Multi-omics analysis reveals genetic regulatory mechanisms of muscle traits in wild and domesticated Bactrian camels

Bactrian camels, large domesticated animals adapted to extreme environments, have evolved under natural and artificial selection to suit their living conditions and meet human needs. In arid and semi-arid regions, they provide valuable resources through economically important traits such as meat, milk, and wool production, contributing significantly to both economy and ecology. However, research on gene function, adaptive evolution, and molecular mechanisms underlying complex traits in Bactrian camels remains limited, constraining the full utilization of their breeding potential and conservation efforts. To address this gap, we performed whole-genome resequencing (WGS) on 35 domesticated Bactrian camels from the Chinese Sunite local population and integrated this data with publicly available WGS data from 112 Asian Bactrian camels. Our comprehensive analysis revealed significant genetic differences and genomic features between wild and domesticated Bactrian camels. We further integrated 27 epigenomic (ATAC-seq) and transcriptomic (RNA-seq) datasets from eight biologically important tissues of four Bactrian camels, along with skeletal muscle scRNA-seq and scATAC data. This allowed us to identify tissue-specific genes, regulatory elements, and genes under positive selection.Our integrated analysis identified target genes and their upstream regulatory elements, including potential regulatory transcription factors, with a focus on positively selected regions in Bactrian camel muscle tissue. We constructed regulatory pathways from key SNPs to regulatory elements to genes, and for the first time, identified regulatory elements in major tissues of the Bactrian camel genome. Our results also summarized the single-cell transcriptional landscape of Bactrian camel skeletal muscle, revealing cellular heterogeneity and genetic expression patterns across two developmental stages. This comprehensive regulatory element map provides a valuable resource for genetic and genomic studies in Bactrian camels. It reveals key regulatory networks, important genes, and regulatory elements influencing muscle development, as well as potentially significant functional variants affecting meat production traits. These findings will provide crucial data support for future genetic improvement and breeding efforts in Bactrian camels.