Selection Lines for Residual Feed Intake (RFI) in Yorkshire Swine Weiguo Cai 1, David Casey 2, Jack Dekkers 1 1 Department of Animal Science, Iowa State.

Selection Lines forSelection Lines forResidual Feed Intake (RFI)Residual Feed Intake (RFI)

in Yorkshire Swinein Yorkshire Swine

Weiguo CaiWeiguo Cai11, David Casey, David Casey22, Jack Dekkers, Jack Dekkers11

11Department of Animal Science, Iowa State University, Ames, IA 50011 andDepartment of Animal Science, Iowa State University, Ames, IA 50011 and22Pig Improvement Company, Franklin, KY 42134Pig Improvement Company, Franklin, KY 42134

Measures ofMeasures ofFeed EfficiencyFeed Efficiency

FCR = Feed/gainFCR = Feed/gain FE = Gain/Feed FE = Gain/Feed

Residual Feed Intake = (Residual Feed Intake = (ObservedObserved FI) – ( FI) – (ExpectedExpected FI given ADG, BF, BW) FI given ADG, BF, BW)(Koch et al., 1963)(Koch et al., 1963)

Figure 1. Residual Feed Intake (RFI)

Predicted FI

Obse

rved

FI

RFI Factors contributing to RFIFactors contributing to RFI• Physical activityPhysical activity• Body temp. regulationBody temp. regulation• Basal metabolic rateBasal metabolic rate• DigestibilityDigestibility• Energetic efficiencyEnergetic efficiency• Immune responseImmune response• Food wastageFood wastage• Measurement errorMeasurement error

= FI – b= FI – b1 1 ADG – bADG – b2 2 BF – bBF – b3 3 BWBW.75.75

ObjectivesObjectives

• Develop lines that differ in FI but have similar ADG, BFDevelop lines that differ in FI but have similar ADG, BF

• Estimate genetic parametersEstimate genetic parameters

• Evaluate direct and correlated responses to selectionEvaluate direct and correlated responses to selection

• Develop a resource population toDevelop a resource population to• study the biological / physiological basis of feed intake / efficiencystudy the biological / physiological basis of feed intake / efficiency

• develop selection tools for feed intake / efficiencydevelop selection tools for feed intake / efficiency

Yorkshire RFI Yorkshire RFI Selection ExperimentSelection Experiment

OutlineOutline

Feed intake recording in pigsFeed intake recording in pigs

Design of selection experimentDesign of selection experiment

Results: Direct and correlated responsesResults: Direct and correlated responses

Estimates of genetic parametersEstimates of genetic parameters

Ongoing and future workOngoing and future work

Recording individualRecording individualfeed intake in pigsfeed intake in pigs

Electronic Feeder Electronic Feeder FIREFIRE©© Osborne Inc.Osborne Inc.

Commercial FeederCommercial Feeder

Feed intake dataFeed intake data

Extensive edit procedures Extensive edit procedures for feed intake datafor feed intake data

unexplained transponderunexplained transponderzero tag consumptionzero tag consumptionoutliers from graphsoutliers from graphsetc.etc.

Developed by David CaseyDeveloped by David Casey

Casey, Stern, Dekkers. 2005. Casey, Stern, Dekkers. 2005. J. Anim. Sci. 83:969–982.J. Anim. Sci. 83:969–982.

Identify errors in visits Identify errors in visits (16 criteria)(16 criteria)

Create graphs Create graphs ((each pig)each pig)

Remove unwanted informationRemove unwanted information

Calculate average daily FICalculate average daily FI

Fill-in missing daily FIFill-in missing daily FI

Design of RFIDesign of RFIselection experimentselection experiment

Generation 0Generation 0

Low RFI lineLow RFI line Control lineControl lineselect for RFIselect for RFI Generation 1 Generation 1 RandomRandom

selectionselectionreduce reduce FIFI Generation 2Generation 2

keep adg, bf ~ constantkeep adg, bf ~ constantGeneration 3Generation 3

Generation 4Generation 4

Design of RFIDesign of RFI

selection experimentselection experiment

Generation 2Generation 2parity 1parity 1

90 boars on FIRE90 boars on FIRE©©

90 gilts on FIRE90 gilts on FIRE©©

Random selectionRandom selection

Control LineSelect Line RFI

Generation 1 parity 1Generation 1 parity 1selectionselection

Generation 2Generation 2parity 2parity 2

Select ~12 boarsSelect ~12 boars ~70 gilts~70 gilts

Sibs of Sibs of Selected boarsSelected boars RFI EBVRFI EBV

Traits measuredTraits measured− from ~40 to ~115 kg− from ~40 to ~115 kg

Electronically measured feed intake (FIREElectronically measured feed intake (FIRE©©, Osborne Inc.), Osborne Inc.)

