1. Developing and Implementing A Genetic Improvement Program
Ken Stalder
Professor and Extension Swine Specialist
Department of Animal Science
Iowa State University
Ames, IA

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

3. 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

4. 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

5. 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

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

7. 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.

8. 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

9. Heritability Trait Heritability Number born alive (NBA) .10
Number weaned (NW)
.05
Sow longevity (SPL)
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

10. 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

11. 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.

12. 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:
Use of records – does no good record data if you don’t make use of it.
USE records to assist in making selection decisions.

13. 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.

14. 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

15. 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

16. 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

17. 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

18. 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

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

21. 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

22. 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.

23. 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.

24. 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

25. 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 pigs/litter
10 index point difference X $.10/pig X 900 pigs = $900 favoring Boar A over Boar B

26. 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.

27. 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

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

29. 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

30. 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

31. 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

32. 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.

34. 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

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

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

37. 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

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

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

40. 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

41. 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

42. 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)

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

44. 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

45. 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.

46. 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.

47. 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.

48. 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

49. 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.

50. 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

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

52. 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

53. 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

54. 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

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

56. 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

57. 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

58. 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

59. 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

60. 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

61. 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)

62. 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.

63. 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

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

65. 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.

66. Types of crossbreeding systems
Rotaterminal Crossbreeding system

67. 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

68. 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

69. 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

70. 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

71. 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.

72. 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

73. 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

74. 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

75. 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%

76. 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%)

77. Thank you for your attention.
Are there any questions?