S., Tong, B., Lenstra, J. A., Han, J., Li, F., Xu, T., Gu, L., Jin, L., Dang, R., Huang, Y., Lan, X., Ren, G., Wang, Y., Gao, Y., Ma, Z., Cheng, H., Ma, Y., Chen, H., Pang, W., Lei, C., & Chen, N.
- Affiliations
- Northwest A&F University (CN)
- Guangxi Academy of Sciences (CN)
- ETH Zurich (CH)
- Inner Mongolia University (CN)
- Utrecht University (NL)
- Chinese Academy of Agricultural Sciences (CN)
- City University of Hong Kong (HK)
- Chinese Academy of Tropical Agricultural Sciences (CN)
- Hainan Provincial Academy of Agricultural Sciences (CN)
- Qinghai University (CN)
- Shandong Academy of Agricultural Sciences (CN)
- Ningxia University (CN)
- Corresponding author
- Pang, Weijun
- Lei, Chuzhao
- Chen, Ningbo
- ORCID
- Xia, Xiaoting
- Zhang, Fengwei
- Li, Shuang
- Luo, Xiaoyu
- Peng, Lixin
- Dong, Zheng
- Pausch, Hubert
- Leonard, Alexander S.
- Crysnanto, Danang
- Tong, Bin
- Lenstra, Johannes A.
- Han, Jianlin
- Li, Fuyong
- Xu, Tieshan
- Gu, Lihong
- Jin, Liangliang
- Dang, Ruihua
- Huang, Yongzhen
- Lan, Xianyong
- Ren, Gang
- Wang, Yu
- Gao, Yuanpeng
- Ma, Zhijie
- Chen, Hong
- Pang, Weijun
- Lei, Chuzhao
- Chen, Ningbo
- Venue
- Genome biology
- Published
- 2023-09-18
- Volume
- 24
- Issue
- 1
- Pages
- 211-211
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC10507960
- OpenAlex
- W4386830828
- Cited by
- 53
- References
- 87
- Citations by year
- 2026: 10 · 2025: 22 · 2024: 21
- FWCI
- 9.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- CityU Scholars (submittedVersion, cc-by)
- CGSPace A Repository of Agricultural Research Outputs (Consultative Group for International Agricultural Research) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- ETH Zürich Research Collection
- Funders
- China Agriculture Research System-the National Beef Cattle and Yak Industrial Technology System (CARS-37)
- National Natural Science Foundation of China (31872317, 32102523, 32072720, No. 31872979)
- The Fellowship of China Postdoctoral Science Foundation (2021T140564, 2020M683587)
- Shaanxi Youth Science and Technology New Star (2022KJXX-77)
- Natural Science Basic Research Program of Shaanxi (2021JQ-137)
- Fundamental Research Funds for the Central Universities
- National Key Research and Development Program of China (SQ2021YFF1000041)
- Inner Mongolia Science & Technology Plan (2021ZZ0204)
- The Key Research and Development Program of Shaanxi Province (2022ZDLNY01-04)
- 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 › Agricultural and Biological Sciences › Agronomy and Crop Science › Livestock Farming and Management
- Keywords
- structural variants, introgression, cattle, Mongolian cattle, climate change adaptation, chromosome-level genome assembly, long-read sequencing, north-south gradient, Bos indicus, banteng, epidermal differentiation, skin barrier, breed differentiation
- MeSH terms
- Adaptation, Physiological, Animals, Cattle, China, Disease Susceptibility, Asia, Eastern, Tuberculosis, Bovine
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