Table 2 Co-located QTNs and candidate genes as well as the related homologs

chr1.S_2694039

1

2,694,039

2.06

3VmrMLM-S

BLUP

SUG

6.085

1.20 × 10^− 7

GRMZM2G035377

AT5G22940 (F8H)

a member of glycosyltransferase family 47

[70]

1.47

3VmrMLM-M

ALL

SIG

16.89

1.16 × 10^− 18

GRMZM2G085691

AT5G03450

Transducin/WD40 repeat-like superfamily protein

GRMZM2G388684

AT2G36870 (XTH32)

xyloglucan endotransglucosylase/hydrolase 32

[71]

GRMZM2G085827

AT3G11470

4’-phosphopantetheinyl transferase superfamily

GRMZM2G085872

AT4G31040 (DLDG1)

Chloroplast membrane protein that modulates H + homeostasis

[72]

LOC_Os08g12780 (ARE1)

chloroplast envelope membrane protein

[73]

GRMZM2G085885

AT5G35100 (CYP28)

Cyclophilin-like peptidyl-prolyl cis-trans isomerase family protein

[74]

GRMZM2G086242

AT4G31040 (DLDG1)

Chloroplast membrane protein that modulates H + homeostasis

[72]

LOC_Os08g12780 (ARE1)

chloroplast envelope membrane protein

[73]

chr1.S_25147299

1

25,147,299

3.91

3VmrMLM-S

HB

SIG

8.856

1.70 × 10^− 10

GRMZM2G023364

NA

NA

1.35

3VmrMLM-S

BLUP

SUG

3.577

4.94 × 10^− 5

GRMZM2G326869

AT2G29200 (PUM1)

a member of the (APUM) proteins containing PUF domain

[75]

GRMZM2G376074

AT3G49600 (UBP26)

Encodes a ubiquitin-specific protease

[76]

GRMZM2G077045

AT1G25580 (SOG1)

Encodes suppressor of gamma response 1 (SOG1)

[77]

chr1.S_258002397

1

258,002,397

NA

BLINK

HB

NA

NA

2.97 × 10^− 10

GRMZM2G107120

NA

NA

NA

MLMM

HB

NA

NA

1.48 × 10^− 6

GRMZM2G703998

NA

NA

NA

SUPER

HB

NA

NA

1.70 × 10^− 7

GRMZM2G055037

AT5G45100 (BRG1)

one of the BRGs (BOI-related gene)

[78]

NA

FarmCPU

HB

NA

NA

6.92 × 10^− 7

GRMZM2G319281

AT3G50690

Leucine-rich repeat (LRR) family protein

GRMZM2G044762

AT3G46940 (DUT1)

DUTP-PYROPHOSPHATASE-LIKE 1

[79]

GRMZM2G045314

AT4G34460 (AGB1)

GTP binding protein beta 1

[80]

LOC_Os03g46650 (RGB1)

guanine nucleotide-binding protein subunit beta-like

[40]

GRMZM2G046101

AT4G34480

O-Glycosyl hydrolases family 17 protein

chr1.S_282470596

1

282,470,596

NA

MLMM

YC

NA

NA

1.32 × 10^− 6

GRMZM5G837018

AT3G49650

P-loop containing nucleoside triphosphate hydrolases superfamily protein

1.07

3VmrMLM-S

YC

SIG

7.483

4.36 × 10^− 9

chr2.S_218342905

2

218,342,905

NA

SUPER

BLUP

NA

NA

4.16 × 10^− 7

GRMZM2G453845

AT4G00690

UB-like protease 1B

0.42

3VmrMLM-M

ALL

SIG

19.08

7.09 × 10^− 21

GRMZM2G151905

AT3G08960 (KA120)

ARM repeat superfamily protein

[81]

GRMZM2G151975

AT1G09900

Pentatricopeptide repeat (PPR-like) superfamily protein

GRMZM2G151979

NA

NA

chr3.S_113480155

3

113,480,155

1.41

3VmrMLM-S

HB

SUG

4.371

7.24 × 10^− 6

GRMZM2G062080

AT5G05520

Outer membrane OMP85 family protein

1.79

3VmrMLM-M

ALL

SIG

24.09

6.18 × 10^− 26

GRMZM2G395549

AT3G11130 (CHC1)

CHC1 heavy chain subunit of clathrin

[82]

GRMZM2G093347

AT1G27450 (APT1)

Adenosine phosphoribosyl transferase (E.C:2.4.2.7)

