Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  1  

Supplemental Figure 1. Assembled transcript size distribution for the joint

assembly across 503 diverse maize inbred lines. All transcripts within a locus are

included in the distribution except transcripts smaller than 500 nucleotides, which

were excluded from all analyses.

0" 0" 269"

49896"

24776"

12505"

6528" 5713"2065"221" 34" 10"

0"

10000"

20000"

30000"

40000"

50000"

60000"

<"150"

150"to"250"

251"to"500"

501"to"750"

751"to"1000"

1001"to"1250"

1251"to"1500"

1501"to"2000"

2001"to"3000"

3001"to"4000"

4001"to"5000"

>"5000"

Num

ber'of'Transcripts'

Transcript'Size'(bp)'

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  2  

Supplemental Figure 2. Number of rice genes and proteins per Oases defined

locus. Transcripts were assembled and grouped into loci with the Velvet/Oases

pipeline and aligned to the Oryza sativa v7 proteins with WU BLASTX. Number of

O sativa genes (A) and proteins (B) per Velvet/Oases locus for loci in which

every transcript had an alignment to an O. sativa protein at greater than 70%

coverage and 70% identity. Number of O. sativa genes (A) and proteins (B) per

Velevet/Oases locus for loci in which one or more transcripts did not have an

alignment to O. sativa at greater than 70% coverage and 70% identity.

7980%

235%

13% 3%

7867%

337%

24% 3%

12046%

473%

41% 9%

11854%

646%

60% 9%

1%2%3%>=%4%

A% B%

C% D%

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  3  

Supplemental Figure 3. Unweighted pair group method with arithmetic mean

tree of 503 diverse maize inbred lines based on 485,179 working set SNP

markers.

