Evaluating Genetic Sources
Identifying and evaluating alternative genetic sources can be a daunting task for producers. Large numbers of live animal and semen suppliers exist, and all claim to have the ideal genetic package to meet the industry needs. While the claims may indeed be true, producers must be able to understand the fundamental process of evaluating genetic value and how genetic improvement principles can be applied when choosing among alternative sources. This fact sheet will guide the producer through a step-wise process that can assist them in identifying the optimal genetic source for their operation.
Successful genetic improvement programs are anchored around answers to, and knowledge of, the following seven step process:
- Identify Role in the Industry
- Set a Breeding Objective
- Decide which Traits to Select for
- Obtain Genetic Information
- Determine the Mating System
- Measure Genetic Improvement
- Present the Product at its’ Best Advantage
Therefore, the objectives of this fact sheet are:
- Identify key factors for each step in the genetic improvement process
- Provide producers with the knowledge and background to evaluate alternative genetic sources
Identify Role in the Industry
Flow of genetic material is commonly viewed in a multi-tiered pyramid (Figure 1) structure with the genetic nucleus placed at the top, indicative of smaller herd size, specific emphasis on pure lines or breeds, and intense selection for many traits. Multiplication occupies the middle of the pyramid and is indicative of larger herd sizes, multiplication and expansion of the number of superior nucleus animals, single and/or multiple crossing of pure lines or breeds, and a lower level of selection intensity that is generally coupled with selection for fewer traits. The base of the pyramid represents commercial production, where large numbers of parent animals produced in multiplication are mated using specific crossbreeding schemes to produce a pig and pork that meet a specific market demand. Therefore, producers must know where they intend to fit in the pyramid scheme and what specific market(s) they are going to serve prior to selecting a genetic source. For example, if an operation purchases end-product parent animals, producer involvement in the genetic improvement process is limited to the desired selection criterion placed on the parents. In contrast, if a herd practices internal multiplication, genetic (selection and mating) and management decisions both play much larger roles within the herd and with respect to source(s) of animals and/or semen used.
In addition, all pork is produced under the assumption that there is consumer demand for the product. However, consumers are steadily increasing demand for differentiated pork products allowing new markets to develop and serve. Differentiation may include breed specifications or specific attribute levels that will influence: 1) the source of genetic material, 2) the degree and focus of selection emphasis placed on traits, and 3) the overall cost (genetic and production) of producing the differentiated product(s). Thus, the producer’s knowledge of their “role” in the industry must be identified and unwavering (at least in the short term) when selecting a genetic source to meet their markets demand.
Set a Breeding Objective
In general terms, “What are the ideal attributes of the pig and product (pork) that you are going to market?” Breeding objectives become a give and take for many reasons, including: 1) genetic progress trough selection is a slow process and a process that gets slower each time you add an additional trait to the breeding objective, 2) relationships between production efficiency and product quality are not always favorable, and 3) the economic value of traits differ across environments, herds, and markets. Thus, producers must define the attribute levels they desire for the given market and develop a breeding program to meet the defined objectives.
As an example, a breeding objective may be 1) To produce market hogs with 57% lean weighing 280 pounds live and marketed at 175 days of age; from a female population where 22 saleable market hogs are produced per exposed female per year, or 2) To market 20 pigs per sow per year at an average of 0.80 inches of backfat and a 7.0 square loin muscle at 260 pounds into a market paying a $10.00/cwt of carcass premium for loins that have greater than 3.5% intramuscular fat, a three or darker visual color score, and a loin 24-hour pH of greater than 5.80. These examples represent two entirely different types of end-point markets. Different genetic resources would be needed to fit the product demands, and different numbers of traits are included in the selection program. However, both scenarios describe objectives that are attainable when sound genetic decisions are made.