[41]

chr4.S_233763894

4

233,763,894

1.75

3VmrMLM-S

YC

SIG

7.795

2.08 × 10^− 9

GRMZM2G056867

AT1G51130 (NSE4A)

δ-kleisin component of the SMC5/6 complex

[83]

1.73

3VmrMLM-S

HB

SIG

7.356

5.88 × 10^− 9

GRMZM2G056920

AT3G12130 (KHZ1)

a CCCH zinc-finger and KH domain protein (KHZ1)

[39]

3.49

3VmrMLM-S

BLUP

SIG

15.69

1.91 × 10^− 17

AC204231.3_FG010

NA

NA

0.65

3VmrMLM-M

ALL

SIG

12.33

4.88 × 10^− 14

GRMZM2G063909

AT2G44350 (ATCS)

mitochrondrion targeted citrate synthase

[84]

chr5.S_70070643

5

70,070,643

2.96

3VmrMLM-S

BLUP

SIG

7.437

4.85 × 10^− 9

GRMZM2G044348

AT2G03120 (AtSPP)

homologous to Signal Peptide Peptidases (SPP)

[85]

0.80

3VmrMLM-M

ALL

SIG

8.279

6.64 × 10^− 10

LOC_Os02g02530 (OsSPP1)

signal peptide peptidase 1-like

[86]

GRMZM2G098301

AT1G42540 (GLR3.3)

member of Putative ligand-gated ion channel subunit family

[87]

GRMZM2G098370

AT5G17310 (UGP2)

UDP-glucose pyrophosphorylase

[88]

LOC_Os02g02560 (OsUgp2)

UTP–glucose-1-phosphate uridylyltransferase

[89]

GRMZM2G098420

AT5G17290 (ATG5)

Autophagy protein ATG5

[90]

GRMZM2G098438

AT5G64470

trichome birefringence-like protein

GRMZM2G156924

NA

NA

GRMZM2G156824

AT4G35600 (CST)

a receptor-like cytoplasmic kinase that acts

[91]

GRMZM2G456917

AT3G02570 (PMI1)

protein with phosphomannose isomerase activity.

[92]

chr5.S_73045639

5

73,045,639

NA

BLINK

YY

NA

NA

7.86 × 10^− 7

GRMZM2G029065

AT4G12080 (AHL1)

AT-hook motif nuclear-localized protein 1

[93]

NA

MLMM

YY

NA

NA

7.69 × 10^− 7

GRMZM2G029087

AT5G47120 (ATBI-1)

a homolog of mammalian Bax inhibitor 1 (BI-1)

[94]

NA

FarmCPU

YY

NA

NA

7.86 × 10^− 7

GRMZM2G029879

AT2G44740

cyclin p4

NA

SUPER

YY

NA

NA

1.64 × 10^− 7

GRMZM2G030013

AT4G26000 (PEPPER)

a polypeptide with K-homology (KH) RNA-binding modules

[95]

NA

SUPER

HB

NA

NA

1.16 × 10^− 6

NA

SUPER

BLUP

NA

NA

1.34 × 10^− 6

chr5.S_209582673

5

209,582,673

NA

BLINK

YY

NA

NA

1.14 × 10^− 6

GRMZM2G046885

AT2G22540 (SVP)

a nuclear protein that acts as a floral repressor

[96]

LOC_Os02g52340

MADS-box transcription factor 22-like (OsMADS22)

[97]

NA

SUPER

YY

NA

NA

2.74 × 10^− 7

GRMZM2G012178

AT4G33945

ARM repeat superfamily protein

NA

SUPER

HB

NA

NA

3.47 × 10^− 7

GRMZM2G465430

AT5G47120 (ATBI-1)

a homolog of mammalian Bax inhibitor 1 (BI-1),

[94]

NA

SUPER

BLUP

NA

NA

1.14 × 10^− 6

NA

FarmCPU

YY

NA

NA

1.14 × 10^− 6

4.63

3VmrMLM-S

YY

SIG

43.35

2.52 × 10^− 45

chr5.S_215364939

5

215,364,939

NA

SUPER

HB

NA

NA

7.55 × 10^− 7

GRMZM5G897740

AT5G42223

a defensin-like (DEFL) family protein

NA

SUPER

BLUP

NA

NA

6.43 × 10^− 7

GRMZM2G079013

AT2G32700 (LUH)

a WD40 repeat and LUFS domain containing protein

[98]

