Multi-breed Evaluation

J. Keith BertrandUniversity of Georgia, Athens

Multi-Breed Evaluation (MBE)

Analyzing the data from animals of any breed composition and providing genetic values

(EPDs) for virtually all animals in the data base, regardless of breed composition.

Why Consider Multi-Breed Genetic Evaluation?

• Genetic values can be computed on animals of any breed composition contained in the data base or population.

• There is a potential increase in the accuracy of the genetic values due to the inclusion of additional information.

• Also, there is an opportunity to provide genetic values and services to new clients.

Effects in Model for Genetic Evaluation of Purebred Data

Maternal Permanent Environmental Effect

Direct Genetic Effect + Maternal Genetic Effect +

Model : WWT = Fixed Effects +

Genetic value (EPD) provided by for an animal =

Estimated Genetic Effects

Effects in MBE Model

Maternal Permanent Environmental Effect

Direct Genetic Effect + Maternal Genetic Effect +

Direct Breed Effect + Maternal Breed Effect +

Direct Heterosis + Maternal Heterosis +

Multi-breed Model : WWT = Fixed Effects +

Genetic value provided by MBE for an animal = Est. Breed Effects + Est. Genetic Effects

Estimation of Heterosis and Breed Effects in MBE Model

• Typical system of Equations:

Cb = y

• Application of Bayesian Methodology:

(C + Vp-1)b = y + Vp

-1 p If Vp is very large = data determinesestimate

If Vp is very small = prior (literature) determines estimate

Heterosis

• Heterosis is the increased performance of crossbred animals due to pairing of alleles that originate from different breeds

• Heterosis affects the phenotypic performance of individuals and needs to be taken into inconsideration in the prediction of EPDs

Estimation of Heterosis Breeds are grouped into biological types for

heterosis computations:

British [B], Continental [C], Zebu [Z], Other [O]

10 comb.: BxB, BxC, BxZ, BxO, CxC, CxZ, CxO, ZxZ, ZxO, OxO

Why Group? – With 60 or more breeds represented, more than seventeen hundred or more possible F1 combinations are possible

Estimating Heterosis as the Fraction of F1 Heterosis

Contibuted by Different Breed Combinations

1/16 hBB

1/16 hBZ

1/8 hBC

¼ Hereford [B]

1/8 hBC¼ Angus [B]

1/16 hBZ 1/8 hCZ¼ Brahman [Z]

1/8 hBC½ Gelbvieh [C]

¼ Angus [B]½ Gelbvieh [C] Sire

Dam

hij = F1 heterosis estimate for the i and j breed comb.

Heterosis Est. = 1/16 hBB + 3/8 hBC + 1/8 hBZ + 1/8 hCZ

Accounting For Breed Composition

• Animal pedigrees are traced back as far as possible.

• The breed combinations of these “founder” animals are determined. These founder animals may not be representative of their breed(s).

• All the genes in the animal originated from these founders.

Breed of Founder (BOF) Effects

• Some breeds are fit in model: Angus, Brahman, Charolais, Gelbvieh, Hereford, Limousin, Simmental, etc.

• Some breeds are placed into groups due to small numbers of observations.

Simmental Evaluation: American, British, Continental, Dairy, and Mixed

Gelbvieh Evaluation: British Beef, British Dairy, Continental Beef, Continental Dairy, and Zebu.

Breed of Founder (BOF) Effects• BOF fit in model to account for the genes

from various breeds that are contributed by the founder animals.

• Yearly or generational BOF effects are fit in model to account for genetic trend in the animals of different breeds that enter the population over time.

Animal: ½ Simmental, ¼ Angus, ¼ Brahman

BOF effect = ½ BOFSIML + ¼ BOFANG + ¼ BOFBRA

(BOF effects est. using a combination of data and literature values.)

Breed of Founder by Generation Group Solutions from Gelbvieh MBE

Generation Group

British Beef

Gelbvieh Angus Limousin

< 1980 6.4 46.5 0.0 24.7

1981-1985 11.7 47.8 7.7 24.7

1986-1990 13.6 49.8 14.3 24.5

1991-1995 12.6 50.7 15.2 24.0

1996-2002 10.4 51.4 14.1 23.8

Prior -7.9 58.4 0.0 25.6

Weaning Weight EPD Gametic Trends for Angus and Limousin Animals from AGA MBE

-10

0

10

20

30

40

1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000

Birth Year

Ave

rage

(lb)

Angus

Gelbvieh

Multi-Breed Evaluation (MBE)

MBE applied to a single breed association data set is not meant to provide information on

“true breed differences”.