11st st parity select boarsparity select boars

22ndnd parity select gilts parity select gilts

Ultrasound scan Ultrasound scan – on-test– on-test

– mid-test– mid-test – off-test– off-test

Body weight – weeklyBody weight – weekly

Average daily gainAverage daily gain(ADG)(ADG)

Weigh pigs weeklyWeigh pigs weekly

Linear regression of Linear regression of weight on day: weight on day: ADG ADG

(kg/day)(kg/day)

Ultrasound ScanUltrasound Scan

Backfat (BF) -Backfat (BF) -10th rib10th rib

Loin muscle area (LMA)Loin muscle area (LMA)

Intramuscular Fat (IMF)Intramuscular Fat (IMF)

Summary of dataSummary of dataacross 4 gener. in select lineacross 4 gener. in select line

TraitsTraits NN MeanMean Phen.StdPhen.Std

RFI RFI (kg/d)(kg/d) 836836 00 0.110.11

ADFI ADFI (kg/d)(kg/d) 836836 1.991.99 0.160.16

ADG ADG (kg/d)(kg/d) 836836 0.770.77 0.080.08

BF BF (mm)(mm) 836836 7.957.95 2.902.90

LMA LMA (cm(cm22)) 836836 26.2826.28 4.044.04

IMF IMF (%)(%) 565565 1.741.74 0.390.39

Note: Phen.Std excludes all fixed effects and pen(group) effect

Var(RFI) Var(FI)=0.46

RFI EBV modelRFI EBV model (ASREML)(ASREML)

FIFI = group + sex = group + sex + pen(group) ++ pen(group) +

bb11**(onwt(onwt**gen) + bgen) + b22**(onage(onage**gen) + bgen) + b33**(offwt(offwt**gen) + gen) +

bb44**((ADGADG**gen) + bgen) + b55**((BFBF**gen) + gen) + BVBVRFIRFI + e+ e

ADG and BF pre-adjusted for onwt, onage, offwtADG and BF pre-adjusted for onwt, onage, offwt

Fixed: group and sexFixed: group and sex

Random: pen (group)Random: pen (group)Note: Metabolic weight not includedNote: Metabolic weight not included

Selection response Selection response for RFI and FIfor RFI and FI

1.1 1.1 pp

1.1 1.1 pp

Correlated responses Correlated responses for ADG and BFfor ADG and BF

0.3 0.3 pp

0.3 0.3 pp

Correlated responses Correlated responses for LMA and IMFfor LMA and IMF

0.1 0.1 pp

0.1 0.1 pp

Heritabilities (on diagonal) genetic (below diagonal) phenotypic (above diagonal)

Heritabilities and correlationsHeritabilities and correlationsBased on ASREML 2-trait analysis

0.530.53 IMFIMF

0.620.62 LMALMA

0.610.61 BFBF

0.330.33 ADGADG

0.400.40 FIFI

0.330.33RFIRFI

IMFIMFLMALMABFBFADGADGFIFIRFIRFI

Heritabilities (on diagonal) genetic (below diagonal) phenotypic (above diagonal)

Heritabilities and correlationsHeritabilities and correlationsBased on ASREML 2-trait analysis

0.530.53 IMFIMF

0.070.07 0.620.62 LMALMA

0.040.04-0.05-0.05 0.610.61 BFBF

0.180.18 0.110.11 0.290.29 0.330.33 ADGADG

0.100.10-0.03-0.03 0.440.44 0.650.65 0.400.40 FIFI

0.040.04-0.10-0.10-0.01-0.01-0.01-0.01 0.510.51 0.330.33RFIRFI

IMFIMFLMALMABFBFADGADGFIFIRFIRFI

0.530.53 0.260.26-0.06-0.06 0.270.27 0.230.23 0.150.15IMFIMF

0.070.07 0.620.62-0.05-0.05 0.190.19-0.10-0.10-0.26-0.26LMALMA

0.040.04-0.05-0.05 0.610.61 0.400.40 0.550.55-0.01-0.01BFBF

0.180.18 0.110.11 0.290.29 0.330.33 0.740.74 0.150.15ADGADG

0.100.10-0.03-0.03 0.440.44 0.650.65 0.400.40 0.710.71FIFI

0.040.04-0.10-0.10-0.01-0.01-0.01-0.01 0.510.51 0.330.33RFIRFI

IMFIMFLMALMABFBFADGADGFIFIRFIRFI

Heritabilities (on diagonal) genetic (below diagonal) phenotypic (above diagonal)

Heritabilities and correlationsHeritabilities and correlationsBased on ASREML 2-trait analysis

