1/23/2018

Genomic Analysis of Responses to Heat Gene and/or genetic 1 markers with NDV Heat Stress Stress in Three Chicken Genetic Lines and Heat Stress in US population 2 • Genetic factors influence the physiological Develop response to heat stress and certain genes play a Animal Genomics and Adaptation to Climate Change breeding stock Gene and/or direct or indirect role of controlling thermal 5 with ND genetic markers tolerance to heat stress with NDV and Heat resistance in Objectives Africa Stress in African Objectives indigenous Ying Wang, Ph.D. ecotypes Validate genes • Identify genes, genetic markers and genetic Perot Saelao, Colin Kern, Kelly Chanthavixay, Sihua Jin, Rodrigo A. Gallardo, David pathways associated with heat stress in three and/or genetic Bunn, Terra Kelly, Jack M. Dekkers, Susan J. Lamont and Huaijun Zhou Develop a SNP unique chicken populations in the US using markers associated advanced genetic and genomic technologies 4 with NDV panel for genetic • Identify genes and/or genetic markers associated resistance in selection by 3 Department of Animal Science integrating with heat stress in African indigenous chicken African indigenous ecotypes using whole genome SNP panel. University of California, Davis ecotypes results

Jan 17, 2018

Experimental Populations Experimental Design

Day 14

38-35°C and 50% humidity Leghorn-GB2 Fayoumi-M13 Hy-Line Brown  Leghorns are layers of white eggs that modern commercial layers were derived Day 23 Day 14 Day 20 from. Domestication and selective breeding are leading to individuals that are Day 21 Chronic Heat & NDV Acute Heat (AH) Chronic Heat (CH) more susceptible to stress. NDV inoculation (CH&NDV) 4 hrs post heat 6 days post heat 7  Fayoumi is a breed of chicken originating in Egypt. They had been imported to (10 EID50 ) 9 days post heat stress (38°C) stress (35°C) the US in 1954 by Iowa State University. Fayoumis are a hardy breed, and stress (35°C) particularly well suited to hot climates.  Hy-Line Brown is the world’s most balanced brown egg layer and provides more profit for the poultry producers. Hy-Line Browns are widely distributed in African Sudden stress Adaption countries.

Physiological Responses to Heat Stress Heat PhenotypicalRelated Physiological Trait Result Response Summary in Blood

Heat Stress (HS) vs. Non-Treated (NT) Beneficial Fayoumi Leghorn Response Heat Stress AH CH CH&NDV AH CH CH&NDV Na+ + NS NS NS - NS NS K+ + NS + NS - - NS Stops eating Shunts iCa2+ + NS NS NS + NS + Panting Spread wings and drink more blood Glu NS NS NS + NS + pH - + + - NS NS - Increase respiratory Urine rate Excretion PCO2 - - - NS NS NS NS TCO2 - NS - - NS NS NS + + Lost Na , K and HCO3 - NS - - + NS NS Increase Increase PO2 Lost CO2 2+ plasma pH and sO2 and HCO3 iCa balance BE - NS NS - NS NS NS PO2 + NS + + - NS NS Respiratory Metabolic Acid/Base balance Alkalosis Acidosis imbalance sO2 + + + NS - + - Hct NS - NS NS - NS Hb NS - NS NS - NS (www.rci.com.au; Borges, et al., 2004; Steinmetz, et al., 2007; Soleimani, et al., 2010; Sivakumar, et al., 2010) (Poultry Science, Wang, et al., 2017)

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Transcriptome Profiling Transcriptome Profiling

Liver Hypothalamus

100 120 111 Up-regulated 82 Down-regulated 100 80 66 80 Up-regulated 61 60 Down-regulated 52 60 Gene Gene Description 40 34 name 40 27 HABB Hemoglobin subunit alpha-A 20 17 20 14 Gene 2 Gene 4 Gene description 1 0 1 0 1 Gene Description name 0 name Genes Expressed Differentially of Numbers family A () 0 HSPA8 Heat shock protein 90 beta family member 8

Numbers of Differentially Expressed Genes Genes Expressed Differentially of Numbers FTFC LTLC FTFC LTLC HSP90B1 member 1 FTFC LTLC FTFC LTLC Heat shock protein family A (Hsp70) Acute Heat Chronic Heat & NDV HSPA2 member 2 Acute Heat Chronic Heat & NDV Gene Gene description FT: Fayoumi treated group URM1 related modifier 1 FT: Fayoumi treated group name FC: Fayoumi non-treated group FC: Fayoumi non-treated group CRY1 Cyptochrome circardian regulator 1 LT: Leghorn treated group LT: Leghorn treated group LC: Leghorn non-treated group LC: Leghorn non-treated group

