Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq

Abstract

Skeletal muscle, accounting for approximately 50% of body weight, is the largest and most important tissue. In this study, the gene expression profiles and pathways in skeletal muscle of Pekin duck were investigated and compared at embryonic day 17, 21, and 27 and postnatally at 6 months of age. An average of 49,555,936 reads in each sample was obtained from the transcriptome libraries. Over 70.0% of alternative splicing (AS) in each sample was mainly alternative 5’ first exon (transcription start site)-the first exon splicing (TSS) and alternative 3’ last exon (transcription terminal site)-the last exon splicing (TTS), indicating that TSS and TTS were the most common AS event in Pekin ducks, and these AS events were closely related to the regulation of muscle development at different growth stages. The results provided a valuable genomic resource for selective breeding and functional studies of genes. A total of 299 novel genes with ≥2 exons were obtained. There were 294 to 2806 differentially expressed genes (DEGs) in each pairwise comparison of Pekin duck. Notably, 90 DEGs in breast muscle and 9 DEGs in leg muscle were co-expressed at all developmental points. DEGs were validated by qPCR analysis, which confirmed the tendency of the expression. DEGs related to muscle development were involved in biological processes such as “endodermal cell differentiation”, “muscle cell cellular homeostasis”, “skeletal muscle tissue growth” and “skeletal muscle cell differentiation”, and were involved in pathways such as oxidative phosphorylation, ECM-receptor (extracellular matrix receptor) interaction, focal adhesion, carbon metabolism, and biosynthesis of amino acids. Some DEGs, including MYL4, IGF2BP1, CSRP3, SPP1 and KLHL31, as well as LAMB2, LAMA2, ITGB1 and OPN, played crucial roles in muscle growth and development. This study provides valuable information about the expression profile of mRNAs and pathways from duck skeletal muscle at different growth stages, and further functional study of these mRNAs and pathways could provide new ideas for studying the molecular networks of growth and development in duck skeletal muscle.

Population structure and genomic footprints of selection in five major Iranian horse breeds

“…For example, increased muscle glycogen and muscle fiber hypertrophy are two important phenomena of muscular adaptations to training that can affect strength and stamina of endurance horses respectively (Rivero, 2007). Interestingly, our results highlighted eight genes—ATPase sarcoplasmic/endoplasmic reticulum Ca 2+ transporting 2 ( ATP2A2 ), mitogen‐activated protein kinase 10 ( MAPK10 ), protein kinase AMP‐activated non‐catalytic subunit gamma 2 ( PRKAG2 ), myoferlin ( MYOF ), glutamate decarboxylase like 1 ( GADL1 ), lysine demethylase 2B ( KDM2B ), growth arrest specific 2 ( GAS2 ), and calcium voltage‐gated channel subunit α1 A ( CACNA1A )—as genes participating in muscle contraction (Ropka‐Molik et al, 2017), equine skeletal muscle adaptations to exercise (Bryan et al, 2017), muscular glycogenosis (Laforêt et al, 2006), muscle dystrophy regulation (Davis et al, 2000), regulation of muscle strength (Mahootchi et al, 2020), skeletal muscle differentiation (Kwon et al, 2021), muscle synthesis (Hu et al, 2021), and regulation of muscular hypotonia (Reinson et al, 2016) respectively. However, McQueen et al (2014) also revealed the contribution of an SNP (rs68536711) located in the equine MYOF gene in foals Rhodococcus equi infection susceptibility.…”

Comprehensive Analysis of Transcriptome and Metabolome Reveals Regulatory Mechanism of Intramuscular Fat Content in Beef Cattle

“…ITGB1 -mediated signaling pathway was responsible for regulating the migration and differentiation of satellite cell derived from bovine skeletal muscle . In addition, it may play a crucial role in skeletal muscle growth and development in ducks . On the other hand, a study shows that expression of β1 and β3 integrins in adipose tissues is positively correlated with obesity in humans and integrin signaling regulates insulin signaling in adipocytes in vivo .…”

“…32 In addition, it may play a crucial role in skeletal muscle growth and development in ducks. 33 On the other hand, a study shows that expression of β1 and β3 integrins in adipose tissues is positively correlated with obesity in humans and integrin signaling regulates insulin signaling in adipocytes in vivo. 34 Meanwhile, β1 integrins also interact with the IGF1R 35 and adipocytes express IR/IGF1R hybrid receptors.…”

RNA-Seq Reveals miRNA and mRNA Co-regulate Muscle Differentiation in Fetal Leizhou Goats

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