Identification of LncRNAs related to growth of chicken’s breast muscle using RNA-seq

This experiment was carried out to identify lncRNAs associated with skeletal muscle of the Isfahan native chicken and the Ross 708 commercial broiler chicken. To do this, after extraction of RNA from the breast muscle samples at the age of 28 days, paired-end sequencing was performed using the Illume Hiseq 2000 platform. Hisat2 software was used to align the clean reads to the chicken reference genome and the Stringtie software was used to assemble the transcripts. A total of 1097 lncRNAs were identified as 925 of which were intergenic and 172 were intronic. Also, the number of novel LncRNAs in intergenic and intronic groups were 432 and 128, respectively. Differential gene expression analysis led to the identification of 19 genes and 20 transcripts differentially expressed lncRNAs between two groups. Syntenic analysis showed that differentially expressed lncRNAs are located near by 45 protein encoding genes. Of these, the expression of five gene coding proteins (SCD gene in commercial chickens and GALNT15, KLHDC4, USP7 and ASB1 genes in native chicken) - whose expression was consistent with the expression of their lncRNA - were significantly expressed between two breeds. Functional enrichment analysis of these genes showed that all of them are involved in the skeletal muscle growth. The results of this study showed that the identified lncRNAs probably have the potential to regulate the genes involved in skeletal muscle growth. In this regard, they possibly cause the differences in growth rates between the two chicken breeds.