Genome Resequencing to Identify SNP Markers for Muscle Quality Trait in Broiler Chickens

Meat quality in chickens is an important trait and continuous selective pressures for fast growth and high yield have negatively impacted qualities of the meat. To investigate genetic variations responsible for regulating muscle quality, whole genome resequencing analysis was performed using pooled DNA samples isolated from two broiler chicken lines divergently selected for muscle color [high muscle quality (HMQ) and low muscle quality (LMQ)] along with their random bred control line (RAN). Millions of SNP were identified and only potentially causal genes containing non-synonymous mutations, which can induce amino acid changes, were focused in this study. Totally 2517 SNPs including 1169 for HMQ and 1348 for LMQ showing >75% SNP rates could induce non-synonymous mutations. Of those, SNPs showing over 10 read depths yielded 20 more reliable SNPs including 3 for HMQ and 17 for LMQ. Bioinformatic analysis using Ingenuity Pathway Analysis (IPA) suggested that meat color in chickens appeared to be associated with the functions of ubiquitylation (UBC) and quality and quantity of various subtypes of collagens associated with the interaction between membrane bound receptor (RECK) and matrix metallopepetidase (MMP9) and in muscle. In this study, various potential genetic biomarkers showing amino acid changes were identified in differential meat color lines through the genome resequencing. Pathway analysis of factors involved suggests meat color in chickens appeared to be associated with the functions of ubiquitylation and quality and quantity of various subtypes of collagen in muscle. This work was supported by Arkansas Bioscience Institute and Arkansas Agricultural Experimental Station.