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Duane NormanAnimal Improvement Programs LaboratoryAgricultural Research Service, USDA, Beltsville, MD
[email protected] Board – 2009 (1)
Update on AIPL research since April 2009
What’s new!
NormanNDHIA Board – 2009 (2)
Genomic news from
the bovine g-nome
NormanNDHIA Board – 2009 (2)
NormanNDHIA Board – 2009 (3)
Calling genotypes
Genotypes called by Tad Sonstegard,BFGL, through April 2009
AIPL staff trained to run GenomeStudio
Cluster files shared with 4 commercial labs to allow call harmonization
Labs began providing genotypes in June
News from the bovine
g-nome
NormanNDHIA Board – 2009 (4)
Commercial labs
GeneSeek (Lincoln, NE)
Genetics & IVF Institute (Fairfax, VA)
Genetic Visions (Middleton, WI)
DNA LandMarks(Saint-Jean-sur-Richelieu, QC, Canada)
News from the bovine
g-nome
NormanNDHIA Board – 2009 (5)
Managing sample ID
Web query established for nominations Indicates pedigree status Designates nominator Provides sample status, including rejection reasons
Query used by labs to convert sample ID to registration number and detect ID entry errors
News from the bovine
g-nome
NormanNDHIA Board – 2009 (6)
Genotype database
50,972 SNP called Calling redone to provide additional
genotypes Many corrections required to make
sample ID match Genotypes from Illumina, University
of Missouri, University of Alberta, and Switzerland also included
News from the bovine
g-nome
NormanNDHIA Board – 2009 (7)
SNP selection
Call rate of >90% Not a duplicate Parent-progeny conflicts of <2% Minor allele frequency of >1% Heterozygosity within 20% of
expected For bulls, X heterozygosity of <5%
News from the bovine
g-nome
NormanNDHIA Board – 2009 (8)
Evaluation preparation
Pedigree file created Checked for missing ancestors Pedigree requested for missing
ancestors
Canadian evaluations obtained for cows
Type evaluations obtained for Holsteins
News from the bovine
g-nome
NormanNDHIA Board – 2009 (9)
Genomic evaluations Evaluations official
Holstein and Jerseys (January 2009) Brown Swiss (August 2009)
June 2009 trait changes Net merit calculated as sum of traits
rather than as an individual trait Holstein feet & legs and rear teat
placement added Current Interbull evaluation added at final
selection-index step triannually
News from the bovine
g-nome
NormanNDHIA Board – 2009 (10)
Reliability calculation
Inversion and discounting Gain in daughter equivalents
times 0.6
Simple approximation Could be adjusted for breed or
number of close relatives Used in April 2009 to beat
deadline
News from the bovine
g-nome
NormanNDHIA Board – 2009 (11)
Interbull plans Convert genomic PTAs (August 2009)
Young bulls from France, Netherlands, and New Zealand
EU requires reliability of ≥50% for marketing
Combine using G-MACE (2010) Proven bulls next year (2010) Domestic and genomic evaluations
computed 1–2 weeks earlier to meet Interbull deadlines
Currently genomics and MACE at same time
News from the bovine
g-nome
NormanNDHIA Board – 2009 (12)
Evaluation options National
Include cows as predictors? Include polygenic effect in model?
International Conversion formulas for young bulls
G-MACE to exchange genomic breeding values
Direct multicountry genomic evaluation
News from the bovine
g-nome
NormanNDHIA Board – 2009 (13)
Culling statistic
s
NormanNDHIA Board – 2009 (13)
NormanNDHIA Board – 2009 (14)
Culling status report
New annual AIPL Research Report by Norman, Wright, and Lombard available at AIPL web site (September 2009)
Based on destination (4) and termination (11) codes provided by DRPCs
Separate summaries by parity and breed 6 breeds 2 crossbred groups
− Heterosis of >90% (crossbred, CB)− Heterosis of 50 to 90% (backcross,
BC)
NormanNDHIA Board – 2009 (15)
Destination codes
Frequency*, %Code A
YBS
GU HO JE MS RW
CB
BC
Stayed in herd 70 68
63 67 71
68 68 74
72
Sold for dairy 7 6 6 3 7 7 4 4 5Sold for
slaughter19 2
124 24 1
722 22 1
820
Died 4 6 8 6 5 4 6 5 5
*Lactations completed between 1-1-07 and 12-31-08
NormanNDHIA Board – 2009 (16)
Termination codesFrequency*, %
Code AY BS GU
HO
JE MS RW CB
BC
Stayed in herd
