Developing and Implementing A Genetic Improvement Program Ken Stalder Professor and Extension Swine Specialist Department of Animal Science Iowa State University Ames, IA 50011-3150 E-mail: stalder@iastate.edu

Components of Swine Performance 1. Genetic ability of the pig 2. Environment - nutrition, health, facilities, management practices, etc. Phenotype (Performance) = Genetics + Environment

Goal of Genetics Program Do not allow inferior genetics or the mating system to limit production efficiency Identify a better source if genetics is the limiting factor in obtaining maximum production performance Usually NOT the case Be sure you are using the correct mating system that maximizes performance Be sure that herd health is not limiting performance May require herd depopulation and repopulation with healthy superior genetics Be sure to understand the costs of this choice If relocating operations, may be good time to update genetics and improve health

Genetic Resources Available Genetic Supplier Choice of suppliers Breeds or Lines Choose the lines that excel for the traits that are important in your markets Choice of individual animals within the population (breed or line) of choice Choose the animals that meet your selection criteria The average of those you select compared to the entire group of potential select animals = selection differential Impact the rate of genetic progress

Genetic Resources Available Selection at the Nucleus (GGP), Multiplier (GP), and Commercial (P) levels Genetic improvement through selection is a slow tedious process Be sure that selection is for the traits that are important in your market Keep your eye on the selection goals Mating Systems Use a mating systems that matches your management preference Maximize heterosis Make use of breed complementarity

Structure of a Breeding System Boars – Semen Nucleus(GGP) Future – Embryos Multiplier (GP) Commercial (P)

Heritability The proportion of total variance observed for a given trait that is attributable to genetics or the genes of an individual within a population. Is always denoted by the symbol h2 Two ways to define heritability Heritability in the broad sense Heritability in the narrow sense Heritability is specific to the population and the trait under consideration. If the genetic or environmental variance for the same trait differs in two population then the h2 has to be different.

Most Important Concept in Animal Breeding Heritability Heritability = define - proportion of phenotypic variation that is due to additive gene effects Most Important Concept in Animal Breeding

Heritability Trait Heritability Number born alive (NBA) .10 Number weaned (NW) .05 Sow longevity (SPL) .10 - .15 21 – day litter weight (LWT21) .15 Days to 1152 kg (250 lb.) (D250) .35 Feed efficiency (F:G and G:F) .30 Backfat thickness (BF10) .40

Selection What traits to include in your selection program? Consideration Choose the traits that economically impact the operation Number born alive – is the salable item produced by the sow 21-day litter weight – is what a producers selling weaned pigs is selling (minimum weight required to obtain full value Days to market weight – how long the pig will stay in finishing facilities and feed efficiency (daily maintenance requirements) Backfat and loin muscle depth or area – determines percentage lean in the carcass which is the salable product (meat) for consumption Is the trait measurable

Selection Artificial selection – selection based on criteria established by breeders Selection - allowing only certain individual to reproduce Is the way genetic improvement in a population occurs. Use of individual performance records Use of EPDs Use of DNA genetic information Identified genes Anonymous markers Etc.

Features Necessary for Selection Equal opportunity – No animals receive preferential treatment. Systematic measurement of all animals – example measure backfat the same way, same location, at the same weight on every animal. Environmental adjustments – e.g. parity, season of year, on test weight, etc. δ2G / δ2G + δ2 E = h2 NSIF adjustment factors: http://mark.asci.ncsu.edu/nsif/guidel/guidelines.htm Use of records – does no good record data if you don’t make use of it. USE records to assist in making selection decisions.

Selection What traits to include in your selection program? Consideration Is the trait measurable Can the traits be measured accurately and in a repeatable fashion Influences heritability and the rate at which the traits can be improved. Does the trait have sufficient variation – specifically genetic variation to which selection can be practiced No variation = no improvement in the trait.

