HO genotypes from Switzerland Genomic evaluation of Guernseys Mutations in HCD and in BH2 HCR edits and adjustments Breed base representation BBR for crossbreds April changes Breed check markers ID: 503965
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Slide1
Current and Future Evaluation ChangesSlide2
HO genotypes from
SwitzerlandGenomic evaluation of GuernseysMutations in HCD and in BH2HCR edits and adjustmentsBreed base representation (BBR) for crossbreds
April changesSlide3
Breed check markers
Breed determining SNP introduced in 2010200 SNPs monomorphic in 1 breed and have fewer than 30% of animals homozygous for that allele in another breedInitially used to identify misidentified samplesLater, used to exclude crossbreds from genomic evaluation because purebred equations did not apply accuratelyCurrently, about
10,000
crossbreds excluded with cost of genotyping about
$400,000Slide4
Predicting breed as a “trait”
Reference population is purebred, proven bullsVariable to predict (Y) is breed of animalHolstein bulls are coded 100% HO, 0% JE, and 0% BS, for example
Animal Breed
Holstein percent
Jersey percent
Brown Swiss %
HO
100
0
0
JE
0
100
0
BS
0
0
100Slide5
Results from 2010 (Katie Olson)
Breed
/SNP set
43 K
3 K
600
Holstein
(N = 14,794)
100.0 ± 0.8100.4 ± 3.1100.2 ± 1.9Jersey(N = 919)99.6 ± 2.897.8± 6.398.9 ± 3.6Brown Swiss(N = 96)99.4 ± 2.198.9 ± 3.699.2 ± 5.1
Means and standard deviations
to predict
breed of the validation
(
young animals) data setSlide6
GPTA for crossbreds
(proposed)Compute traditional PTAs on all-breed base Calculate SNP effects using each pure breed’s genotypes, but on all-breed baseApply each breed’s SNP effects
(AY, BS, GU, HO, JE)
to the crossbred genotypes
Combine individual breed GPTAs weighted by genomic breed composition
Convert GPTAs to
within-breed baseSlide7
Reasons for disposal have been reported and stored in DHI records since
1970About 20% of cows die instead of being sold across all lactationsDeath loss per lactation average 7%, higher in later, lower in earlier lactationCow mortality / livabilitySlide8
PL measures cow’s ability to avoid dying
or being culledLIV measures cow’s ability to stay aliveLIV is a subset of PLCost = 1500 pounds * $.75 / pound + $50 disposal = $1200 / deathProductive Life (PL) vs. Livability (LIV)Slide9
Definition
:Reverse of mortality:0 = died this lactation100 = lived this lactationMultiply by average lactation/cow (2.8) so to put on lifetime scale LIV modelSlide10
Data
:92 million records on 32 million cowsMethodology:Same model and software as other major traitsSimilar edits as other traitsMulti-trait with overall culling per lactation, but lactation cull rate will not be reported
Heritability of
1.3
(Miller et al., 2008),
genetic
correlation with lactation PL of
.50LIV model (cont.)Slide11
Breed
Mean
Std Dev
Num. bulls
AY
0.5
2.0
246
BS
0.12.0692GU-0.33.5182HO-1.12.245,840JE-0.21.73,893MS0.71.964Means and Std Dev. of PTALIV (bulls born 1990 or later, minimum 50 daus, .50 rel for PTALIV) Slide12
Trait
HOJE
Milk
.09
-.08
Fat
.21
.01
Protein
.16-.01Prod. Life.70.54SCS-.28-.07Dau. Preg. Rate.40.54Cow Conc. Rate.40.33Heifer Conc. Rate.28.32Num. bulls45,8403,893Correlation of PTALIV with other trait PTAs (bulls born 1990 or later, minimum 50 daus, .50 rel for PTALIV) Slide13
LIV genetic trends 1970-2013 Slide14
Genetic trend in PTALIV - HOSlide15
Year
TraitsAdded
Data
Corr
Gain
1976
3
Protein
DHIA
.964%19945Productive life, SCSDHIA.8419%200018Size, udder, feet / legsBreeds.946%200321Pregnancy rate, calving ease (sire, dtr)DHIA / NAAB.982%200623Stillbirth (sire, dtr)NAAB.982%201425Heifer, cow conceptionDHIA.973%2016Cow deathDHIA> .99< 1%2016316 more health traitsZoetis.92 ??21% ??Added value from more traitsSlide16
Trait
Cases (%) / lactationHeritability(obs
/
thr
)
3
Cost ($)
/ case
Death
171.3 / 4.81,200Mastitis2233.7 / 6.9200Lameness203.7 / 6.3320Metritis102.9 / 5.9330Retained Placenta52.6 / 7.3250Displaced Abomasum21.5 / 8.1250Ketosis52.1 / 5.9200Health trait cases and costs?1Death data from USDA research2Other trait cases and cost from Zoetis data and advertisement3Observed scale and equivalent underlying (threshold model) heritabilitySlide17
Correlation
CANDFS
FRA
NLD
USA SCS, foreign MAST
.87
.87
.
87
.88USA SCS, foreign SCS.94.88.90.88Correlations of SCS and mastitisGenetic correlations estimated by Interbull, Apr 2016Genetic correlation (SCS,MAST) estimated by Zoetis = .45Slide18
Genotyped mates and ET progenySlide19
Single-step genomic equations
OK for JE, still not for HOTraits already recordedAge at first calf, gestation length, persistency, heat toleranceTraits requiring new dataFeed efficiency, health, etc.Sequence mutations plus markersFuture evaluation optionsSlide20
History of SNP Chips