Decide which Traits to Select for
Trait selection is driven by economic analyses, the proportion of variation due to genes (heritability) for the given trait, and the genetic associations between traits (genetic correlations). In swine production, making a standard incremental change in reproductive performance (number born alive, litter weaning weight, number weaned, etc) often will have more economic value than production (growth rate, feed efficiency) or carcass (backfat, loin muscle area, percent lean) traits. Because reproductive traits are considered low to moderately heritable, herd turnover rates do not allow very intense selection of future parent animals, and estimates of breeding value for replacement gilts are based on ancestor’s (parents and grandparents) performance, genetic progress in reproductive performance at all levels of the genetic pyramid tends to be slow and the rate of change in a standard measure of performance more difficult from a genetic perspective. However, superior genetic lines and/or breeds do exist; thus, producers must identify and select females from nucleus and multiplication phases where documented genetic performance for reproduction is available. Genetic emphasis on indicators of sow longevity may also be considered. These may include evaluation of non-productive days, wean-to-estrus interval, litters per sow lifetime, days of sow life, and others that may speed the rate of genetic progress. In addition, reproductive performance is clearly enhanced when heterosis is maximized; making mating decisions a critical step toward improving reproductive efficiency.
In contrast, production and carcass traits are moderate to highly heritable due, in-part, to the ease of accurate measurement on the live animal and the subsequent ability to performance test large numbers of pigs of any sex (boars, gilts, and barrows). These factors make selection of breeding animals economically feasible and effective for identification of replacement animals with superior genetic potential. Coupled with Artificial Insemination (AI), intense selection placed on phenotypes for highly heritable traits allows for a vast reduction in the number of sires needed for mating and the ability to move semen from the nucleus level throughout the pyramid.
Selection to improve pork processing and palatability attributes also has value for the pork industry. Poor processing yields, carcass drip loss, and inconsistent pork color, to name a few, directly influence product value from the packer to the retailer. In addition, tenderness, juiciness, flavor, and visual characteristics such as color, marbling, and wetness influence consumer acceptance and demand in the high-end restaurant, retail, and export markets. In general, heritability estimates for quality indicators are moderate, indicating progress can be made through selection. However, because quality measures are taken postharvest, selection programs primarily use data derived from progeny and/or siblings to estimate breeding value. Progeny testing, in turn, extends the generation interval and results in a slower rate of genetic improvement when compared with traits directly measurable on the individual. The industry as a whole will benefit tremendously if (or when) quality can be determined on the live animal prior to selection.
Correlated response to selection, or the resulting change in one trait when selection is placed on a second trait, is also important in making genetic change. A prime example is improvement in feed conversion efficiency. In most genetic evaluation programs, individual measures of feed intake and feed efficiency are costly and difficult to accurately record. However, because feed conversion is genetically related backfat and total carcass lean, the pork industry has made genetic progress in feed efficiency through selection for reduced backfat, increased rate of lean gain, and/or an increase the percentage of carcass lean without the expense of individual measurement of feed efficiency. Another, less favorable, genetic relationship exists between increased carcass leanness and pork quality attributes. Specifically, recent data from packers and research indicate that leaner and/or heavier muscled pigs tend to have reduced levels of intramuscular fat in the loin, bellies tend to be thinner leading to poor sliceability, and the pork tends to be tougher even under ideal cooking conditions. These antagonistic relationships create challenges for the industry as it tries to produce meat product that meet the needs for the entire pork chain. To capitalize on beneficial relationships and/or to alleviate potential antagonistic genetic relationships among traits, geneticists will often utilize selection index approaches that allow simultaneous selection for combinations of traits with a goal to maximize the aggregate value or net merit of an animal(s) based on known genetic, phenotypic, and bio-economic values for traits undergoing selection. It is important to remember that as the number of traits under selection increases, the response in each individual trait will decrease.
As indicated previously, trait identification and the degree of emphasis placed on traits will be in large part dictated by economics and the market served. Producers must also remember that in all production settings there is value in structural and reproductive soundness as they relate to animal welfare, longevity and lifetime productivity. Non-functional pigs will often result in lower profits and a lack of enterprise sustainability.
