miR-138-5p promotes chicken granulosa cell apoptosis via targeting SIRT1.

Granulosa cell (GC) apoptosis is the main trigger of follicular atresia. MicroRNAs (miRNAs) are 18-22 nt RNAs whose function is primarily determined by their extended seed region and are considered to be involved in the biological functions of follicular development, including follicular atresia, folliculogenesis, and oogenesis. MiR-138-5p is known to act on chicken GCs. In this study, we found that miR-138-5p was enriched in reproductive organs, such as the uterus and ovaries. To examine whether miR-138-5p could regulate the biological process of GCs, miR-138-5p was examined by transfection of cells with a mimic or inhibitor of miR-138-5p. Expression levels of caspase-3 and caspase-9 mRNA and protein were markedly increased or decreased after transfection of the mimic or inhibitor, respectively. Furthermore, following miR-138-5p inhibition, SIRT1, one of the target genes of miR-138-5p, was found to increase the mRNA, which is correlated with the increased levels of BCL2 expression, an anti-apoptotic gene in the chicken GCs. These results suggest that miR-138-5p promotes apoptosis in chicken GCs by targeting SIRT1.

Whole transcriptome analysis reveals the key genes and noncoding RNAs related to follicular atresia in broilers.

Broodiness, a maternal behavior, is accompanied by the atresia of follicles and the serious degradation of poultry reproductive performance. The comparison of follicles between brooding and laying hens is usually an ideal model for exploring the regulation mechanism of follicle atresia. In this study, we selected three brooding hens and three laying hens to collect their follicles for whole transcriptome sequencing. The results demonstrated different expression patterns between the follicles of brooding hens and laying hens. In the top 10 differentially expressed genes with the highest expression, MMP10 was relatively low expressed in the follicles of brooding hens, but other nine genes were relatively highly expressed, including LRR1, RACK1, SPECC1L, ABHD2, COL6A3, RPS17, ATRN, BIRC6, PGAM1 and SPECC1L. While miR-21-3p, miR-146a-5p, miR-142-5p and miR-1b-3p were highly expressed in the follicles of brooding hen, miR-106-5p, miR-451, miR-183, miR-7, miR-2188-5p and miR-182-5p were lowly expressed in brooding hen. In addition, we identified 124 lncRNAs specifically expressed in the follicles of brooding hens and 147 lncRNAs specifically expressed in the follicles of laying hens. Our results may provide a theoretical basis for further exploration of the molecular mechanism of broodiness in broilers.

Whole-genome resequencing reveals aberrant autosomal SNPs affect chicken feathering rate.

Previous studies have shown that the feather growth rate of chicks is determined by two alleles located on the sex chromosome Z; however, in chicken production, feathering is usually not consistently controlled by the sex chromosome. To identify whether the feathering rate is related to autosomal inheritance, whole-genome resequencing was performed in eight chickens with slow- and fast-feathering rate. A total of 54,984 autosomal single nucleotide polymorphisms (SNPs) were identified, including 393 and 376 exonic SNPs in slow-feathering and fast-feathering chickens, respectively. Mutated genes were mainly involved in response to stimuli and growth and reproduction processes. Mutated genes related to slow-feathering rate were mainly involved in wingless-type MMTV integration site signaling pathway and mitogen-activated protein kinase signaling pathway, whereas mutated genes associated with fast-feathering rate were primarily enriched in autophagy, calcium signaling pathway, extracellular matrix-receptor interaction, and Focal adhesion processes. Importantly, two SNPs, involved in feather development, were found in the exonic regions of Wnt signaling genes. These results shed new light on the relationship between genetic mutation and feather growth rate from the perspective of autosomal inheritance and may have economic significance in chicken breeding.

Effects of Lactobacillus plantarum on growth traits, slaughter performance, serum markers and intestinal bacterial community of Daheng broilers.

