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Novel alternative splicing associated with feed efficiency in dairy cattle under distinct diet compositions
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DOI：10.3168/jds.2025-28092.png)
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Abstract
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Feed efficiency (FE) in dairy cattle is influenced by both genetic and environmental factors, including diet composition. Differential expression (DE) of mRNA isoforms was analyzed using publicly available RNA-Seq data to investigate alternative splicing associated with residual feed intake (RFI) under control and High-Concentrate (HC) diets in Holstein and Jersey cattle. Low-RFI (efficient) animals exhibited more extensive transcriptomic responses than their high-RFI counterparts (207 vs. 103 DE isoforms in Holstein; 183 vs. 90 in Jersey), reflecting greater isoform-specific regulation. Under the control diet, DE isoforms were enriched for transcriptional regulation and cellular function pathways, while the HC diet showed a balanced pattern of up- and downregulation affecting growth, signaling, and metabolic pathways. Overlap between DE isoforms and milk production QTLs was characterized based on functional annotations. In Holsteins, overlap decreased from 66.87% under control to 49.69% under HC, while in Jersey, it increased from 45.02% under control to 64.64% under HC. Comparison between low- and high-RFI animals showed a reduction in reproductive QTL overlap in both breeds: Holstein decreased from 29.65% to 18.69%, respectively, and Jersey decreased from 13.27% to 3.50%, respectively. In Holsteins, the mRNA isoforms WDR33_6 and PRKAR2A_3 were identified as DE transcripts associated with dietary treatment and RFI status suggesting potential roles in FE and metabolic adaptation. As an exploratory study, these results indicate mRNA isoform-level differences associated with RFI and dietary responses in Holstein and Jersey cattle. The observed patterns may reflect contrasts between reproductive and milk production-related biological processes, providing initial insights into candidate features associated with productivity and sustainability.
Keywords:
dairy cattle
feed efficiency
alternative splicing
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