Integrative analysis of long noncoding RNA and mRNA reveals candidate lncRNAs responsible for meat quality at different physiological stages in Gushi chicken

Abstract

Long noncoding RNAs (lncRNAs) play important roles in transcriptional and posttranscriptional regulation. However, the effects of lncRNAs on the meat quality of chicken hasn't been elucidated clearly yet. Gushi chickens are popular in China because of their superior meat quality, particularly the tender flesh, and unique flavor. Gushi chickens are popular in China because of their superior meat quality, delicate flesh, and unique flavor. We performed RNA-Seq analysis of breast muscle from Gushi chicken at two physiological stages, including juvenile (G20W) and laying (G55W). In total, 186 lncRNAs and 881 mRNAs were differentially expressed between G20W and G55W (fold change ≥ 2.0, P < 0.05). Among them, 131 lncRNAs presented upregulated and 55 were downregulated. We identified the cis and trans target genes of the differentially expressed lncRNAs, and constructed lncRNA-mRNA interaction networks. The results showed that differentially expressed mRNAs and lncRNAs were mainly involved in ECM-receptor interaction, glycerophospholipid metabolism, ubiquitin-mediated proteolysis, and the biosynthesis of amino acids. In summary, our study utilized RNA-seq analysis to predict the functions of lncRNA on chicken meat quality. Furthermore, comprehensive analysis identified lncRNAs and their target genes, which may contribute to a better understanding of the molecular mechanisms underlying in poultry meat quality and provide a theoretical basis for further research.

Fig 1. Distribution of identified lncRNAs on each chromosome.

The outer ring represents the chicken genome labeled with chromosome number and position. The green circle shows the distribution of identified lncRNAs in G20W, and the orange circle shows the distribution in G55W.

Fig 2. Characteristics of lncRNAs.

(A) Computational pipeline for the systematic identification of lncRNAs. (B) Venn diagram illustrating the overlap of lncRNAs in breast muscle tissue libraries from G20W and G55W chickens. G20W: 20 weeks of age; G55W: 55 weeks of age. Length (C) and chromosomal (D) distribution of Gushi chicken lncRNAs.

Fig 3. Analysis of differentially expressed lncRNAs.

(A) Representative of the degree of similarity between samples. The correlation coefficient is represented by color; deeper color represents a stronger correlation. (B) Clustering analysis of differentially expressed lncRNAs in G20W and G55W. (C) Volcano plot of differentially expressed lncRNAs in G20W and G55W. Green and red represent downregulated and upregulated expression, respectively.

Fig 4. GO analyses of differentially expressed lncRNAs and mRNAs.

(A) Categories of biological processes, cellular components and molecular functions of the target genes of differentially expressed lncRNAs and mRNAs (cis). (B) Categories of the biological processes, cellular components and molecular functions of the target genes of differentially expressed lncRNAs and mRNAs (trans).

Fig 5. KEGG analyses of differentially expressed lncRNAs and mRNAs.

(A) Scatter plot of the top 20 pathways enriched for differentially expressed lncRNAs and mRNAs in breast tissue from G20W and G55W chickens (cis). The abscissa represents the richness factor, and the ordinate represents the enriched pathway terms. The Q-value represents the corrected P (B) Scatter plot of the top 20 pathways enriched for differentially expressed lncRNAs and mRNAs in breast tissue from G20W and G55W chickens (trans). The abscissa represents the richness factor, and the ordinate represents the enriched pathway terms. The Q-value represents the corrected P.

Fig 6. Differentially expressed lncRNA-mRNA interaction network analysis.

Circles represent coding genes, and arrows represent lncRNAs. Red nodes represent upregulated nodes, and green nodes represent downregulated nodes. Yellow nodes represent pathway terms. The node size represents -logP; the smaller the P value is, the greater is the node size. Lines between lncRNA-mRNA represent interactions between them.

Fig 7. Validation of lncRNAs using RT-qPCR.

Data were analyzed by the 2^-ΔΔCt method using β-actin as a reference gene. Each column represents the mean ±SE. Different letters indicate significant differences in expression levels between the two stages (P ≤ 0.05). Black bars represent read from RNA-Seq. Gray bars represent the results of qRT-PCR.