Supplementary Figure 1 a b - Nature · mr36 mr 40 mr73323 2 6 mr2 04 mrr5r583 mr2 57 mr41 mr006...
34
1 1 a b c d Intensity, cps Intensity, cps Time, min m/z, Da 8.0e4 4.0e4 Time, min Intensity, cps Intensity, cps m/z, Da m/z, Da 2 Supplementary Figure 1 Saccharopine identification facilitated by 3 GWAS results. 4 (a) Manhattan plot displaying the GWAS result of the content of mr208 5 and the strongest association pointed by arrow in red. (b) The strongest 6 association between SNP sf0233224406 is 22 kb away from OsLKR, the 7 gene encoding saccharopine dehydrogenase, suggesting mr208 could be 8 saccharopine. (c) Mr208 detected with MRM transition 277/84 in rice 9 grain sample and (d) mr208 was confirmed as saccharopine by comparing 10 the RT and fragmentation pattern with the commercial standard. 11 12
Transcript of Supplementary Figure 1 a b - Nature · mr36 mr 40 mr73323 2 6 mr2 04 mrr5r583 mr2 57 mr41 mr006...
1
1
a b
c
d
Inte
nsity
, cps
Inte
nsity
, cps
Time, min m/z, Da
8.0e4
4.0e4
Time, minIn
tens
ity, c
psIn
tens
ity, c
psm/z, Da
m/z, Da 2
Supplementary Figure 1 Saccharopine identification facilitated by 3
GWAS results. 4
(a) Manhattan plot displaying the GWAS result of the content of mr208 5
and the strongest association pointed by arrow in red. (b) The strongest 6
association between SNP sf0233224406 is 22 kb away from OsLKR, the 7
gene encoding saccharopine dehydrogenase, suggesting mr208 could be 8
saccharopine. (c) Mr208 detected with MRM transition 277/84 in rice 9
grain sample and (d) mr208 was confirmed as saccharopine by comparing 10
the RT and fragmentation pattern with the commercial standard. 11
12
2
13
a b
c
465.1033
Inte
nsity
, cps
Inte
nsity
, cps
Time, min m/z, Da
465.1033
d
mass-to charge (m/z)
Inte
nsity
, cp
s
x105
14
Supplementary Figure 2 Delphinidin 3-O-glucoside identification 15
facilitated by GWAS results. 16
(a) Manhattan plot displaying the GWAS result of the content of mr063 17
and the strongest association pointed by arrow in red. (b) The strongest 18
association between SNP sf0605268699 is 45 kb away from OsC1. (c) 19
Mass peak (RT=5.2min) and spectrum of delphinidin 3-O-glucoside in 20
rice grain sample (d) delphinidin 3-O-glucoside was confirmed by high 21
resolution mass MS and MS/MS spectral pattern. 22
23
3
24
CV (%)
0-50 50-75 75-100 100-125 125-150 150-175 175-200 >200
Pe
rcen
tage
(%
)
0.00
.05
.10
.15
.20
.25
.30
25
H2
0.0-0.1 0.1-0.2 0.2-0.3 0.3-0.4 0.4-0.5 0.5-0.6 0.6-0.7 0.7-0.8 0.8-0.9 0.9-1
Num
ber
of m
eta
bolit
e
0
20
40
60
80
100
120
140
26
Supplementary Figure 3 The coefficients of variation (CV) and the 27
broad-sense heritability (H2) results for each metabolite. 28
(a) Distribution of the phenotypic coefficients of variation (CV) of 29
metabolic traits (n = 587). (b) Distribution of broad-sense heritability (H2) 30
of metabolic traits (P < 0.05, two-way ANOVA) detected in the 31
association panel. 32
33
4
34
Num
ofS
igni
fican
tLo
ci
010
2030
4050
60
1 2 3 4 5 6 7 8 9 10 11 12Genome
Leaf
a
b
1020
3040
50
1 2 3 4 5 6 7 8 9 10 11 12Genome
Num
ofS
igni
fican
tLo
ci Grain
060
35
Supplementary Figure 4 Statistics of the number of the significant 36
association for the mGWAS results in rice leaf (a) and rice grain (b). 37
38
39
5
40
41
1 2 3 4 5 6 7 8 9 10 11 12Genome
8
7
8
7
7
7
9
8
12
8 8
18 9
2116 8
11 7
7810
8
1240
52
2132
710 8
7217 119 8
418
4743
109
108921
167 7
137
1312 132143
6352
6 13 20
color key (-logP)
ApiChr
Lut 6-C-Gdi-C,C-P-api
Nar 7-O-Go-meApi C-H
Peo 3-O-HTri 4'-gg-O-H
LPC (18:1)LPC (16:2)Del 3-O-GApi 7-O-R
C-P-api O-RTri O-R-mH
AlaValTryIle
LPC (12:1)LA
ProTyrArgHisLysPhe0.1
0.5
1.0co
lor
k ey
(CV
)7
7 7
7
7 7
8
7 7
13 7
7 15
7
9
10 11
10 7
7 10
10
12 15
7
42
Supplementary Figure 5 Comparing the association for some same 43
metabolites between rice grains (up) and rice leaf (down). 44
Pro, proline; Tyr, tyrosine; Arg, arginine; His, histidine; Lys, lysine; Phe, 45
phenylalanine; Ala, alanine; Val, valine; Try, tryptamine; Ile, isoleucine; 46
LPC (12:1), lysophosphatidyl choline (12:1); LA, linoleic acid; 47
LPC(18:1), lysophosphatidyl choline(18:1); LPC(16:2), lysophosphatidyl 48
choline(16:2); Api 7-O-G, apigenin 7-O-glucoside; Api 7-O-R, apigenin 49
7-O-rutinoside; C-P-api O-R, C-pentoside-apigenin O-rutinoside; Tri 50
O-R-mh, tricin O-rutinoside-malonylhexoside; Lut 6-C-G, luteolin 51
6-C-glucoside; di-C,C-P-api, di-C,C-pentosyl-apigenin; Nar 7-O-G, 52
naringenin 7-O-glucoside; o-meApi C-P, O-methylapigenin C-pentoside; 53
Peo 3-O-H, peonidin 3-O-hexoside; Tri 4’-gg-O-H, Tricin 54
4'-O-(β-guaiacylglyceryl) ether O-hexoside; Api, apigenin; Chr, 55
chrysoeriol. 56
57
6
m/z, Da
150 250 350 450
Inte
nsity
,cps
0
4e+6
8e+6
1e+7
2e+7
179.2
267.2
297.1
326.9351.0
411.2381.1
447.2
O
OOH
O
O H
O
OH
OH
OH
OH
CH3
O-methylapigenin 6-C-hexoside
Chromosome
0
10
20
30
40
-Log
10(P
)
a
b
00.20.40.60.81
r2
c
d
e
*
RT, min
6 8 10 12
Inte
nsity
,cps
5.0e+5
1.0e+6
1.5e+6
6 8 10 12
Inte
nsity
,cps
5.0e+5
1.0e+6
1.5e+6
2.0e+6
fO-methylapigenin 6-C-glucoside
apigenin 6-C-glucoside (standard)
Os04g11970
Empty vector
RT, min
0
5.0e+4
1.0e+5
1.5e+5
2.0e+5
2.5e+5
Rel
ativ
eco
nten
t
GACA GACACA
n = 146/340p = 4.9 x 10-55
R2 = 77%
O-methylapigenin 6-C-hexoside
8.2
7.9
7.9
58
59
Supplementary Figure 6 Functional annotation of Os04g11970 and the 60
assignment of associated sites. 61
(a) Structure and LC-MS/MS fragmentation of O-methylapigenin 62
6-C-hexoside. Structure and the major fragments of O-methylapigenin 63
6-C-hexoside are shown. (b) Manhattan plot displaying the GWAS result 64