Obtain Genetic Information
Proper selection is based on data collected under a systematic, whole herd testing program where data are adjusted for known sources of environmental variation and subsequently incorporated into a genetic evaluation program that utilizes known relationships among animals to estimate breeding values, expected progeny differences, and/or selection index rankings. Fortunately, virtually all genetic suppliers have access to a common, comprehensive genetic evaluation procedure called Best Linear Unbiased Prediction (BLUP) and they use the Animal Model procedure where all pedigree relationships and data are simultaneously used to estimate an accurate prediction of an animal’s genetic value. The level of incorporation of BLUP and the Animal Model does vary by genetic source, whereby the extent of use throughout the multiplication stage can be dependent on the sex of the pig, the number of generations removed from the nucleus level, and the cost of data acquisition.
The format of genetic evaluation data dissemination varies significantly across genetic sources. Breeding value (BV: value of an animal as a parent) and Expected Progeny Difference (EPD: how progeny of a given animal are expected to perform) are two common forms of data provided to producers making genetic decisions. Both BVs and EPDs are reported in the unit of the trait with the sign (+ or -) of the BV or EPD indicative of the expected change in direction for a trait if an animal is used for breeding (Table 1). The major difference between a BV and an EPD is that BVs are an estimate on the animal. To determine how the progeny of a parent animal are expected to perform, the BV is reduced by one half to account for the sample half of the BV estimate (sample half of the genes) that will be passed on the progeny. In contrast, an EPD (1/2 of an animal’s BV) is a direct estimate of the expected performance of the progeny if an animal were used as a parent. Important points to remember with respect to both BVs and EPDs: 1) BVs and EPDs are comparable only within a genetic line or breed; 2) selection should be made comparing differences among animals under selection and not the absolute value of a BV or EPD; 3) BVs and EPDs are dynamic estimates of genetic value that will change (positive or negative) as additional data are collected and added to the population undergoing selection; 4) the accuracy of a BV or an EPD will increase as additional data are collected and incorporated into the genetic evaluation process, thus older, heavily used animals with multiple records on the individual, relatives, or progeny will enhance the accuracy of an estimate of genetic value.
Table 1: Hypothetical description of Breeding Value and Expected Progeny Difference estimates
|Trait||Unit||Hypothetical Genetic Values EPD=1/2 EBV||Hypothetical Sire Selection Scenario|
|Desireable Directiona||Estimated Breeding Value||Expected Progeny Difference||Sire 1 EPD||Sire 2 EPD||Difference Between Sires|
|Number Born Alive||pig||+||+0.05||+0.025||+0.15||+0.25*||0.10 pig|
|Litter Weight||lbs||+||+3.00||+1.50||+6.00*||-1.00||7.00 lbs|
|Average Daily Gain||lbs/day||+||+0.10||+0.05||+0.22||+0.30*||0.08 lb/day|
|Days to Market||Days||–||-8.20||-4.10||-10.30*||-2.20||8.10 days|
|Loin Muscle Area||in2||+||+0.00||+0.00||+0.35||+0.45*||0.10 in2|
a+ = positive direction for a BV or EPD is desirable, – = negative direction for a BV or EPD is desirable
* Superior EPD or BV within a given trait
Many seedstock suppliers provide percentile rankings for specific traits or indexes rather than estimated BVs or EPDs for animals or semen they offer their customers (Table 2). Percentile rankings offer both challenges and opportunities for the producer. One advantage of percentile rankings is that they compare directly with a measure of selection intensity or the proportion of animals selected compared with the number tested. For example, if the selection criteria are to choose animals with EPDs or indexes within the top 5% of a test group; the producer knows that 95% of the animals did not meet the selection criterion which is good.
In contrast, the top 5% of a group technically can be the one top boar out of 20, the top 5 out of 100, or the top 50 out to 1000, thus the producer must ask the supplier to quantify how many animals are tested within a group. Percentile rankings also ease the process of purchasing groups of animals or sampling semen from multiple sires as is now common in the industry.
Table 2: Example percentile charta describing animal rankings within a population.
|Traits and Indexesb||BF||Days||Lbs||NBA||LWT||TSI||SPI||MLI|
bBF = Backfat EPD, Days = Days to 250 lb, Lbs = Pounds of lean, NBA = Number born alive
LWT = Pounds of 21-day litter weight, TSI = Terminal Sire Index, SPI = Sow Productivity Index, MLI = Maternal Line Index.
