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Genotype by diet interactions in selection lines for residual feed intake in pigs
Mauch, Emily D.1, N.V.L. Serão2, J.M. Young3, J.F. Patience1, N.K. Gabler1,
and J.C.M. Dekkers11 Department of Animal Science, Iowa State University, Ames 50011
2Department of Animal Science, North Carolina State University, Raleigh 276953Department of Animal Sciences, North Dakota State University, Fargo 58108
EAAP ‐ August 29, 2016
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Residual Feed Intake
RFI = Observed ‐Expected
Feed Intake
RFI first proposed by Koch et al., 1963 2
High RFI
Low RFI
ADG, BF & MBW
• Low RFI• More Feed Efficient
• High RFI• Less Feed Efficient
RFI = ADFI - b1*ADG - b2*BF - b3*MBW
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IOWA STATE UNIVERSITY 3
Low RFI[More Feed Efficient]
High RFI[Less Feed Efficient]
Standardn = 172
Challengen = 157
Diets:Standard (n =2,309)
Challenge (n= 314) = ↓Energy [‐18%], ↑Fiber [+175%]
Standardn = 159
Challengen = 157
Diet Challenge:Generations 8, 9, & 10
n = 644
Fed Standard diet during selection
ISU RFI Lines
Est. 2001
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IOWA STATE UNIVERSITY 4
Low RFI[More Feed Efficient]
High RFI[Less Feed Efficient]
Standardn = 172
Challengen = 157
Diets:Standard (n =2,309)
Challenge (n= 314) = ↓Energy [‐18%], ↑Fiber [+175%]
Standardn = 159
Challengen = 157
Diet Challenge:Generations 8, 9, & 10
n = 644
Fed Standard diet during selection
Diet Challenge of ISU RFI Lines
Est. 2001
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Objective
Identify the impact of feeding a low energy, high fiber (Challenge) diet on
1 ) genetic parameters
2) response to selection
3) genomic regions associated with feed efficiency and component traits
in comparison to high energy, low fiber (Standard) diet
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Phenotypes
6
1. Average Daily Gain (ADG), kg/d
Measured every 2 weeks
~40kg‐ ~118 kg
2. Average Daily Feed Intake (ADFI), kg/d
FIRE© Feeders
3. Feed Conversion Ratio (FCR), kg/kg
4. Off‐test Loin Muscle Area (LMA), cm2
5. Off‐test Backfat Depth (BF), mm
6. Residual Feed Intake (RFI), kg/d
n = 2,623
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Genotypes
• 51,098 SNP after quality control
• GWAS by Serão et al., 2016
7
n = 1,692
Standard Diet
• 46, 347 SNP after quality control
n = 311
Challenge Diet
Illumina PorcineSNP60 Beadchip
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Materials & Methods
1) Genetic Parameter Estimation (n = 2,623)
2) Response to Selection (n = 2,623)
3) Single‐SNP Genome Wide Association Studies (GWAS)1. Pigs fed Standard diet reported by Serão et al., 2015 (n= 1,692)2. Pigs fed Challenge diet (n= 311)
8
Bivariate Models in ASReml 3.0• Traits separated by diet
Univariate Modelsin ASReml 4.0
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1) Genetic Parameter Estimation
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Heritability
RFI = residual feed intake, ADFI = average daily feed intake, FCR = feed conversion ratio, ADG = average daily gain, BF = backfat depth, LMA = loin muscle area
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Genetic Correlations between Diets
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2) Response to Selection for RFI
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Line Differences (High RFI minus Low RFI)
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Line Differences (High RFI minus Low RFI)
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Response to selection for RFI under Standard Diet
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Line Differences (High RFI minus Low RFI)
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100%
82%
39%
Observed Response of Challenge diet was 39% of response of Standard diet by Generation 10
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Line Differences (High RFI minus Low RFI)
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100%
47%
Observed Correlated Response under Challenge diet was 47% of predicted
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3) Genome Wide Association Study
(GWAS)
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Residual Feed Intake
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Genetic Parameter Conclusions
• RFI and component traits are moderately to highly heritablewith similar estimates under Standard and Challenge diets
• RFI and component traits under Challenge diet have high, positive genetic correlations to the same trait under Standard diet
• Genetic correlations for RFI, ADFI and FCR across diets tended to be lower
• The observed correlated response for RFI under the Challenge diet was 47% less than predicted based on the genetic correlation across diets
