Animal breeders are making gains and breeding decisions based on gene-marker technology that was once thought to be applicable only to researchers or companies. Today, new gene-marker tools are commercially available at relatively low costs, including those for traits that address the number of pigs born, feed efficiency and growth, backfat and pork quality. Two companies, GeneSeek, a molecular biology company based in Lincoln, Neb., and DNA LandMarks, a genetic testing company in Canada, have purchased the licensing agreements for the United States and for Canada, respectively, for several gene tests from the original researchers, including those from Iowa State University’s laboratory.

A breeder can now submit a blood or tissue sample (whole blood, blood blotter cards, ear notches, docked tails or tissue obtained through a new ear tagging system from Typifix) as DNA sources for the tests to determine the marker genotypes on multiple animals.

So, let’s look at some of the tests that are now available.

Growth, feed efficiency and backfat

Three markers are associated with growth rate and feed efficiency; they are MC4R, HMGA1 and CCKAR.

The MC4R locus (melanocortin-4 receptor) impacts growth and leanness. There are two alleles or variants for this marker, A and G. The A allele is associated with fast growth while the G variant is associated with lean and efficient growth. The producer and breeder can now decide whether to choose the “fast” or the “lean/efficient” growth form of the gene. Pigs that are homozygous for the fast-growth alleles (AA) reach market weight about three days sooner than pigs that are homozygous for the lean allele.

If producers select for the MC4R lean alleles (GG), pigs will have 8 percent less backfat and eat significantly less feed. These results have been well validated and are effective in all breeds except Hampshire. Note that the accompanying table (on page 32) shows the effects of MC4R in two different populations of pigs.

HMGA1 is abbreviated from the gene’s name, high-mobility group A, and is highly associated with backfat and lean growth. HMGA1 markers are consistently associated with fat deposition, growth rate and lean-mass percentage traits across several pig populations. It is important to remember that the T allele is the beneficial allele, and it should be selected to reduce backfat and improve lean percentage. You can test and select animals that are likely to be leaner and produce leaner offspring. Thus, this allele will reduce backfat and improve percent lean in terminal market animals. Feed efficiency improvements also should occur because a reduction in fat deposits reduces the feed required to add weight to the animal.

CCKAR (cholecystokinin type A receptor) gene marker is associated with feed intake controls, hunger and obesity. It has two genetic alleles or variants, G and A. The G allele is dominant to the A allele. Pigs with at least one copy of the G allele (GA or GG), on average, have ~5 percent higher daily feed intake, 3 percent higher daily gain and 3 percent fewer days to reach 180 kg, compared to homozygotes (AA) for the A allele.

Meat quality markers

Producing high-quality pork to meet consumer demand is a selection goal of most swine breeders, and in the past several years markers have been identified that improve pork quality. The two markers associated with meat quality include PRKAG3 and CAST.

  • PRKAG3 (protein kinase, AMP activated, gamma 3 subunit) is the gene marker associated with muscle glycogen content and meat quality. Producers and breeders can select for animals that have the higher pH (about 0.1) and better meat color form of the gene. Other variations have been referred to as the Rendement Napole (RN) gene marker, which has been shown to cause low ultimate pH and water-holding capacity in pork. The RN marker has been largely observed in purebred Hampshire or crossbred animals involving Hampshire. Hence, this gene was also known as the Hampshire effect.

    This new PRKAG3 gene marker determines the presence of the 199Ile, A-variant which is associated with lower glycogen, higher ultimate pH and favorable color in loin and ham tissues. Animals with this genotype (AA) have a pH of nearly 0.1 higher in their loin and ham muscle samples than those that are homozygous for the non-beneficial allele. Thus, producers should select animals with at least one copy of the A allele, with the target of having all animals be AA.  This marker’s effects have been observed in all major breeds, and the test would be very useful in Berkshire and Duroc breeds to remove the gene’s unwanted forms.

  • CAST (calpastatin) is responsible for inhibiting enzymes called proteases that affect meat tenderness post-harvest. Two variants have been identified within the CAST gene area that impact muscle firmness, juiciness, Instron force, cooking-loss chewiness and tenderness scores. Breeders should select for the favorable CAST A alleles.

