Exploiting Genetics Within Your Herd

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The Professional Swine Manager’s role in the genetic system is generally to take the end result of a genetic improvement program and manage the animals in a manner to maximize the expression of their genetic potential. For pork producers there are two main goals: 1) Improve the efficiency of production, and 2) Improve the quality of the end product produced. There are also two approaches that can be taken to accomplish these goals: 1) Improve the management and environment and, 2) Improve the genetic quality. The intent of this presentation is to provide the background necessary to understand how the genetic improvement program interrelates with production management. For genetic improvement there are three basic methods:

1. Selection – Differential reproductive rates are enforced where the more desirable individuals leave more offspring than the less desirable individuals. Selection makes use of additive genetic variation and is used for long term genetic improvement. At the commercial level most of the selection emphasis should be placed on the genetic source.

2. Mating Systems – A systematized approach to the mating of selected animals to produce non-additive genetic change, observed as heterosis. Heterosis does not occur for all crosses or for all measures of performance. In addition, heterosis must be recreated at each generation by the mating system.

3. Importation – The bringing in of genes for specifically required characters into an otherwise satisfactory population. This is commonly done by bringing in new terminal sire lines. Depopulating a herd and repopulating a herd, while not always economically practical, is the most rapid and simplest form of genetic improvement.

Genetic improvement is normally obtained by utilizing some combination of these systems. However, these systems will each differ in how they relate to production management.

Genetic Relationships Between Performance Traits

For genetic improvement through selection variation amongst animals is required. The variation observed in a population is composed of two primary factors, the genotype and the environment. Conventional selection relies on the fact that use of exceptional individuals as parents of the next generation will result in a positive change in the average performance of the population.

Genetic improvement through selection operates only on the genetic component of the animal’s record. The environmental component is not passed from parent to progeny and, therefore, needs to be accounted for when determining the genetic value of an animal. Some of the environmental factors such as parity of sow or sex can be accounted for mathematically. However, other factors such as health, management and feed are accounted for through contemporary grouping. These are referred to as unknown sources of environmental variation.

When making genetic decisions economically important traits should be emphasized, but it is also important to understand the effect that selection has on different traits. Table 1 provides heritability estimates that tell us the strength of inheritance for each trait. Heritability is the percent of the variation in performance due to genetic effects.

For example, backfat has about a 40% heritability. Thus, about 40% of the variation (the phenotypic differences between animals raised in the same group) in backfat is due to gene effects while the remaining variation is due to environment. Selection will be less effective for lowly heritable traits like pigs born alive because they are affected by the environment to a greater extent. Most litter traits have a low heritability, while production and carcass traits have higher values as shown in Table 1. In addition, an estimate of the standard deviation (SD) and economic value for each trait is also provided. The standard deviation tells us how much variation is present in the population and can be used to estimate where an individual animal ranks in the population. Economic values for performance traits allow the producers to know how much emphasis to place on each measure. Economic values may vary from farm to farm due to differences in management factors and markets.

Table 1. Heritability, Standard Deviation and Economic Value of Swine Performance Measures.

Trait Heritability (%) Standard Deviation Economic Value
Number born alive 10 2.5 13.50
21 day litter weight 15 16.0 .50
Feed efficiency 30 .25 -13.00
Days to 230 lb. 35 13 -.17
Backfat probe 40 .20 -15.00
Percentage lean 50 1.5 1.10

The genetic correlation describes the relationship between two traits, in that a gene or more than one gene may be responsible for an enzyme or other product that influences both traits. Genetic correlations range from -1 to 1. A positive genetic correlation indicates that selection for an increase in one trait will result in an increase in the other. A negative genetic correlation indicates that selection for an increase in one trait will result in a decrease in the other. The sign of the genetic correlation does not indicate the favorability of the relationship, only the statistical relationship.

Table 2 illustrates the genetic correlations between carcass measures and production traits. Selection for decreased fat will increase days to market, reduce pounds of feed required per pound of gain, and greatly increase percent muscle. By improving carcass composition pigs will generally be slower growing, have decreased appetites and be more efficient. If number born alive is improved, small increases in 21 day litter weight are observed, and feed efficiency and growth rate are enhanced slightly. Reproductive traits have little relation to carcass traits.

