Phenotypic and genotypic relationships between meat quality characteristics and expression of target genes associated with broiler meat quality defects

The objective of this project was to employ customized Agilent 8x60 chicken whole genome microarray to identify differentially expressed genes associated with white striping (WS) and wooden breast (WB) defects in breast meat collected from commercial broilers with different slaughter age. Following harvest of chicken breasts (n = 184), the breast samples were classified as based on their appearance into non-defect, WS or WB. The defective samples were further grouped based on defect severity (WS = mild, moderate, severe; WB = moderate, severe). A total numbers of 40 samples were selected to represent various degree of the defects. Total RNA from deep-frozen skeletal muscle was isolated, integrity check (RIN > 7.0) and subjected for one-colored microarray hybridization according to Agilent’s instruction. The array was designed (design ID: AMADID G4102A084792) based on the National Center for Biotechnology Information (NCBI) Gallus gallus Annotation Release 103 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Gallus_gallus/103/). Differential gene expression (p-value < 0.05) was confirmed using qPCR and droplet digital PCR. Biological pathways associated with WS and WB were identified. The microarray type used is a slide having 8 arrays with 56,457 features including control probes. A total numbers of 40 arrays were hybridized using one-color dye procedure. The fluorescent signal intensity obtained for each sample were normalized, analyzed and compared as follows. For WS, transcriptome profiles of the samples were compared as follows; severe WS (n=4) vs non-WS (n=4), severe WS vs mild WS (n=7), severe WS vs moderate WS (n=6). Overall, 21 samples were hybridized for the study of WS defect. For WB, three separate comparisons were designed; non-WB1 (n= 3) vs WB1 (n=2), non-WB2 (n=4) vs WB2 (n=3), non-WB3 (n=4) vs WB3 (n=3), where WB1 = samples collected from 49d broilers exhibiting severe WB and mild WS, WB2 = 49 broilers exhibiting severe WB and moderate WS, and WB3 = ≤45d broilers with severe WB and mild WS. Overall, 19 samples were chosen for the study of WB defect.