Revealing Pathways Associated with Feed Efficiency and Meat Quality Traits in Slow-Growing Chickens

Abstract

Here, molecular pathways and genes involved in the feed efficiency (FE) and thigh-meat quality of slow-growing Korat chickens were investigated. Individual feed intake values and body weights were collected weekly to the calculate feed conversion ratios (FCR) and residual feed intake. The biochemical composition and meat quality parameters were also measured. On the basis of extreme FCR values at 10 weeks of age, 9 and 12 birds from the high and the low FCR groups, respectively, were selected, and their transcriptomes were investigated using the 8 × 60 K Agilent chicken microarray. A weighted gene co-expression network analysis was performed to determine the correlations between co-expressed gene modules and FE, thigh-meat quality, or both. Groups of birds with different FE values also had different nucleotide, lipid, and protein contents in their thigh muscles. In total, 38 modules of co-expressed genes were identified, and 12 were correlated with FE and some meat quality traits. A functional analysis highlighted several enriched functions, such as biological processes, metabolic processes, nucleotide metabolism, and immune responses. Several molecular factors were involved in the interactions between FE and meat quality, including the assembly competence domain, baculoviral IAP repeat containing 5, cytochrome c oxidase assembly factor 3, and myosin light chain 9 genes.

Keywords: Korat chicken; feed efficiency; meat quality; slow-growing chicken; transcriptome.

Figure 1

Hierarchical clustering of the top 50 genes (lowest p-values) between high- and low- feed conversion ratio (FCR) in Korat chickens. Samples are shown in columns, and genes are shown in rows. The scaled expression levels are depicted using a color gradient: upregulated and downregulated genes are shown in red and green, respectively. Genes and samples were grouped using hierarchical clustering analyses. The hierarchical clustering of the scaled gene expression matrix was based on Pearson’s correlations and average link aggregation distances.

Figure 2

Correlations between modules and feed efficiency, meat quality traits, or both in the thigh muscles of Korat chickens. Each row corresponds to a module, and each column corresponds to a trait. Each cell contains the correlation coefficient and the p-value in the first and second lines, respectively. The table is color-coded by correlation in accordance with the legend. The module name is shown on the left side of each cell. FCR10 wks; feed conversion ratio at 10 weeks of age; RFI10 wks, residual feed intake at 10 weeks of age; WHC, water-holding capacity; GMP, guanosine monophosphate; IMP, inosine monophosphate; AMP, adenosine monophosphate; Esterlipid, ester carbonyl of phospholipids; CHbend, CH bending; and Carbo, carbohydrate and glycogen.