qtl mapping in magic populations with r/qtl2 · 2019. 9. 25. · 8 magic.7 15.33 20.92 0.71 39 4...
TRANSCRIPT
QTL mappingin MAGIC populations
with R/qtl2
Karl Broman
Biostatistics & Medical Informatics, UW–Madison
kbroman.orggithub.com/kbroman
@kwbromanSlides: bit.ly/MAGIC19
19 years of R/qtl
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Year
Line
s of
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2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019
idea svn git
R
C
doc
2
R/qtl cross types
▶ backcross, doubled haploids, haploid▶ intercross▶ 2-way RIL by selfing or sibling mating▶ phase-known 4-way cross
3
4
R/qtl2 cross types
▶ backcross, doubled haploids, haploid▶ intercross▶ 2-, 4-, 8-, 16-way RIL by selfing▶ 2-, 4-, 8-way RIL by sibling mating▶ 2-, 3-, 8-way advanced intercross▶ 6- and 19-way MAGIC▶ Diversity Outbred (DO) mice▶ F1 of DO × inbred▶ general RIL or AIL
5
Data files
18.173.3366.670.7121.3718.33MAGIC.1616
41.96.33490.7321.7115MAGIC.1515
48.5649.780.7221.1418.67MAGIC.1414
49.354.6752.330.6719.0521.33MAGIC.1213
36.255.6741.560.6620.5814MAGIC.1112
48.5356.330.9130.4630MAGIC.1011
42.45.3375.780.6318.8616.33MAGIC.910
43.237.3350.560.7924.214.33MAGIC.89
37.354390.7120.9215.33MAGIC.78
NA4.33520.7121.5325MAGIC.67
42.255.6738.330.8225.3618.67MAGIC.56
NA6.3354.330.7422.4518.67MAGIC.45
504.67570.6821.0323MAGIC.34
42.334.3349.110.7522.7122MAGIC.23
NA10.545.110.6417.1515.33MAGIC.12
heightbranchesttl_seedspfruitseed_areaseed_weightbolting_daysid1
GFEDCBA
6
Data files
18.173.3366.670.7121.3718.33MAGIC.1616
41.96.33490.7321.7115MAGIC.1515
48.5649.780.7221.1418.67MAGIC.1414
49.354.6752.330.6719.0521.33MAGIC.1213
36.255.6741.560.6620.5814MAGIC.1112
48.5356.330.9130.4630MAGIC.1011
42.45.3375.780.6318.8616.33MAGIC.910
43.237.3350.560.7924.214.33MAGIC.89
37.354390.7120.9215.33MAGIC.78
NA4.33520.7121.5325MAGIC.67
42.255.6738.330.8225.3618.67MAGIC.56
NA6.3354.330.7422.4518.67MAGIC.45
504.67570.6821.0323MAGIC.34
42.334.3349.110.7522.7122MAGIC.23
NA10.545.110.6417.1515.33MAGIC.12
heightbranchesttl_seedspfruitseed_areaseed_weightbolting_daysid1
GFEDCBA
ABAAAACRY2_42916
AAAAAACRY2_102115
BBABBAMN1_104242714
AAAAAABKN11813
AAAAAAMN1_59276012
AAAABAMN1_59286311
AAAAAAMN1_49420510
AAA−AAMN1_4448209
ABAAAAMN1_3951078
AAAABAMN1_3408107
ABBABAMN1_1977876
ABAABAMASC037715
ABBAAAMN1_1129074
ABBAAAMN1_297163
ABBAAAMN1_292912
MAGIC.103MAGIC.102MAGIC.101MAGIC.100MAGIC.10MAGIC.1marker1
GFEDCBA
6
Data files
18.173.3366.670.7121.3718.33MAGIC.1616
41.96.33490.7321.7115MAGIC.1515
48.5649.780.7221.1418.67MAGIC.1414
49.354.6752.330.6719.0521.33MAGIC.1213
36.255.6741.560.6620.5814MAGIC.1112
48.5356.330.9130.4630MAGIC.1011
42.45.3375.780.6318.8616.33MAGIC.910
43.237.3350.560.7924.214.33MAGIC.89
37.354390.7120.9215.33MAGIC.78
NA4.33520.7121.5325MAGIC.67
42.255.6738.330.8225.3618.67MAGIC.56
NA6.3354.330.7422.4518.67MAGIC.45
504.67570.6821.0323MAGIC.34
42.334.3349.110.7522.7122MAGIC.23
NA10.545.110.6417.1515.33MAGIC.12
heightbranchesttl_seedspfruitseed_areaseed_weightbolting_daysid1
GFEDCBA
ABAAAACRY2_42916
AAAAAACRY2_102115
BBABBAMN1_104242714
AAAAAABKN11813
AAAAAAMN1_59276012
AAAABAMN1_59286311
