Phylogenetic Relations and High-Altitude Adaptation in Wild Boar ( Sus scrofa ), Identified Using Genome-Wide Data

The Qinghai-Tibet Plateau (QTP) wild boar is an excellent model for investigating high-altitude adaptation. In this study, we analyzed genome-wide data from 93 wild boars compiled from various studies worldwide, including the QTP, southern and northern regions of China, Europe, Northeast Asia, and S...

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Bibliographic Details
Published in:Animals (Basel) 2024-10, Vol.14 (20), p.2984
Main Authors: Fang, Shiyong, Zhang, Haoyuan, Long, Haoyuan, Zhang, Dongjie, Chen, Hongyue, Yang, Xiuqin, Pan, Hongmei, Pan, Xiao, Liu, Di, E, Guangxin
Format: Article
Language:English
Subjects:
Altitude
altitude adaptation
Analysis
Dextrose
Genes
Genetic aspects
Genomes
Genomics
Glucose
Glucose metabolism
Hogs
Migration
phylogenetic
Phylogenetics
Phylogeny
Population
Quality control
Software
Tibetan
wide genome
wild boar
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Summary:The Qinghai-Tibet Plateau (QTP) wild boar is an excellent model for investigating high-altitude adaptation. In this study, we analyzed genome-wide data from 93 wild boars compiled from various studies worldwide, including the QTP, southern and northern regions of China, Europe, Northeast Asia, and Southeast Asia, to explore their phylogenetic patterns and high-altitude adaptation based on genome-wide selection signal analysis and run of homozygosity (ROH) estimation. The findings demonstrate the alignment between the phylogenetic associations among wild boars and their geographical location. An ADMIXTURE analysis indicated a relatively close genetic relationship between QTP and southern Chinese wild boars. Analyses of the fixation index and cross-population extended haplotype homozygosity between populations revealed 295 candidate genes (CDGs) associated with high-altitude adaptation, such as , , , and . These CDGs were significantly overrepresented in pathways such as the mammalian target of rapamycin signaling and Fanconi anemia pathways. In addition, 39 ROH islands and numerous selective CDGs (e.g., , , and ), which are implicated in glucose metabolism and mitochondrial function, were discovered in QTP wild boars. This study not only assessed the phylogenetic history of QTP wild boars but also advanced our comprehension of the genetic mechanisms underlying the adaptation of wild boars to high altitudes.
ISSN:2076-2615
2076-2615
DOI:10.3390/ani14202984