miRNA–mRNA network regulation in the skeletal muscle fiber phenotype of chickens revealed by integrated analysis of miRNAome and transcriptome

Abstract

Skeletal muscle fibers are primarily categorized into oxidative and glycolytic fibers, and the ratios of different myofiber types are important factors in determining livestock meat quality. However, the molecular mechanism for determining muscle fiber types in chickens was hardly understood. In this study, we used RNA sequencing to systematically compare mRNA and microRNA transcriptomes of the oxidative muscle sartorius (SART) and glycolytic muscle pectoralis major (PMM) of Chinese Qingyuan partridge chickens. Among the 44,705 identified mRNAs in the two types of muscles, 3,457 exhibited significantly different expression patterns, including 2,364 up-regulated and 1,093 downregulated mRNAs in the SART. A total of 698 chicken miRNAs were identified, including 189 novel miRNAs, among which 67 differentially expressed miRNAs containing 42 up-regulated and 25 downregulated miRNAs in the SART were identified. Furthermore, function enrichment showed that the differentially expressed mRNAs and miRNAs were involved in energy metabolism, muscle contraction, and calcium, peroxisome proliferator-activated receptor (PPAR), insulin and adipocytokine signaling. Using miRNA-mRNA integrated analysis, we identified several candidate miRNA-gene pairs that might affect muscle fiber performance, viz, gga-miR-499-5p/SOX6 and gga-miR-196-5p/CALM1, which were supported by target validation using the dual-luciferase reporter system. This study revealed a mass of candidate genes and miRNAs involved in muscle fiber type determination, which might help understand the molecular mechanism underlying meat quality traits in chickens. Improving meat quality has long been a goal of broiler breeding programs, especially for Chinese native breeds 1,2. However, meat quality is difficult to define because it is a complex trait influenced by numerous factors 3. As the main tissue determining meat quality, skeletal muscle is a heterogeneous tissue composed of different types of muscle fibers, varying in their biochemical and structural characteristics. Previous studies have found that different types of muscle fibers can influence meat quality traits, including meat color, tenderness, water-holding capacity, juiciness, and flavor 4,5. In chickens, myofiber can be divided into red and white fibers, which are referred to as oxidative (type I and IIA) and glycolytic fibers (type IIB), respectively. Oxidative fibers exhibit slow contractility and oxidative metabolism based on mitochondrial oxidative phosphorylation, whereas glycolytic fibers have fast contractility and glycolytic metabolism 6,7. Although the differences between various muscle fiber types in physiology and functionality have been well studied, the molecular regulation of their specification and maintenance in chickens remains largely unknown 8,9. miRNAs are highly conserved non-coding small RNAs that regulate gene expression at the post-transcriptional level in most biological processes. Emerging evidence has demonstrated that miRNAs are involved in

Increasing Fat Deposition Via Upregulates the Transcription of Peroxisome Proliferator-Activated Receptor Gamma in Native Crossbred Chickens

“…[29] reported the function of miRNA-122 in adipose tissue by opposite expression trend to PPARG. Intramuscular fat deposition also reported a relationship with miRNA function showed that the expressed miRNAs and there were involved in energy metabolism, glycerophospholipid metabolism, fatty acid elongation, and degradation pathways, insulin signaling, and PPAR function via miRNA-499-5p/SOX6 and miRNAs-196-5p/CALM1 [30,31]. This adipogenic regulation was described by [30] to demonstrate that intramuscular adipocyte differentiation was controlled via miRNA-140-5p promote targeting retinoid X receptor gamma, which co-activated function with PPAR and lead to mRNA levels of the PPARG and A-FABP increased with adipocyte differentiation.…”

Regulation of Non-Coding RNA in the Growth and Development of Skeletal Muscle in Domestic Chickens

“…Liu et al (2020) systematically compared the mRNA and miRNA transcriptomes of oxidative muscle sartorius (SART) and glycolytic muscle pectoralis major (PMM) in Chinese Qingyuan partridge chickens using RNA sequencing. They found that MiR-499-5p and MiR-196-5p were most abundant and upregulated in SART and demonstrated that MiR-499-5p targets SOX6 (a repressor of slow muscle-specific gene expression), whereas MiR-196-5p targets CALM1 (a key component of the cGMP-PKG and calcium signaling pathways), both together regulating slow muscle fiber formation [ 1 ].…”

“…Chicken is a high-quality animal protein and is the most widely consumed meat product in the world ( , accessed on 14 May 2022). Meat is a major end product of poultry production, and the skeletal muscle, which makes up most of the meat and is the most valuable part of chicken meat products, is strongly linked to meat production and quality [ 1 ]. Skeletal muscle formation is based on the process of myogenesis, which is a multi-step process [ 2 ], and in domestic chicken is separated into two stages: embryonic and postnatal.…”

Comparative Transcriptome Analysis Reveals the Mechanism Associated With Dynamic Changes in Meat Quality of the Longissimus Thoracis Muscle in Tibetan Sheep at Different Growth Stages

“…The previous studies have identified that the different types of muscle fibers to influence many meat quality traits such as the water-holding capacity (WHC), tenderness, color, juiciness, and flavor ( 15 ). Liu et al ( 16 ) demonstrated CaN/NFAT as an important signaling pathway, regulating the transformation of the chicken muscle fiber types. Zhu et al ( 17 ) found MYH6 and Ca 2+ signaling pathways to regulate the muscle fiber types of skeletal muscle in large white pigs.…”