of the content of O-methylapigenin 6-C-hexoside. (c) Gene model of 65
Os04g11970. Filled black box represents coding sequence. The grey 66
7
vertical lines mark the polymorphic sites identified by high-throughput 67
sequencing, and the stars represent the associated sites. (d) A 68
representation of the pair-wise r2 value (a measure of LD) among all 69
polymorphic sites in Os04g11970, where the darkness of the color of each 70
box corresponds to the r2 value according to the legend. (e) Box plot 71
indicate O-methylapigenin 6-C-hexoside content; plotted as a associated 72
site at Chr4. vf0406561691. (f) LC-MS chromatograms of in vitro 73
enzyme assays showing the enzyme activity of recombinant Os04g11970 74
(up). Protein extract from E. coli containing pDEST15 empty vector were 75
used as a negative control (down). 76
77
8
78
cluster 2
cluster 1
cluster 3
cluster 4
cluster 5
cluster 6
a
mr365
59555955mrmmmmrr15
88688886mrr88 mr019 2333333333333333mr2rmrmmmmr23
mr0555mrmmmrr10
111118888888mrmmmrr88
mr591
mr070
6311313131mr6mr6mr636777mmmmmm
mr604
mr009mr771
49349mrr49mr678
mr282
mr531mr852
884484848444r8rmrmmr88
mr587
mr062634334334344mr6mmrrmrmmr63
mr495
mr246mr489
mr717
9419 14411mrr94
77676mrr77
332232333323mrmrmmrr22
4488844844488mr4mmr44
3093mrmrr93
mr158
479977979799799797mrmmrmmrr47
mr42241004110mrm 44mrmmrrr41
000000000000000000mrmmrmmrmrmmr107464646mrmmmmrr74
5202mr5r52
mr189
mr572
mr667
9188818mr9mrmr91
4474477mr4r44
9319mr9r93
mr229mr56284949849mrmmr84
0700700707707mrmmrr10
064640 40664646mr0mmrmmmrr06
mr078
41411441444mrrmmmmr14
mr215
mr373
mr672mr650
mr711mr218
829mrmrmmrmmr82
mr230 0100mr0mmr01
mr629
mr042
7757575755mr7mrrr77
578778788778mr5mrmmr57
474mr4rr4mrmrr47
mr567 7585858mr7mmmrmr75
mr488 98588558585mr9mmmmmrmm88 r989929992mr9r99
99899989898mr9mrmmmrmrr99
mr527 mr075
47070mr4r47
mr0804294294292229mr44mr42
85888
mr628956mr9r95
mr556
388mrr38
30mrr13
mr846mrmrr84
5171717mrr51
mr005
9626mr9r96
mr069
mr551
mr844
747mrmmr74
mr051
777777mr7mrr77
475mr4mr47
27373mr2r27
91919191mrmr19
mr284mr28
957mrr95
mr514r51 mr317r31
474mrmrr14
27676mr2r27
mr068
49mrmmmrmr14
mr480953mrr95
mr529mr838
mr041
mr555
mr839
mr505
mr020
3636mrr13
mr586
mr513r51
mr534
mr695
mr357r35
mr548rr54mr477347mr347r34mr411
mr050
mr319
mr512
mr444
mr421r42
mr074
mr025mr516
616mrmrmr261r26
88418188818mr4m44 r4142323mr4mrmrr42
65858888mrrmrmr658939393mrmmrm mmmmr89
mr835689989889889mrmrmrmrmmmmmmr68
mr077
666696696999mr6mrmmrrr69
646464444564mmrr56
982828282882mrrmrmrmrmrmmmr98
0070707777777077770r7mrmmrrmmmr77
9444449444699rmrmrmmmmmrr69
mr542
446
mr024
7777778979999799999777r8rmrmmrmmmmmmr89
792222222922929929292mrmrmmmmr79
mmmmmmr427mr54mr54m44 r42
mr4123181813111mrmmmmmmmrrmrmr31
mr781
mr620
4545mrr14
mr169mr621
90606mr9r90
mr569mmr56
819191r8rmrmmmmmr81
6116166mrmmmrmrmmmmrmmrr16
mr610
333873377877377737373377373mrmmrr87
64644969644464mr9mrrmmmr96 22212212122122mr2mmmrmmmmmmmmmmmmrmr21
74774777mrmrmrmmmmmr17 691691699191r6mmmmmmmmmmmmrr6959999999999mrmrmrmrmrmmmr59
mr644
8808008080808080mr8r88 559595959mr5mmrmr59
mr815
77773733777377373mrrmrr73909959909mr5mrrrmrrmrmr mmr59683883368868mrmmmr68
mr263mr709
327777mr3mmrrmrmrmmmmmr32 9191999999191919119199199mr9mrmmrrmr91
0868688686mrrrmmmmrmmrr08
20220220202200202022mr2mmrmmmmrmrmr2293233232mr9mmmmmmmr93
33333333333333mrmmmmrmmrr3rr33mr925
111111111rmmrrmr11
mr77317191171117117mr9rrmmmmmmmmmmmrmmrr91
mr609
mr0136363663636336336mrmmrmrrmmr63 mr173
222424244474747444422242442424742424mr7rmrmmmmmmmmmmmmrmr74
29292222222mrmmmmrrmmmmmmmr12
522952522255552252222552522529525rmrmmrmrmrmrmmr9500000000100001rmrrrmrmrmr00 4414112144414214mrmmmmrmrmrmrmr0101010000101010111111r21mr209
1992111mrr21
951mrmr9r95 mr264
mr68577mrmrr17
508000808mrmrrmrrmrr50
mr306
mr865
mr362
mr057
111211111rrmrmmmmr21
417mr4r41 mr055
mr465mrr46
21717mrmrr21
mr389r38
669696666mrmmmmmrmm
444444461411414mrmrmrrmrrmmmm 44
08808060008000808rrrmmrmrmmmrrrmmrrr60
577rrmrmmrrmmmmmmmmmmmrmmmmmmmmmmmr57
mr090
94774777447mrrmmmr94
9779709099mr0mrrmrrmmmrr09
666866666666666666mrmmmrr86
38838838863336363333338mr6rmrmrmrmmmmmmm4141111 r63
92222222222mrmmmmmmr92 00000000800800880808mr28mmrmrr 8802222222222222222222
55535334335533335533r4mrmmmmmmmmmmmrmrmr4333333433333333333333333mrmrmmmmmrmr43
m 04
66666756557565667mrmr75
mr52399999999999999mmrmr99
mr731
399973mr7mmrr73
mr492 242424rmrmrmrm22 r12
188118811111mrrmrmr11 3703370030033mr7mmmmr70
mmmmmmmmmmmmmm
8mrmrmrmmmmmmmr 6r86
mr843
mr584
mr231mr582mr718118m 18r71
mr579
65656696mmr9r96660006000mrmmmmmrmrr66
mr854
mr430269992626999mr2mmmmmr26
0929220mrr09
mr837r83
557mr5r55
757575775mrmmr57mr5535393mrr53
mr983mr98
78000mrmrmr78
m
mr030
42424444242mrmmmmrmrr42mr522
mr028
7444444444mr7mr74
7545554755545445mr7mrmmmmmmmmrr75
3099090090999099mr3rmrmmr30
mr4mr4mr8mmmmrmmmr84mr43862mr031
867786867667mr8mrrr86
75755797755mrmmmmmmmrmr97
mrmrmr
71010010000011010mr7mmmmmrr71
97666977666767666676mrmmrmmmmrmmmrr97mr413
31616mr3r31
mr002
mr810
832mr8mmrmrr83
mr661
mr304mr30
4848mrr84
mr730
mr716
mr518r51
mr221 mr225
56333mr5mrmmmr56 mr981
46060mr4mrmrr46
774mr7mrmmmmr77
778777mr7mr77
mrmrm 25225r32mr353
374mr3mmmr37
mr958
mr806
575557mrmrmmrm8 r15mr403
mr049m 42mr842r84
mr740
mr13445959559595mr4mr45
8333333mr8mrmrmrr83 mr014
mr283rr28
mr32mr 23233r32
659959mrmmr65
mr736
mr800
4414444141mr4mmr44
37577575mrmrmmr37
51919mr2323r51
915159 5mrrmmmmrr91
mr172
69797979mr6mrmmmmrmr69
59659696966966696mrmrmrrmmmrmr59
mr262
mr258
8242422mrmrmrrrmrmr82
42525252525mr4mr42
35959595955mrr35
38448mrmrr38
mr391
mr235
mr122mr248
mr250
929929mrmrmmr9290101110mrmrmrr90
mr268
mr690
mr896
6767766mrmrr16
