Analysis of Differential Gene Expression and Novel Transcript Units of Ovine Muscle Transcriptomes

Abstract

In this study, we characterized differentially expressed genes (DEGs) between the muscle transcriptomes of Small-tailed Han sheep and Dorper sheep and predicted novel transcript units using high-throughput RNA sequencing technology. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that 1,300 DEGs were involved in cellular processes, metabolic pathways, and the actin cytoskeleton pathway. Importantly, we identified 34 DEGs related to muscle cell development and differentiation. Additionally, we were able to optimize the gene structure and predict the untranslated regions (UTRs) for some of the DEGs. Among the 123,678 novel predicted transcript units (TUs), 15,015 units were predicted protein sequences. The reliability of the sequencing data was verified through qRT-PCR analysis of 12 genes. These results will provide useful information for functional genetic research in the future.

Comparative Transcriptome Analysis Identifying the Different Molecular Genetic Markers Related to Production Performance and Meat Quality in Longissimus Dorsi Tissues of MG × STH and STH Sheep

“…The GO terms and pathways with p < 0.01 and Q < 0.01 were considered to be significantly enriched. We selected the DEGs from the GO terms and pathways that included the keywords "development", "growth", "muscle", "fiber", "myofibril", "myoblast", and "fat" (the potential targets involved in sheep production performance and meat quality, according to previous studies) [1,3,9,19]. A correlation analysis [29,30] between the significantly different indexes of the production performance and meat quality (p < 0.001) and the DEGs was conducted using the edgeR package with generalized linear mixed models (GLMMs) [31] to identify the multiple-traitand trait-associated DEGs in the two sheep.…”

“…Mutton is an important protein source for humans and accounts for a large percentage of meat consumption in China [1]. With improvements in human living standards, the demand for high-quality meat and nutrition has also increased.…”

“…Comparative transcriptome analyses have also identified some important differentially expressed genes (DEGs), particularly metallothionein 3 (MMP3), related to a curly fleece in Chinese Tan sheep [13]. Overall, the genome-wide screening of crossbred and indigenous sheep breeds has identified some specific trait-associated genetic molecules, including MYOD1, MYOG, and IGFBPs [1,3,14]. However, understanding of the differences between the phenotypic and genetic aspects of different sheep breeds remains limited.…”

Correlation between gene expression profiles in muscle and live weight in Dzhalginsky Merino sheep

“…There are several methods to study gene expression, including sequencing cDNAs obtained by reverse transcription Zhang et al, 2014), estimating the number of cDNAs by hybridization on biochips (Lobo et al, 2012), and reverse transcription-quantitative real-time PCR (Sun et al, 2014). The latter method is the most accurate and is used to validate the results obtained with microarray hybridization (Lobo et al, 2012).…”

Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos

“…Although some DEGs between skeletal muscles have recently been identified in several species, such as pigs [ 18 , 19 ], mice [ 20 ], turkey [ 8 ], sheep [ 21 ], and dog [ 22 ], the molecular mechanism underlying muscle development in duck remains unclear. Here, we analyzed the DEGs between duck breeds with different growth rates using RNA-Seq technology.…”