Oh7B

MS224

CML_323

ND167

W85

NY_159__Neveh_Yaar_

YELLOW_3-4

CML_465

W821G

W609S

ND247

CML_421

CG65

H52

B97

B2

ND251

12iK

C123

CG10

C15SD15

T234

Sg1533

A627

A635

MEF156-55-2

B10

A

Va99

L_289

B105B107

B99

Ky226

A155

K47

CML_220

CML_322

Oh40B

W601S

AR228

38-11

PHG47

PHV63

F44

A305

EAST_028

A385

A12

H5

CG108

CO216

TZU-CHIAO-HSI-WU_105

YING-55

B104

4578_INBRED

CH701-30

LH59

KUNG-70

B7

M14

CI187-2

W9

B108

CI91B

CML_202

W23

A662

PHK76

Va14

Mo47

Os426

NC472

VaW6

Sg18

SD107

PHT55

B14A

CR_22_INBRED

W64A

B109

Mo45

CL18

SD42

PHG29

52220

FC46

W_7151

ND245

ND283

B106

N527

PHR36

MoG

WXB6

Va52

B114

PHJ40

H71

NC340

Mt42

A649

B98

R226

K201

Hi26

YE_4

LH60

W812G

CO237

I159

DKFBHJ

23W

G22_T122

W24

B54

W55280-2

K41

B14

W813G

CML_218

NY6371

B103Il14H

CI_40H

CML_491

G80

CML_144

SG_30A

H121

N218

N193

SD40

A427

ND260

B64

R229

MS222

W610S

ND1

N501

NKS8324

4554_INBRED

CO117

M162W

B90

N7A

Ki3

37A

LH39

ND101

MS132

B8

B164

PHG39

B112

M37W

S216W

G3_T5a

Hy

846A

ND246

NC342

P39

L317

CML_444A171

K64

FR19

A632

Pa778

W153R

A71

Il101T

N538

A679

HUANYAO

H84

LH145

CH753-4

I29

CG106

K4

PHT77

PHN11

A401

Mo5

IDS69

DKPB80

N216

CM105

C103

W606S

Ia_453

A322

K150

F431

Yu796_NS

CML_277

CML_91

PHB09

OC19

DE4

CML_176

B91CML_228

CML_376B79

NC318

KO679Y

EP1

A340Tr

ND265

MS67

MS221

CO255

DKHBA1

W817G

R197

MS225

NC412

W608S

A415-1-3_INBRED

H110

R168PHG80

CML_216

B77

B75

CI64

R78

CL27

Va38

NC298

B111

W605S

CM99

CML_254

H124w

CML_264

W811G

CO258

B121

W22

Pa468

Ki43

W809G

NP87

Ky228

AusTRCF_306238

Mo23W

MS106

B68

CR1HT

ND230

Ky21

R101

T232

NC236

CML_456

N534

U267Y

33-16

LH149

CI31A

A15

CM48

Va102

Pa392

B73

B66MS211

Os420

Oh7

Mo7

CML_52

INBRED_309

B37

W803G

Mo15W

MS223

W820G

CML_511

INBRED_109

A663

N28

N217

NC358

Chi-tan_120

N199

OH33

R134

HP301

MS12

CO236

4722

Pa891

CML_509

C102

W818G

R225

R181B

W810G

Mo28W

W802GNK

740

H113

LH38

B113

R53

W37A

Va85

WU-TAN-TZAO

R113

U_123

DKIB02

MS226

LP5

W701BC

E2558W

A659

A572

B115

CML_108

Eng-Li_Chih

NC356

B85

CO125

W815G

CL17

N28Ht

Ia5125B

W117Ht

Tx303

PHG35

N545

CI90CCI28A

W607S

S116W

Hi28

B101

Mo39

GE54

DKIB014

LH1H114

H14

YE-CHI-HUNG

INBRED_141

CM174

INBRED_100

A680

MS142

PHG50

CI21E

NO._380

04033V

MS116

CO257

NC250

CML_312

DE3

A321

W59E

Mp339

NC13

MS24A

MS153

4F-35_BKA239

CML_247

CML_197

MS72

LH93

LH82

PHG72

NKH8431

HUOBAI

N6

Pa405

S_56

C68

CO245

A674

Ki11

CML_505

H95

Mo24W

I205

B-18_INB

R.FR.SUP

ERGOLD

F115

CI3AOh43

CM174

Il778d

A258

T242

AS5707

LH143_maintainer

B88

A188

A554

NC222

NC344

B42

A374

CML_488

B87

K55

CH157

CML_287

B84

B119

NC264

A797NW

H96

R4

K148

S306

W

INBRED_305

SD102

H99

DK4676A

Mo30W

PHW17

4226

CML_448

W816G

DE811

F2834T

H122w

Mo44

CML_161

N197

R177

CO158

T146

IDS28

R71

F7

H91

YONG_28

DK78371A

A334

YANG

W814G

A682

WR3

DKMBNA

PHZ51

C42

B52

LH123HT

HP72-11

SD44

CSJ3

R227

A208

W182BN

ND262

C49A

CML_451

GE129Pa880

156A

SD101

CO192

N209

CH9

T9

Mo17

Mo3

DKMBPM

W703

S406

W

N28E

NC230

N542

NC232

A673

K155

W819G

CML_251

CO256

LH61

WD

B120

R30

H49

A661

T141

Pa762

CO106

N215

CL22

B-28

CM7

DKMFD-13D

B110

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  4  

Supplemental Figure 4. Linkage disequilibrium mapping of an example B73

reference gene to the B73 reference genome sequence. Pairwise r2 values

between single nucleotide polymorphisms (SNPs) anchored to the B73 maize v2

reference sequence and a SNP in GRMZM2G057778. (A) r2 values for all of the

chromosome 1 SNPs. (B) Zoomed in region where significant SNPs were located.

The grey boxes show annotated genes in the 5b annotation and the red box

shows the known position for GRMZM2G057778.

A"

B"

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  5  

Supplemental Figure 5. Linkage disequilibrium mapping interval size

distribution. Representative transcript assemblies (RTAs) were mapped to the

reference sequence assembly based on linkage disequilibrium using pairwise r2

values between single nucleotide polymorphisms (SNPs) anchored to the B73

maize v2 reference sequence and SNPs in the RTAs.

LD Mapping Interval Size (Mb)

Freq

uenc

y

0 2 4 6 8 10

050

010

0015

0020

00

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  6  

Supplemental Figure 6. Distribution of mapped versus unmapped

representative transcript assemblies (RTAs). Mapping was based on linkage

disequilibrium mapping between single nucleotide polymorphisms (SNPs) in the

reference sequence assembly and SNPs in the RTAs. Purple indicates overlap

between the two distributions.

Representative Transcript Assembly Size

Freq

uenc

y

0 1000 2000 3000 4000 5000 6000

050

010

0015

0020

00Mapped to ReferenceUnmapped to Reference

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  7  

Supplemental Figure 7. Relationship between reference gene and

representative transcript assembly (RTA) size and average gene expression

across 503 inbred lines. Mapping of RTAs was based on linkage disequilibrium

mapping between single nucleotide polymorphisms (SNPs) in the reference

sequence assembly and SNPs in the RTAs. Expression levels are reported in

fragments per kilobase exon model per million mapped reads (FPKM).

