When it comes to discoveries in pork quality, the Halothane and the Napole genes are the superstars of gene markers. 

The Halothane or stress gene, discovered in 1990, is a single-point mutation on chromosome 6. A commercial test has been developed to identify the carrier and mutant genotypes.

Laboratories all over the world were looking for more definitive information on the Napole gene, which was discovered in the late 1990s by a joint effort in Europe. The Napole mutation is actually a single-gene effect but it’s dominant so finding animals carrying the two bad alleles or the carrier carrying the one bad allele was very difficult until the DNA test was developed.

“The Napole and Halothane genes account for 30 percent to 40 percent of the variation in meat quality,” says Rodney Goodwin production research director for the National Pork Board. “Most other genes don’t have near that effect.”

Both mutations in these genes now have commercial genetic tests, which have allowed the industry to work toward phasing them out in an effort to reduce pale soft exudative pork and improve pork quality.

Reducing both bad forms of the genes has been a long battle, in part because they also contribute to some positive growth characteristics in the animal, which has divided industry opinions.

“The biggest challenge in working on genetics for pork quality has been the antagonistic relationship with positive economic traits,” says Rhonda Miller, meat scientist, Texas A&M University.

The industry was reluctant to eliminate the stress gene, due to a positive correlation with carcass yield. However, Goodwin points out there is “no negative correlation between production traits and pH, color, tenderness, juiciness, and that’s a very positive thing. Most quality traits seem to be a different set of traits independent of production traits.”

“The Napole and Halothane genes are the best known genes, but there are other pork-quality genes, as well,” says Max Rothschild, Iowa State University geneticist and U.S. pig genome coordinator. He points to the following areas:

  • Significant effects on intramuscular fat or marbling have been detected on chromosomes 1, 6 and 7.
  • Chromosomes 6 and 7 quantitative trait loci explain 14 percent to 18 percent of the phenotypic variation for backfat.
  • Two genome regions located on chromosomes 5 and 15 have significant effects on the meat’s ultimate pH in Berkshire/-Yorkshire F2 pigs and in commercial breeds.
  • The genome region on chromosome 5 explains approximately 4 percent of the phenotypic variance in pH.
  • Chromosome 15 genome region explains 4 percent to 6 percent of pH variance, and presents favorable alleles,  in the Berkshire breed. Rothschild notes that this effect is seen in other commercial lines and there is now a commercial genetic-marker test relating to pH levels.
  • Meat color also has significant marker-trait association. The chromosome 15 genome region affects meat quality due to the additional mutations found in the gene causing the Napole effect.
  • The chromosome 17 QTL affects both color score and reflectance measurements of pork.

No genome-wide significant genome regions have been detected for water-holding capacity, drip loss or cooking loss, though some suggestive regions have been discovered for all three categories.

Work with sensory panel evaluations have found some suggestive genome regions, though more work is needed to confirm this. Calpastatin, or CAST, has been mapped in a genomic region for tenderness, and is a specific inhibitor of calpains, which appears to impact tenderness.

“The CAST gene has been shown to have a correlation to tenderness,” says Rothschild. “There has been additional data and research that show in some populations, these genes have an effect on muscling.”

Developing markers that can be tested on live animals are the most valuable benefit of gene-mapping, says Goodwin. Without live markers, you would have to use biopsy, littermate or related-animal studies to evaluate an animal’s quality traits. That can be hit-and-miss, and take a lot longer to develop genetic improvements.

As exciting and successful as the work on mapping pork-quality traits has been thus far, the real potential lies in future research.

“Genetic research gives us a better understanding of some factors that drive pork quality,” says Miller. “The industry has made a lot of changes in animal handling, chilling and transportation to reduce meat-quality variation, but it still exists, which means genetics play a big role in controlling quality. We need to understand the genetic factors that drive pork quality to determine the best management practices for quality and consistency.”

Heritability for most pork-quality parameters is about 30 percent, but could be as high as 50 percent for some categories. Goodwin says genetics probably account for 30 percent to 40 percent of meat-quality variation.

“Day-to-day variation in pork quality is still a big issue,” says Goodwin. “The industry has made a valiant effort to control chilling, management and other factors, but we need to stabilize the genetic component so we can work on the other areas.”

Overall, pork quality is an area where the gene-mapping benefits are clear. Attempts to eliminate the Napole and Halothane genes have had a huge impact on pork quality, and it wouldn’t have been possible without live-marker tests that resulted from gene-mapping research. 

Editor’s note: This is Part II in a series on the swine genome.