Proteomics Analysis of Breast Muscle Tissue Associated with the Phenotypic Expression of Feed Efficiency in a Single Male Broiler Line

A preliminary proteomics investigation was conducted on breast muscle that were obtained from high and low feed efficiency (FE) broiler phenotypes previously analyzed for global gene expression (transcriptomics) (Kong et al., 2011, Poult. Sci. 90:2535-2542). Shotgun proteomics was carried out by the UAMS Proteomics Core Facility, Little Rock, AR using in-gel trypsin digestion and tandem mass spectrometry on breast muscle samples obtained from broilers exhibiting high FE or low FE phenotypes (n=4 per group). The high FE group had greater body weight gain (P = 0.004) from 6-7 wk but consumed the same amount of feed (P = 0.30) as the low FE group resulting in higher (P < 0.001) FE of 0.65 + 0.01 compared to 0.46 + 0.01 for the low FE group. Analysis revealed that ~1500 proteins were identified of which ~400 showed differential abundance (P < 0.05) with the expression of 237 proteins in normalized data being different by 30% or more (≥ 1.3 fold) between high and low FE phenotypes. Interpretation of the proteomic results was facilitated by a commercial software program (Ingenuity Pathway Analysis, IPA. The IPA program identified mitochondrial dysfunction and oxidative phosphorylation as being in the top differentially expressed canonical pathways (up-regulated in high FE tissue) in the proteomic dataset. Upstream analysis (based on differential protein abundance of downstream molecules) predicted that peroxisome proliferator-activated receptor gamma, co-activator 1 alpha (PGC1a) and nuclear respiratory factor 2 (Nrf2) would be activated in the high FE phenotype. Upstream analysis also indicated that muscle damage, myopathy, and hypertrophy were predicted to be inhibited in breast muscle of the high- compared to the low FE phenotype. The overlay and prediction functions of IPA revealed both similarities and differences between the transcriptomics (Kong et al., 2011) and proteomics datasets. Although targeted protein expression analysis is needed to verify the proteomics findings, the results provide additional insight into the fundamental molecular landscape of feed efficiency in breast muscle of broilers as well as further support for a role of mitochondria in the phenotypic expression of FE.  Funding provided by USDA-NIFA (#2013-01953), Arkansas Biosciences Institute (Little Rock, AR) and the Agricultural Experiment Station (Univ. of Arkansas).