Relative Economic Value of Swine Traits Unit Phenotypic Standard Deviation Value per Unit Value per Standard Deviation Relative Economic Value NBA Pig 2.5 28.28 70.7 -39.28 LW21 Lb. 16 0.53 8.48 -4.71 D250 Day 15.6 -0.2 -3.12 1.73 F/G 0.25 -20 -5 2.78 ADG Lb/Day 0.19 12 2.28 -1.27 BF in 0.15 -12 -1.8 1.00 NW 2.4 38.6 92.64 -51.47 Lifetime Pigs Weaned 6 72 -40.00

STAGES - Swine Testing And Genetic Evaluation System National Swine Registry (NSR) Duroc, Hampshire, Landrace, Yorkshire Include F1 (Landrace x Yorkshire) data to make maternal data more accurate Multi-trait animal model Daily across-herd EPDs on association computer Across-herd summaries published semi-annually Breed specific variance components and adjustments www.nationalswine.com

Postweaning Data Pigs scanned at or near 250 pounds (~115 kg) Most ideally set this off-test weight at your ideal market weight Most breeders scan every 3-4 weeks Boars, gilts, and barrows Record weight, backfat, loin muscle area Data sent to NSR office same day Results returned to breeder next day

STAGES Program Components Records of ancestry (Pedigree) Performance measurement program EBV estimation program Public access to the genetic rankings Indexes to combine traits that economically influence selection decisions

Data Procedures Litter data recorded in farrowing house Pedigree information (sire and dam) Date farrowed Number born alive Number after transfer (number allowed to nurse) 21-day litter weight Data sent to NSR office when litter is recorded

EPD -- Predicts the difference in performance of an animal’s offspring relative to the performance of progeny of an average sire or dam

What Is An EPD? Actual difference in performance a producer can expect from future progeny of a sire or dam, relative to the future progeny of an average parent of the same breed or line

EPDs Are Expressed in Units of the Trait Measured: Days/113 kg [250 lbs] (days) Backfat (mm, inches) Number Born Alive (no. pigs) Litter Weight (kg, lbs.) Intramuscular Fat (%) Etc.

Selection Identifying the traits for selection Once identified, how do you apply the selection? Independent culling levels? Selection index What is a selection index? It is a composite measure of the economic value of the genetic merit of an individual (gilt or boar) for a given set of performance traits, such as backfat, average daily gain, etc., relative to the contemporary group of individuals being scored. The ranking based on the index is the basis for selection decisions.

Selection Types of indexes Terminal Sire Index (TSI) A bio-economic index that ranks individuals for use in a terminal crossbreeding system. TSI includes only EPDs for post-weaning traits. It weights the EPDs for backfat, days to 250 pounds, pounds of lean, and feed/pound of gain relative to their economic values. Each point of TSI represents $1 for every 10 pigs marketed or 10 cents per pig produced by a particular sire. Used to select terminal sires

TSI Example Value is $.10/pig for each point Sire A has TSI of 118 Sire B has TSI of 108 Difference of 10 TSI index points Sire 100 litters @ 9 pigs/litter 10 index point difference X $.10/pig X 900 pigs = $900 favoring Boar A over Boar B

Selection Types of indexes Sow Productivity Index (SPI) A bio-economic index that ranks individuals for reproductive traits. SPI weights the EPDs for number born alive, number weaned, and litter weight relative to their economic values. Each point of SPI represents $1 per litter produced by every daughter of a sire.