Probiotics are expected to be an ideal alternative for antibiotics in the poultry industry. This study aimed to investigate the effect of Lactobacillus plantarum on growth traits, slaughter performance, serum markers and intestinal bacterial community of Daheng broilers. A total of 2400 healthy one-day-old Daheng broilers were randomly divided into 5 groups with 6 replicates per group and 40 individuals per replicate. Birds in control group were fed a basal diet, and others were fed basal diets supplemented with 105 , 106 , 107 and 108  CFU/kg Lactobacillus plantarum, respectively. It turned out that adding Lactobacillus plantarum to diet could significantly improve the serum immune performance of broilers (p < 0.05), enhance the antioxidant capacity to a certain extent (p > 0.05), but had no significant effect on growth traits and slaughter performance. Moreover, Lactobacillus plantarum could improve the diversity of intestinal bacterial community, but with the increase of addition concentration, the diversity would gradually decrease. In conclusion, Lactobacillus plantarum can be used as feed additive in broiler production, but whether it is more effective than antibiotics needs further investigation.

Transcriptomics analysis of Daheng broilers reveals that PLIN2 regulates chicken preadipocyte proliferation, differentiation and apoptosis.

BACKGROUND: Intramuscular fat content, an important meat quality trait, strongly affects flavor, juiciness, and tenderness. Sex hormones regulate lipid metabolism, and female hormones stimulate fat deposition, thereby making the female chickens always fatter than males. In this study, the effect of sex on IMF deposition was screened following transcriptomics in chickens. METHODS AND RESULTS: Results confirmed significantly higher IMF content of 150-day female chickens as compared to the male chickens. The female chickens manifested higher serum TG, LDL-C, and VLDL, and significantly lower HDL-C contents than male chickens. Moreover, differential expression of genes involved in lipid metabolism were obtained in the muscle and liver between female and male chicken, which could partly interpret the possible reasons for the sex-mediated differences of IMF content. Cellular results revealed that inhibition of PLIN2 significantly inhibited chicken preadipocyte proliferation and induces apoptosis of preadipocytes, as well as promoted adipocyte differentiation. CONCLUSIONS: According to our results, PLIN2 may be considered as a molecular marker for poultry meat quality and applying this gene in early breed selection.

Small RNA sequencing of pectoral muscle tissue reveals microRNA-mediated gene modulation in chicken muscle growth.

Sichuan mountainous black-bone (SMB) chicken is a small-sized black-feathered chicken breed with low amount of meat, while Dahen (DH) chicken has a larger body size and a faster growth rate. MicroRNAs (miRNAs) are involved in various physiological processes, but their role in chicken muscle growth remains unclear. We aimed to investigate the miRNAs and pathways participating in the muscle growth of chicken. MiRNA profiles of four SMB chickens and four DH chickens were detected by small RNA sequencing. A total of 994 known miRNAs were identified, among which gga-miR-1a-3p, gga-miR-148-3p and gga-miR-133a-3p exhibited the highest enrichment in both breeds of chickens. Thirty-two miRNAs were differently expressed between SMB and DH chickens. The differently expressed miRNAs were mainly associated with fatty acid metabolism, immunity and MAPK activation-related processes. Kyoto encyclopaedia of genes and genomes (KEGG) analysis showed that miRNAs were involved in the immunity-related and MAPK signalling pathways. Moreover, miR-204 was downregulated in DH chicken compared with SMB chicken, and significantly inhibited the expression of MAP3K13, which is involved in the MAPK pathway. It was confirmed through luciferase reporter assays that miR-204 specifically inhibited the activity of MAP3K13. Our results helped demonstrate the potential molecular mechanisms of muscle growth in chickens and provide valuable information for chicken breeding.

Population genomics identifies patterns of genetic diversity and selection in chicken.