Design of directDesign of directline comparisonline comparison

Generation 3Generation 3 Parity 2Parity 2

Selection lineSelection linen=50n=50

Control lineControl linen=38n=38

88 gilts on FIRE88 gilts on FIRE

identify extremes at 70 kg identify extremes at 70 kg

(gene expression)(gene expression)

TraitTrait

Line difference (select-control) Line difference (select-control) estimated based onestimated based on

EBV EBV in selection linein selection line

DirectDirectcomparison comparison

RFI, RFI, g/dg/d -124-124 -93***-93***

FI, FI, g/dg/d -175-175 -123***-123***

ADG, ADG, g/dg/d -24-24 -22-22NSNS

BF, BF, mmmm -0.77-0.77 0.0630.063 NS NS

*** significant at P<.01, NS Not significant at P<.10*** significant at P<.01, NS Not significant at P<.10

Estimates of lineEstimates of line differencesdifferences

SummarySummary

46% of variation in FI is not related to ADG and BF 46% of variation in FI is not related to ADG and BF = RFI = RFI

RFI has substantial heritability (0.33)RFI has substantial heritability (0.33)

4 generations of selection for RFI has resulted in 4 generations of selection for RFI has resulted in

significant change in RFI (93-124 g/d) significant change in RFI (93-124 g/d)

RFI selection has slightly reduced ADG and BFRFI selection has slightly reduced ADG and BF

Yorkshire selection & control lines

for Residual Feed Intake

Integration of Functional Genomics and Quantitative Integration of Functional Genomics and Quantitative Genetics to Improve Feed Efficiency in PigsGenetics to Improve Feed Efficiency in Pigs

Dekkers, Tuggle, Anderson, Nettleton, HonavarDekkers, Tuggle, Anderson, Nettleton, HonavarIowa State UniversityIowa State University

Rekaya, Barb, HausmanRekaya, Barb, HausmanUniversity of Georgia and USDA-ARS-RARCUniversity of Georgia and USDA-ARS-RARC

NRI Grant no. 2005-35604-15618

Gene expressionGene expressionstudiesstudies

Low RFI gilts

Select line

Restr. feeding

SR

Ad Libitum

SA

Restr. feeding

CR

Ad Libitum

CA

High RFI gilts

Control line

Liver Fat

Gene ExpressionGene ExpressionMicroarrayMicroarray

Measure the level of expression ofMeasure the level of expression of>20,000 probes for genes across >20,000 probes for genes across

genomegenome

Source: http://www.affymetrix.comSource: http://www.affymetrix.com

Image from Hybridized GeneChipImage from Hybridized GeneChip

RNA

4 4 4 4

~70 kg~70 kg

LimitedLimitednumbersnumbers

Biological basis ofBiological basis ofdifferences in RFIdifferences in RFI

Residual Feed Intake = (Residual Feed Intake = (ObservedObserved FI) – ( FI) – (ExpectedExpected FI given ADG, BF, BW) FI given ADG, BF, BW)(Koch et al., 1963)(Koch et al., 1963)

Figure 1. Residual Feed Intake (RFI)

Predicted FI

Obse

rved

FI

RFI

New grant funded by New grant funded by National Pork BoardNational Pork Board

and and Iowa Pork Producers AssociationIowa Pork Producers Association

Factors contributing to RFIFactors contributing to RFI• Physical activityPhysical activity• Body temp. regulationBody temp. regulation• Basal metabolic rateBasal metabolic rate• DigestibilityDigestibility• Energetic efficiencyEnergetic efficiency• Immune responseImmune response• Food wastageFood wastage• Measurement errorMeasurement errorRichardson and Herd 2004

Ann CrockAnn Crock Jennifer KerkmanJennifer Kerkman Matt WolfeMatt WolfeJay Lampe Jay Lampe Bryce MartinBryce Martin Benny MoteBenny MoteNapapan PiyasatianNapapan Piyasatian Ryan VoylesRyan Voyles Doug NewcomDoug NewcomJeremy BurkettJeremy Burkett Nick BerryNick Berry Tom BaasTom BaasSender LkhagvadorjSender Lkhagvadorj Long Qu Long Qu Chris TuggleChris TuggleYangfang WangYangfang Wang Dan NettletonDan Nettleton Lloyd AndersonLloyd Anderson

PIC/Genus for providing FIREPIC/Genus for providing FIRE©© feeders feedersISU Center for Integrated Animal GenomicsISU Center for Integrated Animal Genomics

Monsanto Choice GeneticsMonsanto Choice GeneticsUSDA-CSREES NRI Grant no. 2005-35604-15618USDA-CSREES NRI Grant no. 2005-35604-15618

AcknowledgementsAcknowledgementsWeiguo Cai, David CaseyWeiguo Cai, David Casey

John Newton and personnel at ISU Bilsland farmJohn Newton and personnel at ISU Bilsland farm