Upload
badru
View
44
Download
0
Embed Size (px)
DESCRIPTION
Genomic Prediction Results. Measuring Genetic Similarity. Cattle genome sequenced in 2004 30 chromosome pairs (including X,Y) 3 billion letters from each parent Illumina Bovine SNP50 TM Chip 58,000 genetic markers in 2007 39,835 used in genomic predictions Cost about $200 per animal. - PowerPoint PPT Presentation
Citation preview
2007
Paul VanRaden, Curt Van Tassell, George Wiggans, Paul VanRaden, Curt Van Tassell, George Wiggans, Tad Sonstegard, and Jeff O’ConnellTad Sonstegard, and Jeff O’Connell
Animal Improvement Programs Laboratory and Bovine Functional Genomics Laboratory, USDAAgricultural Research Service, Beltsville, MD, [email protected]
2008
Genomic Prediction ResultsGenomic Prediction Results
NAAB DSEC April 2008 (2) Paul VanRaden200
8
Measuring Genetic SimilarityMeasuring Genetic Similarity
Cattle genome sequenced in 2004• 30 chromosome pairs (including X,Y)• 3 billion letters from each parent
Illumina Bovine SNP50TM Chip• 58,000 genetic markers in 2007• 39,835 used in genomic predictions• Cost about $200 per animal
NAAB DSEC April 2008 (3) Paul VanRaden200
8
How Related are Relatives?How Related are Relatives?
Example: Full sibs • are expected to share 50% of their
DNA on average, with SD of 5% • may actually share 40% to 60% of
their DNA because each inherits a different mixture of chromosome segments from the two parents.
• SD 3.5% reported previously was low
NAAB DSEC April 2008 (4) Paul VanRaden200
8
SimulatedSimulated Results (Apr 2007) Results (Apr 2007)
1777 older and 500 younger bulls
10,000 SNPs and 100 QTLs
Reliability vs parent average REL • 58% vs 36% for young bulls• Higher REL if major loci and
Bayesian methods used, lower if many loci (>100) affect trait
NAAB DSEC April 2008 (5) Paul VanRaden200
8
SimulatedSimulated Results (2008) Results (2008)
8271 older and 1984 younger bulls
40,000 SNPs and 500 QTLs
Provided timing, memory test
Reliability vs parent average REL • 79% vs 37% expected for young bulls• 76% vs 37% observed in simulation
NAAB DSEC April 2008 (6) Paul VanRaden200
8
GenotypedGenotyped Bulls (Feb 2007) Bulls (Feb 2007)from Cooperative Dairy DNA Repositoryfrom Cooperative Dairy DNA Repository
DNA of bulls stored in Beltsville (BFGL)
2560 proven bulls used to computed predictions• Bulls born 1994-1996 with >75% reliability
of Net Merit• Plus ancestor bulls born 1952-1993
659 later bulls used to test predictions• Born 2001 with >75% reliability of Net Merit
NAAB DSEC April 2008 (7) Paul VanRaden200
8
Proposed Genotyping (Apr 2007)Proposed Genotyping (Apr 2007)
0
400
800
1200
1990 1994 1998 2002 2006
Nu
mb
er o
f B
ulls
ancestors
proven
predicted
calves
Data cutoff
NAAB DSEC April 2008 (8) Paul VanRaden200
8
Current Genotyped Animals (n=6005)Current Genotyped Animals (n=6005)
0
200
400
600
800
100019
50
1970
1990
1992
1994
1996
1998
2000
2002
2004
2006
2008
Year of Birth
Nu
mb
er o
f A
nim
als
Predictor
Predictee
Young
NAAB DSEC April 2008 (9) Paul VanRaden200
8
AcknowledgmentsAcknowledgments
Funding: • NRI grants 2006-35205-16888, 16701• CDDR Contributors (NAAB, Semex)
Genotyping and DNA extraction:• BFGL, U. Missouri, U. Alberta,
GeneSeek, GIFV, and Illumina
Computing from AIPL staff
NAAB DSEC April 2008 (10) Paul VanRaden200
8
Genomic MethodsGenomic Methods
Direct genomic evaluation• Inversion for linear prediction, REL• Iteration for nonlinear prediction
Combined genomic evaluation• Traditional PA or PTA, subset PA or
PTA, and direct genomic combined by REL in 3 x 3 selection index
• Nonlinear genomic predictions used
NAAB DSEC April 2008 (11) Paul VanRaden200
8
Nonlinear and Linear Regressions Nonlinear and Linear Regressions for marker allele effectsfor marker allele effects
NAAB DSEC April 2008 (12) Paul VanRaden200
8
Actual Results (Feb 2007 data)Actual Results (Feb 2007 data)
