I OWA S TATE U NIVERSITY Department of Animal Science Developing and Implementing A Genetic...

IOWA STATE UNIVERSITYDepartment of Animal Science

Developing and Implementing A Genetic Improvement Program

Ken StalderProfessor and Extension Swine Specialist

Department of Animal ScienceIowa State UniversityAmes, IA 50011-3150

E-mail: [email protected]


1. Genetic ability of the pig

2. Environment - nutrition, health, facilities, management practices, etc.

Phenotype (Performance) = Genetics + Environment

Components of Swine Performance


Goal of Genetics Program

Do not allow inferior genetics or the mating system to limit production efficiencyIdentify 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

Nucleus(GGP)

Multiplier (GP)

Commercial (P)

Boars –

Semen

Future – Embryos


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 heritability1. Heritability in the broad sense2. 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.


Heritability

define - proportion of phenotypic variation that is due to additive gene effects

MOST IMPORTANT CONCEPT IN ANIMAL BREEDING

V

V V V V VA

A D I EP ET hV

VA

P

2 =

Heritability


Heritability

TraitTrait HeritabilityHeritability

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 / δ2

G + 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

Trait 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 Lb. 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 Pig 2.4 38.6 92.64 -51.47

Lifetime Pigs Weaned Pig 6 12 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 postweaning 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

0

10

20

30

40

50

60

70

80

90

100

1 2 3 4 5 6 7 8 9 10 >10

Number of litters per sow

Cum

ulat

ed p

erce

ntag

e of

cul

led

sow

s

Failure to breed Lameness Old Age Other


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

weaningSerenius et al. 2004.


Phenotypic evaluation


Feet and leg evaluation

Conditions shown to negatively impact sow longevity

Buck-kneed front legs Straight rear pasterns


Phenotypic selection


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:1. Health of herd2. Management level3. Cost4. 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

Breed 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 Boar libido

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

1. Individual heterosis – Most common heterosis discussed Impacts the terminal offspring, the largest group of pigs

on a commercial pork operation.

2. Maternal heterosis Impacts maternal traits for both the sow and her

offspring

3. Paternal heterosis Impacts the boar or terminal sire and has little if any

impact on offspring


Types of Heterosis1. Individual

Advantage of a crossbred offspring over purebred parents


Types of Heterosis2. 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 abilityPhoto courtesy A.K. Johnson


Types of Heterosis3. 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 maximize1. Individual Heterosis –

Impacts the greatest number of animals and hence the greatest profit potential

Largest number of traits likely influenced to some degree

2. Maternal Heterosis – Influences both the sow and the piglet Impacts a large portion of the breeding herd Can have a great impact on profitability

3. 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)

Market Hogs

PietrainOr Duroc, or P X D

Live animals or semen

Y x L Female100% Maternal HeterosisX

Market Hogs100% Individual HeterosisIn the terminal offspring

Must find a producer that will make the Yorkshire x Landrace crossbred replacement gilts.

Advantage: easy to manage, all matings are the sameDisadvantage: difficulty finding animals and the desired cross for the program


Example of an Internal Multiplication program for a Terminal Crossbreeding program

Landrace

Market Hogs

Yorkshire

Pietrain, HampshireOr Duroc, or P X D, H X D

Y x L Female100% Maternal Heterosis

X

X

Market Hogs100% Individual HeterosisIn the terminal offspring

15% of herd

85% of herd


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

1. Genetic improvement (measuring growth, backfat, phenotypic evaluation, etc.)

2. Tracking animals through the production system

3. 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)

4. Computerized record keeping and genetic evaluation system really needed

5. Increased knowledge of workers (for example a person proficient in gilt selection is a must)

6. Production of maternal line barrows (typically less value that terminal market hogs)

7. 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)

CrossbredMarket hogs

All pigsgo tomarket

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.

Crossbredfemales

Crossbredfemales

Landrace

Yorkshire



CrossbredMarket hogs

All pigsgo tomarket

Crossbredfemales

Landrace

Crossbredfemales

Crossbredfemales

Duroc

Yorkshire



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

Crossbredfemales

Terminal Boars =Duroc, Pietrain, Hampshire, D x P, H X D

All pigsgo tomarket

Crossbredfemales

Crossbredfemales

Landrace

Yorkshire

X


Rotaterminal Crossbreeding System(3 Breed)

All pigsgo tomarket

15% of herd – Best sows

Landrace

Crossbredfemales

Crossbredfemales

Crossbredfemales

Chester White

Yorkshire

85% of herd –Rest of sows

Crossbredfemales

DurocBoars

Maternal line barrowsgo to market

X


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

EquilibriumCrossbreeding 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 100.0 100.0 75.0 87.5 87.5 84.4 85.7

4 breed rotation 100.0 100.0 100.0 87.5 93.8 93.8 93.3

5 breed rotation 100.0 100.0 100.0 100.0 93.8 96.9 96.8

6 breed rotation 100.0 100.0 100.0 100.0 100.0 96.9 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

1389 65% 2137

1389 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.

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