Transcriptome and co-expression network analysis reveals the molecular mechanism of inosine monophosphate-specific deposition in chicken muscle

Genome-wide association analysis reveals genetic loci and candidate genes for white diarrhea in Jingyuan chickens

In order to investigate the basic genetic structure of dysentery in Jingyuan chickens and to explore the genetic markers associated with dysentery resistance in chickens, the present study was based on the genome-wide association analysis (GWAS) technique to investigate the candidate SNPs and genes associated with dysentery resistance in Jingyuan chickens, and a total of 12 SNPs were associated with dysentery resistance in Jingyuan chickens. In addition, some important candidate genes inciuding frizzled class receptor 4 (FZD4), DDB1 and CUL4 associated factor 13(DCAF13), regulating synaptic membrane exocytosis 2 (RIMS2), transmembrane protein 8C (TMEM8C), and RIC1 homolog (RIC1) were identified by selection signal analysis, gene annotation, and enrichment analysis. These results can be used as potential molecular selection markers for chicken dysentery resistance in Jingyuan chickens in order to improve the breeding of disease resistance in Jingyuan chickens.

Integrating lipidomics and metabolomics to reveal biomarkers of fat deposition in chicken meat

Local chicken breeds in China are highly regarded for their superior meat flavor. This study utilized lipidomics and non-targeted metabolomics to identify biomarkers influencing intramuscular fat (IMF) deposition in the breast muscle of 42- and 180-day-old Jingyuan chickens. Results revealed that IMF content was higher in the breast muscle of 180-day-old Jingyuan chickens compared to 42-day-old chickens (P < 0.01). We identified 248 differentially expressed lipids (DELs) and 1042 differentially expressed metabolites (DEMs). The breast muscle of 180-day-old chickens contained higher levels of TG, fatty acid (FA) and cholesteryl ester (CE), with C16:1 and C18:1 being particularly abundant. Integration of non-targeted metabolomic analyses emphasized glycerolipid metabolism and vitamin digestion and absorption as the main pathways distinguishing between 42- and 180-day-old chickens. Additionally, the differential metabolites LysoPS 18:1, LysoPC 20:3, LysoPC 18:2, LysoPI 20:3, and Pantothenic acid contributed to enhanced meat flavor in Jingyuan chickens.

Explorations on Key Module and Hub Genes Affecting IMP Content of Chicken Pectoralis Major Muscle Based on WGCNA

Inosine monophosphate (IMP) is a substance that enhances flavor and plays a crucial role in the umami taste of chicken muscle. It is also an influential factor in determining chicken's economic value. However, the molecular regulatory network underlying the IMP content in muscle remains unclear. To address this issue, we performed transcriptome sequencing on 20 pectoralis major muscle samples from 120-day-old Guangde feathered-leg chicken and used weighted gene co-expression network analysis (WGCNA) to identify key regulatory factors that influence IMP content. The weighted gene co-expression network was constructed using a total of 16,344 genes, leading to the identification of 20 co-expression gene modules. Among the modules that were identified, it was observed that the purple module (R = -0.51, p = 0.02) showed a significant negative correlation with the IMP content. This suggests that the genes within the purple module had the ability to regulate the IMP content. A total of 68 hub genes were identified in the purple module through gene significance (GS) > 0.2 and module membership (MM) > 0.8. The STRING database was used for a protein-protein interaction (PPI) network of hub genes. Furthermore, troponin I type 1 (TNNI1), myozenin 2 (MYOZ2), myosin light chain 2 regulatory cardiac slow (MYL2), and myosin light chain 3 regulatory cardiac slow (MYL3) involved in the "ATP-dependent activity", "cAMP signaling pathway" and "cGMP-PKG signaling pathway" were identified as central regulators that contribute to IMP content. These results offer valuable information into the gene expression and regulation that affects IMP content in muscle.

Integration of transcriptome and machine learning to identify the potential key genes and regulatory networks affecting drip loss in pork

Low level of drip loss (DL) is an important quality characteristic of meat with high economic value. However, the key genes and regulatory networks contributing to DL in pork remain largely unknown. To accurately identify the key genes affecting DL in muscles postmortem, 12 Duroc × (Landrace × Yorkshire) pigs with extremely high (n = 6, H group) and low (n = 6, L group) DL at both 24 and 48 h postmortem were selected for transcriptome sequencing. The analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA) were performed to find the overlapping genes using the transcriptome data, and functional enrichment and protein-protein interaction (PPI) network analysis were conducted using the overlapping genes. Moreover, we used machine learning to identify the key genes and regulatory networks related to DL based on the interactive genes of the PPI network. Finally, nine potential key genes (IRS1, ESR1, HSPA6, INSR, SPOP, MSTN, LGALS4, MYLK2, and FRMD4B) mainly associated with the MAPK signaling pathway, the insulin signaling pathway, and the calcium signaling pathway were identified, and a single-gene set enrichment analysis (GSEA) was performed to further annotate the functions of these potential key genes. The GSEA results showed that these genes are mainly related to ubiquitin-mediated proteolysis and oxidative reactions. Taken together, our results indicate that the potential key genes influencing DL are mainly related to insulin signaling mediated differences in glycolysis and ubiquitin-mediated changes in muscle structure and improve the understanding of gene expression and regulation related to DL and contribute to future molecular breeding for improving pork quality.

Transcriptome analysis reveals the role of long noncoding RNAs in specific deposition of inosine monphosphate in Jingyuan chickens

Inosine monphosphate (IMP) is one of the important indicators for evaluating meat flavor, and long noncoding RNAs (lncRNAs) play an important role in its transcription and post-transcriptional regulation. Currently, there is little information about how lncRNA regulates the specific deposition of IMP in chicken muscle. In this study, we used transcriptome sequencing to analyze the lncRNAs of the breast and leg muscles of the Jingyuan chicken and identified a total of 357 differentially expressed lncRNAs (DELs), of which 158 were up-regulated and 199 were down-regulated. There were 2,203 and 7,377 cis- and trans-regulated target genes of lncRNAs, respectively, and we identified the lncRNA target genes that are involved in NEGF signaling pathway, glycolysis/glucoseogenesis, and biosynthesis of amino acids pathways. Meanwhile, 621 pairs of lncRNA-miRNA-mRNA interaction networks were constructed with target genes involved in purine metabolism, fatty acid metabolism, and biosynthesis of amino acids. Next, three interacting meso-networks gga-miR-1603-LNC_000324-PGM1, gga-miR-1768-LNC_000324-PGM1, and gga-miR-21-LNC_011339-AMPD1 were identified as closely associated with IMP-specific deposition. Both differentially expressed genes (DEGs) PGM1 and AMPD1 were significantly enriched in IMP synthesis and metabolism-related pathways, and participated in the anabolic process of IMP in the form of organic matter synthesis and energy metabolism. This study obtained lncRNAs and target genes affecting IMP-specific deposition in Jingyuan chickens based on transcriptome analysis, which deepened our insight into the role of lncRNAs in chicken meat quality.