Genetic progress is made through selection of animals with superior genetic ability whether based on and EPD or a percentile rank. Genetic superiority is measured as the amount by which an animal exceeds the average performance of a test group or population. Remember that within any normally distributed test population half of the animals will be above and half below the mean level of performance. So, genetic progress is made through selection of animals or groups of animals that surpass the 50th percentile or have EPDs that are favorable compared with the breed or line average. Therefore, regardless of the trait(s) under selection, producers should understand and ask the suppliers for information on the average levels of performance and select individuals or groups of individuals from within the upper 50th percentile. This goal is much easier to achieve on the sire side rather than the female side, particularly if breeding herd female culling rates are too large that females below the 50th percentile must be used to maintain herd size.
Producer need to have some caution when selection is based on index values alone. By design, a selection index allows for superiority in one trait to compensate for inferiority or a lower level of performance in second (or additional) traits. For example, a terminal sire index may include growth rate and backfat depth, two economically important traits, into a single measure (index value) of genetic merit. However, two or more animals with the same index value may have different EPDs for backfat and growth rate (Table 3) with one being superior in growth and having greater backfat while the other(s) may be leaner with slower growth. This concept illustrates the value of individual trait EPDs or BVs along with the index value(s) when determining an animal’s genetic potential and when determining the optimal percentile when selecting animals based on an index.
Increasingly, genetic suppliers are expanding the industry’s knowledge of genetic markers and genes that influence phenotypic performance. This knowledge base will only continue to expand and will make the process of genetic selection even more efficient and accurate in the future. Currently, genetic marker and specific allele testing is used extensively at the nucleus level and, through a process of mating, specific forms of genes (alleles) or markers are passed from generation to generation through targeted mating thus assuring that they are present in the parent animals used at the commercial level.
Table 3: Relationship between Expected Progeny Differences (EPDs) and Index measures of genetic value.
|Expected Progeny Differencea||Terminal Sire Indexb|
|Sire||Backfat||Days to 250||Lbs of Lean||TSI|
bTerminal Sire Index = Bio-economic genetic index combining EPDs for Backfat Depth, Days to 250 Pounds and Pounds of Lean.
Two major genes identified in pigs, the Porcine Stress Syndrome Gene (Hal-1843) and the Rendement Napole Gene, have been extensively studied across the world and most genetic suppliers have chosen to remove the detrimental forms because of the extensive pork quality problems associated with the mutant alleles. Overall, molecular genetic tools offer promise to the tried and true process of quantitative selection and will continue to enhance the accuracy of genetic selection processes.
The one intangible when collecting data and making selection decisions is related to what you can’t or don’t often see, specifically, the animals. Biosecurity, distance, faith in numbers, and faith in people are often reasons given for failure to view the animals prior to a live or semen purchase. All reasons described can be very good or very poor justification for failure to view the animals, but producers should reserve the right to reject animals that arrive with superior performance data, yet are unable to function in the environment due to issues related to health, structure, movement, and/or other abnormalities. Accountability on the part of the seedstock supplier is expected when making an investment in genetic resources.
Determine a Mating System
Mating strategies exist to optimize output following selection of superior animals. Mating animals more alike based on phenotype (positive assortative mating) or relationship (line breeding and inbreeding) are methods commonly used to rapidly improve traits with moderate to high heritability estimates and for traits where intense selection, such as sire line choice, can be practiced. Matings based on animals that differ in phenotype (negative assortative mating) or lack of close relationship (out-crossing or crossbreeding) are commonly used to bring together complimentary performance for traits with the goal to make a complete package. Traits characterized as lowly heritable (reproduction) commonly benefit most when mating unrelated animals. Mating systems utilized on production units will often be some combination of closely and distantly related animals because enterprise efficiency require integration of both concepts.