8535553535mrmmmmr85
3763767767776mrmmm77777 r37
443343444343434443mrrmmmmrmmr4493883833893833838mrmmrmmmmrmrmrrmmr93
mr9084676676677667mrmmmmmmmmrmmmmrr46
560606060060056566mr5mrmrr56
9737339773733733mr9m 9mmmmmrmrmmrmrr97
35005050055350005mrmmmmmmrrmrr3560160160101001160mrmrr60
mr279
mr801
390909090399909000099mr3mmmmmmmmmmr39
68686868686668mrmmrrmrmrrmr68
mr698
933333mrmmrmmmrrmmr93970707970mr9mmmmrmr97
41666661161161mr4rmmrmmm 4rmmr41
mr1266mmm 2mmm 62
75055005557mrmmrr33333333333333r75
9555555595555555555mr9rmmmmmr95
0080880800008mrmmmmmr00
42424224224mrmrmmrmrr14
mr241 mrmmmrmr249458458558mr4mmrmmmmm 58mmr45
mr301851515155185mrrmmmrmmmmr85
92828292828mr9mmmr92
mr738
mr869
03333333333333mrmrmmmrr0r03
943434334434444334434334mrmmmrmrmrmmrmrrr94
82525258252555525mr8mmrmmmmmr82mr175
01666mrmrmmrmrr01
mr034
mr649
910101011010101910100mrmmmmmrrmrmr91
030303333mrmrmrrr1029999999999mr2mrmrr29
mr244mr137
mr804
7299292992922mr7rmrmmmrmmmmmrr72
mr387
mr855mr 55m 55m 555rm 5mmm 555558555m 85m
mr612
mrmrmmmmm
mr052
mr707
82622666226266262262662222268 6mrmrmrmmmmmr82
349494949mrmrmrmrr34290090mr2mmrr29
70000000mrmrr70550505505mrmrmmr55
3959593955595mr3mmrr39
7011701000mrmmmr70
363636363mrmrmrmr36
44000404400mr4mmmrmrmmrmmrmr44
73232732333332mrmrmmmmmmmmmmr73mr266
4343434rr14mr240
mr5mmmr58338583r58
mr257
4mrmrmmrmmrmmmrmrm 1r41mr006
45656565655656565mr4rrmmrmmmm3232323 r45
878878887878877878mr8mmmmmmrmmmr87
mr680r68
mr297
86336363mrr86
mr011
3838mrmrmr13993mrr99
89888889899mrmmmmrr89
mr176
0818818188188mrmmmrmmmmr08
mrmmmmmmmmmr
8505500505055050500mrmrmmrmmmrmrmmmmr85
328832828283228mr3mmmmmm mmmmmr32
8313313133133mr8mmmmmrmmrmmrmmrrmm 8mmrmmmr83 mr494
48484r4r48
961661mr9mmmrmr96
760606060060mrmrmr76
980808800980mrmrm111111 r98
46146616166mr4mrmrmmr46
97474774747974mrmrmrmmr9737mrmrmmmrmrrmmrrmrrm
44r37
482482882828224mr4mrmmrrmmr48
950595mr9mrmmmmmr95
mr817282828288288mrmmrr1209555mrmmrmmmrmr mm8
r09
33737mr3mrr33
093099309mrmrmmrmmmrr09
27272727mrmr1265757mrmmmmmr65
mr677
mr265476676676767676776676766766mrmmmrmmmmmrmr47
56565565565655665655mrmmmmmrmmr 6mmr15
236366333236336mrmmmrmmmr23 57177171775mrmmmmmr5mr570434433mrmrmrmmrmmr049090090090900mrr90
mr206
70000070mrmmrrmmmmrrmmr 022222mrmrmmmmmmmmrr70
mr625r62
9343333mr9mmmmmr93
338mr3r33
mr449r44
437mr4r434646mrmr14
mr4mrmrmmmmr 711r47mr503
624244442mrmmmmmmmr62 788888888888mrmmmrmmrmrmr78
626622mrmrr62397mrmmmmmm mr6mrr6r39
mr50229339299399393mrmrmmmr29
mr946
836366mr8rmr83
878789887879887787798mr9mmrmrmmmmr98
mr045766667666666666666mr7mrmmrmr76
mr533
8757575757587575757575mr8mmmmmmrmmmmm 5r87
mr029
2717mrmmmrmmmrr27
95454555445mrmmr95
828228822mr8mrm71717171717177 r82
6276272mrmr62
687787mrmrr68
mr585
mrmmmr393933939933mrmmmrmrr39
622mrr62084848mrmmmmmmr08mr072
mr061
mr023
mr382r38
mr071
mr545
mr688r686232mrmrmr62mr201mmr20
mr45454r45r 45545rrmr017
784848488444844mrmmmmmrmmmr78
24744mr2mrmr24
mr793r79
mr510mr692
mr140
mr704
568mr5mr56
mr507r50
mr496
10mrmr11mr371
mr728
mr809
mr795
43434mr4r43
mr969
mr525rr52
mr324mr120
294mrr29
mr570r57
60000mrmrr60mr814
mr343r34463mr4r46
mr949
mr272
mr037
mr348mrr34
mr581r58
1mmr100198898mr9mrmrr98
45353mrr45
mr594r59
090mrr10
mr528rr52
mr794
mr526mrr52
mr802432mr4rr43
mr224
mr676
mr803
mr239mr311
mr807
mr864r86
mr204
845mrmr84
285285mr2rmrr28 mr355
mr451r45
540mr5r54
mr326
mr885mr332mr340r34
m
mr816
791917mrmrrmmmrr79
94545945455454554mrmmmmmmrmmrmmmrrr94
mr722
mr693
mr329
mr799
mr180
mr287
mrmmmmmmr
mr812
mr663mr307
mr179
mr699
mr656
mr171mr305r30
84141mr8r84mr648
9909909mrmrmr9994244222422mr9mmr94 mr813
mr210
mr712mr181
mr208
9050505mr9r90
334344mr3mrrrmmmrr33
mrmrmmmmmmrmrrmmr
9489448mr9mmmrr94
mr255
mr254
333mr876
mr664
mr616 mr104 mr053
mr106
mr0830404040 04mrmmrr04
77999mrrmrmr77mr259 01221222mrmrmmrr01
mr497
mr46697797797mrmmmrmrmr19
mr286
091919mrr09
920200mrrmrr92mr617
725mr7r72
mr926
339mr3mrmmmmr33
0808880mrrmrr10
mr798mr900
76876mrmmr76
mr115mmr11
708mrr70mr720
mr056
mr923
53000mrr53mr032
mr9270366mrr03
mr408
mr414
mr332
mr896
mr653
mr908
mr903
mr876
mr904
unknown
flavonoids
others
AA and NA ders phenolamines fatty acids
vitamines terpenoids
positive
negative
mr051
mr018
mr041
mr231
mr059
mr422
mr533
mr412
b
sub network 2
sub network 1
sub network 3
79
Supplementary Figure 7 The PCA (a) and GGM (b) results of rice 80
grain. 81
AA and NA ders, amino acid and nucleic acid derivatives.82
9
50 100 150 200 250 300
Inte
nsity
, cps
0
4e+6
8e+6
1e+7
77.0
91.1117.1
144.1
161.0
50 100 150 200 250 3000
4e+6
8e+6
Inte
nsity
, cps
77.1
91.1
117.1
127.1
144.1
186.1 203.1
50 100 150 200 250 300
Inte
nsity
, cps
0
1e+7
2e+7
77.1 91.1
105.1117.1
128.0
144.1
204.1 247.2
265.1
m/z, Da
50 100 150 200 250 300
Inte
nsity
, cps
0
4e+6
8e+6
1e+7
77.090.9
103.1
117.1
130.2
144.1
191.1
273.9 291.0
NH2
NH
NH
NH
CH3
O
NH
NH
O
NH
NH
O
aTryptamine
N-acetyltryptamine
N-benzoyltryptamine
N-cinnamoyltryptamine
83
10
b
50 100 150 200 250 300
Inte
nsity
, cps
0
8e+5
2e+6
61.1 77.0 89.1 105.1
115.1
132.1
160.1
177.1
NH2
NH
OH
50 100 150 200 250 300
Inte
nsity
, cps
0
2e+7
4e+7
77.1
95.1
105.1
115.2
132.1143.1
160.1
210.1 229.0 249.0264.1 280.9
NH
NH
OH
O
m/z, Da
50 100 150 200 250 300
Inte
nsity
, cps
0
5e+4
1e+5
2e+5
77.1
105.1
115.2132.1
160.1
209.2
265.1
281.1
297.2
NH
NH
OH
OOH
Serotonin
N-benzoylserotonin
N-salicyloylserotonin
84
85
Supplementary Figure 8 The mass spectrum and structure of some 86
metabolites for GGM results. 87
(a) Tryptamine related metabolites and (b) serotonin related metabolites. 88
89
90
11
mr896 (N-Benzoyltryptamine) 91
92
93
mr903 (N-Benzoylserotonin) 94
95
96
97
