RNA deep sequencing reveals novel transcripts and pathways involved in the unsaturated fatty acid metabolism in chicken

Abstract

Fatty acids in chicken meat especially the unsaturated fatty acids (UFA) contribute in the nutritional value, meat quality, and human health. A deeper knowledge in the genomics of fatty acids (FA) is important as it identifies effective markers to be used in marker-assisted breeding in chickens for higher UFA leading to the economic benefits in chicken production industry. Therefore, this study aimed to investigate trancriptome profilling in the liver tissues collected from chicken with divergent UFA contents in the breast muscle tissues using RNA deep-sequencing. Liver tissues from chicken with higher (n = 3) and lower (n = 3) UFA were analysed using Illumina HiSeq 2500. The total number of reads produced for each liver sample ranged from 24.30 to 29.97 million. Approximately 367 genes were differentially regulated with the significance level of p-adjusted value <0.05. Among them, 187 genes were up-regulated and 180 were down-regulated (P < 0.01, FC > 1.5) in higher UFA group. Differentially regulated genes in high UFA liver samples were enriched in metabolic processes such as heme binding, sodium channel activity, and iron ion binding. Pathway analysis identified the metabolic pathways, ECM receptor interaction, focal adhesion, peroxisome, Wnt signaling and TGF-Beta signaling pathways which may play important roles in UFA metabolism. Differential gene expression analysis identified candidate genes in the ATP synthesis, apovitellenin, cytochrome P450, hydroxysteroid, solute carrier and stearoyl-CoA desaturase family. These differentially expressed genes and pathways may lead to UFA variation and could be used as genetic marker for UFA traits in chickens. However, further validation is required to confirm the effect of these genes in the UFA-related molecules metabolism in other chicken populations.