Genome-wide association study of meat quality traits in a White Duroc×Erhualian F2 intercross and Chinese Sutai pigs

PLoS One. 2013 May 28;8(5):e64047. doi: 10.1371/journal.pone.0064047. Print 2013.


Thousands of QTLs for meat quality traits have been identified by linkage mapping studies, but most of them lack precise position or replication between populations, which hinder their application in pig breeding programs. To localize QTLs for meat quality traits to precise genomic regions, we performed a genome-wide association (GWA) study using the Illumina PorcineSNP60K Beadchip in two swine populations: 434 Sutai pigs and 933 F2 pigs from a White Duroc×Erhualian intercross. Meat quality traits, including pH, color, drip loss, moisture content, protein content and intramuscular fat content (IMF), marbling and firmness scores in the M. longissimus (LM) and M. semimembranosus (SM) muscles, were recorded on the two populations. In total, 127 chromosome-wide significant SNPs for these traits were identified. Among them, 11 SNPs reached genome-wise significance level, including 1 on SSC3 for pH, 1 on SSC3 and 3 on SSC15 for drip loss, 3 (unmapped) for color a*, and 2 for IMF each on SSC9 and SSCX. Except for 11 unmapped SNPs, 116 significant SNPs fell into 28 genomic regions of approximately 10 Mb or less. Most of these regions corresponded to previously reported QTL regions and spanned smaller intervals than before. The loci on SSC3 and SSC7 appeared to have pleiotropic effects on several related traits. Besides them, a few QTL signals were replicated between the two populations. Further, we identified thirteen new candidate genes for IMF, marbling and firmness, on the basis of their positions, functional annotations and reported expression patterns. The findings will contribute to further identification of the causal mutation underlying these QTLs and future marker-assisted selection in pigs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adiposity / genetics
  • Animals
  • China
  • Color
  • Crosses, Genetic*
  • Female
  • Genome-Wide Association Study*
  • Hydrogen-Ion Concentration
  • Linkage Disequilibrium / genetics
  • Male
  • Meat / standards*
  • Muscle Proteins / metabolism
  • Muscles / metabolism
  • Polymorphism, Single Nucleotide / genetics
  • Sus scrofa / genetics*


  • Muscle Proteins

Grant support

Funding was provided by the Key Project of National Natural Science Foundation of China (No. 31230069), the National Natural Science Foundation of China (No. 31101697), and the Development Programs for Basic Research of China (973 Programs, No. 2012CB722502 and 2012CB124702). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.