12
mr904 (N-Cinnamoyltryptamine) 98
99
100
mr908 (N-Salicyloylserotonin) 101
102
103
104
13
1000 grain weight 105
106
107
Grain length 108
109
110
111
14
Grain thickness 112
113
114
Grain width 115
116
117
15
Hull color 118
119
120
Seed color 121
122
123
Supplementary Figure 9 The related Manhattan plots (up) and 124
quantile-quantile plots (down). 125
126
16
127
0 2 4 6 8 10 120
500
1000
1500
2000
2500
3000
mean=3.0
95% quantile = 5.3
128
Supplementary Figure 10 Permutations of number of homologous or 129
co-linear loci occurred by chance. 130
Given the number of loci studied between two species, an average of 3.0 131
out of 42 homologous or co-linear loci could possibly be due to chance 132
alone. The 95% quantile of the distribution for metabolite- metabolite loci 133
of homolog or co-linear is 5.3. 134
135
17
136
−lo
g(P
)
0
2
4
6
Chr8
rice
r2
0.60.4
0.20
0.8
sf0802256337
2.20 2.22 2.30 2.32 (Mb)2.26
Os08g04500 Os08g04540OsTDC1
Os08g04560 Os08g04620 Os08g06400
82.69 82.79 82.89 82.99 83.09 (Mb)
GRMZM2G362828 GRMZM2G063363 GRMZM2G021388 GRMZM2G021277 GRMZM2G016254
●
●●
●●
●
●●
●
●
●
●
●●
●
●●●●●●
●
●●
●
●
●●●●●●●
●
●●
●●●●●●●●●●
●
●
●●●
●
●●
●●●●●●
●
●
●
●
●●
●
●
●
●
●
●●●●
●●
●
●
●
●●
●
●●
●
●
●
●
●
●
●●
●
●
●
●●
●
●
●
●●●
●
●
●●●●
●●●●
●
●●●
●
●●●●
●●
●●●
●
●
●
●
●
●
●
●
●
●
●
●●●●●
●
●●●●●●●●
●
●●●●●
●
●●●
●●
●
●●
●●
●
●●●●●●●●●
●
●
●●
●
●●●
●●●●●●●
●
●●●
●
●
●●
●
●●
●●●●
●●
●●●●●
●
●
●●
●●●●
●●
●
●●●●
●●●●
●
●●●●
●
●
●
●●●●●
●
●
●
●
●
●●
●●
●●
●●
●●●
●●
●
●
●●
●
●
●●●●●
●●
●●
●●
●●●
●
●●●
●
●
●●
●
●
●
●
●●
●
●
●
●●●●●●●●
●
●●●●●
●
●●
●
●
●
●
●●
●
●●
●●
●
●●●●
●●
●●
●
●
●●
●
●
●
●
●●
●●
●●●●●●●●●●●●●
●
●
●
●
●
●●
●●●
●
●
●●
●●
●
●
●
●
●
●●
●
●●
●
●
●
●
●
●
●
●
●●
●
●●
●
●●●●●
●
●
●
●●
●
●
●
●●
●
●●
●●●●
●
●
●●
●
●
●
−lo
g(P
)
0
5
10
15
Chr10
PZE-110043443maize
a
137
138
0
5
10
15
−lo
g(P
)
Chr1
30.63 30.65 30.70 30.75 (Mb)
ricesf0130643809
Os01g53330OsUGT-3
Os01g53350 Os01g53470 Os01g53520
200.20 200.16 (Mb)
GRMZM2G031308GRMZM2G078771GRMZM2G381025
●
●
●
●
●●●
●
●
●●●
●
●
●●●●●●●
●
●
●
●
●
●
●●
●
●
●
●●●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●●●
●
●
●●
●
●
●
●
●
●
●●
●
●
●
●
●
●●●
●
●
●
●●
●
●
●
●
●
●●●●
●
●
●
●●
●
●
●
●
●●
●
●
●●
●●●●
●●
●
●●●
●●●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●
●●●
●
●
●
●
●
●
●
●
●
●
●
●
●●●●●
●
●
●
●
●
●
●●
●
●
●
●●●
●
●●
●
●●
●
●●●
●
●
●
●
●
●
●
●
●
●●●
●
●●
●
●
●
●●
●
●
●
●
●
●
●
●
●●
●●
●
●●●●
●
●
●
●
●●
●●●●
●●●●
●●●
●
●
●
●
●
●
●●●
●
●
●
●
●
●
●●●
●●
●
●●
●
●●
●●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●●●
●●
●
●
●
●
●
●
●
●
●
●●●●●
●●●●
●
●●
●
●
●●●●●
●●
●
●
●
●●
●●
●
●●
●
●●●●
●
●●
●
●●●
●●
●
●
●●●
●
●
●
●
●
●●●
●
●
●●
●
●
●●●
●●
●●●●●●
●●●●●●●
●●●●●●
●●●●●
●●●
●
●●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●●
●
●●●
●●
●
●
●
●
●
●
●●
●
●
●
●
●●
●
●●●●●
●●
●
●
●●●
●
●
●●
●
●
●
●
●
●
●
●
●●
●
●●●●
●●●
●●●
●
●
●●
●●
●
●
●●
●
●
●●
●
●
●
●
●
●●●
●
●
●●
●
●●
●
●
●
●
●
●●
●
●●●●
●●
●●
●
●
●●●
●
●
●
●
●
●
●
●●
●
●
●●
●
●
●
●
●
●
●
●
●●
●
●●
●●
●●●●●●●●●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●●●
●
●
●
●
●
●●●
●●●●●
●
●
●
●
●
●●
●
●●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●●
●●●●●
●●●
●
●
●
●
●●●
●●
●
●
●
●●
●
●
●●
●
●
●
●
●
●●●●
●
●
●●
●
●
●
●
●
●
●
●●
●
●
●
●●
●
●
●
●●
●
●
●●
●
●
●●●●
●
●●
●
●
●
●●
●
●
●
●●
●
●
●
●●●
●
●
●●●●●●●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●●
●●●
●
●
●
●
●●●
●
●
●●
●
●
●
●
●
●
●●
●●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●●●●
●
●
●
●
●
●
●
●●●●
●
●●
●
●●●●
●
●
●●
●
●●●
●
●
●
●●
●
●●●
●
●
●●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●●●
●
●●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●●●●
●
●
●
●●
●
●
●
●
●
●
●●
●●●
●●●
●
●
●
●
●
●
●●
●
●●
●●
●
●
●
−lo
g(P
)
0
4
6
2
chr3.S_200219661maize
r2
0.60.4
0.20
0.8
200.18200.20
Chr3
b
139
18
0
1
2
3
4
5
6
7
●
●
●
●
●●
●
●●
●
●
●●
●
●
●
●
●
●●●
●
●●●●
●●●●
●
●
●
●
●
●
●
●
●
●
●●
●●●●
●
●
● ●●●
●
●●
●
●
●
●
●
●
●
●●
●
●
●
●
●●●●
●●●●
●●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●●
●●●●●●●
●
●
●
●
●
●●
●●●
●
●
●
●
●
●●●
●
●
●
●●
●
●
●
●
●●
●
●
●
●●●
●
●●
●
●
●●
●
●●●
●
●●
●
●●
●
●●
●
●
●
●●●
●
●●
●●●●
●●
●
●●
●●●●●
●
●
●
●●
●
●●●●●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●●●●
●●●●●
●
●
●●●●
●
●●●
●●●
●
●●
●●
●
●
●●●
●
●
●
●
●
●
●●●●●
●
●●●●●●
●●
●●●●●●●●●●●
●●●
●
●●
●●●●
●
●●●●
●●
●●●●
●
●●
●
●
●●●
●
●●●●
●
●
●
●
●
●
●
●●●●●●●
●●
●●
●
●●
●
●
●
●●
●●●●●●
●
●●●
●
●
●●
●
●
●●
●
●●●
●
●●
●
●
●●
●
●●●
●
●●
●
●
●●
●
●●
●
●
●
●
●
●
●●●
●
●
●
●●
●●●
●
●
●●
●
●●●
●
●●
●●
●
●●
●
●
●
●
●
●
●●
●
●
●
●
●●●
●
●
●●●
●●
●●
●
●
●
●●
●
●
●
●
●●●
●
●
●
●
●●
●
●●
●
●
●●
●●
●
●
●
●●
●
●
●
●
●
●
●
●●
●
●●
●●●
●
●●
●
● ●
●
●
●
●
●●
●
●
●●●
●
●
●●●●●
●
●●
●
●●●●●●
●
●
●
●●
●
●
●
●
●●●
●
●
●●
●
●●●
●
●●
●●●
●
●
●
●
●●
●
●
●
●
●
●
●●
●
●
●
●
●
●●
●
●●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●●
●
●●
●●
●
●
●●
●●
●
●
●
●
●
●●
●●
●●
●●●
●
●
●
●
●
●●
●
●●
●
●●
●
●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●●●●●
●
●
●●●●●
●●
●●●●
●
●
●
●
●
●
●●●●●●
●●●
●
●● ●
●
●
●
●
●●●●●
●
●
●
●
●●
●●
●●●●
●●
●
●●
●●●
●●
●
●●●
●
●
●●
●●
●
●●●●
●●
●
●
●●
●
●●●●
●
●●
●
●
●
●
●●
●
●●
●
●
●
●
●
●
●●●
●
●●●●●●●
●
●
●
●●
●
●
●
●
●
●●●●
●
●
●●●●
●
●
●
●●●●●
●
●●
●
●
●●●●
●●
●●●●
●
●●●●●●
●
●
●
●●
●
●
●●●
●
●
●
●
●
●
●
●●●
●
●
●●
●
●
●
●●●●●●●●●●●●
●
●
●
●
●●●
●●●● ●●●●
●●
●●●●●
●●
●
●
●●●
●●
●
●
●●
●●
●
●●
●●
●
●●●
●●●●●●●●●●●●●
●●●●●●●
●
●
●
●
●
●
●●●
●●
●
●
●
●●●●
●●●●
●
●
●●
●
●●
●
●
●
●
●
●
●
●
●●●
●
●
●●
●
●
●
●●●
●●
●
●
●
●
●
●
●
●●●●●●
●
●●
●
●●
●
●●●●
●
●
●
●●
●●
●●
●
●
●●
●●
●●
●
●
●
●●●●●
●
●
●●●
●
●
●●●●●● ●
●●●●●
●
●
●●
●
●
●
●●
●●
●●
●
●
●