Selection Types of indexes Maternal Line Index (MLI) An index for seedstock that is used to produce replacement gilts for crossbreeding programs. MLI weights EPD's for both terminal and maternal traits relative to their economic values, placing approximately twice as much emphasis on reproductive traits relative to post- weaning traits Each point of MLI represents $1 per litter produces by every daughter of a sire. Use to select maternal sires and to cull sows

Selection Types of indexes Ideally idexes should be developed based on the economic situation in your country. Country specific indexes

Selection Once indexes are calculated and you have identified the animals with acceptable breeding value indexes, what other selection methods are needed? Molecular marker tools Major genes Stress gene (HAL) Napole gene (RN-) Candidate genes Estrogen receptor gene (ESR) MC4R influencing both growth rate and feed efficiency Mapped genes PRKAG3 & CAST both genes influence meat quality

Use of HAL and RN- markers Breeders have tested for these markers world wide. Several million tests run – HAL nearly removed from all lines RN- still exists in mostly Hampshires Recommendation: Test and remove bad (undesirable) alleles

Selection Once indexes are calculated and you have identified the animals with acceptable breeding value indexes, what other selection methods are needed? Phenotypic selection Feet and leg evaluation on boars and gilts Genitalia evaluation on all boars and gilts Underline evaluation on maternal line boars and gilts Replacement boars and gilts might have the very best numbers but may have feet and leg soundness or other issues that make it difficult or impossible for them to breed. From a genetic improvement standpoint they have no value

Selection Typically, phenotypic traits are selected upon by employing Independent Culling Levels type of selection What is independent culling? Selection method in which minimum acceptable phenotypic level is assigned to a trait being evaluated. Selection of culling based on pigs meeting specific levels of performance for each trait included in the breeder's selection program. Example After you have established that any gilt meeting a Maternal Line Index score of 95 and have found that 60 out of 100 gilts meet this value you then proceed to score feet and leg soundness. Score leg soundness in a group of breeding gilts on a scale of 1 to 10 with 10 being best. You keep anything that scores a 6 and above.

Selection of Crossbred Gilts Select at a weight of 175 – 240 lbs Faster growing gilts - better appetites Structurally sound Level designed, loose structured Large feet with equal toe size Wide chest, spring of rib (not flat sided) Flexible joints, particularly pasterns on both front and rear legs No swollen joints

Selection of Crossbred Gilts Underlines Small, evenly spaced, well defined nipples No inverted teats No blind or infantile teats Backfat---0.60-0.80 in. is ideal Favor docile, calm gilts over those that are excitable and difficult to handle

Incidence of failure to breed, lameness and culling for old age, in the sows according to litter parity Dagorn & Aumaitre, 1978

Phenotypic evaluation Indirect Selection for Longevity Buck kneed fore legs were shown to be negatively associated with: Age at first farrowing, Farrowing interval, Total number born, and Piglet mortality from birth to weaning Serenius et al. 2004.

Phenotypic evaluation Indirect Selection for Longevity Feet and leg evaluation Conditions shown to negatively impact sow longevity Buck-kneed front legs Straight rear pasterns

Phenotypic selection Indirect Selection for Longevity Conditions shown to positively impact sow longevity Weak front pasterns

Phenotypic selection Many thought that we could just breed by the numbers Phenotypic selection Independent culling levels Do impact traits that influence profitability Keep your best sows in the herd for a long time Impact fitness Role with animal well being

Selection for Sow Longevity Generally not been a large focus directly at the nucleus level Trait is measured at the end of productive life Trait in direct conflict with making rapid genetic change Selection pressure, if any is placed, is directed at indicator traits affecting sow longevity Feet and leg soundness Backfat Other conformation traits

Crossbreeding Effects on Sow Longevity Mean age and number of litters produced were lower in purebred Yorkshire sows when compared to crossbred sows (Jorgensen, 2000) Purebred sows had higher culling for locomotion and reproductive failure Crossbreds averaged 3.61 parities at culling while the purebreds averaged only 3.01 (Sehested and Schjerve, 1996)

Mating Systems Purebreeding – used at the nucleus level & some level at multiplication* Inbreeding Linebreeding Outcrossing

Mating Systems Crossbreeding – used at the multiplication level and at the commercial level Static Systems Rotational Systems Static Rotational Systems System choice is dependent on: Health of herd Management level Cost Other System goal = maximize heterosis or hybrid vigor

Hybrid Vigor or Heterosis The average performance of the offspring compared to the average performance of its parents Example average daily gain Line A = 800 g / d Line B = 800 g / d Parental average = 800 g / d Group of progeny from these parents average daily gain = 950 g / d Hybrid vigor = 950 – 800 = 150 / 800 = 18.8% Why maximize heterosis? It is FREE producers are wasting money if you do not take advantage of it.