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0 50000 100000 150000

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Reference 5b Gene Size (bp)

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n (F

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1000 2000 3000 4000 5000

020

6010

0

Mapped RTA Size (bp)

Avg

Expr

esio

n (F

PKM

)

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Unmapped RTA Size (bp)

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Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  8  

Supplemental Figure 8. Natural variation for vegetative and floral transition

traits measured on a set of diverse inbred lines. (A) Growing degree days (GDD)

to pollen shed measured on 409 lines, (B) GDD to silk measured on 409 lines,

and (C) last juvenile leaf measured in 424 inbred lines. Phenotypic data was

measured in 2010 and 2011 using a randomized complete block design with two

replications per year, and best linear unbiased predictions (BLUPs) are shown.

GDD to Pollen Shed

Freq

uenc

y

1000 1200 1400 1600 1800

040

80

GDD to Silking

Freq

uenc

y

1000 1200 1400 1600 1800 2000

020

6010

0

Last Juvenile Leaf

Freq

uenc

y

4 6 8 10 12 14

040

8012

0

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  9  

Supplemental Figure 9. Manhattan plots of Genome Wide Association Analysis

(GWAS) results for growing degree days (GDD) to silk. (A) Manhattan plot of

GWAS results using single nucleotide polymorphism markers. Genome-wide

significance threshold was set using simpleM method (p = 2.7 x 10-7). (B)

Manhattan plot of GWAS results using gene expression level as the independent

variable. Significance threshold was set using Bonnferoni correction (1.04 x 10-6).

GRMZM2G171622))

Rap2.7)(vgt1)%

A"

B"

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  10  

Supplemental Table 1. Joint representative transcript assemblies (RTAs) with

evidence of transcript splitting. Evidence is based on WU BLASTX searches

against the Oryza sativa v7 and Sorghum bicolor v1 protein sequences.

Groups of Contigs with Evidence of Being Split

Number of Contigs in

Group Source of Evidence joint_Locus_101800, joint_Locus_87723 2 Oryza sativa joint_Locus_1136070, joint_Locus_1657260 2 Oryza sativa joint_Locus_1181568, joint_Locus_684853 2 Oryza sativa joint_Locus_128958 joint_Locus_71128 2 Oryza sativa joint_Locus_13275, joint_Locus_44373 2 Oryza sativa joint_Locus_1436 joint_Locus_2447 2 Oryza sativa joint_Locus_14577 joint_Locus_52134 2 Oryza sativa joint_Locus_15049, joint_Locus_9104 2 Oryza sativa joint_Locus_15397, joint_Locus_66342 2 Oryza sativa joint_Locus_170691, joint_Locus_58823 2 Oryza sativa joint_Locus_18904 joint_Locus_52436 2 Oryza sativa joint_Locus_19415, joint_Locus_9081 2 Oryza sativa joint_Locus_19580 joint_Locus_2763 2 Oryza sativa joint_Locus_22285, joint_Locus_48776 2 Oryza sativa joint_Locus_37766, joint_Locus_8573 2 Oryza sativa joint_Locus_5302, joint_Locus_5612 2 Oryza sativa joint_Locus_63974, joint_Locus_858915 2 Oryza sativa joint_Locus_70405, joint_Locus_998528 2 Oryza sativa joint_Locus_992235, joint_Locus_99675 2 Oryza sativa joint_Locus_1023, joint_Locus_12688 2 Oryza sativa and Sorghum bicolor joint_Locus_13191 joint_Locus_33468 2 Oryza sativa and Sorghum bicolor joint_Locus_15285 joint_Locus_7314 2 Oryza sativa and Sorghum bicolor joint_Locus_16444, joint_Locus_24503 2 Oryza sativa and Sorghum bicolor joint_Locus_16532, joint_Locus_49312 2 Oryza sativa and Sorghum bicolor joint_Locus_16590 joint_Locus_8781 2 Oryza sativa and Sorghum bicolor joint_Locus_16908 joint_Locus_78814 2 Oryza sativa and Sorghum bicolor joint_Locus_20577, joint_Locus_5374 2 Oryza sativa and Sorghum bicolor joint_Locus_21508 joint_Locus_2908 2 Oryza sativa and Sorghum bicolor joint_Locus_21598 joint_Locus_88988 2 Oryza sativa and Sorghum bicolor joint_Locus_22934, joint_Locus_28470 2 Oryza sativa and Sorghum bicolor joint_Locus_23191, joint_Locus_97093 2 Oryza sativa and Sorghum bicolor joint_Locus_23614 joint_Locus_4673 2 Oryza sativa and Sorghum bicolor joint_Locus_24263 joint_Locus_34966 2 Oryza sativa and Sorghum bicolor joint_Locus_30036, joint_Locus_36156 2 Oryza sativa and Sorghum bicolor joint_Locus_30048, joint_Locus_62843 2 Oryza sativa and Sorghum bicolor

