Identification of RNA isoforms expressed in skeletal muscle of native and commercial chickens by sequencing method

This experiment was conducted to investigate and identify the isoforms related to the structure of muscular proteins between Isfahani native and Ross commercial chickens with different growth rates. We extracted total RNA from breast muscle samples of two groups at end of 4 weeks of age. After paired-end sequencing of samples using the Illumina Hiseq 2000 platform, Hisat2 was applied to align clean reads to chicken reference genome. Then, Cufflinks package was used to assemble transcripts and identify significantly differentially expressed genes. The statistical comparison of the isoforms between two groups revealed 259 isoforms with significant difference in expression, of which 161 isoforms were up-regulated and 98 isoforms were downregulated in commercial chickens. Among the commercial chicken isoforms, four genes (ACTC1, ATF3, CYR61 and FABP4) were upregulated with two different isoforms. In addition, in commercial chicks, the frequency of isoforms associated with slow contraction fibers was greater than that of rapid contraction fibers. Functional study showed that the isoforms in commercial chickens were more related to cell proliferation and differentiation, hypertrophy growth and biosynthesis of muscle proteins, whereas in native chickens, mainly they were associated to immune processes, carriers of ions and metals, binding to metals, DNA and RNA, and factors contributing to degradation of muscle proteins. The results of this study showed that such changes may have been able to strengthen the ability to maintain and overcome the severe environmental and nutritional conditions during the developmental period of the chicken by reducing the level of requirements and enhancing immunity and adaptability in native chicken.