genetic architecture of methane emissions from dairy cows marcin...pszczola et al. jas, 2017 which...
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Poznań University of Life Sciences
Genetic architecture of methane emissions from dairy cows
Marcin Pszczoła, Sebastian Mucha, Tomasz Strabel, Ewa Selll-Kubiak
FACULTY OF VETERINARY MEDICINE AND ANIMAL SCIENCESDepartment of Genetics
and Animal Breeding
GRANT NO: OPUS 2013/09/B/NZ9/03179
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CH4
= Greenhouse
gas
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CH4 = 2% –
12% energy loses
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Does genetic variance in CH4
exist?
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27% of variation in daily CH4
emission is heritable
Pszczola et al. JAS, 2017
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Which genes control CH4
emission?
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CH4
Eructation(~90% )
Breath(~1-2% )
Gas
(~9-8% )
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Measuring scheme
Probe
Feedingbin
Automated milking system
Milking device
FTIR GASMET equipment
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Collected CH4
dataFarm 1 Farm 2
227 54
/ day 24,336 1,535
2014-NOV 2016-FEB2016-JUN 2016-SEP
2016-FEB 2016-MAR
39,680 39,680
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Daily CH4
emission
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GWAS
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MethodBayesian Variable Selection
(BayZ)
Assumptions:
),0(),0(
~ 2
2
1
0
g
g
NN
σσ
β1
0
:yprobabilitwith :yprobabilitwith ππ
1π = 0.001
500k MCMC iterations for posterior means
15k BURN-IN
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ModelFixedLactation (1 or 2+)General lactation curve (3rd
ord. Leg. pol.)Year-week of the measurement
(accounting
for Farm)
RandomAnimal (2nd
ord. Leg. pol.)Permanent environment (2nd
ord. Leg. pol.)Error
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Identified
SNP
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50 SNP with BF>10
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3
SNP with BF>30
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Variance explained
TOTAL0.154%
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Variance explained
TOTAL0.154%
10>BF<300.122%
BF>300.032%
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Previously reported QTL
*cow qtlDB (www.animalgenome.org)
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Previously reported QTL
milk production & composition
body size
*cow qtlDB (www.animalgenome.org)
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Previously reported QTL
health status
feed efficiency
milk production & composition
body size
*cow qtlDB (www.animalgenome.org)
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*BIOMART (Ensembl Bos Taurus UMD 3.1)
5 candidate genes found
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*BIOMART (Ensembl Bos Taurus UMD 3.1)
NTHL1, TSC2,
PKD1BTA 25
PPP1R16BBTA 13
CYP51A1BTA 4
5 candidate genes found
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GO TERMSmetabolism
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GO TERMSmetabolism
lipids steroidsnitrogen lysosome
(Energy)
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GO TERMSmetabolism
lipids steroidsnitrogen lysosome
(Energy) protein synthesis & gradation
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GO TERMSmetabolism
lipids steroidsnitrogen lysosome
(Energy) protein synthesis & gradation
blood vessel endothelial cells
regulation
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GO TERMSmetabolism
lipids steroidsnitrogen lysosome
(Energy)
development
protein synthesis & gradation
blood vessel endothelial cells regulation
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GO TERMSmetabolism
lipids steroids
endothelial barrier
nitrogen lysosome(Energy)
development
protein synthesis & gradation
blood vessels
blood vessel endothelial cells
regulation
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GO TERMSmetabolism
lipids steroids
endothelial barrier
nitrogen lysosome(Energy)
development
protein synthesis & gradation
blood vessels
digestive tract
blood vessel endothelial cells
regulation
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GO TERMSmetabolism
lipids steroids
endothelial barrier
nitrogen lysosome(Energy)
development
protein synthesis & gradation
blood vessels
digestive tract
blood vessel endothelial cells
regulation
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Conclusions
small proportion of the genetic variance explained
QTL in genomic regions for traits related to CH4
Candidate genes possibliy relevant to CH4 emission
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Poznań University of Life SciencesFACULTY OF VETERINARY MEDICINE
AND ANIMAL SCIENCESDepartment of Genetics
and Animal Breeding
CH4
emission has complex
genetic architecture