Transcriptomic analysis of long non-coding RNA and mRNA in pigeon squab pectoralis muscle development

1. As one of the most widespread poultry species in the world, pigeons have been bred primarily for meat production due to their high nutritional value and good taste. Their breast muscle is an important economic product as it determines the yield and quality of meat from pigeons. 2. Long non-coding RNA (lncRNA) plays an important role in transcription and post-transcriptional regulation, but research on the molecular mechanisms of this process in pectoral muscle development in pigeon squabs is lacking. 3. Herein, RNA sequencing was used to analyse these mechanisms in pigeon squabs at different ages: 3(D3), 14 (D14) and 25 d (D25). A total of 56 169 differentially expressed (DE) lncRNA and 29 939 DE mRNA were identified among the three age groups, of which 483 were differentially co-expressed. A lncRNA–mRNA interaction network was constructed, and cis-trans identification, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. 4. The results showed that lncRNA affected muscle development through the cell cycle, cytoskeleton in muscle cells, motor proteins, extracellular matrix (ECM) receptor interaction, focal adhesion, and other signalling pathways. Five DE lncRNA and mRNA were selected (<i>LTCONS_00073284,LTCONS_00012834</i>, <i>LTCONS_00032767</i>, <i>LTCONS_00041298</i>, <i>LTCONS_00028245;TNNC1</i>, <i>XIRP1</i>, <i>PITX3</i>, <i>COL4A6</i>, and <i>TNNT3</i>). Their expression patterns were validated by reverse transcription-quantitative polymerase chain reaction (RT-QPCR), which were consistent with the high-through sequencing results.