By integrating long-read and short-read transcriptomics with whole-genome resequencing, the team uncovered specific transcript variants and genetic variations linked to superior feed utilization, providing new molecular targets and more efficient ways for fish breeding.
Feed is the largest cost component in aquaculture and also a major source of environmental pressure, making improvements in feed efficiency is a central goal for sustainable fish production. Feed efficiency describes an animal's ability to convert dietary nutrients into body mass, and even modest gains generating substantial economic benefits while reducing nutrient waste discharged into aquatic ecosystems. Conventional indicators such as feed conversion ratio often obscure genetic variation because they are ratio-based, whereas residual feed intake (RFI) more accurately captures inherent differences in feed utilization. At the molecular level, AS enables a single gene to generate multiple transcript isoforms with distinct functions. However, how AS, together with genetic variants such as single nucleotide polymorphisms, contributes to feed efficiency in fish remains poorly understood.
A study (DOI: 10.48130/animadv-0025-0030) published in Animal Advances on 09 January 2026 by Yongkai Tang's team, Chinese Academy of Fishery Sciences, demonstrates that AS, shaped by underlying genetic variation, is a key regulatory mechanism influencing feed efficiency in Jian carp, providing novel molecular insights and potential targets for breeding more efficient and sustainable aquaculture strains.
In this study, a multi-layered transcriptomic and genomic analysis was applied to investigate how AS and genetic variation are associated with feed efficiency differences between low residual feed intake (LRFI) and high residual feed intake (HRFI) Jian carp. First, AS events were systematically identified and classified from liver transcriptomes, revealing 23,997 AS events in the LRFI group and 23,938 in the HRFI group, with both groups showing similar AS profiles dominated by alternative 3′ splice sites and exon skipping, indicating that overall AS composition was conserved between efficiency phenotypes. Next, transcript expression was quantified across all samples, leading to the detection of 70,422 expressed transcripts. Clustering analysis based on transcript abundance largely separated LRFI and HRFI individuals, demonstrating distinct global transcriptional patterns associated with feed efficiency. Differential expression analysis further identified 200 differentially expressed transcripts, including 71 alternatively spliced transcripts derived from 64 differential alternative splicing genes (DASGs). Functional enrichment analyses of these DASGs showed their involvement in biological processes related to protein interaction and regulation, while pathway analysis highlighted metabolic and stress-related pathways, notably lysine degradation and fatty acid degradation, which are closely linked to feed utilization. Building on these results, detailed gene-level analyses focused on two key DASGs, acsl4a and Hadha. Structural and expression analyses revealed that functional splice variants of acsl4a were more highly expressed in efficient fish, whereas a specific Hadha isoform with distinct structural features was upregulated in inefficient fish, suggesting isoform-specific roles in lipid metabolism. These transcriptomic findings were largely validated by qRT-PCR, confirming the robustness of the expression patterns. Finally, whole-genome resequencing was used to characterize SNPs associated with DASGs, revealing that these genes harbored a higher proportion of splice-altering and missense SNPs than the genome-wide background, providing genomic evidence that genetic variation may influence feed efficiency through modulation of AS.
These findings provide a new perspective on the biological basis of feed efficiency in fish. By pinpointing specific alternatively spliced transcripts and associated SNPs, the study opens the door to molecular marker-assisted breeding for more efficient carp strains. Improved feed efficiency not only lowers production costs but also reduces nitrogen waste and environmental impacts, contributing to more sustainable aquaculture systems.
