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

Chicken prolactin (PRL) is a physiological candidate gene for egg production. Variations of T8052C and G8113C in exon 5 of PRL gene may associate with chicken egg production. The objective of the study was to investigate the association of these two single nucleotide polymorphisms in PRL gene with egg production of Recessive White chickens and Qingyuan Partridge chickens. Genotyping was performed by polymerase chain reaction-ligase detection reaction (PCR-LDR) method. The T8052C and G8113C of PRL were significantly associated with age at first egg (AFE) and total egg number at 300 days of age (EN 300). A significant association was also found between T8052C-G8113C haplotypes and AFE as well as EN300, the H2H3 was the most advantageous diplotype for egg production. We putatively drew the conclusion that these two SNPs in PRL gene as well as their haplotypes could be used as the potential molecular markers for egg production traits in chicken.

Back and thigh skin of chickens showed significant differences in the thickness and the feather follicle density and size, which are important traits for slaughtered chickens' appearance. In the present study, global gene expression profiling was conducted in the back and thigh skin of chickens using Microarray technology. The results showed that 676 genes were differentially expressed between back and thigh skin. The expression of the differentially expressed genes (DEGs), including PPP1R3C, IGF1, PTCHD1, HOXB6, FGF9, CAMK4, SHH, BMP8B, FOXN1 and PTGER2, was validated by real‐time quantitative polymerase chain reaction (RT‐qPCR), and the results were consistent with microarray results. Functional analysis revealed that the DEGs were significantly involved in cell proliferation, differentiation, apoptosis, adhesion and transport process, and the pathways were significantly mapped into the ECM‐receptor interaction, peroxisome, focal adhesion, Hedgehog and PPAR signalling pathways. Protein–protein interaction network analysis suggested that signalling pathways related to feathers morphogenesis and development, such as Wnt, FGF, MAPK, SHH and BMP signalling pathways, occupied important positions in the network. Genes involved in these signalling pathways and adhesion molecules might play a vital role in skin and feather follicle development. Further single nucleotide polymorphism (SNP) association analysis of Wnt3A showed that the AC genotype of SNP g.255361 C>A significantly increased the feather follicle density of thigh skin. Our findings may provide new insights on candidate genes and pathways related to skin and feather follicle formation of chickens.

ABSTRACT. The micromolar calcium-activated neutral protease gene (CAPN1) is a physiological candidate gene for meat tenderness. Four previously identified single nucleotide polymorphism (SNP) markers located within the CAPN1 gene were evaluated for their associations with variation in the meat tenderness of a Chinese indigenous chicken breed, a higher meat quality breed (i.e., Qingyuan partridge chicken), and the commercial Recessive White chicken breed. WarnerBratzler shear force measurements were used to determine tenderness phenotypes for all animals; intramuscular fat (IMF) content and rate of water loss in the breast muscles were also measured. Genotyping was performed by the polymerase chain reaction-ligase detection reaction method. Polymorphisms were identified for all markers, except CAPN1 2546. The frequency of allele T was zero, and allele C was fixed for CAPN1 2546 in the studied populations. The SNP CAPN1 3535 in the CAPN1 gene was significantly associated with tenderness and other meat quality traits, where animals inheriting the AA genotype had smaller shear force values, lower water loss rates, and higher IMF contents. Moreover, H1 (AAA) was the most advantageous haplotype for meat tenderness. The results of this study confirm some previously documented associations. Furthermore, novel associations have been 1393-1403 (2015) identified that, following validation in other populations, could be incorporated into breeding programs to improve meat quality.