Introduction to Swine Genetics for Small and Beginning Farmers



The performance of pigs is the result of two influences: genetics and environment. Because the genetics of a pig plays an important role in its performance and meat quality, all pig producers should be familiar with the potential and application of genetic selection. This factsheet provides an introduction to genetic principles and selection strategies for beginning pig farmers.



  • Summarize core genetic principles
  • Describe selection strategies


Swine Genetics 101



At conception, genetic information from the sire and dam combine to create the genotype of the offspring. The pig’s genotype is simply the genetic makeup for the animal. For most economically important traits, the pig’s genotype can be thought of as setting an upper limit for an animal’s performance, sometime called the genetic potential. Whether the pig’s genetic potential is realized or not is usually heavily influenced by environment.  Environment is a collective term for all the non-genetic influences on an animal. Environment includes but is not limited to nutrition, housing, health status, and thermal conditions. The phenotype—physical appearance or performance —of a pig is the result of the animal’s genotype and environment. The relationship between phenotype, genotype, and environment is often summarized as the following equation:


Phenotype = Genotype + Environment


Heritability is the proportion of differences in performance among animals that is due to genetic differences (Whittemore, 2006). Table one summarizes heritability estimates for selected traits. A range of values is given because these values are estimates from different populations. Although these are estimates, it is well established that some traits are less heritable than others. Another way of saying the same thing is that some traits are more heavily influenced by environment than by genotype.


Reproductive traits usually have a heritability of less than 25% and are considered lowly heritable. For traits that are lowly heritable, working on improving the environmental conditions to support a desirable outcome may be a more practical approach than genetic selection over the short term. For example, prewean mortality has a very low heritability and so a producer trying to reduce prewean mortality should first address environmental challenges leading to prewean mortalities. Improving prewean mortality or other lowly heritable traits through genetic selection is possible, but it will take a considerable amount of focused effort and time.


Alternatively many growth and carcass traits have a heritability of more than 30% and are considered moderately to highly heritable. Carcass backfat and loin muscle area are highly heritable traits and so introduction of a boar with superior phenotype for these traits into the breeding herd will result in rapid improvement in carcass backfat and loin muscle area in the resulting offspring.


Nearly all traits are not the result of one gene—a segment of DNA that is the basic unit of heredity (AnimalSmart, 2015). Rather, multiple genes typically influence and interact with each other to impact a combination of traits (Cassady and Robison, 2006). Positively correlated traits are those traits that when an increase is made in one trait, there is an increase in the other as well. For example, loin eye area is positively correlated with percent lean. Thus, if we select for a larger loin eye area we are also selecting for a leaner carcass. Negatively correlated traits have the opposite relationship—as one increases the other decreases. Sometimes negative correlations are actually beneficial. For example, loin eye area is negatively correlated with back fat depth, thus, an increase in loin eye area is generally associated with a decrease in backfat depth—a beneficial outcome if the goal is to improve muscling and percent lean. Some genetic relationships are antagonistic. For example, continued selection of pigs with greater muscle will generally result in a reduction of maternal performance for traits such as conception rate, pigs born alive, pigs weaned, and weaning weight of the litters.


Selecting Animals for Breeding


Identification and selection of pigs with superior phenotypes, even for lowly heritable traits is important. There are basically four ways that we evaluate our animals/traits to determine which individuals we should use for breeding.  These include visual appraisal, production testing, progeny testing, and marker-assisted selection. Typically a combination of methods should be used to insure that productive breeding decisions are made.


Visual Appraisal


The first method for evaluating breeding animals is visual appraisal or the eye test.  This method of selection is based on the phenotype of the animal or what the animal looks like when compared to other animals in a group. For selection decisions where traits are highly heritable, and the animals compared are of a similar age or stage of life, this can be a good method.  However, it may not be the best method for achieving genetic progress.  One of the negatives of visual appraisal is that we may overlook a superior animal due to the simple fact of age or weight variation within a group. For example, if we are selecting replacement gilts from a group of gilts with a wide range in age variation the older gilts in the group will likely be larger and more developed and will thus be more likely to be kept for breeding stock.