Hybrid Vigor or Heterosis Why maximize heterosis? It is FREE producers are wasting money if you do not take advantage of it. It has its effects on those traits that involve fitness that typically influence profitability the most Conception rates – does a sow become bred or not Number born and number born alive – limits the number of pigs that will eventually be sold Longevity – how long the sow remains in the breeding herd Etc. Make sure the mating system of choice is implemented correctly 100% of the time.

Breed Complementarity No breed of pigs is perfect or ideal for all traits Crossbreeding allows the opportunity to mix breeds to create a breed mix that is more ideal than any of the parent breeds would have been. Ideally, a crossbreeding plan would mix breeds that complement each other; The strong points of one breed may offset the weaker characteristics of another, resulting in more complete, problem-free pigs.

Breed Complementarity Traits Excelling Berkshire Meat quality Chester White Number born alive, meat quality Duroc Growth, meat quality, lean growth Hampshire Carcass cutability Landrace Milking ability, number born alive Meishan Number born alive, thrifty piglets at birth Pietrain Carcass cutability (lean and heavy muscled) % lean Poland China Boar libido Spotted Yorkshire Number born alive, growth rate

Compensatory mating Mating of individual animals to correct problems in one animal by mating it to an animal that excels in that area Examples: A sow might be slightly buck kneed so you might consider mating it to a boar that has exception set to the knee so to produce offspring that have near ideal set to the front leg A sow might have a little too much fat so you consider mating to a sire that is leaner than average so to produce offspring that are near ideal for backfat.

Types of Heterosis Individual heterosis – Maternal heterosis Most common heterosis discussed Impacts the terminal offspring, the largest group of pigs on a commercial pork operation. Maternal heterosis Impacts maternal traits for both the sow and her offspring Paternal heterosis Impacts the boar or terminal sire and has little if any impact on offspring

Types of Heterosis 1. Individual Advantage of a crossbred offspring over purebred parents

Types of Heterosis 2. Maternal Advantage of a crossbred mother over a purebred mother Advantage for the sow Impact on the sow Greater number of eggs ovulated Greater conception rate Greater farrowing rate Advantage for the piglet Heavier weaning weights Number weaned Primarily due to mothering ability Photo courtesy A.K. Johnson

Types of Heterosis 3. Paternal Advantage of a crossbred father over a purebred father Sperm production Semen volume Libido Not as important as maternal heterosis

Heterosis Order of importance to maximize Individual Heterosis – Impacts the greatest number of animals and hence the greatest profit potential Largest number of traits likely influenced to some degree Maternal Heterosis – Influences both the sow and the piglet Impacts a large portion of the breeding herd Can have a great impact on profitability Paternal Heterosis – Typically only influence the boar itself Least amount of profit gained if used for the paternal traits influence by heterosis

Relationship between heterosis and heritability Traits Heritability Heterosis Reproductive Low High Health Low High Growth Moderate Moderate Carcass High Low

Using Heterosis Disadvantage Superior performance observed in crossbred individuals is not transmitted upon mating Gene combinations are not transmitted to progeny Only individual genes are transmitted to progeny Additive gene action = heritability, EPDs, EBVs Gene combinations are rearranged or lost when crossbred animals are mated together Random segregation of alleles during meiosis

Genomic Selection Genomic selection actually just extends our current approach to selection. Enhancing these proven methods by using more information to calculate EPDs. Genomic selection does not eliminate the need to have good data on important families and individuals within our populations. Genomic selection is selection based on actual DNA sequences where the variation in DNA sequences among individuals is used, along with pedigree and individual performance data, to predict the EPDs for individuals with increased accuracy. In the future we may be able to predict the value of combinations of genes and their interaction. Ultimately yielding more accurate predictions and faster rates of genetic progress