●
●
●
●●●
●
●●●●●●●●●●●●●
●
●●
●●
●●
●
●●●●●●●●●
●
●●
●
●●●
●
●
●
●●●●
●
●●●●●●
●●●●●●●
●●
●
1
2
3
4
5
6
7
0
rice sf0123644140
r2
0.60.4
0.20
0.8
Os01g41430RUGT-5
215.75
GRMZM5G888620
215.80
Chr1
23.55 23.60 (Mb)
Os01g41450
23.50
215.85 (Mb)
−lo
g(P
)−
log
(P)
chr3.S_215786480
Chr3
maize
c
140
−lo
g(P
)
0
2
4
6
Chr6
rice
r2
0.60.4
0.20
0.8
sf0603183527
3.18 3.21 3.24 3.27 3.30 3.33 (Mb)
Os06g06780 Os06g06880 Os06g06980 Os06g07020
78.80 78.90 79.00 79.10 79.20 79.30 79.40 (Mb)
GRMZM2G342243 GRMZM2G041822 GRMZM2G127948 GRMZM2G086277
●●●
●
●
●●
●
● ●
●
●
●
●●●
●
●●
●
●
●
●●
●●
●
●
●
●
●
●●●●●
●
●●
●
●
●
●
●
●●●●
●
●
●
●●●●●●
●
●
●
●
●
●●
●●
●●●●
●●
●
●●
●
●
●
●
●
●
●●●●
●●
●
●●
●
●
●
●●
●●●●●
●
●
●
●●
●
●
●●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●●●
●
●●
●
●
●
●
●
●
●
●●
●●
●
●
●●
●
●
●
●
●
●●
●
●● ●
●
●
●
●
●
●
●
●
●●●●
●●●●●
●
●●●●
●●●●
●
●
●●
●
●●
● ●●●●●●●●●
●
●●●
●
●●
●
●
●●●●
●●
●
● ●
●
●●
●
●●●
●●
●●
●●●●
●●
●●
●
●
●
●
●
●
●
●
●
●
●●
●●
●
●
●
●
●●
●
●●●
●
−lo
g(P
)
0
2
4
6
8
10SYNGENTA0813
Chr6
maize
d
141
19
RT, min
6 7 8 9 10 11 12 13 14
Inte
nsity
,cp
s
1.0e+5
2.0e+5
3.0e+5
4.0e+5
11.4
Apigenin
Apigenin 7-O-glucoside
8.7
RT, min
6 7 8 9 10 11 12 13 14
Inte
nsity
,cp
s
2.0e+5
4.0e+5
6.0e+5
8.0e+5
1.0e+6
1.2e+6 Apigenin (standard)
11.4
Empty vector
Os11g25454
0
2
4
6
−lo
g(P
)
Chr11
14.03 14.13 14.23 14.33 (Mb)
rice sf1114353342
Os11g25454 Os11g25720 Os01g53470 Os01g53520
3.20 3.30 (Mb)
GRMZM2G085854GRMZM2G085054
−lo
g(P
)
0
4
6
2
chr4.S_3210771maize
r2
0.60.4
0.20
0.8
3.263.24
Chr4
8
2.3 2.5 2.7 2.9 3.1 3.3 3.5 3.7 3.9 4.1●
●●
●
●
●●
●
●●
●●
●●
●
●
●●
●
●
●●
●
●
●●
●●
●
●
●
●
●
●
●
●●
●
●
●
●
●●●
●●
●●
●●●
●
●
●●●
●
●●●
●●●
●●
●
●
●
●
●●
●●●●
●●●●
●
●
●
●●
●●●
●
●
●●
●●●●
●
●
●●
●●
●
●●●●●●
●
●
●●
●●●●
●
●
●●
●
●●●●●●
●
●
●
●
●
●●●●
●
●
●
●
●
●
●
●●
●● ●
●●
●●
●
●●
●
●
●●
●
●●
●
●
●
●
●
●
●
●
●●●
●●
●
●
●
●
●
●
●
●
●●
●
● ●●
●
●●●
●
●
●
●
●●●●●●●
●●
●
●
●
●●
●
●
●
●●●
●
●
●
●
●●●
●●●●●●
●●●
●●
●●
●●●●●●
●
●●
●●
●
●●●
●
●●●
●
●
●
●
●
●
●
●●
●
●
●
●
●●
●
●
●●
●●
●
●●
●
●●
●●
●
●
●
●
●●
●●
●
●
●
●
●
●
●●
●
●
●
●●
●
●●●
●●
●●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●●●
●●
●
●
●
●●●●
●●●
●
●●●
●●
●
●
●●●●
●
●
●
●
●
●
●
●
●●●
●
●
●●
●●
●
●●
●
●●
●
●
●
●
●
●
●●
●
●
●●
●●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●●
●●
●
●
●
●●
●
●
●
●
●
●●
●●
●●
●●
●
●
●
●●●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●●
●
●●
●●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●●
●
●●●
●●
●
●●●●
●
●
●
●
●
●
●●●
●
●
●
●
●●●●●●
●
●
●
●●
●
●
●
●
●
●
●
●
●●
●
●
●
●●
●
●
●
●●
●●
●●●●
●
●
●
●●●
●
●
●
●●
●●
●
●
●●
●
●
●
●●
●
●
●
●
●
●
●●●●
●
●
●●●●
●
●
●
●●
●
●
●
●
●
●●
●
●
●
●●
●
●
●
●
●●●
●●
●
●
●
●
●
●●
●●●
●●●●●●
●
●●●
●●
●
●
●●
●
●
●
●
●
●●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●●
●
●
●
●
●●
●●
●
●
●
●
●●●
●●
●
●
●
●
●
●
●
●
●●
●
●
●●●
●
●
●
●●●
●
●●●●
●
●●●●●
●
●
●●
●
●●
●
●
●
●●
●●●●●
●
●
●
●
●
●
●
●
●●●● ●
●
●
●
●
●●●
●●
●●●●
●
●●●●
●●
●●
●
●
●
●
●
●●
●
●
●●●
●
●
●
●
●●●
●
●
●
●●
●●●
●
●●
●
●
●
●
●
●
●
●●
●●●
●
●
●
●●
●
●
●
●
●
●●
●●●●●●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●●
●
●
●●
●
●●●
●●
●●
●
●
●
●●
●
●
●
●●●●
●●
●
●●
●●
●
●
●●●●
●
●●●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●●●●●
●
●
●
●
●
●
●
●●
●
●
●
●●●
●
●
●●●●
●
●
●
●
●●
●
●
●
●●●
●●●●●●●
●●
●
●
●
●●●●●●●
●●
●●
●●
●●
●
●
●●●
●
●●
●
●
●
●●
●
●
●●
●●
●
●●
●
●
●
●
●
●●●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
e
f
142
143
Supplementary Figure 11 Colinear genomic regions and the 144
20
homologous loci (or genes) of tryptamine (a), 3’, 4’, 5’-tricetin 145
O-hexoside (b) chrysoeriol (c), caffeic acid (d) and apigenin 146
7-O-glucoside (e) between rice grain and maize kernel. (f) Annotation of 147
Os11g25454 as the candidate gene underlying the mGWAS for apigenin 148
7-O-glucoside and identified the function by in vitro. LC-MS 149
chromatograms of in vitro enzyme assay shows the enzyme activity of 150
recombinant Os11g25454 (up). Protein extract from E. coli containing 151
pDEST15 empty vector were used as a negative control (down). 152
153
21
At3GlcT
At3AraT
At3RhaT
Vv3GlcT
Ph3GlcT
Pf3GlcT
Hv3GlcT
Zm3GlcT
Os11g25454
UGT84A1
UGT84A2
At5GlcT
Ph5GlcT
Pf5GlcT
Vh5GlcT
Os07g32060
Os01g53460
Os06g18010
Os06g18140
GRMZM2G383404
Os06g18670
Os06g18790
At7RhaT
At7GlcT
DbB5GlcT
NtIS5a
Gt3GlcT
Os02g37690
CmF7G2RhaT
BpA3G2GlcAT
UGT79B1
IpA3G2GlcT
PhA3G2RhaT
Os11g26950
91
100
100
95
100
100
100
100
99
100
100
100
100
97
100
97
99
100
91
92
100
100
100
99
100
62
100
100
82
60
73
0.1 154
Supplementary Figure 12 Phylogenetic analysis of glucosyltransferase 155
genes from the plant glucosyltransferase family. 156
The neighbor-joining tree was constructed using aligned full-length 157
amino acid sequences. Bootstrap values from 1, 000 replicates are 158
indicate at each node. Bar = 0.1 amino acid substitutions per site. 159
160
22
161
metabolites
mr004 mr584 mr430 mr582 mr082 mr543 mr069
Rel
ativ
e co
nten
t
0
2e+4
4e+4
6e+4
8e+4
WT975
metabolites
mr004 mr584 mr430 mr582 mr082 mr543 mr069
Rel
ativ
e co
nten
t
0
1e+5
2e+5
WT123
c
d
WT 9 7 5
Rel
ativ
e ex
pres
sion
0
100200300400
Os06g18790
WT 1 2 30
1
8000
16000
Os06g18670
a b
Os06g18670
Os06g18790
162
Supplementary Figure 13 The transgenic results of Os06g18670 and 163
Os06g18790. 164
The expression level of Os06g18670 (a) and Os06g18790 (b) 165
respectively; (c and d), the relative content of some flavonoids in rice 166
transgenic individuals. WT, the transgenic background variety ZH11. The 167
23
P value is calculated using the Student’s t tests. Data are shown as the 168