Visual appeal is very beneficial for helping select and/or cull for physical traits that could be problematic long term, such as feet and leg soundness, leg conformation and other structural traits, number of functional teats, and external genitalia size and shape. The Replacement Gilt Evaluation and Selection Pocket Guide—available through the Pork Information Gateway—provides a visual reference and summary of key criteria to consider when visually evaluating replacement gilts (Stalder et al., 2010).


Production Testing


Production testing allows producers to make selection decisions based on an animal’s performance when compared to its contemporaries.  Recording performance data is common for most swine farms and is typically used to monitor production dynamics and highlight strengths or weaknesses within the operation. If performance data is collected in a uniform and precise manner and maintained accurately over the productive lifetime of a breeding animal, performance data can be used to evaluate breeding decisions. One of the most challenging aspects of production testing for use in genetic improvement is the requirement of maintaining the exact identification of an animal and its parents throughout its lifetime (Bates, 2006). Misidentification of animals and other data errors will greatly reduce the utility of production records as tools for making breeding decisions.


The National Swine Improvement Federation (NSIF) has developed guidelines for uniform swine improvement programs. These guidelines provide a framework for collecting and comparing performance data important for genetic selection of pigs (NSIF, 2003). Performance data that is relatively easily measured on farm include: birth date, number born alive, weaning date, number weaned, and age at marketing. Collecting data on weight at weaning and market requires a scale, but is easily measured on farm. Backfat thickness and loin eye area are important carcass traits that may be possible to measure by working with your processor or through the use of digital ultrasound.


Standardizing or adjusting records for known environmental factors that influence the performance is necessary to compare individuals in a herd or group on an equal basis.   For example, the parity—number of litters previously farrowed—is known to affect litter size with sows usually farrowing the most live pigs around parity 4 or 5. In order to compare two sows in terms of number born alive an adjustment should be made for parity of the sows. Table 2 summarizes parity adjustment factors for number born alive.


Another example of a common measurement used to compare growth rate in market pigs is Days to 250 lb. Days to 250 lb is not determined by serially weighing an individual pig until it reaches 250 pounds, rather there is a formula that can be used to standardize weight for age and gender of the pig (NSIF, 2003):


Adjusted days = actual age + [(desired weight – actual weight) X ((actual age – A) / actual weight)]


where A = 50 for boars and barrows and 40 for gilts


Using the adjustment equation, pigs farrowed within a short window of time (two weeks) can be compared directly when individual weights on the entire group is collected at a single time point. Adjustments are derived from research data and have been proven to be effective means to compare data within a variable group of contemporary animals. Adjustment information is available from NSIF for many important swine production traits.


In many swine breed organizations, data collected on the farm is sent for central processing and when analyzed in computer models a resulting Breeding Value is estimated. Breeding Values (BV—a measure of an animal’s value as a parent) and Expected Progeny Differences (EPDs—a measure of an animal’s genetic contribution to their progeny) often allow for comparison of animals across herds and allow for selection of targeted animals to improve specific traits (Cleveland and See, 2006; Moeller, 2006).


Progeny Testing


Progeny testing can be thought of as an extension of production testing where production records are kept on the offspring of an individual and are used to estimate the parent’s and the individual pig’s breeding value or genetic merit. Progeny testing is used commonly by swine genetic companies and offers the most value for traits that are not easily measured on the live animals such as meat quality and individual feed efficiency. Progeny testing is used to estimate a sire’s BV for reproductive traits that are only expressed in his daughters. Progeny testing increases the time and associated resources needed to collect and maintain data on important traits. In combination with traits that can be measured directly on the individual, adding data on progeny will enhance genetic value assessments. When pedigree information (sire, dam, grand sires, grand dams, siblings, half siblings, and progeny) is combined with progeny testing, EPDs can be generated. Expected Progeny Differences will increase in accuracy as additional information is added, particularly as more progeny records are included. Thus, as the animals have progeny of their own and more records are established, confidence in an animal’s EPD for the traits of interest increases.