August 2003 PTAs for 2650 older bulls to predict January 2008 daughter deviations for 569 younger bulls (total = 3119 bulls)
Results computed for 27 traits: 5 yield, 5 health, 16 conformation, and Net Merit
Nonlinear A used, B didn’t work
NAAB DSEC April 2008 (13) Paul VanRaden200
8
Marker P-Values for Net MeritMarker P-Values for Net Merit
NAAB DSEC April 2008 (14) Paul VanRaden200
8
Marker Effects for Net MeritMarker Effects for Net Merit
NAAB DSEC April 2008 (15) Paul VanRaden200
8
Marker Effects for MilkMarker Effects for Milk
NAAB DSEC April 2008 (16) Paul VanRaden200
8
Marker Effects for Final ScoreMarker Effects for Final Score
NAAB DSEC April 2008 (17) Paul VanRaden200
8
Reliabilities and R-square values comparing Reliabilities and R-square values comparing traditional to genomic predictionstraditional to genomic predictions
Squared corr (x100)
Reliability
Traditional Genomic Genomic
Trait PA Genomic PA Realized Gain
Net Merit 8 21 36 54 18
Milk 30 44 38 54 16
Fat 15 39 38 65 27
Protein 31 43 38 51 13
Fat % 28 58 38 72 34
Protein % 32 51 38 66 28
NAAB DSEC April 2008 (18) Paul VanRaden200
8
Reliabilities and R-square values comparing Reliabilities and R-square values comparing traditional to genomic predictionstraditional to genomic predictions
Squared corr (x100)
Reliability
Traditional Genomic Genomic
Trait PA Genomic PA Realized Gain
Prod Life 9 19 28 47 19SCS 7 23 32 54 22DPR 15 23 25 40 15SCE 19 23 31 36 5DCE 24 27 31 36 5Final Score 24 32 28 37 9
NAAB DSEC April 2008 (19) Paul VanRaden200
8
Expected vs Observed ReliabilityExpected vs Observed Reliability
Reliability for predictee bulls • Average across traits: 57% expected
vs. 48% observed vs. 30% PA• Observed range 72% (fat pct) to 36%• PTA regressions .8 to .9 of expected
Redo 2003 cutoff using April data
Develop REL and PTA adjustments
NAAB DSEC April 2008 (20) Paul VanRaden200
8
Clones and Identical TwinsClones and Identical Twins21HO2121, 21HO2125, 21HO2100, CAN6139300, CAN613930321HO2121, 21HO2125, 21HO2100, CAN6139300, CAN6139303
Traditional Genomic
Bull Dtrs NM$ REL NM$ REL
Triton - ETN 98 -363 82 -371 91
Triad - ETN 26 -306 68 -370 91
Trey - ETN 108 -395 83 -371 91
Loyalty 108 -185 78 -196 87
Lauriet 83 -203 76 -196 87
NAAB DSEC April 2008 (21) Paul VanRaden200
8
X, X, YY, , Pseudo-autosomalPseudo-autosomal SNPs SNPs
487 SNPs
35 SNPs
0 SNPs
35 SNPs
NAAB DSEC April 2008 (22) Paul VanRaden200
8
SNPs on X ChromosomeSNPs on X Chromosome
Each animal has two evaluations• Expected genetic merit of daughters• Expected genetic merit of sons• Difference is sum of effects on X• SD = .1 σG, smaller than expected
Correlation with sire’s daughter vs. son PTA difference was significant (P<.0001), regression close to 1.0
NAAB DSEC April 2008 (23) Paul VanRaden200
8
SNP Density ComparisonSNP Density Comparison2130 older and 261 younger bulls2130 older and 261 younger bulls
REL of PA
Genomic REL
Trait 10K 20K 40K
Net Merit 35 45 49 48
Milk 37 49 52 51
Fat 37 52 55 57
Protein 37 52 54 53
Productive Life 28 44 45 42
SCS 31 44 45 47
Dtr Preg Rate 21 44 49 46
NAAB DSEC April 2008 (24) Paul VanRaden200
8
Genetic Evaluation AdvancesGenetic Evaluation Advancesand increases in genetic progressand increases in genetic progress
Year Advance % Gain
1935 Daughter-dam comparison 100
1962 Herdmate comparison 50
1974 Modified cont. comparison 5
1977 Protein evaluated 4
1973 Records in progress 10
1989 Animal model 4
1994 Net merit, PL, and SCS 50
2008 Genomic selection >40
NAAB DSEC April 2008 (25) Paul VanRaden200
8
ConclusionsConclusions
Genomic predictions significantly better than parent average (P < .0001) for all 26 traits tested
Gains in reliability from 2650 bulls (Feb data) equivalent on average to 9 daughters with records
April data included 5285 proven bulls, more analysis needed