GRMZM2G078887

AT3G07090

Interacts with C3H59 via its WD40 domain and C-terminal region

GRMZM2G376595

AT1G04010 (PSAT1)

aphosphoserine aminotransferase

[99]

chr7.S_170643809

7

170,643,809

1.37

3VmrMLM-S

BLUP

SIG

8.732

2.28 × 10^− 10

GRMZM2G436082

AT2G41770 (STL1)

cellulose synthase complexes

[100]

0.54

3VmrMLM-M

ALL

SIG

13.75

1.75 × 10^− 15

GRMZM2G133400

AT5G13720

Uncharacterized protein family

[101]

GRMZM2G133392

AT5G27320 (GID1C)

a gibberellin (GA) receptor

[102]

GRMZM2G133358

AT3G60910

S-adenosyl-L-methionine-dependent methyltransferases superfamily protein

GRMZM2G433767

AT3G63470

serine carboxypeptidase-like 40

GRMZM2G133275

AT2G28420

Vicinal oxygen chelate (VOC) superfamily member

LOC_Os07g46360 (OsGly I)

glyoxalase family protein

[103]

chr9.S_110657959

9

110,657,959

NA

SUPER

HB

NA

NA

2.53 × 10^− 7

GRMZM2G110408

AT2G30950 (VAR2)

Metalloprotease

[37]

NA

SUPER

BLUP

NA

NA

1.74 × 10^− 6

GRMZM2G110646

AT1G68000 (PIS1)

phosphatidylinositol synthase 1

[104]

NA

FarmCPU

HB

NA

NA

1.27 × 10^− 6

chr9.S_110659989

9

110,659,989

NA

SUPER

HB

NA

NA

9.31 × 10^− 7

GRMZM2G110408

AT2G30950 (VAR2)

Metalloprotease

[37]

NA

SUPER

BLUP

NA

NA

1.74 × 10^− 6

GRMZM2G110646

AT1G68000 (PIS1)

phosphatidylinositol synthase 1

[104]

chr9.S_111331253

9

111,331,253

3.76

3VmrMLM-S

HB

SUG

5.44

5.59 × 10^− 7

2.18

3VmrMLM-S

BLUP

SUG

3.612

4.54 × 10^− 5

2.31

3VmrMLM-M

ALL

SIG

14.75

1.72 × 10^− 16

chr9.S_152202624

9

152,202,624

1.94

3VmrMLM-S

BLUP

SUG

5.023

1.51 × 10^− 6

GRMZM2G178072

AT3G24010

a member of the Inhibitor of Growth family homeodomain proteins

0.88

3VmrMLM-M

ALL

SIG

8.909

1.50 × 10^− 10

GRMZM5G865819

AT2G20370 (UMR3)

a xyloglucan galactosyltransferase

[105]

GRMZM2G137779

AT2G20370 (UMR3)

a xyloglucan galactosyltransferase

[105]

chr10.S_3188051

10

3,188,051

2.91

3VmrMLM-S

BLUP

SIG

10.37

4.85 × 10^− 12

GRMZM2G356817

AT3G14470 (LRR4)

NB-ARC domain-containing disease resistance protein

[106]

0.83

3VmrMLM-M

ALL

SIG

12.36

4.55 × 10^− 14

GRMZM2G356839

NA

NA

GRMZM2G058481

AT3G08600

transmembrane protein, putative

GRMZM2G058531

AT3G08570

Phototropic-responsive NPH3 family protein

LOC_Os02g35970 (CPT1)

coleoptile phototropism protein 1-like

[107]

GRMZM5G862857

NA

NA

GRMZM2G058595

AT2G30520 (RPT2)

a phototropin-interacting NRL protein

[108]

chr10.S_12754330

10

12,754,330

3.59

3VmrMLM-S

YY

SIG

15.03

8.91 × 10^− 17

GRMZM2G137407

AT5G58380 (SIP1)

a CBL-interacting protein kinase

[109]

4.07

3VmrMLM-S

BLUP

SIG

13.53

2.94 × 10^− 15

LOC_Os12g02200 (OsCIPK14)

CBL-interacting protein kinase 14-like

[110]

2.23

3VmrMLM-M

ALL

SIG

30.22

4.06 × 10^− 32

GRMZM2G063394

AT1G76390 (PUB43)

Plant U-box type E3 ubiquitin ligase

[111]

GRMZM5G802395

NA

NA

chr10.S_28506964

10

28,506,964

NA

MLMM

YY

NA

NA

1.06 × 10^− 6

10.28

MLM

YY

NA

NA

1.38 × 10^− 6