Table 2. Genetic Correlations Between Swine Performance Measures.

21 day litter wt

Feed Efficiency

Days to Market


% Muscle

Number born alive





21 day litter weight





Feed efficiency





Days to market







Heterosis Effects on Performance Targets

Crossbreeding is an important part of commercial swine production systems because of the improvement in efficiency from heterosis and the potential to exploit differences between breeds. A terminal, static cross in which all offspring are market animals takes the greatest advantage of differences in strengths of lines or breeds. Lines that have superior genetic merit for reproduction provide the females and lines that are superior for production traits provide the males. The pigs marketed then have high genetic potential for production and the sow herd has high merit for reproductive traits. Heterosis has the most significant benefit in maternal performance and factors effecting fertility in boars (Table 3). Ultimately in commercial pork production, selection and crossbreeding are combined to achieve the highest level of performance.

An example of heterosis is a cross between lines A and B. Let’s assume that number of pigs born alive average 10 and 11 for A and B, respectively, and that the daughters produced from this cross average 11.5 pigs/litter. The heterosis for number born alive in these AxB females can be calculated as follows:

Maternal heterosis for number born alive = [(11.5 – ((10+11)/2)) / 10.5] x 100 = 9.5%

Maternal heterosis of 9.5% is equal to the 1 pig/litter advantage the crossbred female has over the average performance of the pure line parents.

In commercial production knowing the levels of maternal, paternal and individual heterosis are important when setting performance targets. One fairly common example is the comparison of the F1 females (AxB) to the backcross female (AxAB).

The expected heterosis of a cross is determined by the amount of genes the parents have in common. This can be determined by the amount of breed in common, i.e. A and B are unrelated, therefore, the offspring have 100% heterosis. Therefore, the F1 has 100% heterosis and the backcross has 50% heterosis. In the previous example, the AxB female had a 1 pig/litter advantage due to heterosis, however if the AxAB female were used in the sow herd this advantage, due to heterosis, is expected to be only .5 pigs/litter.

Table 3. Estimates of Heterosis for Measure of Swine Performance



Heterosis (%)


Maternal Heterosis


# of Embryos



Litter size


7 – 10

21 day litter weight




Paternal Heterosis


Testicle weight



Total sperm



Conception rate


10 – 14


Individual Heterosis


Avg. Daily Gain



Feed Efficiency






Genotype by Environment Interactions

A pig’s genes are expressed in the environment where it is reared. The pig cannot grow in the absence of an environment containing feed and water nor can an inherited resistance to disease be expressed in the absence of the disease organism (Table 4). Therefore, the testing and selection of animals should take place in environments that are very similar to which the progeny will be exposed.

However, it is equally important that testing and selection take place in an environment that distinguishes between genotype. Take for example, the impact of genotype by environment interaction on the choice of nutritional program for the evaluation of lean growth rate. It is only at higher levels of energy and protein that differences in lean growth and fatness become evident.

Table 4. Interaction Between Genetic Resistance to E coli K88 and the Presence of the Organism in the Environment

Incidence of Diarrhea (%)


Without K88

With K88

Litters by sire A



Litters by sire B



If the environment in which animals are tested and selected differs greatly from the commercial environment, it is necessary that there is no severe genotype by environment interaction where the selected animals turn out to be worse in the commercial environment. The most common example of this situation is in the breeding herd where some sow genotypes excel in productivity when the housing environment consists of gestation crates.

These same sows when group housed and placed in a pasture environment may be inferior to another genotype which is more durable in that environment, but will not be superior when housed in gestation crates.

Most often the quality of the commercial environment does not allow the full expression of genetic potential. When making changes or upgrades in the source of breeding animals, an upgrade in management and environment is required if the new, improved genotypes are to express their full potential.

Genetic Lag

The swine breeding herd is often thought of as a pyramid. The point or top tier(s) of the pyramid represents nucleus animals. These animals are usually pure line animals in a genetic improvement program selected for specific traits. The multiplier tier(s) cross the nucleus lines for production of parent gilts and boars to be used on commercial farms. The commercial tier then crosses the parent boar and gilt lines from the multiplier tier to produce the market hogs that are slaughtered.