BACKGROUND: There are hundreds of phenotypically distinguishable domestic chicken breeds or lines with highly specialized traits worldwide, which provide a unique opportunity to illustrate how selection shapes patterns of genetic variation. There are many local chicken breeds in China. RESULTS: Here, we provide a population genome landscape of genetic variations in 86 domestic chickens representing 10 phenotypically diverse breeds. Genome-wide analysis indicated that sex chromosomes have less genetic diversity and are under stronger selection than autosomes during domestication and local adaptation. We found an evidence of admixture between Tibetan chickens and other domestic population. We further identified strong signatures of selection affecting genomic regions that harbor genes underlying economic traits (typically related to feathers, skin color, growth, reproduction and aggressiveness) and local adaptation (to high altitude). By comparing the genomes of the Tibetan and lowland fowls, we identified genes associated with high-altitude adaptation in Tibetan chickens were mainly involved in energy metabolism, body size maintenance and available food sources. CONCLUSIONS: The work provides crucial insights into the distinct evolutionary scenarios occurring under artificial selection for agricultural production and under natural selection for success at high altitudes in chicken. Several genes were identified as candidates for chicken economic traits and other phenotypic traits.

Comparative transcriptome analysis reveals regulators mediating breast muscle growth and development in three chicken breeds.

Objective: The goal of this study was to investigate the mechanisms of muscle growth and development of three chicken breeds. Participants: Eighteen chickens, including three different breeds with different growth speeds (White Broiler, Daheng, and Commercial Layers of Roman), were used. Methods: Total RNA from breast muscle of these chickens was subjected to a gene expression microarray. Differentially expressed genes (DEGs) were screened and functional enrichment analysis was performed using DAVID. Seven DEGs were confirmed by quantitative reverse transcription PCR. Results: Overall, 8,398 DEGs were found among the different lines. The DEGs between each two lines that were unique for a developmental stage were greater than those that were common during all stages. Functional analysis revealed that DEGs across the entire developmental process were primarily involved in positive cell proliferation, growth, cell differentiation, and developmental processes. Genes involved in muscle regulation, muscle construction, and muscle cell differentiation were upregulated in the faster-growing breed compared to the slower-growing breed. DEGs including myosin heavy chain 15 (MYH15), myozenin 2 (MYOZ2), myosin-binding protein C (MYBPC3), insulin-like growth factor 2 (IGF2), apoptosis regulator (BCL-2), AP-1 transcription factor subunit (JUN), and AP-1 transcription factor subunit (FOS) directly regulated muscle growth or were in the center of the protein-protein interaction network. Pathways, including the extracellular matrix (ECM)-receptor interaction, mitogen-activated protein kinase (MAPK) signaling pathway, and focal adhesion, were the most enriched DEGs between lines or within lines under different developmental stages. Conclusions: Genes involved in muscle construction and cell differentiation were differentially expressed among the three breeds.

Enhancement of Nutrient Composition and Non-Volatile Flavor Substances in Muscle Tissue of Red Drum (Sciaenops ocellatus) Through Inland Low Salinity Saline-Alkaline Water Culture.

The red drum (Sciaenops ocellatus), a globally significant marine aquaculture species, boasts formidable osmoregulatory capabilities and remarkable adaptability to low salinity, making it an ideal candidate for commercial cultivation in inland low salinity saline-alkaline waters. However, studies on the fundamental nutritional composition and flavor quality of S. ocellatus in these inland low salinity saline-alkaline waters remain unreported. This study delves into the impact of inland low salinity saline-alkaline environments on the basic nutritional components and nonvolatile flavor substances (including free amino acids and free nucleotides) in the muscle tissue of S. ocellatus. The findings reveal that redfish cultivated in these conditions exhibit a significant increase in the crude fat, ash, and protein content in their dorsal muscle tissue, coupled with a decrease in moisture content (p < 0.05), indicating an enhancement in the nutritional value of the dorsal muscle tissue. Furthermore, this cultivation environment significantly elevates the content of free amino acids in the muscle tissue (p < 0.05), particularly those contributing to umami and sweet tastes, while reducing the relative content of bitter amino acids. Although the total content of free nucleotides decreased, the equivalent umami concentration (EUC) in the muscle tissue markedly increased (p < 0.05) due to the synergistic effect of umami amino acids and flavor nucleotides, enhancing the umami taste characteristics. Therefore, inland low salinity saline-alkaline aquaculture not only elevates the nutritional value of S. ocellatus muscle tissue but also improves its umami flavor characteristics. This discovery opens new perspectives for further research into the impact of inland low salinity saline-alkaline environments on the flavor properties of marine animals.

