Objectives: - Identify alleles that adapt chickens to the stress of a changing environment. - Identify alleles that improve nutrient utilization in production lines of chickens. - Identify novel alleles in African chickens where birds have been naturally selected to be more tolerant of climate variation.

1. Adapting Chicken Production to
Climate Change through Breeding
• PD: Carl J. Schmidt, University of Delaware
• coPI: Susan J. Lamont, Iowa State University
• coPI: Max Rothschild, Iowa State University
• coPI: Michael Persia, Virginia Tech University
• coPI: Chris Ashwell, North Carolina State University
• USDA-NIFA-AFRI Climate Change Award #2011-67003-
30228;

2. Expectations for 2060
Alexander Ruane, NASA

3. • Adaptation to increased incidence of heat waves:
– Genes that respond to heat stress will play a
role in adaptation to heat
– Birds with better responses to heat will have
alleles that can confer adaptation to heat
stress.
• Mitigation:
– Mitigation will occur, in part, by improving
feed efficiency.
– Identifying alleles that improve feed efficiency
will mitigate impact of poultry industry on
climate change
Adapting Chicken Production To Climate
Change Through Breeding

4. Post Hatch Temperatures
HATCH
D42
D42
D21
HEAT STRESS
CONTROL
38°C for 8 hrs daily
25°C 25°C
25°C 25°C
37°C 25°C

5. Materials and Methods
39oC
25oC
22 23 24 25 26 27 28 41 42
Days Post-Hatch
35oC for 8hrs/day
Necropsy (D7, D21, D28, D42)

6. Use of Genomics to Address
Climate Challenges
• Heat stress causes an estimated annual economic loss of $125-165
million in the U.S. poultry industry alone (St-Pierre et al. (2003)).
• There is potential to breed birds that are more resilient to
increasing temperatures using genomics
• Genome Wide Association Study (GWAS): A technique used to
analyze an associations between SNP and traits
• Rationale: Fayoumis underwent natural selection for heat
tolerance. Inbreeding resulted in fixation of alleles at highest
frequency. Commercial broilers selected for muscle mass.
• Objective: To determine genetic regions associated with response
to heat stress in an AIL
• Goal: To breed chickens more robust in tolerating increased
temperatures

7. Advanced Intercross Line
X
Broiler Fayoumi
F2 generation chicks
• F18 and F19 generations used in this study (468 birds)
Genotyping
•600K Affymetrix Axion GW GT chicken array
Statistical analyses
•Heritability: EMS traditional ANOVA method in JMP based on sire variance
GWAS: Bayes B in GenSel (Fernando and Garrick (2009))

8. Heritability
Phenotype Heritability
Body weight d 21 (g) 25%
Body weight d 28 (g) 36%
∆ Body weight d 28-21 (g) 21%
∆ Body temp d 22-20 (°F) 6%
∆ Body temp d 28-22 (°F) 10%
Breast weight % (g) 19%
 Genetic control exists for these unique traits under heat stress;
therefore, they will respond to genetic selection for improvement

9. • First time GWAS reported on novel phenotypes measured
during heat stress
– Body temp: effects detected on chr 27 and 14
– Body weight: effects detected on chr 1, 2, 4, 6 and 7
– Digestibility: effects detected on chr 19, 20 and 21
– %Breast weight: effect on chr 1 explaining >15% of
genetic variance
•Body temperature: novel QTL identified
•Body weight: novel QTL identified
•Novel QTL identified:
% Breast weight: region may be a good candidate for selection
for improved production in hot climates.

10. GWAS from Advanced Intercross Line. Identified 120
QTLs for response to heat stress.

11. African Chicken Ecotype Analysis:
Shared Runs Of Homozygosity GSEA
11
AA recycling
Kinase activation
Environment
Oxidative
stress
High UV regions

12. PCA plot of populations
European
African

13. Illinois (legacy line) Ross (modern broiler)

14. 14
Glycogen
Glucose-1-phosphate
Glucose-6-Phosphate
Glucose
Blood for use by other tissues
PYGL
PGM1
G6PC
SLC2A2
Phosphorylase*
Phosphoglucomutase
Glucose 6-Phosphatase
Facilitated Glucose Transporter
Fructose-6-Phosphate
Fructose-bisphosphatase 2
Up in Heat Stress
Not Detectable
Detected, no difference
* = rate limiting enzyme

