Integrative genotype-environment association and single-cell transcriptomic analyses identify candidate mechanisms of environmental adaptation in pigs.
- 1College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
- 2Animal Breeding and Genomics, Wageningen University and Research, Wageningen 6700 AH, The Netherlands.
- 3Department of Animal Science, Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
Abstract
As one of the earliest domesticated and most globally ubiquitous livestock, pigs (Sus scrofa) have undergone profound environmental adaptation while following human expansion across diverse bioclimatic zones. Despite their evolutionary significance, the genomic mechanisms enabling pigs to thrive in disparate ecological settings remain poorly understood. Here, we present a comprehensive global analysis using a dataset of 1,151 pig genome sequences representing 146 distinct populations. By integrating three complementary genotype-environment association (GEA) frameworks including redundancy analysis (RDA), BayPass, and latent factor mixed models (LFMM), we identified genomic regions and candidate genes associated with environmental variation. Our analysis detected several candidate genes associated with high-altitude adaptation, particularly those involved in ultraviolet radiation response. By integrating lung single-cell RNA sequencing analysis (scRNA) from high-altitude and commercial breeds, we identified ASXL1 as a candidate gene potentially involved in high-altitude adaptation. Meanwhile, scRNA revealed candidate regulatory pathways, including the NOTCH signaling pathway, that were overlooked by traditional GEA methods, suggesting the complex regulatory landscape of physiological adaptation. Together, this study integrates large-scale population genomics and scRNA to provide insights into the genetic associations and regulatory landscapes potentially contributing to environmental adaptation in domestic pigs, advancing our understanding of livestock evolutionary responses to diverse ecological conditions.
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BibTeX
@article{li2026integrative,
title = {{Integrative genotype-environment association and single-cell transcriptomic analyses identify candidate mechanisms of environmental adaptation in pigs.}},
author = {Dong Li and Tiantian Yuan and Xiang Li and Yu Quan and Xuekai Tian and Ye Cheng and Yulong Wang and Xinglong Wu and Boyuan Sun and Wansheng Liu and Yu Jiang and Rongrong Ding and Martien A M Groenen and Martijn F L Derks and Taiyong Yu},
journal = {Molecular biology and evolution},
year = {2026},
month = oct,
doi = {10.1093/molbev/msag260},
url = {https://europepmc.org/article/MED/42851070},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - Integrative genotype-environment association and single-cell transcriptomic analyses identify candidate mechanisms of environmental adaptation in pigs.
AU - Dong Li
AU - Tiantian Yuan
AU - Xiang Li
AU - Yu Quan
AU - Xuekai Tian
AU - Ye Cheng
AU - Yulong Wang
AU - Xinglong Wu
AU - Boyuan Sun
AU - Wansheng Liu
AU - Yu Jiang
AU - Rongrong Ding
AU - Martien A M Groenen
AU - Martijn F L Derks
AU - Taiyong Yu
PY - 2026
DA - 2026/10/01
JO - Molecular biology and evolution
DO - 10.1093/molbev/msag260
UR - https://europepmc.org/article/MED/42851070
AB - As one of the earliest domesticated and most globally ubiquitous livestock, pigs (Sus scrofa) have undergone profound environmental adaptation while following human expansion across diverse bioclimatic zones. Despite their evolutionary significance, the genomic mechanisms enabling pigs to thrive in disparate ecological settings remain poorly understood. Here, we present a comprehensive global analysis using a dataset of 1,151 pig genome sequences representing 146 distinct populations. By integrating three complementary genotype-environment association (GEA) frameworks including redundancy analysis (RDA), BayPass, and latent factor mixed models (LFMM), we identified genomic regions and candidate genes associated with environmental variation. Our analysis detected several candidate genes associated with high-altitude adaptation, particularly those involved in ultraviolet radiation response. By integrating lung single-cell RNA sequencing analysis (scRNA) from high-altitude and commercial breeds, we identified ASXL1 as a candidate gene potentially involved in high-altitude adaptation. Meanwhile, scRNA revealed candidate regulatory pathways, including the NOTCH signaling pathway, that were overlooked by traditional GEA methods, suggesting the complex regulatory landscape of physiological adaptation. Together, this study integrates large-scale population genomics and scRNA to provide insights into the genetic associations and regulatory landscapes potentially contributing to environmental adaptation in domestic pigs, advancing our understanding of livestock evolutionary responses to diverse ecological conditions.
SN - 0737-4038
SN - 1537-1719
ER -