| Heterosis refers to the phenomenon that hybrid progeny of different species or different breeds of a specie is superior to parents in growth,reproduction,resistance,etc.Mule is an interspecific hybrid of horse and donkey,with heterosis phenotypes such as muscle endurance,cognitive ability,body size,disease resistance and longevity.In this study,transcriptome sequencing of muscle,brain and skin tissues of horses,donkeys,mules and hinnies was performed to obtain the differentially expressed genes(DEGs)and differential alternatively spliced genes(DASGs).Through the functional enrichment,the pathways and genes associated with the phenotype related to the heterosis of mules have been found.Finally,a partial differential splicing event was verified by using full-length transcriptions.The main findings are as follows:1.Differentially expressed genes between the mules and their parents,hinnies and their parents in muscle,brain and skin tissues were obtained by transcriptome analysis.According to the expression relationship between hybrid animals and their parents,the differentially expressed genes were divided into five types,high-parent dominance genes,low-parent dominance genes,over-dominance genes,under-dominance genes and additivity genes.Among them,high-parent dominant genes and low-parent dominant genes can correspond to the existing dominant hypothesis,while superdominant genes and ultralow dominant genes are consistent with the definition of overdominant hypothesis.After classifying the differentially expressed genes,pathway enrichment analysis was performed on each gene set,and the pathways related to the control organ size were enriched in the overdominant gene set,which may be related to the traits of the mules’ big body size.2.By clustering the alternative splicing events of all samples,it was found that the difference in the proportion of alternative splicing events can reflect the differences between different tissues and different animals.Further,the bioinformatics method was used to calculate the difference between the mules and thiers parents,the hinnies and thiers parents in the muscle,brain and skin tissues,and no more than 12.64% genes were found both in differentially expressed genes and differential alternatively spliced genes.Pathway enrichment analysis with differential splicing genes significantly enriched the muscle contraction pathway in muscle tissue,which may be related to the muscular endurance in mules.In brain tissue,neuronal system and axon guidance pathway are enriched,which may be related to the cognitive ability of mules.3.The pathway enrichment analysis was perfromed with differentially expressed genes and differentially alternatively spliced genes.The muscle contraction pathway was significantly enriched in muscle tissue,including 48 differentially expressed genes,26 differentially alternatively spliced genes,and 8 genes are both of them.In the eight genes,the TNNC2 gene can regulate the contraction of skeletal muscle.When the expression of RYR1 gene increases,the content of type I muscle fiber increase,too.And the type I muscle fiber is mainly responsible for endurance activities.This provides a reliable candidate gene list for explaining the heterosis of mule in muscle endurance.4.Through the quality controlling and correction,a total of 121,384 full-length transcriptions were obtained from the Full-length transcription of the mule.These transcripts can cover a total of 6,311 genes and 951 genes of 1,402 differentially spliced genes.In summary,through the transcriptome analysis of mules,hinnies and their parents,we identified differentially expressed genes and differential alternative splicing genes between different tissues of different animals,providing a gene list possiblely related to the musclar endurance,cognition and body size by enrichment analysis.Validating some differential alternative splicing genes by the full-length transcriptome data. |
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