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  11  

joint_Locus_3425 joint_Locus_584 2 Oryza sativa and Sorghum bicolor joint_Locus_34360 joint_Locus_64012 2 Oryza sativa and Sorghum bicolor joint_Locus_34600, joint_Locus_59279 2 Oryza sativa and Sorghum bicolor joint_Locus_34661 joint_Locus_38040 2 Oryza sativa and Sorghum bicolor joint_Locus_35404 joint_Locus_69145 2 Oryza sativa and Sorghum bicolor joint_Locus_36466 joint_Locus_94778 2 Oryza sativa and Sorghum bicolor joint_Locus_42803, joint_Locus_55328 2 Oryza sativa and Sorghum bicolor joint_Locus_43723 joint_Locus_44651 2 Oryza sativa and Sorghum bicolor joint_Locus_44942, joint_Locus_8079 2 Oryza sativa and Sorghum bicolor joint_Locus_47209, joint_Locus_93036 2 Oryza sativa and Sorghum bicolor joint_Locus_49248 joint_Locus_59920 2 Oryza sativa and Sorghum bicolor joint_Locus_49864 joint_Locus_5136 2 Oryza sativa and Sorghum bicolor joint_Locus_5057 joint_Locus_9360 2 Oryza sativa and Sorghum bicolor joint_Locus_57418, joint_Locus_7640 2 Oryza sativa and Sorghum bicolor joint_Locus_5776, joint_Locus_7919 2 Oryza sativa and Sorghum bicolor joint_Locus_58467, joint_Locus_6159 2 Oryza sativa and Sorghum bicolor joint_Locus_62194, joint_Locus_6893 2 Oryza sativa and Sorghum bicolor joint_Locus_710645, joint_Locus_9883 2 Oryza sativa and Sorghum bicolor joint_Locus_10093 joint_Locus_9200 2 Sorghum bicolor joint_Locus_114747, joint_Locus_87789 2 Sorghum bicolor joint_Locus_11613, joint_Locus_28214 2 Sorghum bicolor joint_Locus_122107, joint_Locus_42479 2 Sorghum bicolor joint_Locus_12610 joint_Locus_48952 2 Sorghum bicolor joint_Locus_1364, joint_Locus_4786 2 Sorghum bicolor joint_Locus_14038, joint_Locus_22911 2 Sorghum bicolor joint_Locus_14765 joint_Locus_82989 2 Sorghum bicolor joint_Locus_16057 joint_Locus_5437 2 Sorghum bicolor joint_Locus_16727 joint_Locus_3124 2 Sorghum bicolor joint_Locus_1703 joint_Locus_5334 2 Sorghum bicolor joint_Locus_17685, joint_Locus_36037 2 Sorghum bicolor joint_Locus_17880 joint_Locus_428 2 Sorghum bicolor joint_Locus_180 joint_Locus_4968 2 Sorghum bicolor joint_Locus_18464 joint_Locus_9339 2 Sorghum bicolor joint_Locus_19976, joint_Locus_40814 2 Sorghum bicolor joint_Locus_20351 joint_Locus_3181 2 Sorghum bicolor joint_Locus_20499, joint_Locus_25554 2 Sorghum bicolor joint_Locus_21224, joint_Locus_89453 2 Sorghum bicolor joint_Locus_23200 joint_Locus_62640 2 Sorghum bicolor joint_Locus_23469 joint_Locus_51487 2 Sorghum bicolor joint_Locus_23512, joint_Locus_39332 2 Sorghum bicolor joint_Locus_24351 joint_Locus_25115 2 Sorghum bicolor joint_Locus_25134 joint_Locus_25725 2 Sorghum bicolor joint_Locus_26344, joint_Locus_8926 2 Sorghum bicolor

