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

Shan Gao,Zhichao Wang,Xuelei Dai,Yu Jiang,Hojjat Asadollahpour Nanaei,Bin Wei,Xihong Wang,Yu Wang,Zongjun Li,Junjie Shao

doi:10.3390/ani10060980

Abstract

Simple SummaryMules 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.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.

Highlights

Heterosis, known as hybrid vigor, refers to the phenomenon that hybrids exhibit superior performance in areas such as stress resistance, fertility, growth rate, and biomass production compared with their parental inbred lines [1,2,3]
Our results showed that more than of 601, 427, and 482 million clean reads were retained from muscle, brain, and skin tissues, respectively, after removing the adaptor and low-quality reads
Our results showed that the gene expression the divergence between hybrids and either of their parents can be indicated by differentially expressed genes (DEGs) and differential alternative splicing (DAS) genes

Summary

Introduction

Known as hybrid vigor, refers to the phenomenon that hybrids exhibit superior performance in areas such as stress resistance, fertility, growth rate, and biomass production compared with their parental inbred lines [1,2,3] This phenomenon has been widely used in breeding programs, by mating two different pure-bred lines, to improve the quantity of both crops [4,5,6] and livestock production [7,8,9]. Animals 2020, 10, 980 model defines that allelic interactions at a single locus or more loci lead to increased vigor. Unlike these two models, the third model explains interactions between nonallelic genes, which are created due to new combinations in the hybrid. With the development of functional genomics and the improvement of RNA sequencing (RNA-seq) technologies, the molecular basis of heterosis has been investigated at the transcriptional level of gene expression in several plant and animal species such as cattle [14], mice [15], pig [16], chicken [17], coral reef butterflyfish [18], and crossed lamb [19]

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