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;

Expectations for 2060

Alexander Ruane, NASA

• 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

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

Materials and Methods39oC

25oC

22 23 24 25 26 27 28 41 42

Days Post-Hatch35oC for 8hrs/day

Necropsy (D7, D21, D28, D42)

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

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 arrayStatistical analyses•Heritability: EMS traditional ANOVA method in JMP based on sire variance GWAS: Bayes B in GenSel (Fernando and Garrick (2009))

HeritabilityPhenotype 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

• 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.

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

African Chicken Ecotype Analysis: Shared Runs Of Homozygosity GSEA

11

AA recycling

Kinase activation

Environment

Oxidative stress

High UV regions

PCA plot of populations

European

African

Illinois (legacy line) Ross (modern broiler)

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

FBP2

Fructose-bisphosphatase 2

Up in Heat Stress

Not Detectable

Detected, no difference

* = rate limiting enzyme

Gluconeogenesis & Glcogenolysis

ImmunityLipid Synthesis

Amino Acids

Lipolysis Inhibition of Cell cycle

Beta-Oxidation

Up in Heat StressUp in Control

Glutathione Production

Pentose Phosphate Pathway

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

16Red- Manuscripts or theses writtenBlack- data collected, awaiting student to analyze

Total Mass

Normalized Mass

Impact of Heat Stress on Breast Muscle Growth

Diameter

Circumference

Area

Impact of Heat Stress on Hypertrophy

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

Probiotic and body temperature under heat stress

Bicarbonate Levels and Probiotic(not only impacts temperature)

PROBIOTIC

CONTROL

CO2 +H20 «--» H2CO3 «--» HCO3-

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.

• 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

Enriched in Ross 708Enriched in Illinois

Model for Differences in Breast Muscle Growth Post-Hatch Days 6-21