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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND GENOMIC APPROACHES TO IMPROVE EFFICIENCY OF SWINE PRODUCTION AND PRODUCT QUALITY

Location: Reproduction Research

Title: Genome-wide association of meat quality traits and tenderness in swine

Authors
item Nonneman, Danny
item Shackelford, Steven
item King, David
item Wheeler, Tommy
item Wiedmann, Ralph
item Snelling, Warren
item Rohrer, Gary

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 16, 2013
Publication Date: September 1, 2013
Repository URL: http://handle.nal.usda.gov/10113/57863
Citation: Nonneman, D.J., Shackelford, S.D., King, D.A., Wheeler, T.L., Wiedmann, R.T., Snelling, W.M., Rohrer, G.A. 2013. Genome-wide association of meat quality traits and tenderness in swine. Journal of Animal Science. 91(9):4043-4050.

Interpretive Summary: Pork quality has a large impact on consumer preference and perception of eating quality and is largely driven by tenderness and juiciness scores, which are related to shear force, cooking loss and pH. Water loss from meat during postmortem storage reduces profitability and consumer appeal. Other measures of pork quality, such as color and intramuscular fat, also affect consumer satisfaction ratings to a lesser extent, but may influence purchase decisions. Factors like genetics, cooking temperature and packing plant procedures also affect meat quality and tenderness. While several candidate genes have been proposed for pork quality, only a few causative genes have been identified. Numerous QTL studies have been reported for pork quality using different breeds and crossbred populations, but limited studies have been done using dense genetic markers in commercial animals. This study was done to identify additional genes affecting economically important pork quality traits. A dense genome-wide analysis was performed for pork quality traits (intramuscular fat, slice shear force, color, purge, cooking loss and pH) collected from 531 to 1,237 barrows and gilts of a Landrace-Duroc-Yorkshire population using the Illumina PorcineSNP60 Beadchip, which provides dense genetic marker coverage. Associations were detected with regions of the swine genome for all traits. Intramuscular fat had the greatest number of SNP associations, followed by pH, purge, cooking loss, shear force and color. Two genomic regions contained associations for multiple traits; one on chromosome 1 was associated with slice shear force, moisture loss and pH, and another on chromosome 6 was associated with purge and intramuscular fat. Candidate genes were identified in associated regions for all meat quality traits and several previously identified gene associations were confirmed. These results suggest that markers in these regions should be useful for genetic improvement of pork quality traits in commercial populations.

Technical Abstract: Pork quality has a large impact on consumer preference and perception of eating quality. A genome-wide association was performed for pork quality traits [intramuscular fat (IMF)], slice shear force (SSF), color attributes, purge, cooking loss, and pH] from 531 to 1,237 records on barrows and gilts of a Landrace-Duroc-Yorkshire population using the Illumina PorcineSNP60 BeadChip. Associations were detected using MTDFREML for all traits. Intramuscular fat had the greatest number of SNP associations, followed by pH, purge, cooking loss, shear force, and color. Two regions contained associations for multiple traits; one on SSC1 at 255 Mb near calcineurin subunit B (PPP3R2) was associated with SSF, moisture loss, and pH, and one on SSC6 from 28 to 29.5 Mb for purge and IMF containing the candidate genes glucose-6-phosphate isomerase (GPI) and KCTD15. Some of the other compelling candidate genes in regions associated with meat quality include CEBPA, SNAI1, and FAM132A for IMF, CAPN1 for SSF, GLUL for pH, and PRKAG3 and ITGB1 with cooking loss.

Last Modified: 12/21/2014
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