Abstract

Background:
Pesisir cattle are one of the indigenous livestock genetic resources in Indonesia. They have a high capacity to adapt to tropical environments. However, information about their transcriptomic profile is limited.

Aim:
This study aimed to analyze the liver transcriptomic profile and identify differentially expressed genes in Pesisir cattle with distinct phenotypes (high and low body weight) using RNA-seq technology.

Methods:
Liver tissue samples were taken from 2 groups of adult female Pesisir cattle: high body weight (LivHigh01) and low body weight (LivLow01). RNA was extracted, and libraries were prepared. Sequencing was performed using the Illumina NovaSeq 6000 platform. Bioinformatics analysis included quality control, read mapping, gene expression quantification, and differential gene expression (DGE) analysis. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for variant calling and functional analysis.

Results:
Gene expression distribution across samples was relatively uniform. Differential gene expression (DGE) analysis identified a limited number of significant genes, predominantly downregulated genes. Gene Ontology (GO) analysis revealed the involvement of genes in immune system processes and responses to stimuli, albeit with limited statistical significance. In contrast, KEGG analysis identified 2 significantly enriched pathways, namely, glycosphingolipid biosynthesis and nicotinate and nicotinamide metabolism. Genetic variation analysis demonstrated an increased proportion of missense variants in the high body weight group.

Conclusion:
Differences in body weight in Pesisir cattle are not driven by global changes in gene expression but rather by the specific regulation of a subset of genes involved in energy metabolism pathways and cellular functions.

Key words: Body weight; Differential gene expression; Liver transcriptome; Pesisir cattle; RNA-seq.