Shrimp Cultured in Low-Salt Saline-Alkali Water has a Better Amino Acid Nutrition and Umami─Comparison of Flavors between Saline-Alkali Water- and Seawater-Cultured Litopenaeus vannamei.

The advantages of Litopenaeus vannamei farming in saline-alkali water have gradually attracted attention, but few studies have focused on its flavor. In this study, L. vannamei cultured in saline-alkali water (SS) and ordinary seawater (CS) (both have a breeding time of 120 days) were selected for analysis (n = 5). High-performance liquid chromatography (HPLC) was used to measure free amino acids and flavoring nucleotides in the muscles of L. vannamei, while the taste activity value (TAV) and equivalent umami concentration (EUC) were used to analyze the degree of umami. The total essential amino acids (TEAA) in the SS group were 238.41 ± 46.24 mg/mL, significantly higher than that in the CS group (107.06 ± 15.65 mg/mL). The total amount of flavor nucleotides in the SS group was 2948.51 ± 233.66 µg/mL, significantly higher than those in the CS group (2530.37 ± 114.67 µg/mL). The content and TAV of some free amino acids (Glu, Cys-s) in the SS group were significantly higher. Meanwhile, due to the significant increase in IMP, the synergistic effect of free amino acids and flavored nucleotides leads to higher EUC. The significant separation of SS and CS samples in principal component analysis (PCA) indicates a significant difference between the two groups. Our results indicate that shrimp cultured in saline-alkali water has a stronger umami. This study enriches the basic theories related to the flavor of salt-alkali water crustaceans.

Effects of different dietary fiber supplement strategies on incidence of acute gastrointestinal injury in ICU patients: A prospective observational study.

OBJECTIVE: This study aimed to explore the effects of dietary fiber (DF) supplement strategies on the incidence of acute gastrointestinal injury (AGI) in critically ill patients. DESIGN: A prospective observational study. SETTING: The study was conducted in the First Affiliated Hospital of Soochow University from April 2021 to March 2023. METHODS: Using a five-day dietary log counted the amount of DF supplement. The best fitting trajectories of DF supplement were determined based on the latent class trajectory modelling (LCTM). The data of AGI were evaluated on the day 5 (D5) and day 7 (D7) after intensive care unit admission. RESULTS: A total of 179 patients were included in the study. The LCTM yielded a four-trajectories of models, named; Sustained Low - Group, Slowly Rising - Group, Early Supplement & Slowly Rising - Group and Rapidly Rising - Group, respectively. The incidences of AGI on D5 and D7 were 51.4 % and 40.0 %, respectively. There was an increased risk in the grade of AGI in the Sustained Low - Group compared with the Rapidly Rising - Group on D5 [odds ratio (OR), 4.8; 95 % confidence interval (CI), 1.9-12.1] and D7 (OR, 12.0; 95 % CI, 3.9-37.0); and an increased risk in the Slowly Rising - Group on D5 (OR, 3.6; 95 % CI, 1.3-9.9). CONCLUSION: The supplement of DF in critically ill patients may be insufficient and the incidence of AGI is high. Sustained low and slow rising DF supplement may be associated with an increased risk in the AGI. IMPLICATIONS FOR CLINICAL PRACTICE: The clinical staff could focus on the supplementation of not only the three macronutrients, but also DF in critically ill patients.

A hybrid attentional guidance network for tumors segmentation of breast ultrasound images.