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  12  

joint_Locus_27342 joint_Locus_8701 2 Sorghum bicolor joint_Locus_29789 joint_Locus_64917 2 Sorghum bicolor joint_Locus_30595 joint_Locus_60531 2 Sorghum bicolor joint_Locus_30978, joint_Locus_40567 2 Sorghum bicolor joint_Locus_32394 joint_Locus_50124 2 Sorghum bicolor joint_Locus_32779 joint_Locus_87139 2 Sorghum bicolor joint_Locus_35795 joint_Locus_59202 2 Sorghum bicolor joint_Locus_36014, joint_Locus_93686 2 Sorghum bicolor joint_Locus_36121, joint_Locus_53598 2 Sorghum bicolor joint_Locus_37564 joint_Locus_3950 2 Sorghum bicolor joint_Locus_41520 joint_Locus_9987 2 Sorghum bicolor joint_Locus_42693 joint_Locus_7017 2 Sorghum bicolor joint_Locus_44248 joint_Locus_9508 2 Sorghum bicolor joint_Locus_46683 joint_Locus_5174 2 Sorghum bicolor joint_Locus_5528 joint_Locus_6957 2 Sorghum bicolor joint_Locus_5661, joint_Locus_5738 2 Sorghum bicolor joint_Locus_6643, joint_Locus_89384 2 Sorghum bicolor joint_Locus_138968, joint_Locus_496829, joint_Locus_873258 3 Oryza sativa joint_Locus_22803 joint_Locus_48527, joint_Locus_57710 3

Oryza sativa and/or Sorghum bicolor

joint_Locus_1025038, joint_Locus_13866, joint_Locus_245649 3 Oryza sativa or Sorghum bicolor joint_Locus_10465 joint_Locus_33158, joint_Locus_71675 3 Oryza sativa or Sorghum bicolor joint_Locus_3082, joint_Locus_35141, joint_Locus_4733 3 Oryza sativa or Sorghum bicolor joint_Locus_1258598, joint_Locus_128691, joint_Locus_162710, joint_Locus_685105 4 Oryza sativa joint_Locus_71606, joint_Locus_72742, joint_Locus_73948, joint_Locus_84041 4 Oryza sativa and Sorghum bicolor joint_Locus_14312, joint_Locus_235130, joint_Locus_319977, joint_Locus_53297 4

Oryza sativa and/or Sorghum bicolor

joint_Locus_132552, joint_Locus_20427, joint_Locus_23530, joint_Locus_32486 joint_Locus_770308, joint_Locus_93556 joint_Locus_121873, joint_Locus_70068 joint_Locus_55224, joint_Locus_557202, joint_Locus_83732 11

Oryza sativa and/or Sorghum bicolor

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  13  

Supplemental Table 2. Gene Ontology (GO) slim terms for the 8,681 representative transcript assemblies.

Main Category Subcategory Total Percent biological_process biological_process 4 0.25% biological_process biosynthetic process 161 9.91% biological_process carbohydrate metabolic process 102 6.28% biological_process catabolic process 62 3.82% biological_process cell cycle 3 0.18% biological_process cell death 25 1.54% biological_process cellular component organization 26 1.60% biological_process cellular homeostasis 8 0.49% biological_process cellular process 301 18.53% biological_process DNA metabolic process 65 4.00% biological_process generation of precursor metabolites and energy 14 0.86% biological_process lipid metabolic process 49 3.02% biological_process metabolic process 202 12.44%

biological_process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process 141 8.68%

biological_process photosynthesis 3 0.18% biological_process pollen-pistil interaction 5 0.31% biological_process protein metabolic process 75 4.62% biological_process protein modification process 154 9.48% biological_process response to abiotic stimulus 3 0.18% biological_process response to biotic stimulus 1 0.06% biological_process response to stress 17 1.05% biological_process signal transduction 10 0.62% biological_process translation 51 3.14% biological_process transport 142 8.74% cellular_component cellular_component 2 0.46% cellular_component cell wall 3 0.68% cellular_component cytoplasm 46 10.50% cellular_component cytoskeleton 9 2.05% cellular_component cytosol 4 0.91% cellular_component endoplasmic reticulum 4 0.91% cellular_component extracellular region 4 0.91% cellular_component Golgi apparatus 4 0.91% cellular_component intracellular 48 10.96% cellular_component membrane 202 46.12% cellular_component mitochondrion 9 2.05% cellular_component nuclear envelope 1 0.23% cellular_component nucleoplasm 6 1.37% cellular_component nucleus 55 12.56% cellular_component peroxisome 3 0.68% cellular_component plastid 3 0.68% cellular_component ribosome 31 7.08% cellular_component thylakoid 2 0.46% cellular_component vacuole 2 0.46% molecular_function binding 173 11.66%