When considering mating options, sire choices are often considered the most powerful and rapid method of making genetic change for performance, carcass, and reproductive traits due to sire use over many females resulting in large numbers of progeny. For terminal traits, sire lines or breeds should be selected based on genetic value for the combination of traits that have economic value for the market. In general, the impact of heterosis (Table 4) on reproductive characteristics of the boar is observed early in life, typically following onset of sexual maturity. Heterosis expression is limited in boars over 12 months of age resulting in similar reproductive performance for a pure bred compared with a crossbred boar. Sire choice does influence reproductive performance of daughters and care must be taken to identify superior sires when the intent is to produce replacement females even when matings are to produce crossbred progeny.
Crossbreeding is a powerful tool for improving reproductive performance because heterosis is clearly expressed in the crossbred female (Table 4). Using an estimate of 8% heterosis for number of pigs born alive, a group of crossbred females, compared with pure females averaging 10 pigs born alive per litter, would be expected to have a number born alive of 10.8 pigs just by being a crossbred. When coupled with within breed selection for increased reproductive performance, opportunities are tremendous.
The optimal mating system will be production setting specific. The decision to purchase or produce replacement females within the population will generally establish the complexity of a mating system.
Table 4: Heterosis estimates for swine traits.
|Trait||Individual Heterosis (%)||Maternal Heterosis (%)||Paternal Heterosis (%)|
|Number of Embryos||0.0||7-8||0.0|
|Number Born Alive||0.5||7-10||0.0|
|21-d Litter Weight||10.0||27||0.0|
|Loin Muscle Area||1.0||2.0||0.0|
Producers purchasing replacement females and boars (live or semen) from a single genetic source generally use a source-specific mating plan that will typically maximize heterosis in the female, male, and progeny populations while also identifying or suggesting criteria for selection of males used in mating plan. Purchasing replacements is also the easiest option with regard to making matings (all the same line), maintaining records, and production flow (all pigs go to harvest), but comes with added investment costs, the risk of introducing disease, and lack of control of most genetic decisions.
Internal multiplication (generally of female lines) offers the ability to fine-tune genetic decisions through farm level selection and mating decisions. More complex internal multiplication systems may include production of male lines, but the added complexity and strain on facilities and personnel resources often prohibit this approach. Internal female production is generally accomplished either through static crossing systems or rotational crossing systems with the goal of optimizing heterosis when balanced against the economic costs of the alternatives. Internal multiplication may provide additional biosecurity through a reduction in the risk of live animal introductions.
Static crossing systems, often described as grand-parent (Figure 2) or great grand-parent (Figure 3) multiplication systems require maintenance of pure line(s) or breed(s) of females that serve as the base level for production of crossbred parent females.
Maternal line semen from a complimentary breed(s) or line(s) is often introduced to make the crossbred matings and semen is introduced to multiply pure line females as well. Semen introductions avoid having multiple lines on the site and allow the producer to exploit the opportunity to find and use a superior quality animal or line within the breeding plan. Use of multiple lines and production of pure bred pigs create additional management needs and will increase the costs of semen from high genetic value sires when using static crossbreeding mating plans.
Rotational crossbreeding programs continue to be used in the swine industry because they require less intense management while capitalizing on a large proportion of the available heterosis for traits of importance. Breed or line complimentarily is very critical to the success of rotational crossbreeding systems because replacement females and market hogs are produced simultaneously, creating the need for a balance of carcass, production, and reproduction attributes. The most common and most feasible rotational system includes three distinct lines or breeds. A three-breed rotation (Figure 4) captures significantly more heterosis (86%) than a two-breed rotation (67%) while reducing the added complexity of introducing and managing a complementary fourth breed needed for the four-breed rotation (93%).
Rota-terminal crossbreeding systems, where the replacement female population produced in rotation through identification of superior mothers, combines the advantages of static and rotational crossbreeding systems. Rota-terminal systems allow high levels of heterosis in the replacement female and up to 100% heterosis in the majority of market swine produced.
Rotations, in comparison to static crosses, reduce the need to continually maintain (via pure matings or introduction) purebred females which add a level of complexity to breeding management. Because multiple generations (multiple parities) are in production at any given time, an effective female record keeping system is need to ensure appropriate matings are made. An advantage of rotational and/or rota-terminal systems is that each female in production, regardless of breed composition, is a candidate for production of replacement females. With effective performance assessment, superior performing females based on standardized phenotypic data, can be mated to males with greater genetic potential to produce candidates for selection and the remaining females can be mated for the production of high value market hogs.