PURPOSE: In recent years, breast cancer has become the greatest threat to women. There are many studies dedicated to the precise segmentation of breast tumors, which is indispensable in computer-aided diagnosis. Deep neural networks have achieved accurate segmentation of images. However, convolutional layers are biased to extract local features and tend to lose global and location information as the network deepens, which leads to a decrease in breast tumors segmentation accuracy. For this reason, we propose a hybrid attention-guided network (HAG-Net). We believe that this method will improve the detection rate and segmentation of tumors in breast ultrasound images. METHODS: The method is equipped with multi-scale guidance block (MSG) for guiding the extraction of low-resolution location information. Short multi-head self-attention (S-MHSA) and convolutional block attention module are used to capture global features and long-range dependencies. Finally, the segmentation results are obtained by fusing multi-scale contextual information. RESULTS: We compare with 7 state-of-the-art methods on two publicly available datasets through five random fivefold cross-validations. The highest dice coefficient, Jaccard Index and detect rate ([Formula: see text]%, [Formula: see text]%, [Formula: see text]% and [Formula: see text]%, [Formula: see text]%, [Formula: see text]%, separately) obtained on two publicly available datasets(BUSI and OASUBD), prove the superiority of our method. CONCLUSION: HAG-Net can better utilize multi-resolution features to localize the breast tumors. Demonstrating excellent generalizability and applicability for breast tumors segmentation compare to other state-of-the-art methods.

The segmentation effect of style transfer on fetal head ultrasound image: a study of multi-source data.

The generalization ability of the fetal head segmentation method is reduced due to the data obtained by different machines, settings, and operations. To keep the generalization ability, we proposed a Fourier domain adaptation (FDA) method based on amplitude and phase to achieve better multi-source ultrasound data segmentation performance. Given the source/target image, the Fourier domain information was first obtained using fast Fourier transform. Secondly, the target information was mapped to the source Fourier domain through the phase adjustment parameter α and the amplitude adjustment parameter ß. Thirdly, the target image and the preprocessed source image obtained through the inverse discrete Fourier transform were used as the input of the segmentation network. Finally, the dice loss was computed to adjust α and ß. In the existing transform methods, the proposed method achieved the best performance. The adaptive-FDA method provides a solution for the automatic preprocessing of multi-source data. Experimental results show that it quantitatively improves the segmentation results and model generalization performance.

The shared microbiome in mud crab (Scylla paramamosain) of Sanmen Bay, China: core gut microbiome.

Introduction: The mud crab, Scylla paramamosain, holds great commercial significance as a marine crustacean widely cultivated in the Indo-Pacific region. Understanding the core gut microbiota of aquatic animals is crucial for their overall health and growth, yet the core gut microbiota of mud crab remains poorly characterized. Methods: In this study, we gathered gut samples from mud crabs across five locations within Sanmen Bay, China. Through the utilization of high-throughput sequencing, we delved into the composition of the gut microbial community and identified the core gut microbiome of mud crab. Results: Our results demonstrate that the gut microbial diversity of mud crab did not exhibit significant variation among the five sampling sites, although there were some differences in community richness. At the phylum level, we identified 35 representative phyla, with Firmicutes, Proteobacteria, Bacteroidota, and Campilobacterota as the dominant phyla. Among the 815 representative genera, we discovered 19 core genera, which accounted for 65.45% of the total sequences. These core genera were distributed across 6 phyla, and among them, Photobacterium exhibited the highest average relative abundance. Discussion: Photobacterium has probiotic activity and may play a crucial role in enhancing the immune response of the host and maintaining the diversity of the gut microbiota. Moreover, we observed a positive correlation between the relative abundance of core genera and the stability of the gut microbial community. Furthermore, our findings revealed distinct differences in gut microbial composition and specific taxa between the sexes of mud crab. These differences subsequently influenced the functionality of the gut microbial community. Overall, our investigation sheds light on the core gut microbiota of mud crab, emphasizing the importance of core gut microbial communities in maintaining the health and growth of these commercially significant marine crustaceans.

