Evidence map›Paper›PMID 37723525›Full record

ArticleGenome biology2023

Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment.

Xiaoting Xia, Fengwei Zhang, Shuang Li, Xiaoyu Luo, Lixin Peng, Zheng Dong, Hubert Pausch, Alexander S Leonard, Danang Crysnanto, Shikang Wang and 20 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.

0numbers the graph read from it
0cells of the map it votes in
40citing papers in PubMed
17.2field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

40 citing papers in PubMed, 49 citations in OpenAlex.

  1. Article
  2. Review
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  6. Review
  7. The chromosome-level genome of Chinese indicine cattle breed provides insights into bovine adaptation and immunity.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026
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  9. Genome-wide detection of copy number variations in indigenous Red Sindhi cattle using ddRAD sequencing.Mammalian genome : official journal of the International Mammalian Genome Society · 2025
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  10. Review
  11. Genome assemblies of IndianNAR genomics and bioinformatics · 2025
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

30 authors at 13 institutions in 5 countries.

Xiaoting Xia *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Fengwei Zhang *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Shuang Li *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Xiaoyu Luo *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Lixin Peng *National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, China.
Zheng Dong *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Hubert PauschAnimal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
Alexander S LeonardAnimal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
Danang CrysnantoAnimal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
Shikang WangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Bin TongThe State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.
Johannes A LenstraFaculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
Jianlin HanLivestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya.
Fuyong LiDepartment of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China.
Tieshan XuTropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
Lihong GuInstitute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China.
Liangliang JinKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Ruihua DangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Yongzhen HuangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Xianyong LanKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Gang RenKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Yu WangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Yuanpeng GaoCollege of Veterinary Medicine, Northwest A&F University, Xianyang, Yangling, China.
Zhijie MaQinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China.
Haijian ChengKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Yun MaKey Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China.
Hong ChenKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
Weijun PangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China. pwj1226@nwafu.edu.cn.
Chuzhao LeiKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China. leichuzhao1118@nwafu.edu.cn.
Ningbo ChenKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China. ningbochen@nwafu.edu.cn.ORCID http://orcid.org/0000-0001-6624-5885
Northwest A&F University · CNETH Zurich · CHNorth West Agriculture and Forestry University · CNChinese Academy of Tropical Agricultural Sciences · CNCity University of Hong Kong · HKGuangxi Academy of Sciences · CNHainan Provincial Academy of Agricultural Sciences · CNInner Mongolia University · CNInstitute of Animal Sciences · CNNingxia University · CNQinghai University · CNShandong Academy of Agricultural Sciences · CNUtrecht University · NL

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundStructural 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.

resultsIn 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.

conclusionsOur findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance.

Indexed as

Adaptation, PhysiologicalDisease SusceptibilityAnimalsAsia, EasternCattleChinaTuberculosis, BovineEast Asian cattleGenome assemblyLong-read sequencingStructural variation

Identifiers

PMID37723525
PMCPMC10507960
OpenAlexW4386830828

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.