Detailed record keeping, semen delivery, and space allocation are required for internal multiplication systems, but the rewards can certainly outweigh the effort from disease control or disease maintenance perspectives as long as biosecurity protocols maintain effectiveness. Internal production will often require additional labor and management capabilities to increase the opportunity for success.
Measure Genetic Improvement
Measuring true genetic progress requires discipline and long-term commitment. At the nucleus and multiplication levels comprehensive records of ancestry and individual performance for large numbers of traits allows genetic trends to be calculated and analyzed. Because commercial herds lack sufficient resources to evaluate individual market animals and instead rely on group averages, variation and trend analyses for production and carcass traits are difficult to assess and compare directly across layers of the genetic pyramid. In addition, while extensive production databases exist for breeding herds at the commercial level and do not match the information required to evaluate genetic progress, particularly when commercial level females are crossbred and animals higher in the pyramid are more likely to be pure bred.
Also, the commercial level is two generations behind improvement at the nucleus level due to genetic lag, or the time required to distribute superior animals and or semen to the commercial level. Thus, comparisons between commercial and seedstock levels are difficult to make and may lead to an improper assessment of progress without forethought into the process.
The key to measuring or monitoring genetic progress is rooted in establishing a set of measurable, consistent, accurate characteristics to describe annual progress. For production measures, data comparisons with nucleus level performance and within the commercial herd need to be compared under standard starting and ending weights, days on feed, standard diets, standard housing and feeding facilities, or some other definable characteristic that allows direct comparisons to be made. Carcass measures of backfat depth, lean percentage, dressing percent and others must be collected at similar end-point weights, at similar carcass locations, and with comparable times off of feed to have value within a herd and in comparison to the nucleus level. Also, data should be balanced or adjusted based on sex of the pig due to the inherent sex differences in performance and carcass measures. Comparisons of reproductive performance between commercial and the nucleus lines are difficult due to crossbreeding at the commercial level. However, in the case of reproduction (and performance and carcass) traits, documented genetic trends for traits or indexes provided by the seedstock supplier can provide a tool for assessing predicted progress at the commercial level. Seedstock suppliers should always have trend data available for review by the customer because nucleus level progress, even though two generations removed from commercial production, is one of the most important indicators of progress opportunities for the commercial segment.
Present the Product at is’ Best Advantage
The best genetics will not overcome deficiencies in management, facilities, or health. Investment in genetics is a long-term, expensive commitment that should be approached based on realistic expectations of the conditions (environment) under which the genetics are to perform and requires a match with a genetic supplier that can provide genetics to meet the conditions. Environmental conditions will dictate choice of genetics and, conversely, genetic performance will be dictated by the ability to optimize the environment. Poor choices on either side of the equation result in less than optimal performance.
Producers must also consider the ‘product’ they are producing, whether it be a weaned pig, a replacement female, or a pork chop to a white-table cloth restaurant, and realize that they are a small part of the much larger pork chain. Genetic success, similar to financial success, comes as result of producing a product that has value, is backed by integrity, and produced with pride in knowledge that pork production helps feed the world
Successful identification a superior genetic material requires discipline and a systematic approach. The optimal source will match a producer’s genetic needs with the market and the physical, fiscal, and management resources available. By following the seven step plan described in this paper, producers will be able to identify high quality genetic sources and use this knowledge to optimize genetic efficiency in their operations.
1. Ahlschwede, WT, Christians, CJ, Johnson, RK, Robison, OW. Crossbreeding systems for commercial pork production. 1987. Pork Industry Handbook Factsheet-39. Purdue University Cooperative Extension, West Lafayette, Indiana.
2. STAGES (Swine Testing and Genetic Evaluation System), Duroc Active Sires, October 2004. Available at: http://www.ansc.purdue.edu/stages/duroc/percentile.htm . Accessed April 26, 2005.