Effect of Domestication on Nonvolatile Flavor Substances in Mud Crabs (Scylla paramamosain): A Way to Improve the Quality of Commercial Crabs.

In this study, the best domestication time for mud crabs (Scylla paramamosain) that were domesticated in the same region was explored. MC crabs (Mang Cai City, Vietnam), TS crabs (Taishan City, Guangdong Province, China), and NB crabs (Ningbo City, Zhejiang Province, China) were used as experiment groups, which were all domesticated in the Sanmen area for 28 days. Then, free amino acids and flavor nucleotides in muscles and hepatopancreas were determined. In MC and NB crabs, flavor amino acids in hepatopancreas and equivalent umami concentration (EUC) of flavor nucleotides in the hepatopancreas and muscles were lower than those of CK1 and CK3 crabs before domestication (0 day). There was no significant difference between MC and CK1 and between NB and CK3 crabs after 28 days of domestication. The content of umami amino acids, the total content of flavor nucleotides, and EUC in the hepatopancreas in TS crabs were lower than those in CK2 crabs and were still lower than those in CK2 crabs after 28 days of domestication. Therefore, it takes at least a month to domesticate mud crabs. The theoretical basis and technical reference for the directional cultivation of the flavor quality of mud crabs were provided in this study..

Characterization of the expression profile of calpain-3 (CAPN3) gene in chicken.

Calpain-3 is a skeletal muscle-specific protease and participates in the regulation of myogenesis. In this study, we quantified the expression of calpain-3 (CAPN3) mRNA in a Chinese local chicken breed (Sichuan Mountainous Black-boned chicken [MB]), to discern the tissue and ontogenic expression pattern. Meanwhile, we compared the CAPN3 mRNA expression pattern in MB chicken at 10 weeks with a commercial meat type chicken line (S01) of the same age to identify the unique expression pattern under different genetic background. A real time quantitative PCR (qRT-PCR) assay was developed for an accurate measurement of its expression in various tissues from chickens at different ages (0, 2, 4, 6, 8, 10, and 12 weeks). Expression of the CAPN3 mRNA was detected in the selected tissues, regardless of age. The breast muscle and leg muscle tissues had a significantly higher expression than the other tissues from the same individual (P < 0.01). Overall, the CAPN3 mRNA level exhibited a "rise-decline" developmental change in detected tissues except for brain. The S01 chicken had a higher expression of the CAPN3 mRNA in detected tissues than the MB chicken at 10 weeks. The present expression data of chicken CAPN3 gene may provide some information to shed light on the tissue and ontogenic expression pattern during chicken development.

Characterization of the expression profiles of calpastatin (CAST) gene in chicken.

The calpain system, a Ca(2+)-activated protease family, plays an important role in postmortem tenderization of skeletal muscle due to its involvement in the degradation of important myofibrillar and associated proteins, as well as in cytoskeletal remodeling and regulation of muscle growth. In this study, we quantified the expression of calpastatin (CAST) in two Chinese chicken breeds (mountainous black-bone chicken breed (MB) and a commercial meat type chicken breed (S01)), to discern the tissue and age-related specific expression pattern and its potential role on muscle tissue metabolism. Real-time quantitative PCR (RT-qPCR) assay was developed for accurate measurement of CAST mRNA levels in various tissues from chicken with different ages (0, 2, 4, 6, 8, 10, and 12 week). CAST mRNA was detected in collected organs. The heart and leg muscle tissues had the highest expression of CAST than other tissues from the same chicken (P < 0.01). Age-related expression pattern of CAST gene was evident in breast muscle, liver, and brain tissues (P < 0.05), but not in heart and leg muscle tissues (P > 0.05). Overall, the CAST mRNA level exhibited a "rise-decline-rise-decline" developmental change in breast muscle and liver, with the highest expression at 2 weeks and the lowest expression at 8 weeks. The S01 chicken had significantly higher expression of CAST in breast muscle and heart than the MB chicken (P < 0.05) at 10 weeks. Our results suggested the CAST expression may be related to muscle fiber development.

