Characterization and Comparative Analyses of Muscle Transcriptomes in Dorper and Small-Tailed Han Sheep Using RNA-Seq Technique

Abstract

The sheep is an important domestic animal and model for many types of medically relevant research. An investigation of gene expression in ovine muscle would significantly advance our understanding of muscle growth. RNA-seq is a recently developed analytical approach for transcriptome profiling via high-throughput sequencing. Although RNA-seq has been recently applied to a wide variety of organisms, few RNA-seq studies have been conducted in livestock, particularly in sheep. In this study, two cDNA libraries were constructed from the biceps brachii of one Small-tailed Han sheep (SH) and one Dorper sheep (DP). The Illumina high-throughput sequencing technique and bioinformatics were used to determine transcript abundances and characteristics. For the SH and DP libraries, we obtained a total of 50,264,608 and 52,794,216 high quality reads, respectively. Approximately two-thirds of the reads could be mapped to the sheep genome. In addition, 40,481 and 38,851 potential coding single nucleotide polymorphisms (cSNPs) were observed, respectively, of which a total of 59,139 cSNP coordinates were different between the two samples. Up to 5,116 and 5,265 respective reference genes had undergone 13,827 and 15,684 alternative splicing events. A total of 6,989 reference genes were extended at the 5’, 3’ or both ends, and 123,678 novel transcript units were found. A total of 1,300 significantly differentially expressed genes were identified between the two libraries. These results suggest that there are many differences in the muscle transcriptomes between these two animals. This study addresses a preliminary analysis and offers a foundation for future genomic research in the sheep.

Comparative analysis of the liver tissue transcriptomes of Mongolian and Lanzhou fat-tailed sheep

“…In the two sheep breeds, we found similar AS rates, with 35.69, 34.03, 34.50, 38.33, 37.46, and 30.54% of the reference genes in the six libraries undergoing 24,239,22,283,22,457,26,635,27,093, and 18,700 AS events. This is much lower than that reported for humans (86.0%) (Wang et al, 2008), but is higher than that reported for pigs (18.0%) (Chen et al, 2011), sheep (25.28-26.02%) (Zhang et al, 2013), and rice (33.0%) (Zhang et al, 2010). The most common AS identified in our research was IR, in both Mongolian and Lanzhou fat-tailed sheep.…”

“…The most common AS identified in our research was IR, in both Mongolian and Lanzhou fat-tailed sheep. Our results were similar to those for rice (Zhang et al, 2010), but different from those for pigs (Chen et al, 2011) and Dorper and small-tailed Han sheep (Zhang et al, 2013), in which A3SS was identified as the most common AS. Our results also differed from those of humans (Sultan et al, 2008), in which ES was the primary type of AS.…”

Energy requirements for the maintenance and growth of Dorper-Jinzhong crossbred ram lambs

“…The Dorper breed of sheep is a fast-growing meat-producing sheep originated from South Africa, and is renowned for its hardiness, early sexually maturity, lean carcass and high growth rate. The breed has been widely used as a terminal sire breed to improve the growth performance and carcass traits of lambs (Zhang et al 2013;Xing et al 2014). The Jinzhong breed is an indigenous sheep breed that demonstrates strong adaptability to local conditions in Shanxi province, China.…”

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

“…Studies of gene expression profiles in sheep muscles by Lobo et al (2012) revealed differential expression of MyoD1 and IGFBP4 genes associated with breed and productive qualities. In addition, Zhang et al (2013) studied gene expression in two sheep breeds by RNA sequence analysis and revealed significant differences in more than 1,300 genes. Continued research has allowed these researchers to describe 34 genes with differential expression related to the development and differentiation of muscle cells .…”