Comparative Transcriptome Profiling Analysis Uncovers Novel Heterosis-Related Candidate Genes Associated with Muscular Endurance in Mules

SIMPLE SUMMARY: Mules have better and greater muscle endurance than hinnies and their parents. However, the molecular mechanisms underlying heterosis in their muscles are still much less understood. In this study, we conducted comparative transcriptome and alternative splicing analysis on the heterosis mechanism of muscular endurance in mules. Our results showed that 8 genes were significantly enriched in the “muscle contraction” pathway. In addition, 68% of the genes with alternative splicing events from the mule muscle tissue were validated by the long transcript reads generated from PacBio sequencing platform. Our findings provide a research foundation for studying the genetic basis of heterosis in mules. ABSTRACT: Heterosis has been widely exploited in animal and plant breeding programs to enhance the productive traits of hybrid progeny from two breeds or species. However, its underlying genetic mechanisms remain enigmatic. Transcriptome profiling analysis can be used as a method for exploring the mechanism of heterosis. Here, we performed genome-wide gene expression and alternative splicing (AS) analyses in different tissues (muscle, brain, and skin) from crosses between donkeys and horses. Our results indicated that 86.1% of the differentially expressed genes (DEGs) and 87.2% of the differential alternative splicing (DAS) genes showed over-dominance and dominance in muscle. Further analysis showed that the “muscle contraction” pathway was significantly enriched for both the DEGs and DAS genes in mule muscle tissue. Taken together, these DEGs and DAS genes could provide an index for future studies of the genetic and molecular mechanism of heterosis in the hybrids of donkey and horse.