Research Progress in Interfacial Characteristics and Strengthening Mechanisms of Rare Earth Metal Oxide-Reinforced Copper Matrix Composites.

The existence of a small amount of rare earth metal oxides (REMOs) can greatly affect the structure and function of copper matrix composites owing to improvement of surface and interface properties between REMOs and metal matrix, and there are still some challenges concerning interfaces and complex interfacial reactions. This review summarizes the interfacial characteristics and strengthening mechanisms of REMO-reinforced copper matrix composites, including fabrication methods for solving rare earth metal oxide-dispersion problems and characterization of the microstructure and properties of REMO-reinforced copper matrix composites. In particular, the strengthening effects of various rare earth metal oxide-reinforced copper matrix composites are systematically summarized. The interface characteristics of composites from a thermodynamics standpoint and the strengthening mechanism are emphatically investigated and discussed in order to help unveil design principles and to provide reference for future research of REMO-reinforced copper matrix composites.

Characterization of lncRNA/circRNA-miRNA-mRNA network to reveal potential functional ceRNAs in the skeletal muscle of chicken.

Skeletal muscle, comprising approximately 40% of body mass, is a highly complex and heterogeneous tissue serving a multitude of functions in the organism. Non-coding RNAs (ncRNAs) are known to participate in skeletal muscle development as critical regulators. However, the regulatory mechanisms of ncRNAs on chicken muscle traits are not well understood. In the present study, we collected the leg muscle from male embryos of Tibetan chicken at embryonic (E) 10 and E18 for RNA sequencing. A total of 6,583 differentially expressed mRNAs (DEMs) including 3,055 down-regulated and 3,528 up-regulated were identified in E18. We identified 695 differentially expressed lncRNAs (DELs) (187 down-regulated and 508 up-regulated) and 1,906 differentially expressed circRNAs (DECs) (1,224 down-regulated and 682 up-regulated) in E18. Among the 130 differentially expressed miRNAs (DEMIs), 59 were up-regulated and 71 were down-regulated in E18. Numerous DEMs and target genes for miRNAs/lncRNAs were significantly enriched in the muscle system process and cell cycle. We constructed a miRNA-gene-pathway network by considering target relationships between genes related to skeletal muscle development and miRNAs. A competing endogenous RNA (ceRNA) network was also constructed by integrating competing relationships between DEMs, DELs, and DECs. Several DELs and DECs were predicted to regulate the ADRA1B, ATP2A2, ATP2B1, CACNA1S, CACNB4, MYLK2, and ROCK2 genes. We discovered the crosstalk between the ncRNAs and their competing mRNAs, which provides insights into ceRNA function and mechanisms in the skeletal muscle development of chicken.

Integration analysis of metabolome and transcriptome profiles revealed the age-dependent dynamic change in chicken meat.

To explore the chemical composition of chicken meat during different growth and development periods, the dynamic alterations of the metabolite composition were determined using LC-MS/MS-based metabolomics. Together, 573 metabolites were identified in chicken meat from five age stages. Generally, pentadecanoic acid, stearic acid, creatine, carnosine, IMP, L-histidine and L-isoleucine presented an upward trend with age, while anserine, DHA, L-aspartic acid, LPA 18:1 and LPI 18:1 decreased with age. The main pathways of chicken meat metabolism affected by age were fructose and mannose metabolism, arachidonic acid metabolism, steroid hormone biosynthesis, riboflavin metabolism, biosynthesis of unsaturated fatty acids, and linoleic acid metabolism. Using transcriptomic profiling data, we conducted Pearson correlation analysis between gene expression and metabolite profile data in each age comparison. Integration analysis of metabolome and transcriptome would be helpful to understand the biological processes underlying the development of meat quality and explore valuable biomarkers for specific metabolite accumulation.