The time it takes for any genetic improvement made in the selection program of the top tier of the pyramid to trickle down to commercial market hogs is called genetic lag. In each tier of the pyramid the length of time that animals are used and their relative genetic superiority to younger animals influences the genetic level experienced at the lower levels of the pyramid. Genetic lag will be different in each production system and can easily range from 4 to 10 years. This means that the genetic level of performance of market hogs today was selected in the nucleus lines 4 to 10 years ago and the improvements being made in the nucleus herds today will not be observed in market hogs until 4 to 10 years from now. If the genetic lag is reduced it means that the pork producer will see the genetic improvements in the market hogs’ performance sooner. Genetic lag is determined by several of the following variables:

1. The rate of genetic progress taking place in the nucleus herd.

2. The genetic superiority of the nucleus boars and gilts transferred to multiplier herds.

3. The length of the generation interval at each level of the pyramid.

4. The number of steps in the breeding system, including the multiplier and customer herds.

The seedstock supplier determines the rate of genetic progress in the nucleus herd by the design and implementation of their genetic improvement program at the nucleus level. Most seedstock suppliers can provide information on the genetic trend (annual genetic improvement) that they have been able to achieve for each trait selected on in their nucleus herd(s). The seedstock supplier that is selected to provide animals to the breeding herd should be making annual improvements in traits of importance to the commercial program.

The genetic progress in the nucleus herd(s) can also be accelerated by the replacement rate of the nucleus breeding herd. At the nucleus level boars are often replaced after six months of use and females are replaced when younger gilts are available that are genetically superior based on expected progeny differences (EPDs).

Table 5 (NSIF-FS9) illustrates the effect the replacement rate on genetic improvement per year in NSIF Index units. If a high levels of genetic improvement per year is to be attained, the results in Table 5 would indicate that boars probably should not be used for more than 1 year and sows should not be kept for more than 4 litters.

Table 5. The Effect of Boar and Sow Age on Genetic Improvement per Year in NSIF Index Units1

Number of

Boars are used in the herd for

Litters / sow

3 months

6 months

1 year

2 years

3 years





































1This value needs to be added to 100 to obtain the NSIF index of the progeny of the selected boars and gilts.

It is important to realize that genetic lag is not only important when genetic improvement is taking place at the nucleus level. It should also be noted that the difference between the commercial herds and the seedstock suppliers is the genetic lag. The structure of the genetic transfer system will determine how wide this gap is between the seedstock supplier and the commercial producers.

At the multiplier level the most common system follows the three tiers where replacement boars and gilts come to the multiplier level from the nucleus and the multiplier subsequently provides replacement boars and gilts to the commercial operations. Every additional multiplication step that is added to the system moving the commercial boar and gilt replacements further from the genetic improvement program at the nucleus level increases genetic lag.

Most multiplier herds are operated in typical commercial fashion with standard replacement rates. Selection is usually not performed among the crossbred progeny at the multiplier level because of the large proportion of females required and the increased genetic cost that it would create. Genetic improvement is made at the multiplier levels by routine replacements from the nucleus level where continuous genetic improvement is occurring. Genetic lag can be addressed at the multiplier level through selection of boars.

It is generally not cost effective to operate a selection program at the commercial level. However, genetic lag can be reduced by regular replacement of breeding stock with superior individuals and boars can be replaced at an average age of one year to minimize genetic lag. The opportunity to reduce genetic lag at the commercial level is in the quality of seedstock selected. It is possible to purchase boars of superior genetic merit directly from the nucleus level and this can reduce genetic lag by about 1/2 year.

AI can reduce genetic lag in two primary ways:

1. When AI is used the boar:sow ratio will decrease, reducing the number of boars needed; allowing fewer, superior boars to be selected.

2. AI offers the opportunity to reduce genetic lag by using superior sires from the nucleus levels at all levels of the production pyramid.