Marker Assisted Selection


The fourth method to consider is marker-assisted selection.  This method involves collecting and analyzing a DNA sample for specific markers that have a measurable effect on a trait.  An example would be the test for Porcine Stress Syndrome (PSS).  Porcine stress syndrome is a group of conditions that include acute stress, sudden death, and pale soft and exudative (PSE) pork (Cowart and Casteel, 2001). Porcine Stress Syndrome is determined by a simple recessive gene and animals can be normal or have no copies of the recessive gene (NN), a carrier which has one copy of the recessive gene (Nn), or stress positive which has two copies of the recessive gene (nn). Pigs that are stress positive for PSS show the most severe impacts of the gene while pigs that are carriers are intermediate in performance. Stress positive pigs will pass this gene onto all of their offspring while carriers will pass this gene onto a portion of their offspring. Testing for PSS involves collecting a blood sample and sending it to a lab for DNA analysis. Additional single gene mutation DNA tests are available in swine, including the Rendement Napole Gene (RN), a gene influencing pork quality. This level of testing may be cost prohibitive for most small and beginning farmers, but most genetic suppliers will provide PSS and other major gene status information on breeding stock or semen they sell.




The pig’s performance is the result of two influences: genetics and environment. Because the genetics of a pig plays an important role in its performance and meat quality, all pig producers should be familiar with the potential and application of genetic selection. Combining visual appraisal with production testing are practical ways for most pig farms to evaluate potential breeding stock while progeny testing and marker assisted selection tools are more commonly used by seedstock companies. Several Pork Information Gateway factsheets discuss genetics and swine breeding in greater detail than is included in this factsheet. These may be good references for additional information and include:

  • Basic Concepts of Genetic Improvement; PIG 06-01-04
  • Genetic Parameters and Their Use in Swine Breeding; PIG 06-01-05
  • Selection Programs for Seedstock Producers; PIG 06-02-02
  • Application of Selection Concepts for Genetic Improvement; PIG 06-02-04
  • Evaluating Genetic Sources; PIG 06-05-01


Animal Smart 2015. Glossary of terms. Available online at http://animalsmart.org/glossary accessed April 25, 2015.


Bates, R.O. and E.R. Cleveland. 2006. Basic concepts of genetic improvement. Pork Information Gateway Factsheet 06-01-04.


Cassady, J. and O.W. Robison. 2006. Genetic parameters and their use in swine breeding. Pork Information Gateway Factsheet 06-01-05.


Cleveland, E. and T. See. 2006. Selection programs for seedstock producers. Pork Information Gateway Factsheet 06-02-02.


Cowart, R.P. and S. W. Casteel. 2001. An outline of swine diseases: A handbook. 2nd edition. Iowa State University Press, Ames, IA.


Moeller, S. 2006. Evaluating genetic sources. Pork Information Gateway Factsheet 06-05-01.


NSIF. 2003. Guidelines for Uniform Swine Improvement Programs. National Swine Improvement Federation. Knoxville, TN. Available online at http://www.nsif.com/guidel/guidelines.htm  accessed April 25, 2015.


Stalder, K.J., C. Johnson, D.P. Miller, T. J. Baas, N. Berry, A.E. Christian, T.V. Serenius. 2010. Replacement gilt evaluation pocket guide. National Pork Board, Des Moines, IA. Available online at http://www.porkgateway.org/FileLibrary/PIGLibrary/References/Replacement%20Gilt%20Evaluation%20-%20Feet%20and%20Leg%20Info.pdf accessed April 25, 2015.


Whittemore, C. T. 2006. Chapter 6: Development and improvement of pigs by genetic selection. In: I. Kyriazakis and C.T. Whittemore editors, Whittemore’s Science and Practice of Pig Production. 3rd Edition. Blackwell Publishing Ltd, Ames, IA.  p 184–262.