AAAAAAMN1_49420510
AAA−AAMN1_4448209
ABAAAAMN1_3951078
AAAABAMN1_3408107
ABBABAMN1_1977876
ABAABAMASC037715
ABBAAAMN1_1129074
ABBAAAMN1_297163
ABBAAAMN1_292912
MAGIC.103MAGIC.102MAGIC.101MAGIC.100MAGIC.10MAGIC.1marker1
GFEDCBA
AAAA−BAAAAAAAAAABBAMASC0742422
BABAAAAAABAAABAAABAAXR1_38121
AAB−AAAAAAAABAAAAAAMN1_139946620
ABBAAAAAAAAABAAAAAAMN1_129606819
AABAAAABBBABBAAAAAAMASC0360918
AAABAABAAAAAAAAABAAMASC0701417
AABAAAAAABABBBAAAAACRY2_42916
AAAAAAAAAAAAAABAAAACRY2_102115
ABABAABAAABABBABABAMN1_104242714
AAAAAAAAAAAAAAAAAABBKN11813
AAAAAAAAAAAAAABAAABMN1_59276012
AABABAAAAAABAAABABAMN1_59286311
ABAAAAAAAAAAAABAAABMN1_49420510
ABBABAAAAAAAAABBAABMN1_4448209
AAAAAAAAAAAABAAAAAAMN1_3951078
ABBAAAAAAAAAABABABBMN1_3408107
BBAAABAAAAAABBAAABBMN1_1977876
AAAAAAAAAAAABABAABAMASC037715
AAAABBABBAABBBBAAABMN1_1129074
AAAAABABBAAABAABAABMN1_297163
AAAAABABBAAABAABAABMN1_292912
ZuWuWsWilTsuSfRschPoOyNoMtLerKnHiEdiCtColCanBurmarker1
TSRQPONMLKJIHGFEDCBA
6
Data files
18.173.3366.670.7121.3718.33MAGIC.1616
41.96.33490.7321.7115MAGIC.1515
48.5649.780.7221.1418.67MAGIC.1414
49.354.6752.330.6719.0521.33MAGIC.1213
36.255.6741.560.6620.5814MAGIC.1112
48.5356.330.9130.4630MAGIC.1011
42.45.3375.780.6318.8616.33MAGIC.910
43.237.3350.560.7924.214.33MAGIC.89
37.354390.7120.9215.33MAGIC.78
NA4.33520.7121.5325MAGIC.67
42.255.6738.330.8225.3618.67MAGIC.56
NA6.3354.330.7422.4518.67MAGIC.45
504.67570.6821.0323MAGIC.34
42.334.3349.110.7522.7122MAGIC.23
NA10.545.110.6417.1515.33MAGIC.12
heightbranchesttl_seedspfruitseed_areaseed_weightbolting_daysid1
GFEDCBA
ABAAAACRY2_42916
AAAAAACRY2_102115
BBABBAMN1_104242714
AAAAAABKN11813
AAAAAAMN1_59276012
AAAABAMN1_59286311
AAAAAAMN1_49420510
AAA−AAMN1_4448209
ABAAAAMN1_3951078
AAAABAMN1_3408107
ABBABAMN1_1977876
ABAABAMASC037715
ABBAAAMN1_1129074
ABBAAAMN1_297163
ABBAAAMN1_292912
MAGIC.103MAGIC.102MAGIC.101MAGIC.100MAGIC.10MAGIC.1marker1
GFEDCBA
AAAA−BAAAAAAAAAABBAMASC0742422
BABAAAAAABAAABAAABAAXR1_38121
AAB−AAAAAAAABAAAAAAMN1_139946620
ABBAAAAAAAAABAAAAAAMN1_129606819
AABAAAABBBABBAAAAAAMASC0360918
AAABAABAAAAAAAAABAAMASC0701417
AABAAAAAABABBBAAAAACRY2_42916
AAAAAAAAAAAAAABAAAACRY2_102115
ABABAABAAABABBABABAMN1_104242714
AAAAAAAAAAAAAAAAAABBKN11813
AAAAAAAAAAAAAABAAABMN1_59276012
AABABAAAAAABAAABABAMN1_59286311
ABAAAAAAAAAAAABAAABMN1_49420510
ABBABAAAAAAAAABBAABMN1_4448209
AAAAAAAAAAAABAAAAAAMN1_3951078
ABBAAAAAAAAAABABABBMN1_3408107
BBAAABAAAAAABBAAABBMN1_1977876
AAAAAAAAAAAABABAABAMASC037715
AAAABBABBAABBBBAAABMN1_1129074
AAAAABABBAAABAABAABMN1_297163
AAAAABABBAAABAABAABMN1_292912
ZuWuWsWilTsuSfRschPoOyNoMtLerKnHiEdiCtColCanBurmarker1
TSRQPONMLKJIHGFEDCBA
1.3994671MN1_139946620
1.2960691MN1_129606819
1.226551MASC0360918
1.1893741MASC0701417
1.1884331CRY2_42916
1.1878411CRY2_102115
1.0424281MN1_104242714
0.7615841BKN11813
0.5929841MN1_59276012
0.5928671MN1_59286311
0.4942051MN1_49420510
0.4447641MN1_4448209
0.3951071MN1_3951078
0.340811MN1_3408107
0.1977871MN1_1977876
0.1746051MASC037715
0.1129071MN1_1129074
0.0297571MN1_297163
0.0292911MN1_292912
poschrmarker1
CBA
6
Control file (json or yaml)