means ± s.e.m., n = 3. mr004, di-C,C-pentosyl-apigenin; mr584, 169
C-hexosyl-luteolin O-p-coumaroylhexoside; mr430, Luteolin 170
6-C-glucoside; mr582, C-hexosyl-apigenin O-p-coumaroylhexoside; 171
mr082, C-hexosyl-apigenin O-feruloylhexoside; mr543, 172
C-hexosyl-chrysoeriol O-hexoside; mr069, di-C, C-hexosyl-apigenin 173
derivative. 174
175
24
176
12 2 13 4 WT 3 9 1 80
1
2
3
4
OX RNAi
p=3.6E-05
p=2.5E-06
p=6.6E-06
Gra
inw
idth
(mm
)
p=5.3E-08
p=5.8E-04
p=3.9E-06
p=1.9E-06
p=9.5E-07
WT
Re
lativ
eex
pre
ssio
n
0
1
2
100
150
200
12 2 13 4
OX
3 9 1 8RNAi
WT0
2
4
6
12 2 13 4
OX
3 9 1 8RNAi
Trig
one
llin
eco
nte
nt(×
106 )
a b
c
177
178
Supplementary Figure 14. Phenotype data in transgenic plants. 179
Shown are bar plots for the mRNA level of Os02g57760 (a) and for the 180
content of trigonelline (b) in transgenic positive individuals. (c) The 181
comparison of grain width between transgenic plants and wild type. The 182
P value is calculated using the Student’s t tests. Data are shown as the 183
means ± s.e.m., n = 3. 184
Supplementary Note 1 185
Metabolites identification and putative annotation strategies. 186
25
We determined the relative levels of 837 distinct metabolic traits in rice 187
grains using a newly developed liquid chromatography-tandem mass 188
spectrometry (LC-MS/MS)-based, widely targeted metabolic profiling 189
method1. Of the 837 metabolic features, 80 were identified based on 190
comparisons of MS/MS spectra, an exact mass number, and retention 191
time with those of authentic standards (Supplementary Data 2). A total 192
of 230 were putatively annotated based on high resolution MS, MS/MS 193
spectra and other strategies, including: i) linking the unknown metabolites 194
to functionally related genes based on genetic mapping2, and/or further 195
verifying the genes using in vivo or in vitro strategies; ii) connecting two 196
metabolites with similar MS/MS spectra3; and iii) combining the 197
Gaussian graphical model (GGM)4 with the similarity of the MS/MS 198
spectra. The details are provided below. 199
To annotate more metabolites, we associated the unknown metabolites 200
with annotated genes based on our high-resolution genetic mapping as 201
previously reported2, For example, the strong association between SNP 202
sf0233224406 located 22 kb from OsLKR5 (encoding saccharopine 203
dehydrogenase) and the mr208 (m/z 277) level suggested that this 204
metabolite could be saccharopine or its derivative. We subsequently 205
identified the mr208 metabolite as saccharopine by comparing the 206
retention time and fragmentation pattern of this metabolite with the 207
commercial standard (Supplementary Figure 1). 208
26
The strong association between SNP sf0605268699 located 45 kb from 209
OsC1 (encoding MYB transcription factor)6 and the mr063 (m/z 210
465.1033) level suggested that this metabolite could be an anthocyanin or 211
its derivative. We subsequently identified the mr063 metabolite as 212
delphinidin 3-O-glucoside by high resolution MS and the fragmentation 213
pattern of this metabolite (Supplementary Figure 2). Using this 214
approach, the mGWAS enabled the putative annotation of more than 40 215
metabolites (Supplementary Data 4). 216
We used the Gaussian graphical model (GGM) to reconstruct pathways 217
involving directly related metabolites. GGM is based on pairwise Pearson 218
correlation coefficients conditioned against the correlation with all other 219
metabolites4. First, we performed Principal component analysis (PCA) on 220
the genotype mean values to summarize the correlations and pinpoint 221
groups of correlated metabolites. We found some obvious clusters, such 222
as the class of flavonoids, some amino acids and terpenoids etc., 223
suggesting strong correlations between them (Supplementary Fig. 7a). 224
For the GGM calculation in this article, a full data matrix was constructed 225
from 502 samples and 587 metabolites. GGM with an empirical Bayes 226
approach7 was employed to estimate partial correlations and reconstruct a 227
GGM network from a given dataset. In addition to the results for the full 228
population, we included the data for separate GGM analyses across the 2 229
genetic subgroups (indica and japonica). We compared the GGM 230
27
networks of three groups filtered by a significant P-value < 2.9E-07 231
based on the Bonferroni correction. Together, the resulting GGM consists 232
of a total of 2119 connections (Supplementary Data 15). In accordance 233
with previous observations, we consistently observed associations 234
between biochemically related metabolites from various metabolic 235
pathways in both the overall network (Supplementary Fig. 7b) and the 236
top list of high-scoring GGM edges: metabolites naringenin 237
7-O-glucoside and apigenin 7-O-glucoside (P-cor = 0.30, Pearson’s 238
correlation coefficient), which are involved in flavonoid metabolism, or 239
threonyl carbamoyl adenosine and 240
[1,2,4]triazolo[1,5-a]pyrimidine-7-carboxamide,4,5,6,7-tetrahydro-N-(2-241
methoxy-5-methylphenyl)-5-oxo- (P-cor = -0.08, Pearson’s correlation 242
coefficient), which represent related nucleic acid derivatives 243
(Supplementary Fig. 7b). Then, we searched for high-score correlating 244
pairs of an unknown and a known metabolite that might provide a 245
biochemical context for the unknown metabolite. For example, the 246
correlation between tryptamine (mr653) and mr904 was 0.09. This pair 247
had the same major m/z 144 fragment (the main ion for tryptamine), 248
suggesting that mr904 was a tryptamine derivative. We putatively 249
