selection lines for residual feed intake (rfi) in yorkshire swine weiguo cai 1, david casey 2, jack...
TRANSCRIPT
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
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
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