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  14  

molecular_function carbohydrate binding 15 1.01% molecular_function catalytic activity 189 12.74% molecular_function DNA binding 82 5.53% molecular_function enzyme regulator activity 9 0.61% molecular_function hydrolase activity 227 15.30% molecular_function kinase activity 21 1.42% molecular_function lipid binding 5 0.34% molecular_function molecular_function 9 0.61% molecular_function motor activity 1 0.07% molecular_function nuclease activity 6 0.40% molecular_function nucleic acid binding 23 1.55% molecular_function nucleotide binding 228 15.36% molecular_function oxygen binding 1 0.07% molecular_function protein binding 163 10.98% molecular_function RNA binding 17 1.15%

molecular_function sequence-specific DNA binding transcription factor activity 17 1.15%

molecular_function signal transducer activity 3 0.20% molecular_function structural molecule activity 34 2.29% molecular_function transferase activity 167 11.25% molecular_function translation factor activity, nucleic acid binding 8 0.54% molecular_function transporter activity 86 5.80%

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  15  

Supplemental Table 3. Single nucleotide polymorphisms (SNPs) in the genome

wide association study (GWAS) SNP set that cause amino acid changes in the

glossy15 protein. Amino acid substitution format is X#Y, where X is the original

amino acid, # is the position of the substitution and Y is the new amino acid.

Asterisk indicates the most significant SNP detected in GWAS.

Amino Acid Substitution

Causal SNP Location

SNP alleles

R26L 95739788* T/G L45F 95,739,846 C/G R57S 95,739,880 C/A P69A 95,739,916 G/C

Supplemental Data. Hirsch et al. Plant Cell. (2014). 10.1105/tpc.113.119982  

  16  

Supplemental Table 4. Summary of growing degree days to pollen shed Genome Wide Association Study (GWAS)

results. The most significant SNP per gene model is reported.

Gene Annotation Chr SNP Position P-value MAF R2 GRMZM2G469551 Homeobox-leucine zipper protein HOX9 1 230,544,444 1.52E-07 0.30 3.6% GRMZM2G044550 Endonuclease/Exonuclease/phosphatase family protein 1 243,990,144 3.86E-08 0.08 3.9%

GRMZM2G444692 Colon cancer-associated protein Mic1-like containing

protein 1 244,073,581 3.86E-08 0.08 3.9% GRMZM2G080355 Stress-enhanced protein 1 1 244,637,069 3.86E-08 0.08 3.9% GRMZM5G859592 Transporter 1 248,589,191 7.59E-08 0.08 3.8% GRMZM2G041770 IFA-binding protein 1 266,951,478 2.42E-07 0.20 3.5% GRMZM2G040965 AFH1 2 193,620,057 3.81E-07 0.11 3.3% GRMZM2G171600 Calmodulin binding protein 3 158,899,098 5.04E-07 0.49 3.3% GRMZM2G171622 CBS domain containing protein 3 158,975,082 2.95E-13 0.46 7.1% GRMZM2G030038 Molecular chaperone, heat shock protein, Hsp40 3 159,677,854 6.03E-07 0.34 3.2% GRMZM2G346639 Nucleic acid binding protein 3 209,913,052 2.44E-07 0.48 3.5% GRMZM2G054651 HVA22 c 4 6,552,572 8.24E-07 0.25 3.1% GRMZM2G135568 Protein transporter 4 39,602,695 2.13E-09 0.02 4.7% GRMZM2G084195 Histone H4 4 156,481,266 5.84E-07 0.03 3.2% GRMZM2G053236 ATP-dependent Clp protease proteolytic subunit 5 188,100,997 6.40E-07 0.26 3.2% GRMZM2G578314 Tetratricopeptide repeat-containing protein 5 208,258,146 1.29E-07 0.10 3.6% GRMZM2G169114 Inner membrane protein ybaL 6 104,858,202 2.48E-07 0.18 3.5% GRMZM2G169089 Diacylglycerol acyltransferase 6 104,859,429 2.83E-08 0.25 4.0% GRMZM2G029685 40S ribosomal protein S24 6 104,966,076 4.58E-07 0.32 3.3% GRMZM5G898887 Serine/threonine-specific receptor protein kinase 7 95,096,143 3.17E-07 0.46 3.4% GRMZM2G578572 BAH domain containing protein 8 57,381,320 2.91E-07 0.05 3.4% GRMZM2G060045 ABC transporter 8 134,740,296 3.84E-07 0.12 3.3% GRMZM2G470513 Transcription initiation factor IIA gamma chain 8 134,843,412 5.23E-07 0.10 3.3%