Weaning Weight EPD Trends for Angus and Limousin Animals from Limousin (NALF) and

Gelbvieh (AGA) Evaluations

-30

-20

-10

0

10

20

30

1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000

Birth Year

Ave

rage

(lb)

An-NALFLi-NALFAn-AGALi-AGA

Incorporation of Outside EPDs Into MBE Evaluation

• Significant numbers of sires from another breed may be present in the data set.

• Similar to the evaluation of heterosis and BOF effects, the data and the outside EPD can be combined.

• The outside EPD information can be used to better evaluate and rank a set of bulls within a breed. This assumes no sire by breed-of-dam interactions.

• The base of external EPDs has no influence on the EPDs predicted in the MBE

Rank Correlation Between External EPDs and Gelbvieh MBE EPDs of Angus Sires When External

Information is Ignored or Included

AAA Accuracy

External EPDs Ignored

External EPDs Included

No. of Sires

0.0 - 0.2 0.39 0.62 192

0.2 - 0.4 0.26 0.75 505

0.4 – 0.6 0.27 0.82 299

0.6 - 0.8 0.33 0.91 575

0.8 – 1.0 0.19 0.95 258

Incorporation of Outside EPDs Into MBE:Magnitude of Outside vs MBE EPDs

An Example:

Two high accuracy Angus bulls with AAA weaning EPDs of 60 and 20 lbs may not have the same magnitude of EPD in the MBE for another breed. However, if the two bulls have very little data in the MBE, the difference in their EPDs out of the MBE will be close to 40 lbs.

Multi-Breed Evaluation (MBE)

Does MBE provide EPDs?

People expect sire EPDs to predict the difference in the expected average performance between the progeny of two sires provided they were mated to dams of the same genetics, including breed type.

Sire A EPD = 30 lbs, Sire B EPD = -5 lbs

Expected difference in the average performance of future progeny produced by two sires = 30 – (-5)) = 35 lbs

Does MBE provide EPDs?

Sire A: 1/2 Limousin, 1/2 Brahman

Sire B: 100% Limousin

Bred to genetically similar Limousin dams

EPDA - EPDB = provides a prediction of thedifference in the additive transmitting abilitiesbetween sires A and B.

Average perf. of progA - average perf. of progB =

TAA - TAB + (1/2 F1 hetCZ)

What’s Next For MBE

Prototype Multi-Breed Evaluation (MBE)

• Several breeds have proposed the pooling of their data sets for a prototype MBE for growth traits.

• Breed associations will be responsible for creating the necessary cross-link identification of animals.

• Consortium will begin building the data base containing pedigrees from all breeds and assigning animal identification to use in MBE. Goal is to have an initial analysis completed sometime this summer in order to evaluate hardware and software requirements.

Inclusion of Records From Early Weaned

Animals

• Records from animals outside of acceptable age ranges are eliminated (BIF recom-mendation for weaning weight: 160-250 days.

• Weaning weight records from early weaned animals eliminated due to age range edits.

• Consortium asked to solve the problem.

Implementation of Models For Longitudinal Data

• Growth traits could be considered as repeated or longitudinal measures across time on the same animal.

• Fitting models that account for the longitudinal nature of growth would allow for weight at any age to be included in the evaluation

Several Measures on the Same Animal W

eigh

t

Age (days)

1 125 205 365 735

Partitioning of Animal Differences Using Using A Random Regression Model

yjk = 0j + 1j(A) + 2j(A2) + 3j(A3) + jk

ij = i + aij + pij +mil +peil +eij

yjk = (0 + a0j + p0j +m0l +pe0l +e0j)

+ (1 + a1j + p1j +m1l +pe1l +e1j)(A)

+ (2 + a2j + p2j +m2l +pe1l +e2j)(A2)

+ (3 + a3j + p3j +m3l +pe3l +e3j)(A3)

+ jk

Breeding Values (BV) Computed From Random Regression Models

BV of animal j at age n =

a0j + a1j(An) + a2j(An2) + a3j(An

3)

Hypothetical Weight EPDs From Random Regression Model Analysis

Age

1 205 365

EP

D

Summary

• MBE combines prior literature estimates and performance and pedigree information to provide EPDs for animals of various breed combinations.

• At the request of several breed associations, NBCEC will conduct a prototype MBE for growth traits on a pooled data set.

• NBCEC is conducting research to improve MBE.