Litter size markers

In a time when there’s a glut of pigs on the market, litter sizes may not be a focus area. But, of course, increasing litter size also improves efficiencies, as it requires fewer sows and less feed. Two new markers called ESR and EPOR, which stand for estrogen receptor and erythopoietin receptor, respectively, are commercially available.

  • The ESR gene marker is associated with litter size, and a large swine breeding company has used it for many years. It was first discovered in Meishan pigs. Estrogen is a key female hormone that plays a significant role in many reproductive functions, including embryo survival, fetal development, fertility, maintenance of fertility and secondary sexual characteristics. Animals that carry one copy of the favorable gene variation will, on average, have 0.4 more pigs per litter. Sows that are homozygotes (carry two copies) for this marker would average 0.8 pigs more per litter. This test is effective in breeds or lines involving Large White or Yorkshire breeds and crossbred sows related to these breeds.
  • EPOR has been shown to be associated with uterine capacity and litter size. Researchers at USDA’s Meat Animal Research Center in Clay Center, Neb., conducted a study using sow lines selected for increased ovulation rate. Such sows have been associated with having the favorable allele for the EPOR marker. Furthermore, sows with the favorable alleles have increased uterine capacity, which likely contributes to increased live births.

Where to begin with molecular markers?

Our advice to producers is to begin testing herd boars and/or those in the boar studs that they use to make pure matings. For boars used to develop terminal-sire lines, the best approach is to determine the status of all herd boars and those in boar studs for growth and meat quality markers. Similarly, all boars used to make maternal purebred matings should be tested using the litter size markers.

Once producers have those results, they can determine the frequency of the alleles (good and bad) for the sire breeds or lines. They can use this information to determine whether it’s necessary to test females from each breed or line. From there, producers can determine which alleles to fix or ensure that animals carry two copies of the alleles in a given breed or line. Producers can then select for the preferred animals and cull those without the desirable alleles.

What’s the transition to developing breeding programs?

Many of these markers or genes are best used in combination. Use of all five markers, including MC4R, CCKAR, PRKAG3, CAST and HGMA1, would be beneficial to develop a terminal line for improved growth, leanness and meat quality. MC4R (growth allele) and HGMA1 could be used to develop a line that grows fast and has some backfat improvement. Similarly, selecting animals that have the MC4R (lean allele) and HGMA1 could be used together to make even faster progress in improving breeding stock’s leanness and efficiency. The PRKAG3 and CAST could be used in combination to improve meat quality. Furthermore, some breeders may choose to select animals for all of the growth and meat quality markers to develop pure-breed animal lines that excel in producing lean, high-quality pork.

Maternal lines should be developed with favorable alleles for both the ESR and EPOR markers. This use will enhance the chances of the lines having larger litters, which is important to the efficiencies and profitability of any pork operation.

Breeders and producers should work to develop the best multi-gene combination that meets customer needs for maternal and terminal lines. Extension swine specialists and others in the industry are available to advise breeders once results are obtained.

Testing, at what cost?

The cost for the marker tests varies ($12 to $16 for two genes and up to $35 for all genes), depending on how many tests are done. Check the GeneSeek or DNA LandMarks Web sites for more cost information.

While testing is not inexpensive, especially if attempting whole herd tests, you can gather useful information by testing sub-populations of animals at a much lower cost. This allows a strategy to be in place before entire whole-herd testing programs are required to determine the status for all of the markers available.

Of course, there are other tests to remember. Breeders should ensure that their herds are free of the Porcine Stress Syndrome (PSS) gene. If producers are concerned that their animals might have this particular defect, they should test the animals using the Hal1843 marker. There also are tests for the NAPOLE gene, Insulin-like Growth Factor (IGF) that’s been associated with meat quality in pigs, F4 resistance to E. coli F4 ab/ac in pigs and the Hampshire breed test. Lastly, tests are available that identify porcine reproductive and respiratory syndrome and porcine circovirus 2.  

Used in thoughtful combinations, these gene markers offer real benefits for future genetic and economic improvement for swine breeders and commercial pork producers alike. PK

Targeting Carcass Traits

Shown here is an example of the effects of the MC4R molecular marker. Pigs that are homozygous for the fast growth alleles (AA) reach market weight about three days sooner than pigs that are homozygous for the lean allele. Pigs with the GG form will have 8 percent less backfat and eat significantly less feed than their counterparts.