Transcriptome Profiling AldosteroneAldosterone Signaling Signaling in Epithelial in Epithelial Cells in Hypo Cells

Breast muscle

100 Up-regulated 79

80 AH Hypothalamus AH Hypothalamus Down-regulated

60 Leghorn (Activation of Transport) Ion (Activation

40 30 Gene Gene Description name •Leghorn: Activation 20 15 14 CRY1 Cryptochrome circadian clock 1 Hypothalamus 6 5 ) •Fayoumi: Inhibition 0 3 0 Gene •Leghorn: Activation Numbers of Differentially Expressed Genes Genes Expressed Differentially of Numbers FTFC LTLC FTFC LTLC Gene Description

name Breast Muscle •Fayoumi: Inhibition Ion Transport Ion

Acute Heat Chronic Heat & NDV UNC45B Unc-45 myosin B AH( Hypothalamus AH( Hypothalamus FT: Fayoumi treated group CEP85 Centrosomal protein 85 •Leghorn: Inhibition FC: Fayoumi non-treated group Solute carrier family 20 (phosphate Liver SLC20A2 •Fayoumi: Activation

LT: Leghorn treated group transporter), member 2

Activation of Activation Fayoumi LC: Leghorn non-treated group Heat shock protein family B (small) HSP88 member 8

Hy-Line Brown Phenotypic Results Hy-Line Brown GWAS Results

Heat Stress (HS) vs. Non- Beneficial treated (NT) Response AH CH CH&NDV Significant SNPs associated with Na+ + + + + heat stress K+ + + + + iCa2+ + + NS + Glu NS - NS pH - - - NS Hy-Line Brown Body Weight Gain Acute Heat Chronic Heat Chronic Heat & NDV PCO2 - 180 * NS - - Phenotype TCO2 - - - - sO2 Hct Hb K HCO3 Na TCO2 150 Significance * HCO3 - - - - 120 Var99.5 Alpha0.05 1 1 1 4 1 2 1 BE - 90 - - - PO2 +

60 - NS NS Body Weight Gain (g) Gain WeightBody 30 sO2 + - + NS

0 Hct - NS + D14(AH)D14 (AH) D20(CH)D20 (Ch1) D23(CH&NDV)D23 (Ch2) Hb - NS +

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Hy-Line Brown GWAS Results Hy-Line Brown GWAS Results

 D14 sO2  D20 K+

Position Gene Gene Description Note Position Gene Gene Description PSPC1* Paraspeckle component 1 FTvs.LT=1.82 (Liver at AH) CDX4 Novel genes MIR6641 Gga-mir-6641 USP12-LIKE Novel genes Chr2: MPHOSPH8 M-phase phosphoprotein 8 Chr4: SLC16A2 Solute carrier family 16 member 2 179257601 PARP4 Poly(ADP-Ribose) Polymerase Faymily Member 4 12459540 RLIM Ring finger protein, LIM domain interacting GJA3 Gap junction protein alpha 3 MIR1573 Gga-mir-1573 GJB2 Gap junction protein beta 2 UPRT Uracil phosphoribosyltransferase homolog

Hy-Line Brown GWAS Results Summary

 D23 Na+

1. Each tissue had a distinct transcriptome response within both genetic lines during heat stress and NDV infection.

2. Fayoumi utilized a more effective gene regulatory strategy to maintain electrolyte and acid-base balance.

3. SNPs and gene regions associated with heat stress have Position Gene Gene description Note PTPRG* Receptor-type -protein FTvs.FC=1.82 (Liver at AH) been identified in Hy-Line Brown and potentially provide phosphatase gamma precursor SYNPR Synaptoporin Chr12: candidate genes and genetic markers associated with heat SNTN Sentan, cilia apical structure protein 13124388 THOC7 THO complex 7 stress resistance. SLC25A26 Solute carrier family 25 member 26 SUCLG2 Succinate-CoA ligase GDP-forming beta subunit

Acknowledgements

• UC Davis – Drs. Huaijun Zhou, Rodrigo Gallardo, David Bunn and Terra Kelly – Zhou lab: Dr. Colin Kern, Dr. Neil Huefner, Perot Saelao, Kai Mon, Tae Hyun Kim, Kelly Chanthavixay, Sihua Jin – Gallardo Lab: Dr. Ali Nazmi, Alejandra Figueroa

• Iowa State University – Drs. Sue Lamont, Jack Dekkers

• Hy-Line International – Drs. Petek Settar, Janet Fulton

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