Using AI at any level of the pyramid can reduce genetic lag by approximately 1/2 year, depending on the selection intensity placed on natural service and AI boars. If AI is used at all levels of the production pyramid and gilts are obtained from a source with consistent genetic improvement, the genetic lag can be reduced to its lowest possible level of about 3 1/2 years.

For commercial managers to reduce genetic lag, the most attention should be paid to the selection of the breeding stock supplier. The genetic supplier must be realizing genetic progress through the use of a performance testing and genetic evaluation program and then rapidly disseminating this improvement through its multiplication system. The commercial producers then must use genetic information when purchasing breeding animals along with acceptable health, reproductive soundness, and skeletal structure. Incorporation of an AI program will also greatly reduce genetic lag if the AI boars that are selected come from the nucleus level. If no change is made in the way that commercial boars are selected genetic lag may not be changed. And finally, by reducing the time that commercial boars are used to 1 year or less will result in a reduction in genetic lag at the commercial level.

Porcine Stress Syndrome

The stress gene has a deleterious effect on pork quality, but may have a positive impact on percentage lean in the carcass. The carcass advantages of stress-positive pigs over normal pigs are more than offset by the possible death losses that can occur. In the present marketing structure the stress carrier pigs can provide a carcass merit advantage, but research has shown that there is ultimately a reduction in pork quality.

No breed is entirely free of the PSS problem and, likewise, no breed can be termed categorically stress-susceptible. PSS is inherited as a simple recessive gene, meaning that both the sire and the dam must be at least carriers of the gene. A single genetic locus is involved in transmission of this gene. The normal gene is called (N) and the mutant halothane gene is called (n). Canadian researchers (O’Brian and MacLennan, 1992) discovered that PSS is associated with a single base pair mutation on the HAL gene. A DNA-based test has been developed that can identify normal, stress carrier, and stress positive animals. Every individual has two copies of every gene. Pigs are classified as normal (homozygous nonmutant or NN) when both copies of the HAL gene are normal. Stress carrier pigs carry one copy of the mutation and one normal gene and are termed heterozygous monomutant (Nn). In stress positive pigs both copies of the gene have the mutation and these pigs are called homozygous dimutant (nn).

In pork production it is very important to know the stress status of the breeding stock in your herd. Yours seedstock supplier can provide this information. The DNA-based blood test can be used to remove stress-positive and stress-carrier animals from the breeding herd. If you elect to use the stress carrier animals to improve your percentage lean, manage them wisely. Use stress positive animals only for terminal breeding. Never keep any gilts back from a known carrier. Provide good management for boars and market hogs. If the sow herd is stress free, using a stress positive boar will produce 100% stress carriers, and using a stress carrier boar will produce 50% stress free and 50% stress carriers.

Some of the undesirable meat characteristics and PSS can be minimized by observing simple management practices at marketing. The following are suggestions for reducing losses associated with handling market hogs:

1. Avoid crowding in holding pens and trucks. Make sure loading and unloading facilities are well-designed to minimize excitement. Train personnel in animal behavior and be patient.

2. Eliminate the opportunity for fighting. Do not mix pigs that have not been reared together. Handle pigs quietly at all times and refrain from use of an electric prod.

3. Avoid extremes in temperature and other environmental conditions. Do not move pigs during the hottest part of the day.

4. Do not require pigs to walk long distances; avoid driving pigs over slippery surfaces; do not feed pigs 12 to 24 hours prior to marketing; and spread the stress over long periods of time and allow time for adjustment.

5. Include a 2 to 4 hour resting period in preslaughter handling. Use showering for cooling if temperatures are high.

How to Maximize Genetic Potential

In order to maximize genetic potential at the commercial level the nucleus source for breeding herd replacements must be making constant genetic progress. The breeding herd replacements put into commercial production must also be selected according to genetic potential and compatiablity (heterosis). In addition, when replacement gilts are selected within herd some objectivity should be used for keep/cull decisions.

To realize genetic potential from an animal the genotype must be allowed to express itself. This mean having access to appropriate feed, water, facilites, disease. In order to monitor expression of genetic potential and to make appropriate adjustments to feeding and management programs current, accurate, and useful performance records are required.