15. Gluconeogenesis
& Glcogenolysis
Immunity
Lipid
Synthesis
Amino Acids
Lipolysis
Inhibition of
Cell cycle
Beta-Oxidation
Up in Heat
Stress
Up in Control
Glutathione
Production
Pentose
Phosphate
Pathway

16. Additional Transcriptome Studies
Completed
• Hypothalamus –thesis written
• Cerebellum
• Pituitary - published
• Breast Muscle- two
manuscripts
• Liver submitted
• Duodenum- thesis written
• Jejunum
• Ileum
• Large Intestine
• Ventricles and Atria
• Spleen- thesis written
• Bursa
16
Red- Manuscripts or theses written
Black- data collected, awaiting student to analyze

17. Total Mass
Normalized
Mass
Impact of Heat Stress on Breast Muscle Growth

18. Diameter
Circumference
Area
Impact of Heat Stress on Hypertrophy

19. Impact of Probiotic on Chicken
• Probiotic: B. subtilis added to feed
• Claimed to improve performance of birds.
• Tested this with Ross 708, industry standard
broiler line.
• Results: 3% increase in feed efficiency

20. Probiotic and body temperature under
heat stress

21. Bicarbonate Levels and Probiotic
(not only impacts temperature)
PROBIOTIC
CONTROL
CO2 +H20 «--» H2CO3 «--» HCO3
-

22. Impact of Studies
• 120 quantitative trait loci affecting response to heat stress mapped
in Broilers.
• Layer GWAS study complete- currently analyzing data.
• African and European birds SNP mapped and compared to identify
differences that might provide clues to growth selection in different
climates.
• Over 1500 Transcriptome libraries collected from the majority of
chicken tissues under control and heat stress. Expression of over
800 genes modulated by heat stress.
• Largest impact on genes affecting chaperones, intestinal integrity,
response to oxidative stress, cell cycle regulation, and immunity.
• Morphometric data from broilers indicates impact of heat stress on
hyperplasia, not hypertrophy.
• Probiotic may be effective in providing resilience to acute heat
stress.

23. • Project Directors
– Carl Schmidt –Delaware
– Sue Lamont –ISU
– Michael Persia – ISU (Virginia
Tech)
– Max Rothschild – ISU
– Chris Ashwell – NC State
• Delaware: 3Yr Post-Doc
Available 2017-2020
– Amanda Wagner Research
Associate
– Janet de Mena M.S. Completed
– Shurnevia StricklandM.S.
Completed
– Brooke Aldrich, M.S. Completed
– Liang Sun, graduate student
– Rick Davis, graduate student
– Allen Hubbard graduate student
– Modupe Adetunji graduate
student
– Colin Kern graduate student
– Elizabeth Pritchett graduate
student
– Allison Rogers graduate student
– Doyinsola Adetunji undergraduate
– Rachel Derita, undergraduate
– Brittany Hazard, undergraduate
– Seretha Suah, undergraduate
– Blair Schneider undergraduate
– Sara Jastrebski M.S. student
• Iowa State University
– Michael Kaiser, Research Associate
– Erin Sandford, graduate student.
– Derrick Coble, graduate student
– Angelica Bjorkquist, graduate
student
– Damarius Fleming, graduate
student
– Hongyan Sun, graduate student,
– Jianqin Zhang, visiting scholar
– Qinghua Nie, visiting scholar
– Zhiqiang Li, visiting scholar
– Ling Lian, graduate student
– Mahoussi Aholoupke,
undergraduate intern
– Kelsey Casebere, undergraduate
research assistant
– Neva Nachtrieb, research associate
– Kevin Bolek, graduate student
– Raj Murugesan, graduate student
– J.J. Green, graduate student
– Mallory, graduate student
– Kelsey Nesheim, undergraduate
student
– Cody McDonald, undergraduate
student
– Ceslie Ozbun, undergraduate
– Alysha Gareis, undergraduate
– Suneel Onteru, post doctoral
fellow,
– Xia Zhao, graduate student
– Muhammed Walugembe, graduate
student
– Liz Bobeck, post doctoral fellow
• North Carolina State
– Alex Zavelo, graduate student
– Zack Lowman, graduate student
– Mary Pat Bulfin, undergraduate
student

24. 24

25. Enriched in Ross 708
Enriched in Illinois
Model for Differences in Breast Muscle Growth
Post-Hatch Days 6-21