Effects of Different Rearing Systems on Lueyang Black-Bone Chickens: Meat Quality, Amino Acid Composition, and Breast Muscle Transcriptome

Abstract

The quality of poultry products depends on genotype, rearing system, and environment. The aim of this study was to investigate the effects of different rearing systems on meat quality, amino acid composition, and breast muscle transcriptome from Lueyang black-bone chickens. Lueyang black-bone chickens (n = 900) were randomly divided into three groups (cage, flat-net, and free-range groups), with three replicates per group (100 chickens per replicate). At 16 weeks, a total of 36 healthy chickens (six males and six females per group) were collected, and their breast muscles were sampled to detect meat quality parameters, amino acid composition, and fatty acid contents. Furthermore, breast muscles from six random hens in each group were used for RNA-seq analysis. The results revealed that the values of pH, shear force, inosine monophosphate (IMP), palmitic acid, and linoleic acid in the free-range group were significantly higher than those in the caged group (p < 0.05). Fat content in the free-range group was significantly lower than in the caged and flat-net groups (p < 0.05). Glutamate (Glu) levels, the amino acid crucial for the umami taste, was significantly higher in the free-range group than in the caged group (p < 0.05). Meanwhile, there was no significant difference between the free-range and flat-net groups (p > 0.05). The breast muscle transcriptome results showed that there were 291, 131, and 387 differently expressed genes (DEGs) among the three comparison groups (caged vs. free-range, flat-net vs. caged, and flat-net vs. free-range, respectively) that were mainly related to muscle development and amino acid metabolism pathways. To validate the accuracy of the transcriptome data, eight genes (GOS2, ASNS, NMRK2, GADL1, SMTNL2, SLC7A5, AMPD1, and GLUL) which relate to fat deposition, skeletal muscle function, and flavor formation were selected for Real-time Quantitative PCR (RT-qPCR) verification. In conclusion, these results suggested that rearing systems significantly influenced the meat quality and gene expression of Lueyang black-bone chickens. All the data proved that free-range and flat-net systems may provide better flavor to consumers by affecting the deposition of flavor substances and the expression of related genes. These findings will provide a valuable theoretical basis for the rearing system selection in the poultry industry.

Keywords: Lueyang black-bone chicken; different expressed genes; meat quality; rearing system; transcriptome.

Figure 1

Gene expression clustering heat map under three rearing systems. Each column in the heat map represents the expression of different genes in the same sample, and each row represents the expression of the same gene in different samples. Red genes are up-regulated, and blue genes are down-regulated in the affected samples.

Figure 2

Top 20 GO and KEGG enrichment of DEGs. KEGG pathway (A–C) and GO term (D–F) enrichment were conducted with DEGs of three groups (caged vs. free-range, flat-net vs. caged, and flat-net vs. free-range). The vertical ordinate is the pathway name and the horizontal coordinate value is the ratio of enriched genes to total genes. The sizes of the point indicate how many DEGs are in the pathway, and the colors of different points correspond to different p-value ranges.

Figure 3

PPI network of candidate differently expressed genes. In the network, the higher the score of the interacting genes, the deeper the color of the lines between them, indicating a stronger interaction between two genes. The lines are directional, with the source gene pointing to the target gene along the direction of the number on the line. The larger the circle representing the gene, the more the interactions of the gene.

Figure 4

Validation of candidate DEGs under three rearing systems using real-time quantitative PCR. For each gene, different lowercase letters (a–c) indicate significant differences (p < 0.05).