Transcriptome Analysis for Pork Color – the Ham Halo Effect in Biceps Femoris.

Pork color is a major indicator of product quality that guides consumer purchasing decisions. For hams, consumers prefer a uniform pink color. Recently, industry has received an increase in consumer complaints about the lightness and non-uniformity of ham color, primarily lighter color in the periphery termed “ham halo” that is not caused by manufacturing procedures. This effect is seen in fresh and processed hams and the outer, lighter muscle is associated with lower myoglobin concentrations, pH and type I fibers. The objective of this study was to identify differences in gene expression profiles between light and normal colored biceps femoris muscle from pork hams. RNA was extracted from light and normal colored biceps femoris muscle from samples from the same animal showing an extreme ham halo effect, and over 50 million paired-end reads (2x75bp) per library were sequenced on an Illumina NextSeq 500. Seventy-six to 82% of trimmed high quality reads were mapped to the Sscrofa 10.2 assembly and unplaced scaffolds. Differentially expressed genes (DEGs) were identified using DESeq2 and GFOLD. DESeq2 identifies DEGs between groups and GFOLD identifies DEGs in samples from an individual animal. A total of 14,809 transcripts were expressed in biceps femoris; 14,766 were expressed in both light and normal muscle. DESeq2 identified 340 DEGs with 318 genes being more highly expressed in normal colored muscle. Within each animal, GFOLD identified an average of 768 DEGs. GFOLD identified 50 DEGs identified in at least 8 of the 10 animals, all of which were more highly expressed in normal colored muscle. Gene ontology (GO) enrichment analysis of these genes identified transition between fast and slow fibers, and skeletal muscle adaptation and contraction as the most significant biological process terms. Of the 340 DEGs, 319 mapped to 275 unique chromosomal regions; there were 33 clusters of 2 or more genes within 200 kb of a neighboring gene or long non-coding RNA, suggesting co-transcription of DEGs. Sixty-one DEGs resided within 200 kb of 93 unique QTL or SNP associations for color traits, pH, driploss, cookloss, purge, water-holding capacity or fiber type. The evaluation of gene expression by RNA-Seq identified DEGs between regions of the biceps femoris with the ham halo effect that may be candidate genes that contribute to the variation in color, pH and water-holding capacity of pork. USDA is an equal opportunity provider and employer.