Multi-omics integration analysis reveals the regulatory impact of CNVs for slaughter traits in cattle

Copy number variations (CNVs) represent a crucial class of genomic variations that modulate gene expression and contribute to phenotypic diversity. In this study, we systematically identified 124,790 CNVs across genome using Bovine HD SNP array. A CNV-based genome-wide association study (GWAS) identified 17 and 3 significant CNV segments associated with lean meat percentage (LMP) and dressing percentage (DP), respectively. The expression quantitative trait locus (eQTL) analysis revealed 621, 399 and 20 expression CNV regions (eCNVRs) significantly associated with gene expression in muscle, liver, and fat tissues. Further investigation through differentially expressed alternative splicing (DEAS) analysis detected 15,450 and 12,356 alternative splicing events (ASE) related to LMP in muscle and liver tissues. Notably, integration analysis of CNV-GWAS, eQTL and splicing quantitative trait locus (sQTL) uncovered a significant 14-kb deletion encompassing two candidate genes (ILVBL and SYDE1). Moreover, we identified a 12-kb duplication for LMP with enhancer signals of the GC gene, suggesting its potential regulatory impact on gene expression. Our study identified several associated CNVs for slaughter traits and elucidated their regulation of gene expression, providing novel insights into the genetic architecture of complex traits and advancing precision breeding strategies in cattle.