Transcriptomic analysis for pork color – The ham halo effect in biceps femoris

Authors: Nonneman, Danny - Dan; Keel, Brittney; Lindholm-Perry, Amanda; Rohrer, Gary; Wheeler, Tommy; Shackelford, Steven; King, David - Andy

Submitted to: Meat and Muscle Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/17/2021
Publication Date: 3/14/2022
Citation: Nonneman, D.J., Keel-Mercer, B.N., Lindholm-Perry, A.K., Rohrer, G.A., Wheeler, T.L., Shackelford, S.D., King, D.A. 2022. Transcriptomic analysis for pork color – The ham halo effect in biceps femoris. Meat and Muscle Biology. 6(1):1-8. Article 13050. https://doi.org/10.22175/mmb.13050.
DOI: https://doi.org/10.22175/mmb.13050

Interpretive Summary: Uniform pink color is a primary determinant of consumer acceptance of cured ham product. Recently, industry has received an increase in consumer feedback about 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 concentration, pH, and percentage type I muscle fibers. The goal of this study was to compare gene expression profiles from light and normal colored biceps femoris to identify potential biomarkers associated with the ham halo defect and meat color traits. We identified hundreds of differentially expressed genes that provide candidates for the phenotypic differences of the ham halo defect and provide insights into metabolic pathways responsible for biological differences in the lean color of pork.

Technical Abstract: Pork color is a major indicator of product quality that guides consumer purchasing decisions. Recently, industry has received an increase in consumer complaints about the lightness and nonuniformity 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 concentration, pH, and type I fibers. The objective of this study was to identify differences in gene expression profiles between light and normal-colored portions of the biceps femoris muscle from pork hams. RNA-sequencing (RNA-seq) was performed for paired light and normal-colored muscle samples from 10 animals showing the ham halo effect. Over 50 million paired-end reads (2×75 bp) per library were obtained. An average of 99.74% of trimmed high-quality reads was mapped to the Sscrofa 11.1 genome assembly. Differentially expressed genes (DEGs) were identified using both the DESeq2 and GFOLD software packages. A total of 14,049 genes were expressed in the biceps femoris; 13,907 were expressed in both light and normal muscle, while 56 and 86 genes were only expressed in light and normal muscle, respectively. Analysis with DESeq2 identified 392 DEGs with 359 genes being more highly expressed in normal-colored muscle. A total of 61 DEGs were identified in the DESeq2 analysis and identified in at least 7 of the 10 individual animal analyses. All 61 of these DEGs were up-regulated in normal-colored muscle. Gene Ontology enrichment analysis of DEGs identified the transition between fast and slow fibers and skeletal muscle adaptation and contraction as the most significant biological process terms. The evaluation of gene expression by RNA-seq identified DEGs between regions of the biceps femoris with the ham halo effect that are associated with variation in pork color.