Example of a Terminal Crossbreeding program (purchase all replacements) Must find a producer that will make the Yorkshire x Landrace crossbred replacement gilts. Advantage: easy to manage, all matings are the same Disadvantage: difficulty finding animals and the desired cross for the program Pietrain Or Duroc, or P X D Live animals or semen Y x L Female 100% Maternal Heterosis X Market Hogs Market Hogs 100% Individual Heterosis In the terminal offspring

Example of an Internal Multiplication program for a Terminal Crossbreeding program Yorkshire Landrace X 15% of herd Pietrain, Hampshire Or Duroc, or P X D, H X D Y x L Female 100% Maternal Heterosis X 85% of herd Market Hogs Market Hogs 100% Individual Heterosis In the terminal offspring

Other types of mating systems Rotational Roto-terminal Choice of system is largely driven by how a producer wants to source replacement gilts Purchase Trading out of pocket expense for ease of management and implementation of mating system Implement a terminal cross mating system

Other types of mating systems Rotational Roto-terminal Choice of system is largely driven by how a producer wants to source replacement gilts Produce your own gilts – Internal multiplication program Trading management ability for out of pocket expense (although cost of production is not greatly different when all costs for raising your replacement gilts are actually totaled Rotational mating system Roto – terminal mating system Use of boars or semen becomes a secondary choice in these systems Producer needs more management when producing their own gilts Genetic improvement (measuring growth, backfat, phenotypic evaluation, etc.) Tracking animals through the production system Properly sized internal multiplication system within your operation (Having sufficient number throughout the year when needs vary i.e. seasonal breeding problems to deal with) Computerized record keeping and genetic evaluation system really needed Increased knowledge of workers (for example a person proficient in gilt selection is a must) Production of maternal line barrows (typically less value that terminal market hogs) Tracking specific sow matings (maternal line vs terminal line matings within the same system)

Rotational crossbreeding system Advantages: Raise your own replacements so you control your genetic program Entire herd devoted to terminal production, just retaining the best gilts from the best mothers in the herd. Disadvantage: Do not take advantage of specialized sire and dam lines Essentially all breeds utilized must excel at maternal (number born alive, milking ability or 21-day litter weights), terminal (growth, feed efficiency, etc.), and meat quality (pH, marbling, etc.) traits. How many breeds or lines can really do this? Requires the use of many breeds of boars in a given herd Can be difficult to manage if numerous gilts from differing crosses are maintained.

Rotational Crossbreeding System (2 Breed) The crossbred gilts are mated to Yorkshire boars and those three way cross gilt are then mated to Landrace boars or semen. The four-way cross gilts are mated to Yorkshire boars or semen and so forth. Crossbred females Landrace Yorkshire All pigs go to market Crossbred Market hogs

Rotational Crossbreeding System (3 Breed) Landrace Crossbred females Duroc Yorkshire Crossbred Market hogs All pigs go to market Crossbred females

Rotational Crossbreeding System (3 Breed) In the three breed rotational crossbreeding system, the three way crossbred gilt is mated to Berkshire boars and those four way cross gilt are then mated to Chester White boars or semen. The five way cross gilts are mated to Duroc boars or semen and then finally we are back to the six way cross gilts being mated to the original boar in the order, the Berkshire boars or semen and so forth. In all cases, replacement gilts are retained from the most productive sows. The order in which the boars are used does not matter but once it is set must use the appropriate breed of boar on a given sow The sow herd could be made up of 3, 4, 5 and 6 way cross females at any given time. Each sow needs to be mated to the correct breed of boar to ensure that the most heterosis possible is captured.