annotated mr904 as N-cinnamoyltryptamine by comparing the MS and 250
fragmentation patterns with tryptamine (Supplementary Data 15). Over 251
30 metabolites were putatively annotated using this approach 252
28
(Supplementary Data 4 and 15). 253
Supplementary Note 2 254
The process and criterion for the assignment of candidate genes 255
responsible for the variation of metabolic traits based on mGWAS. 256
To confirm the candidate genes responsible for the variation of metabolic 257
traits, we mined the candidate genes using the following methods: i) 258
estimating the allelic effect of each genotypic class in close proximity to 259
the most significant peak SNPs and confirming the associated SNP/InDel; 260
ii) looking for a protein or protein cluster that was biochemically and/or 261
biologically related to the associated metabolic trait encoded at these loci; 262
iii) performing cluster analysis of the candidate genes relative to 263
homologous genes with known functions; iv) cross-referencing with 264
results from linkage mapping and v) verifying the candidate genes 265
according to the tissue-specific expression pattern. 266
For example, SNP sf0310132518 located 12 kb from Os03g18130 267
(encoding a putative asparagine synthetase) was significantly associated 268
(P = 5.7E-07, LMM, n = 502) with asparagine (mr173). The high 269
sequence identity (68% at the amino acid level) between Os03g18130 and 270
AtASN2 suggested that Os03g18130 encoded an asparagine synthetase. 271
This hypothesis was supported by the preferential expression of 272
Os03g18130 together with a higher accumulation of this metabolite in the 273
29
rice grain. 274
We also observed a 2 bp deletion that resulted in a frame shift in 275
Os04g11970. This deletion was highly significantly associated with the 276
variation (P = 6.7E-47, LMM, n = 502) and the absence of 277
O-methylapigenin C-hexoside, strongly suggesting the loss of function 278
allele for this candidate. 279
SNP sf0524319598 located in Os05g41645 (encoding a putative 280
chalcone synthase), was significantly associated (P = 3.3E-52, LMM, n = 281
502) with C-pentosyl-apigenin O-rutinoside (mr080). The high sequence 282
identity (48% at the amino acid level) between Os05g41645 and AtTT4 283
suggested that Os05g41645 encoded a chalcone synthase underlying this 284
flavonoid. 285
SNP sf0137818225 located 27 kb from Os01g65260 (encoding a 286
putative amido phosphor ribosyltransferase) was significantly associated 287
(P = 2.5E-10, LMM, n = 502) with threonyl carbamoyl adenosine 288
(mr408). The above data strongly suggested that Os01g65260 encoded an 289
amido phosphor ribosyltransferase that was involved in the accumulation 290
of threonyl carbamoyl adenosine. 291
Together, more than 30 candidate genes were newly disclosed by 292
examining the mGWAS data from the rice grain alone in addition to 30 293
genes that were previously identified in studies using either mutants or 294
recombinant and natural populations (Supplementary Data 14). 295
30
Supplementary Note 3 296
Comparative mGWAS between rice and maize. 297
Comparative linkage mapping between crop plants, such as wheat, maize, 298
and rice8,9, has revealed good correspondences among QTLs in crop 299
plants for traits including seed size, shattering habit, and flowering time 300
etc., and has been suggested as a useful tool for predictions of the loci of 301
homologous major genes10-12. This concept was modified and extended in 302
our mGWAS for candidate gene mining based on the co-linear mapping 303
of the targeted metabolic trait(s) between species (e.g., searching for 304
candidates within homologous or co-linear regions co-mapped by the 305
same metabolites detected in both species). Because orthologous genes 306
between rice and maize may vary in their substrate specificity (e.g., 307
responsible for similar but not exactly the same metabolite), metabolites 308
with similar structures were also included in the comparison. 309
In this study, rice (Nipponbare, MSU version 6.1) and maize (B73, 310
RefGen_v2) genomes were used for the identification and 311
characterization of homologous regions. The sequence alignment analysis 312
was based on a VISTA sequence alignment algorithm program13. 313
Detailed information concerning the homologous fragments between the 314
two species is available from the VISTA database 315
(http://genome.lbl.gov/vista/index.shtml)14. 316
We previously performed metabolic profiling of 983 metabolic features 317
31
in 702 diverse maize accessions and identified hundreds of significant 318
locus-trait associations in maize kernel through mGWAS15. To 319
investigate the common genetic control of metabolism between rice and 320
maize, we focused on the 123 co-detected metabolic features in rice 321
grains and maize kernels (Supplementary Data 4). The co-detected 322
metabolic traits in both species were used to filter out loci through 323
mGWAS in the rice and maize grain. The calculated genome-wide 324
threshold was set at P = 1.8E-06 (MLM, n = 339) for maize17 and P = 325
1.3E-06, 1.8E-06 and 4.1E-06 (LMM, n = 502) for the whole panel, 326
indica and japonica rice2, respectively. According to these thresholds, we 327
obtained a total of 420 (Supplementary Data 16) and 292 328
(Supplementary Data 17) loci for the 123 co-detected metabolic features 329
in rice and maize, respectively. We searched for homologous loci mapped 330
by the same metabolites or metabolites of similar structures between 2 331
species by referring to the VISTA database 332
