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

<div><p>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 <i>MSTN</i> 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 (<i>FGF5</i>) knockout goats (FGF5^+/- group) and three goats with disrupted expression of both the <i>FGF5</i> and <i>MSTN</i> genes (FM^+/- group). The sequence reads were obtained using the Illumina HiSeq 2000 system and mapped to the <i>Capra hircus</i> 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 <i>MSTN</i> and that these genes are likely downstream targets of <i>MSTN</i> 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 <i>MSTN</i> knockout goat, which is a valuable resource for studying goat genomics.</p>