RNA-seq reveals transcriptome changes in goats following myostatin gene knockout

Myostatin (MSTN) is a powerful negative regulator of skeletal muscle mass in mammalian species that is primarily expressed in skeletal muscles, and mutations of its encoding gene can result in the double-muscling trait. In this study, the CRISPR/Cas9 technique was used to edit MSTN in Shaanbei Cashmere goats and generate knockout animals. RNA sequencing was used to determine and compare the transcriptome profiles of the muscles from three wild-type (WT) goats, three fibroblast growth factor 5 (FGF5) knockout goats (FGF5(+/-) group) and three goats with disrupted expression of both the FGF5 and MSTN genes (FM(+/-) group). The sequence reads were obtained using the Illumina HiSeq 2000 system and mapped to the Capra hircus reference genome using TopHat (v2.0.9). In total, 68.93, 62.04 and 66.26 million clean sequencing reads were obtained from the WT, FM(+/-) and FGF5(+/-) groups, respectively. There were 201 differentially expressed genes (DEGs) between the WT and FGF5(+/-) groups, with 86 down- and 115 up-regulated genes in the FGF5(+/-) group. Between the WT and FM(+/-) groups, 121 DEGs were identified, including 81 down- and 40 up-regulated genes in the FM(+/-) group. A total of 198 DEGs were detected between the FGF5(+/-) group and FM(+/-) group, with 128 down- and 70 up-regulated genes in the FM(+/-) group. At the transcriptome level, we found substantial changes in genes involved in fatty acid metabolism and the biosynthesis of unsaturated fatty acids, such as stearoyl-CoA dehydrogenase, 3-hydroxyacyl-CoA dehydratase 2, ELOVL fatty acid elongase 6 and fatty acid synthase, suggesting that the expression levels of these genes may be directly regulated by MSTN and that these genes are likely downstream targets of MSTN with potential roles in lipid metabolism in goats. Moreover, five randomly selected DEGs were further validated with qRT-PCR, and the results were consistent with the transcriptome analysis. The present study provides insight into the unique transcriptome profile of the MSTN knockout goat, which is a valuable resource for studying goat genomics.