Developing and Implementing A Genetic Improvement Program

1. 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

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

9. Heritability

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: • 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. USErecords 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

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 • www.nationalswine.com

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 100 litters @ 9 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---0.60-0.80 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 parityDagorn & 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. 2004.

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

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 – • 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