DNA-based technologies and
approaches for the genetic
improvement of beef cattle
Alison Van Eenennaam, Ph.D.
Animal Genomics and Biotechnology
Cooperative Extension Specialist
Department of Animal Science
University of California, Davis, CA U.S.A.
Ph: (530) 752-7942
alvaneenennaam@ucdavis.edu
http://animalscience.ucdavis.edu/animalbiotech
Van Eenennaam NM 3/6/2015
Animal Biotechnology and Genomics Education
Animal breeders have used selection
on phenotypes to great effect!
Animal Biotechnology and Genomics Education
However breeding based on objective
performance recording has been
spectacularly successful…..
Average milk production per lactation of US Holstein cows has nearly doubled during the past 40 years
Image from: Dekkers, J.C.M, and F. Hospital, 2002. The use of molecular genetics in the
improvement of agricultural populations. Nature Reviews Genetics 3: 22-32
Animal Biotechnology and Genomics Education
Do you Support or Oppose
these Government Policies
http://agecon.okstate.edu/faculty/publications/4975.pdf
80% Of Americans Support Mandatory
Labels On Foods Containing DNA
Animal Biotechnology and Genomics Education
The bovine genome is similar in size
to the genomes of humans, with an
estimated size of 3 billion base pairs.
Human &
cattle
genomes
are 83%
identical
Van Eenennaam NM 3/6/2015
Animal Biotechnology and Genomics Education
What is a Genetic Marker ?
A DNA sequence
variation that has
been associated
with a given trait in
one or more
populations
Van Eenennaam NM 3/6/2015
Animal Genomics and Biotechnology Education
We want to use DNA markers (SNPs) in
addition to pedigree and performance
information to help select the best animals
If cross two carriers then get ¼ (25%) chance of carrier
GT ♂ x GT ♀
¼ GG
Van Eenennaam NM 3/6/2015
½ GT
¼ TT
Animal Biotechnology and Genomics Education
Simple (qualitative) traits

Genotype = phenotype
–
–
–
–
–
Gender (male, female)
Coat color
Certain genetic diseases
Double muscling
Horns
Van Eenennaam NM 3/6/2015
Animal Genomics and Biotechnology Education
SIMPLE TRAITS
(Qualitative)
e.g. Polled
Genetic conditions
COMPLEX TRAITS
(Quantitative)
e.g. Marbling
GENETICS
100 %
GENETICS
ENVIRONMENT
Van Eenennaam NM 3/6/2015
Animal Genomics and Biotechnology Education
Tests for quantitative traits
– before 2010 1-100 SNPs





Meat Tenderness
Quality Grade (Marbling)
Beef Cattle Feed Efficiency
Meat Yield
Disease Resistance
Animal Genomics and Biotechnology Education
DNA TEST FOR MARBLING EXPLAINS 15%
of GENETIC VARIATION IN THE TRAIT
DNA
TEST
OTHER
GENES
85%
37%
GENETICS
Van Eenennaam NM 3/6/2015
63%
ENVIRONMENT
EPD
estimates
all genes
Animal Genomics and Biotechnology Education
What is wrong with having only a
few markers for quantitative traits?


A few markers are not sufficient to account for
much (<20%) of the additive genetic variation
– so little obvious relationship between
phenotype and DNA-test results and little
genetic progress likely to result from markerassisted selection (MAS)
Need to have lots of markers to explain more
of the genetic variation
Van Eenennaam NM 3/6/2015
Animal Genomics and Biotechnology Education
High-throughput genotyping
technology enabled the development
of high density “SNP chips”
The sequencing of the bovine genome allowed for the
development of a 50,000 SNP chip, then the 800,000 SNP
chip; and now whole genome sequencing is being done on
AI bulls (3 billion base pairs)!
Van Eenennaam NM 3/6/2015
Need to integrate DNA information into
National Cattle Evaluation (NCE)
“Information from DNA tests only has value in
selection when incorporated with all other available
forms of performance information for economically
important traits in National Cattle Evaluation (NCE),
and when communicated in the form of an EPD with
a corresponding BIF accuracy.
For some economically important traits (e.g. feed
efficiency), information other than DNA tests may not
be available. Selection tools based on these tests
should still be expressed as EPD within the normal
parameters of NCE ” (Tess, 2008).
Animal Genomics and Biotechnology Education
Information sources for EPDs – DNA
just one source of data for GE-EPD
r
r
Accuracy (r) – correlation
between test result and
actual genetic merit
Van Eenennaam NM 3/6/2015
Animal Genomics and Biotechnology Education
American Angus Association performs
weekly evaluations with genomic data
Van Eenennaam NM 3/6/2015
Bovine Respiratory Disease Consortium
Angus predictions (r) are not very
accurate in Red Angus (Data provided by Dorian Garrick)
Trait
Trained in Black
Angus/Validated
in Black Angus
Trained in Black
Angus/Validated
in Red Angus
BirthWt
0.64
0.27
WeanWt
0.67
0.28
YearlingWt
0.75
0.23
Fat
0.70
0.21
Rib Eye Area
0.75
0.29
Marbling
0.80
0.21
CalvEase (D)
0.69
0.14
CalvEase (M)
0.73
0.18
Angus = ASREML 5-fold validation Red Angus = correlation
Training on de-regressed EPDs Saatchi et al (GSE)
Animal Genomics and Biotechnology Education
AN: Angus
BM: Beefmaster
BN: Brangus
BR: Brahman
BU: Braunvieh
CA: Chiangus
CH: Charolais
HH: Hereford
HL: Line 1 HH
Van Eenennaam NM 3/6/2015
GV: Gelbvieh
LM: Limousin
MA: Maine Anjou
RA: Red Angus
SA: Salers
SG: Santa Gertrudis
SH: Shorthorn
SM: Simmental
Approximate genetic
distance between
breeds using data from
the 2,000 Bull Project.
Larry Keuhn, USDA MARC
http://www.nbcec.org/topics/
BeefBreeds.pdf
Bovine Respiratory Disease Consortium
Hype cycle: the over-enthusiasm or "hype" and
subsequent disappointment that typically happens
with the introduction of new technologies
Van Eenennaam NM 3/6/2015
Animal Genomics and Biotechnology Education
Realized accuracies (r) resulting from
genomic selection prediction equations
trained in US beef cattle breeds
Van Eenennaam NM 3/6/2015
Van Eenennaam et al. 2104. Annual Review Animal Biosciences 2:105-139.
Other breeds? Current status of genomicpredictions in US beef industry 2/11/2015
Via Angus Genetics Incorporated (AGI)
Angus
Charolais
Via GeneSeek/NBCEC – perhaps using Garrick/Golden software in future
Hereford - thru ABRI/Breedplan - currently
Simmental
Gelbvieh
Limousin
Red Angus
Shorthorn - finishing training population
Maine-Anjou - going thru validation
Via John Genho
Santa Gertrudis
Rex Ranch & Deseret
Brangus - getting near to it
Van Eenennaam NM 3/6/2015
Dorian Garrick, Personal
communication
Bovine Respiratory Disease Consortium