Types of crossbreeding systems Rotaterminal Crossbreeding system

Rotaterminal crossbreeding system Is a compromise between the terminal and rotational system Use rotational system to produce gilts and a terminal system to produce offspring for market. More heterosis realized than with rotational alone Still can save replacement breeding stock Still must buy terminal sire Can select traits in individual breeds via the terminal sire Can focus on strengths and weaknesses of certain breeds

Advantages of Rotaterminal System Can purchase startup females once Reduced health risk Suitable for AI Maternal heterosis is 86% (3-breed maternal cross) or 66.7% (2-breed maternal cross) 100% heterosis in market pig

Rotaterminal Crossbreeding System (2 Breed) 15% of herd – Best sows 85% of herd – Rest of sows Terminal Boars = Duroc, Pietrain, Hampshire, D x P, H X D Crossbred females Landrace Yorkshire All pigs go to market X Crossbred females

Rotaterminal Crossbreeding System (3 Breed) 15% of herd – Best sows Landrace Crossbred females Chester White Yorkshire 85% of herd – Rest of sows Crossbred females Duroc Boars All pigs go to market X Maternal line barrows go to market

Amount of heterosis capture in a rotational or rotaterminal situation The amount of individual heterosis and maternal heterosis capture in the rotational crossbreeding system is dependent on the number of breeds utilized. In the rotaterminal situation, the same can be said however, the loss of individual heterosis only applies to the growth and performance associated with the replacement gilts. Most concerned with the maternal heterosis. Remember in the rotaterminal system, 85% of the offspring attain 100% individual heterosis.

Heterosis percentage in rotational crosses Generation number Equilibrium Crossbreeding System 1 2 3 4 5 6 2 breed rotation 100.0 50.0 75.0 62.5 68.9 67.2 66.7 3 breed rotation 87.5 84.4 85.7 4 breed rotation 93.8 93.3 5 breed rotation 96.9 96.8 6 breed rotation 98.4

To calculate the number of replacement gilts needed Item Example Average Sow Inventory (A) 2500 Annual Replacement Rate (B) .50 Number Needed / Year A x B = (C) 1250 Number of Days in Isolation (D) 60 Percent of Number Purchased that Farrow a Litter (E) .90 Time Needed to Clean Isolation Facility, Days (F) 7 Number of Replacement Females to Purchase C / E = (G) 1389 Number of Replacement Female Groups 365 days / (D + F) = (H) 5.45 Number of Females Purchased per Group G / H 255

Replacement Gilt Needs Assuming 1389 replacement gilts are needed annually whether they are purchased or internally multiplied. How many gilts will be required once selection takes place? Gilts needed for Breeding Purposes Percentage of Gilts Selected Total Number of Gilts to Produce 1389 80% 1736 65% 2137 50% 3472

Replacement Gilt Needs Assume that 8 offspring reach market weight for each grand-parent female in production in an internal gilt multiplication system Of the 8 offspring each grand-parent female produced 4 (one-half of offspring) are females and each female has 2.2 litters per year (8.8) Percentage of Gilts Selected Total Number of Gilts to Produce Grand-Parent Sows Needed (Assuming a 80% farrowing rate of GP females) Percentage of Herd Devoted to Replacement Gilt Production 80% 1736 246 9.8% 65% 2137 303 12.1% 50% 3472 494 19.8%

Replacement Gilt Needs Does not account for any disease outbreak, fluctuations in farrowing rate (summer vs. other season) Also must produce replacement grand-parent females It is clear that the cost of producing the replacement gilt in an internal multiplication system can vary quite easily Grand-Parent Sows Needed (Assuming a 80% farrowing rate of GP females) Percentage of Herd Devoted to Replacement Gilt Production Grand-Parent Females Needed to Replace GP females (Assumes 50% replacement and 75% conception) Total number of GP sows and % of herd 246 9.8% 75 321(12.8%) 303 12.1% 92 395 (15.8%) 494 19.8% 132 626 (25.0%)

Thank you for your attention. Are there any questions?