An atlas of cell type specific regulatory effects in cattle Article Swipe
Lingzhao Fang
,
Houcheng Li
,
Huicong Zhang
,
Pengju Zhao
,
Qi Zhang
,
Senlin Zhu
,
Tao Shi
,
Yanan Wang
,
J. G. Lü
,
Liu Yang
,
John F. O’Grady
,
David E. MacHugh
,
Yu Wang
,
Zhenyu Wei
,
Xuemei Lu
,
Mingshan Wang
,
Bo Han
,
Weijie Zheng
,
Ao Chen
,
Shamima Akter
,
Nayan Bhowmik
,
Ying Ma
,
R.L. Baldwin
,
Congjun Li
,
Jicai Jiang
,
Li Ma
,
Christian Maltecca
,
Junjian Wang
,
Mian Gong
,
Xiaoning Zhu
,
Qing Lin
,
Xi Yang
,
Di‐Cheng Zhu
,
Jinyan Teng
,
Dailu Guan
,
Bailing An
,
Jilong Ren
,
Yali Hou
,
Fei Wang
,
Bingjie Li
,
Laurent Frantz
,
Greger Larson
,
Zexi Cai
,
Goutam Sahana
,
Yu Jiang
,
Hui‐Zeng Sun
,
Dongxiao Sun
,
George E. Liu
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-6956718/v1
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-6956718/v1
Understanding the genetic and molecular architecture of complex traits and artificial selection is crucial for advancing sustainable precision breeding in cattle and other livestock. Yet, how genetic variation affects cellular gene expression remains elusive in cattle. Here, by integrating 8,866 bulk RNA-seq samples and 999,192 single cells of 81 cell types in 22 bovine tissues, we presented a comprehensive atlas of regulatory variants at the cell type resolution in cattle. By colocalizing with bulk-tissue expression quantitative trait loci (beQTL), we detected 57,043 novel cell-type stratified eQTL and cell-type/state interaction eQTL in 18,153 genes, which also exhibited a stronger tissue/cell-type specificity than beQTL. By examining genome-wide associations (GWAS) of 44 complex traits, these cell-resolved eQTL were colocalized with 505 (24%) additional GWAS loci compared to beQTL. Through integrating this resource with selection signatures between dairy and beef cattle, we provided tissue/cell-specific regulatory insights into cattle breeding. Overall, the current atlas of cell-type-specific regulatory variants will serve as an invaluable resource for cattle genomics and selective breeding.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.21203/rs.3.rs-6956718/v1
- https://www.researchsquare.com/article/rs-6956718/latest.pdf
- OA Status
- gold
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4412152660
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4412152660Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.21203/rs.3.rs-6956718/v1Digital Object Identifier
- Title
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An atlas of cell type specific regulatory effects in cattleWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-07-10Full publication date if available
- Authors
-
Lingzhao Fang, Houcheng Li, Huicong Zhang, Pengju Zhao, Qi Zhang, Senlin Zhu, Tao Shi, Yanan Wang, J. G. Lü, Liu Yang, John F. O’Grady, David E. MacHugh, Yu Wang, Zhenyu Wei, Xuemei Lu, Mingshan Wang, Bo Han, Weijie Zheng, Ao Chen, Shamima Akter, Nayan Bhowmik, Ying Ma, R.L. Baldwin, Congjun Li, Jicai Jiang, Li Ma, Christian Maltecca, Junjian Wang, Mian Gong, Xiaoning Zhu, Qing Lin, Xi Yang, Di‐Cheng Zhu, Jinyan Teng, Dailu Guan, Bailing An, Jilong Ren, Yali Hou, Fei Wang, Bingjie Li, Laurent Frantz, Greger Larson, Zexi Cai, Goutam Sahana, Yu Jiang, Hui‐Zeng Sun, Dongxiao Sun, George E. LiuList of authors in order
- Landing page
-
https://doi.org/10.21203/rs.3.rs-6956718/v1Publisher landing page
- PDF URL
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https://www.researchsquare.com/article/rs-6956718/latest.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://www.researchsquare.com/article/rs-6956718/latest.pdfDirect OA link when available
- Concepts
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Atlas (anatomy), Computational biology, Biology, AnatomyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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