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
CH4
= Greenhouse
gas
CH4 = 2% –
12% energy loses
Does genetic variance in CH4
exist?
27% of variation in daily CH4
emission is heritable
Pszczola et al. JAS, 2017
Which genes control CH4
emission?
CH4
Eructation(~90% )
Breath(~1-2% )
Gas
(~9-8% )
Measuring scheme
Probe
Feedingbin
Automated milking system
Milking device
FTIR GASMET equipment
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
Daily CH4
emission
GWAS
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
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
Identified
SNP
50 SNP with BF>10
3
SNP with BF>30
Variance explained
TOTAL0.154%
Variance explained
TOTAL0.154%
10>BF<300.122%
BF>300.032%
Previously reported QTL
*cow qtlDB (www.animalgenome.org)
Previously reported QTL
milk production & composition
body size
*cow qtlDB (www.animalgenome.org)
Previously reported QTL
health status
feed efficiency
milk production & composition
body size
*cow qtlDB (www.animalgenome.org)
*BIOMART (Ensembl Bos Taurus UMD 3.1)
5 candidate genes found
*BIOMART (Ensembl Bos Taurus UMD 3.1)
NTHL1, TSC2,
PKD1BTA 25
PPP1R16BBTA 13
CYP51A1BTA 4
5 candidate genes found
GO TERMSmetabolism
GO TERMSmetabolism
lipids steroidsnitrogen lysosome
(Energy)
GO TERMSmetabolism
lipids steroidsnitrogen lysosome
(Energy) protein synthesis & gradation
GO TERMSmetabolism
lipids steroidsnitrogen lysosome
(Energy) protein synthesis & gradation
blood vessel endothelial cells
regulation
GO TERMSmetabolism
lipids steroidsnitrogen lysosome
(Energy)
development
protein synthesis & gradation
blood vessel endothelial cells regulation
GO TERMSmetabolism
lipids steroids
endothelial barrier
nitrogen lysosome(Energy)
development
protein synthesis & gradation
blood vessels
blood vessel endothelial cells
regulation
GO TERMSmetabolism
lipids steroids
endothelial barrier
nitrogen lysosome(Energy)
development
protein synthesis & gradation
blood vessels
digestive tract
blood vessel endothelial cells
regulation
GO TERMSmetabolism
lipids steroids
endothelial barrier
nitrogen lysosome(Energy)
development
protein synthesis & gradation
blood vessels
digestive tract
blood vessel endothelial cells
regulation
Conclusions
small proportion of the genetic variance explained
QTL in genomic regions for traits related to CH4
Candidate genes possibliy relevant to CH4 emission
Poznań University of Life SciencesFACULTY OF VETERINARY MEDICINE
AND ANIMAL SCIENCESDepartment of Genetics
and Animal Breeding
CH4
emission has complex
genetic architecture