{"description": "Arabidopsis MAGIC data, Gnan et al (2014)","crosstype": "magic19","sep": ",","na.strings": ["-", "NA"],"comment.char": "#","geno": "arabmagic_geno.csv","founder_geno": "arabmagic_foundergeno.csv","gmap": "arabmagic_pmap_tair9.csv","pmap": "arabmagic_pmap_tair9.csv","pheno": "arabmagic_pheno.csv","genotypes":
"A": 1"H": 2"B": 3
},"geno_transposed": true,"founder_geno_transposed": true
}
7
Control file (json or yaml)
{"description": "Arabidopsis MAGIC data, Gnan et al (2014)","crosstype": "magic19","sep": ",","na.strings": ["-", "NA"],"comment.char": "#","geno": "arabmagic_geno.csv","founder_geno": "arabmagic_foundergeno.csv","gmap": "arabmagic_pmap_tair9.csv","pmap": "arabmagic_pmap_tair9.csv","pheno": "arabmagic_pheno.csv","genotypes":
"A": 1"H": 2"B": 3
},"geno_transposed": true,"founder_geno_transposed": true
}
7
Control file (json or yaml)
{"description": "Arabidopsis MAGIC data, Gnan et al (2014)","crosstype": "magic19","sep": ",","na.strings": ["-", "NA"],"comment.char": "#","geno": "arabmagic_geno.csv","founder_geno": "arabmagic_foundergeno.csv","gmap": "arabmagic_pmap_tair9.csv","pmap": "arabmagic_pmap_tair9.csv","pheno": "arabmagic_pheno.csv","genotypes":
"A": 1"H": 2"B": 3
},"geno_transposed": true,"founder_geno_transposed": true
}
7
Control file (json or yaml)
{"description": "Arabidopsis MAGIC data, Gnan et al (2014)","crosstype": "magic19","sep": ",","na.strings": ["-", "NA"],"comment.char": "#","geno": "arabmagic_geno.csv","founder_geno": "arabmagic_foundergeno.csv","gmap": "arabmagic_pmap_tair9.csv","pmap": "arabmagic_pmap_tair9.csv","pheno": "arabmagic_pheno.csv","genotypes":
"A": 1"H": 2"B": 3
},"geno_transposed": true,"founder_geno_transposed": true
}
7
Control file (json or yaml)
{"description": "Arabidopsis MAGIC data, Gnan et al (2014)","crosstype": "magic19","sep": ",","na.strings": ["-", "NA"],"comment.char": "#","geno": "arabmagic_geno.csv","founder_geno": "arabmagic_foundergeno.csv","gmap": "arabmagic_pmap_tair9.csv","pmap": "arabmagic_pmap_tair9.csv","pheno": "arabmagic_pheno.csv","genotypes":
"A": 1"H": 2"B": 3
},"geno_transposed": true,"founder_geno_transposed": true
}
7
Reading data into R
library(qtl2)arab <- read_cross2("arab_magic.json")
19-way Arabidopsis MAGICKover et al. (2009) PLoS GenetGnan et al. (2014) Geneticsgithub.com/rqtl/qtl2data
8
Reading data into R
library(qtl2)arab <- read_cross2("arab_magic.json")
19-way Arabidopsis MAGICKover et al. (2009) PLoS GenetGnan et al. (2014) Geneticsgithub.com/rqtl/qtl2data
8
Data diagnostics
See Broman et al. (2019) Cleaning genotype data fromSee Diversity Outbred mice. G3 9:1571–1579
See See doi: 10.1534/g3.119.400165
9
Genotype reconstruction
Chr 3 position (Mbp)
2 3 4 5 6
● ●●●● ● ●● ● ● ● ● ●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ● ● ● ●●● ●● ● ● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●● ●●●● ● ●● ● ●● ● ● ●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●Zu
WuWsWil
TsuSf
RschPoOyNoMt
LerKnHi
EdiCt
ColCanBur
● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●MAGIC.244
10
Genotype reconstruction
Chr 3 position (Mbp)
2 3 4 5 6
● ●●●● ● ●● ● ● ● ● ●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ● ● ● ●●● ●● ● ● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●● ●●●● ● ●● ● ●● ● ● ●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●Zu