Normal 69 67 63 66 71 67 68 73 71 Abortion <1 <1 <1 1 1 1 <1 1 1Sold Locomotion 1 1 1 1 <1 <1 1 1 1 Low yield 2 3 3 4 3 3 3 3 3
Reproduction
5 6 6 5 3 6 6 3 4
Mastitis 2 3 3 4 3 3 4 4 4 Other 8 8 11 10 7 9 8 6 7
*Lactations completed between 1-1-07 and 12-31-08
NormanNDHIA Board – 2009 (17)
Left herd but not sold for dairy
Frequency*, %Termination
codeAY
BS
GU HO JE MS RW
CB
BC
Sold Locomotion 4 5 3 4 2 1 4 4 3 Low yield 11 1
29 15 1
412 10 1
415
Reproduction 22 21
18 16 14
23 22 15
16
Mastitis 10 10
11 12 13
13 13 17
16
Other 35 29
35 33 32
36 29 28
29
Died 19 23
24 21 25
16 21 22
21
*Lactations completed between 1-1-07 and 12-31-08
NormanNDHIA Board – 2009 (18) NormanNDHIA Board – 2009 (18)
AM-PM factors
NormanNDHIA Board – 2009 (19)
Cooperative research
Purdue University (Mike Schutz)
Objectives Derive factors to estimate daily
yields from 1 record for 2X milking and 1 or 2 records for 3X milking
Compare factors derived by several methods for their accuracy in predicting true daily yield or somatic cell score (SCS)
AM-PM factors
NormanNDHIA Board – 2009 (20)
Progress to date
Adjustment factors developed for Holstein and Jersey milk yield from 2X and 3X milkings
Preliminary Holstein and Jersey 2X AM-PM factors developed for fat, protein, and SCS
AM-PM factors
NormanNDHIA Board – 2009 (21)
Plans
Verification of 2X AM-PM factors for fat and protein
Development and verification of 3X factors for fat and protein
Determination of whether effect of milking interval on somatic cell count is consistent enough to allow adjustment
All breeds combined for final estimation of adjustment factors
AM-PM factors
NormanNDHIA Board – 2009 (22) NormanNDHIA Board – 2009 (22)
Genetic resistance to
Johne’s disease
NormanNDHIA Board – 2009 (23)
Cooperative studies
Characteristics of milk ELISA scores and factors affecting scores Antel BioSystems (Byrem, Norman)
Estimation of genetic parameters and transmitting ability for milk ELISA scores University of Minnesota (Attala ... Cole)
Johne’s disease
NormanNDHIA Board – 2009 (24)
Milk ELISA characteristics
Average score of 0.04 (±0.18) for 196,412 tests from 696 herds in 16 States from 2002 through 2008 3.2 and 6.1% positives based oncutoffs of 0.40 and 0.10
Same average and SD for 42,778 scores from 25 more comprehensively tested herds in Michigan and Wisconsin 3.0 and 5.6% positives
Johne’s disease
NormanNDHIA Board – 2009 (25)
Milk ELISA (cont.)
Cows with multiple tests within parity (10%) 95% negative for last test if 1st test negative
52% positive for last test if 1st test positive
Cows with multiple tests across parities (27%) 91% negative for last test if 1st test negative
51% positive for last test if 1st test positive
Johne’s disease
NormanNDHIA Board – 2009 (26)
Milk ELISA (cont.) Unusually high percentage (44%) of
untested cows removed from herd by end of current lactation likely indicates selection of which cows to test for Johne’s
Tested cows removed from herd 15% of positive cows 12% of negative cows
Further analysis needed to optimize usefulness of DHI records in evaluation of milk testing for Johne's
Johne’s disease
NormanNDHIA Board – 2009 (27)
Factors affecting scores Cow distribution
by parity
Score distribution by days from calving to test
Birth and test seasons (four 3-mo seasons starting in January) normally distributed
Score distribution by year
Parity 1 2 3 ≥4Cows (%) 45 26 15 14
Test stage (d)
1–60
61–120
121–180
181–240
241–300 301–360
≥361
Scores (%) 12 9 8 11 23 18 20
Year2002 2003 2004 2005 2006 2007
2008*
Scores (%) 4 8 12 14 20 25 16
*partial year
Johne’s disease
NormanNDHIA Board – 2009 (28)
Score factors (cont.)
Scores generally increased with year, parity, and test stage
Birth and test seasons nonsignificant
Low heritability (4%)
Moderate repeatability (26%)
Johne’s disease
NormanNDHIA Board – 2009 (29)
Correlations
185 Holstein AI sires with ≥50 daughters
PTA correlation with breeding value for ELISA score Milk (0.08) Fat (–0.06) Protein (0.03)
Selection based on SCS, productive life, DPR, and net merit could improve resistance to Johne’s
SCS (-0.01) Productive life (–
0.19) DPR (–0.15) Net merit (–0.16)
Johne’s disease