Transcriptome analysis reveals the role of long noncoding RNAs in specific deposition of inosine monphosphate in Jingyuan chickens.

ABSTRACT

Inosine monphosphate (IMP) is one of the important indicators for evaluating meat flavor, and long noncoding RNAs (lncRNAs) play an important role in its transcription and post-transcriptional regulation. Currently, there is little information about how lncRNA regulates the specific deposition of IMP in chicken muscle. In this study, we used transcriptome sequencing to analyze the lncRNAs of the breast and leg muscles of the Jingyuan chicken and identified a total of 357 differentially expressed lncRNAs (DELs), of which 158 were up-regulated and 199 were down-regulated. There were 2,203 and 7,377 cis- and trans-regulated target genes of lncRNAs, respectively, and we identified the lncRNA target genes that are involved in NEGF signaling pathway, glycolysis/glucoseogenesis, and biosynthesis of amino acids pathways. Meanwhile, 621 pairs of lncRNA-miRNA-mRNA interaction networks were constructed with target genes involved in purine metabolism, fatty acid metabolism, and biosynthesis of amino acids. Next, three interacting meso-networks gga-miR-1603-LNC_000324-PGM1, gga-miR-1768-LNC_000324-PGM1, and gga-miR-21-LNC_011339-AMPD1 were identified as closely associated with IMP-specific deposition. Both differentially expressed genes (DEGs) PGM1 and AMPD1 were significantly enriched in IMP synthesis and metabolism-related pathways, and participated in the anabolic process of IMP in the form of organic matter synthesis and energy metabolism. This study obtained lncRNAs and target genes affecting IMP-specific deposition in Jingyuan chickens based on transcriptome analysis, which deepened our insight into the role of lncRNAs in chicken meat quality.

Jingyuan chicken is an excellent local chicken breed listed in the Catalogue of Livestock and Poultry Genetic Resources of China. Its unique growing environment has enabled Jingyuan chicken to develop the characteristics of compact meat, unique flavor, and high nutritional value, which makes it the first choice for chicken food. Inosine monophosphate (IMP) is widely recognized as an important indicator for evaluating the flavor of livestock and poultry meat. To mine potential long noncoding RNAs (lncRNAs) and their regulatory IMP-specific deposition interaction networks, we used transcriptome sequencing to identify 357 lncRNAs that were differentially expressed in breast and leg muscles of 180-d-old Jingyuan hens. We screened the key lncRNAs affecting IMP and three lncRNA-miRNA-mRNA regulatory networks by bioinformatics methods. This provides a new approach to studying IMP-specific deposition, improvement of chicken meat flavor, and breed improvement in Jingyuan chickens.