The full-length transcriptome reveals alternative splicing events involved in regulating feed efficiency in Jian carp (Cyprinus carpio var. jian)

Feed efficiency is a pivotal trait impacting aquaculture's profitability. This study focused on Jian carp to explore the genetic mechanisms underlying the feed efficiency of fish from the perspective of alternative splicing (AS). Through the combined analysis of PacBio full-length transcriptome sequencing and Illumina transcriptome sequencing data, a total of 70,422 full-length transcripts were identified from the liver of Jian carp, among which 200 transcripts showed significant expression differences between the low residual feed intake (LRFI) and high residual feed intake (HRFI) groups. A subset of 71 differentially expressed transcripts (DETs) were identified as alternatively spliced transcripts derived from 64 genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations suggested that these AS events might influence feed efficiency in Jian carp by influencing the lysine degradation and fatty acid degradation pathways. Prediction of amino acid sequences, identification of structural domains, and three-dimensional protein structure predictions revealed significant structural differences between proteins encoded by differentially expressed alternatively spliced transcripts and other transcripts for key candidate genes: acsl4a and Hadha. Whole-genome resequencing was employed to identify single nucleotide polymorphisms (SNPs) within the genome of Jian carp. SNP annotation using SnpEff indicated that a higher proportion of SNPs associated with the 64 differentially spliced genes altered the transcript splicing regions and introduced nonsense mutations compared with the general SNP population. This study unveiled the involvement of AS events in regulating the function of specific genes, thereby affecting the feed efficiency of Jian carp. The findings contribute to the comprehension of the regulatory network governing fishes' feed efficiency and provide potential directions for exploring methods to improve feed efficiency in these fish.