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GWAS Conclusions
• RFI is a highly polygenic trait• Affected by many genes with small effects• No clear overlap of regions identified in GWAS for RFI under Standard versus Challenge diet
• For component traits, some genomic regions overlap under Standard and Challenge diets
• Novel QTL for BF on SSC 2 at 162 Mb in ISU RFI lines
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Overall Conclusions
• RFI appears to be a genetically different trait depending on diet fed, suggesting genotype by diet interactions• rg = 0.82 ± 0.28• Lower response to selection under Challenge diet than predicted• No clear overlap in GWAS results between Standard & Challenge diets
• Diet may play a role in selection for feed efficiency pigs• Deviations from diet fed during selection may result in reduced response in feed efficiency
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Acknowledgements
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Lauren Christian Swine Research Farm
Gary Kuper
Tom Sandve
Dekkers’ Lab Group
ISU RFI Group
ISU AB&G Group
USDA AFRI‐NIFA Grant #20011‐68004‐30336
Duane & Shirley Acker International Fellowship
FIRE© Feeder Donations
Genus PICChoice Genetics
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Appendix
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Diet Differences
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Standard Challenge Difference
Net Energy, Mcal/kg 2.42 1.99 ‐18%
Acid Detergent Fiber (ADF), % 3.5% 12.5% +257%
Neutral Detergent Fiber (NDF), % 9.4% 25.9% +175%
Lysine:Metabolizable Energy (Lys:ME), g/Mcal 2.87 2.94 ____
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Phenotype & Genotype Records
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Phenotypic RecordsLowRFI‐HELF High‐HELF Low‐LEHF High‐LEHF
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Diet Standard & ChallengeBivariate Models, ASReml 3.0
RFI = residual feed intake, ADFI = average daily feed intake, FCR = feed conversion ratio, ADG = average daily gain,
BF = backfat depth, LMA = loin muscle area27
Trait line sex pen‐cohort onage onwt offwt ADG*gen offbf metwt litter idpig
RFI,kg/d X X X X X X X X X X X
ADFI,kg/d X X X X X X
FCR, kg/kg X X X X X X
ADG, kg/d X X X X X X
BF, mm X X X X X X
LMA, cm2 X X X X X X
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Genetic Parameters1 = Standard Diet, 2 = Challenge Diet
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Trait N Mean(SD) h2 c2 σP σg
RFI1, kg/d 2,309 ‐‐‐‐‐‐ 0.24 ± 0.05 0.09 ± 0.03 0.13 0.06
RFI2, kg/d 313 ‐‐‐‐‐‐ 0.35 ± 0.17 0.00 ± 0.00 0.22 0.13
ADFI1,kg/d 2,309 2.02 (0.30) 0.41 ± 0.05 0.02 ± 0.03 0. 20 0.13
ADFI2,kg/d 313 2.47 (0.38) 0.45 ± 0.14 0.00 ± 0.00 0.27 0.18
FCR1, kg/kg 2,309 2.78 (0.41) 0.26 ± 0.05 0.11 ± 0.03 0.26 0.13
FCR2, kg/kg 313 4.26 (0.62) 0.18 ± 0.15 0.04 ± 0.10 0.51 0.21
RFI = residual feed intake, ADFI = average daily feed intake, FCR = feed conversion ratioc2 = common litter effect
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Genetic Parameters1 = Standard Diet, 2 = Challenge Diet
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Trait N Mean(SD) h2 c2 σP σg
ADG1,kg/d 2,309 0.73 (0.11) 0.39 ± 0.05 0.03 ± 0.03 0.09 0.05
ADG2,kg/d 314 0.59 (0.10) 0.52 ± 0.17 0.02 ± 0.09 0.08 0.06
BF1, mm 2,307 17.15 (4.86) 0.59 ± 0.06 0.08 ± 0.03 3.61 2.78
BF2, mm 314 19.16 (5.15) 0.46 ± 0.20 0.10 ± 0.09 4.10 2.78
LMA1, cm2 2,306 42.82 (5.47) 0.52 ± 0.06 0.07 ± 0.03 4.65 3.36
LMA2, cm2 314 43.26 (5.34) 0.47 ± 0.22 0.12 ± 0.10 4.92 3.37
ADG = average daily gain, BF = off‐test backfat depth, LMA = loin muscle area c2 = common litter effect
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Models for Single SNP GWAS
RFI = residual feed intake, ADFI = average daily feed intake, FCR = feed conversion ratio, ADG = average daily gain,
BF = backfat depth, LMA = loin muscle area30
Fixed Effects Random Effects
Trait mu line sex gen‐par scanner onage onwt offwt offbf metwt ADG*gen SNP pig pen‐cohort litter
RFI,kg/d
X X X X X X X X X X X X X X
ADFI,kg/d
X X X X X X X X
FCR,kg/kg
X X X X X X X X
ADG,kg/d
X X X X X X X X
BF, mm
X X X X X X X X X
LMA,cm2 X X X X X X X X X
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AverageDaily Feed Intake
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SSC1 180Mb MC4R
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Feed Conversion
Ratio
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LoinMuscleArea
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Residual Feed Intake
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Residual Feed Intake
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Residual Feed Intake
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