Integrating selective signatures and Cis-eQTLs to prioritize candidate genes potentially related to milk production traits in dual-purpose cattle

This study aimed to identify candidate genes and genetic markers affecting milk production traits in dual-purpose cattle, providing a foundation of data for marker-assisted breeding. Cis-eQTL analysis was performed on 83 Xinjiang brown cattle and 80 Chinese Simmental cattle using whole-genome resequencing and RNA-seq data derived from blood samples. Candidate genes were prioritized by overlapping the eGenes with genes from previous selective signature analyses. In Xinjiang brown cattle, 293,758 cis-eQTLs regulating 1,720 genes were identified, whereas 78,735 cis-eQTLs regulating 569 genes were found in Chinese Simmental cattle. By overlapping the eGenes with candidate genes from previous selective signature analyses, we prioritized 103 genes (e.g., PPP2R3A, GNAI1, and ITGB4) in Xinjiang brown cattle and 26 candidate genes (e.g., MAPK10 and HPSE) in Chinese Simmental cattle as potentially related to milk production traits. These results provide valuable data for the development of new dairy lines in Xinjiang brown cattle and for future genomic selection in dairy-oriented Chinese Simmental cattle.