(http://genome.lbl.gov/vista/index.shtml) and detected 42 loci for 23 333
metabolites or metabolites of similar structures in both species 334
(Supplementary Data 18). 335
To test the significance of our GWAS homolog or co-linearity, we 336
adopted the randomization test of Churchill et al. 199416 to determine the 337
proportion of overlaps expected to occur by chance. The deviation from 338
the random number of GWAS homolog or co-linearity was calculated as 339
32
follows. All SNP hits of co-detected metabolites were randomly 340
distributed over the 420 and 292 identified association positions in the 341
rice and maize kernel, respectively. Then, we counted the number of 342
homolog or co-linearity with each locus for metabolites with the same or 343
similar structures using rice and maize fragments according to their local 344
LD decays. This procedure was repeated 10,000 times and yielded a 345
distribution of expected numbers of loci of homolog or co-linearity. Then, 346
this distribution was compared against the outcome for the actual data. 347
The mean and 95% quantile of the distribution for tge 348
metabolite-metabolite loci of homolog or co-linearity were 3.0 and 5.3, 349
respectively (Supplementary Fig. 10), suggesting that the majority of the 350
observed overlaps could not possibly be explained by chance alone. 351
Next, we looked for homologous gene(s) within the homologous or 352
co-linear loci between rice and maize using an expectation value (E) of 353
10-10 as the significance threshold17. Using this approach, a number of 354
candidate genes were assigned (Supplementary Fig. 11 and 355
Supplementary Data 19), including reported genes for metabolic traits 356
such as tryptophan decarboxylase OsTDC1 (Os08g04540), which 357
catalyzes the conversion of tryptophan into tryptamine in rice18 358
(Supplementary Fig. 11a), and another two flavonoid O-UDP-glucosyl 359
transferases (OsUGT-319 and RUGT-520) underlying the variation of 3’, 4’, 360
5’-tricetin O-hexoside and chrysoeriol, respectively (Supplementary 361
33
Figs. 11b-c). 362
Supplementary References 363
1. Chen, W. et al. A novel integrated method for large-scale detection, identification, and 364
quantification of widely targeted metabolites: application in the study of rice metabolomics. Mol 365
Plant 6, 1769-1780 (2013). 366
2. Chen, W. et al. Genome-wide association analyses provide genetic and biochemical insights into 367
natural variation in rice metabolism. Nat Genet 46, 714-721 (2014). 368
3. Matsuda, F. et al. Metabolome-genome-wide association study dissects genetic architecture for 369
generating natural variation in rice secondary metabolism. Plant J 81, 13-23 (2015). 370
4. Krumsiek, J. et al. Mining the unknown: a systems approach to metabolite identification 371
combining genetic and metabolic information. PLoS Genet 8, e1003005 (2012). 372
5. Kawakatsu, T. & Takaiwa, F. Differences in transcriptional regulatory mechanisms functioning for 373
free lysine content and seed storage protein accumulation in rice grain. Plant Cell Physiol 51, 374
1964-1974 (2010). 375
6. Saitoh, K., Onishi, K., Mikami, I., Thidar, K. & Sano, Y. Allelic diversification at the C (OsC1) 376
locus of wild and cultivated rice: nucleotide changes associated with phenotypes. Genetics 168, 377
997-1007 (2004). 378
7. Schafer, J. & Strimmer, K. An empirical Bayes approach to inferring large-scale gene association 379
networks. Bioinformatics 21, 754-764 (2005). 380
8. Moore, G., Devos, K.M., Wang, Z. & Gale, M.D. Cereal genome evolution. Grasses, line up and 381
form a circle. Curr Biol 5, 737-739 (1995). 382
9. Ahn, S. & Tanksley, S.D. Comparative linkage maps of the rice and maize genomes. Proc Natl 383
Acad Sci U S A 90, 7980-7984 (1993). 384
10. Lin, Y.R., Schertz, K.F. & Paterson, A.H. Comparative analysis of QTLs affecting plant height and 385
maturity across the Poaceae, in reference to an interspecific sorghum population. Genetics 141, 386
391-411 (1995). 387
11. Ming, R. et al. Comparative analysis of QTLs affecting plant height and flowering among 388
closely-related diploid and polyploid genomes. Genome 45, 794-803 (2002). 389
12. Paterson, A.H. et al. Convergent domestication of cereal crops by independent mutations at 390
corresponding genetic Loci. Science 269, 1714-1718 (1995). 391
13. Frazer, K.A., Pachter, L., Poliakov, A., Rubin, E.M. & Dubchak, I. VISTA: computational tools 392
for comparative genomics. Nucleic Acids Res 32, W273-279 (2004). 393
14. Mayor, C. et al. VISTA : visualizing global DNA sequence alignments of arbitrary length. 394
Bioinformatics 16, 1046-1047 (2000). 395
15. Wen, W. et al. Metabolome-based genome-wide association study of maize kernel leads to novel 396
biochemical insights. Nat Commun 5, 3438 (2014). 397
16. Churchill, G.A. & Doerge, R.W. Empirical threshold values for quantitative trait mapping. 398
Genetics 138, 963-971 (1994). 399
17. Dean, R.A. et al. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434, 400
980-986 (2005). 401
18. Kang, S., Kang, K., Lee, K. & Back, K. Characterization of rice tryptophan decarboxylases and 402
34
their direct involvement in serotonin biosynthesis in transgenic rice. Planta 227, 263-272 (2007). 403
19. Kim, B.G. et al. Flavonoid O-diglucosyltransferase from rice: molecular cloning and 404
characterization. J Plant Biol 52, 41-48 (2009). 405
20. Ko, J.H., Kim, B.G., Hur, H.G., Lim, Y. & Ahn, J.H. Molecular cloning, expression and 406
characterization of a glycosyltransferase from rice. Plant Cell Rep 25, 741-746 (2006). 407
408