WuWsWil
TsuSf
RschPoOyNoMt
LerKnHi
EdiCt
ColCanBur
● ●●●● ● ●● ● ●● ● ● ●●●● ● ●●●●●●● ● ●● ●● ● ● ● ● ● ●● ● ● ●●MAGIC.244
Edi Wu
10
Genotype reconstruction
gmap <- insert_pseudomarkers(arab$gmap , step=0.2, stepwidth="max")pmap <- interp_map(gmap, arab$gmap , arab$pmap)
pr <- calc_genoprob(arab, gmap, error_prob=0.002, cores=24)
11
Genome scan
1 3 52 40
10
20
30
40
Chromosome
LOD
sco
refruit length
12
Genome scan
1 3 52 40
10
20
30
40
Chromosome
LOD
sco
refruit lengthhaley−knott
lmm
12
Genome scan
1 3 52 40
10
20
30
40
Chromosome
LOD
sco
refruit lengthhaley−knott
lmmlmm w/loco
12
Genome scan
1 3 52 40
10
20
30
40
Chromosome
LOD
sco
reseed weighthaley−knott
lmmlmm w/loco
13
Genome scan
out_hk <- scan1(pr, arab$pheno , cores=24)
operm_hk <- scan1perm(pr, arab$pheno , n_perm=1000, cores=24)
k <- calc_kinship(pr, cores=24)out_lmm <- scan1(pr, arab$pheno , k, cores=24)
k_loco <- calc_kinship(pr, "loco", cores=24)out_loco <- scan1(pr, arab$pheno , k_loco, cores=24)
14
SNP association scan
1 3 52 40
10
20
30
Chromosome
LOD
sco
re
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fruit length
15
SNP association scan
1 3 52 40
10
20
30
Chromosome
LOD
sco
re
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fruit length
15
SNP association scan
1 3 52 40
5
10
15
20
25
Chromosome
−lo
g 10
p−
valu
e
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fruit length
15
SNP association scan
1 3 52 40
10
20
30
Chromosome
LOD
sco
re
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seed weight
16
SNP association scan
1 3 52 40
5
10
15
Chromosome
−lo
g 10
p−
valu
e
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seed weight
16
SNP association scan
snp_pr <- genoprob_to_snpprob(pr, arab)
out_snps <- scan1(snp_pr, arab$fruit , cores=24)
17
QTL effects
−3
−2
−1
0
1
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Fruit length (chr 2 @ 11.4 Mbp)Q
TL
effe
ct
Bur
Can Col Ct
Edi H
i
Kn
Ler
Mt
No
Oy
Po
Rsc
h Sf
Tsu W
il
Ws
Wu
Zu
18
QTL effects
−3
−2
−1
0
1
●
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Fruit length (chr 2 @ 11.4 Mbp)Q
TL
effe
ct
Bur
Can Col Ct
Edi H
i
Kn
Ler
Mt
No
Oy
Po
Rsc
h Sf
Tsu W
il
Ws
Wu
Zu
●
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least squaresBLUP
18
QTL effects
−4
−2
0
2
4
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Seed weight (chr 1 @ 21.4 Mbp)Q
TL
effe
ct
Bur
Can Col Ct
Edi H
i
Kn
Ler
Mt
No
Oy
Po
Rsc
h Sf
Tsu W
il
Ws
Wu
Zu
●
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least squaresBLUP
19
QTL effects
fl_peak <- max(out_hk, pmap, lodcolumn="fruit_length")fl_pr <- pull_genoprobpos(pr, pmap, fl_peak$chr , fl_peak$pos)
fl_fit1 <- fit1(fl_pr, arab$pheno[,"fruit_length"])fl_blup <- fit1(fl_pr, arab$pheno[,"fruit_length"], blup=TRUE)
20
Goals
▶ Genotype reconstructions from external software▶ General models for RIL and AIL▶ Sequencing-based genotype data▶ Multiple-QTL models▶ QTL × environment interactions▶ Interactive data visualization
21
Slides: bit.ly/MAGIC19
kbroman.org
kbroman.org/qtl2
github.com/kbroman
@kwbroman
22