Table 1 Summary of 32 candidate genes were newly disclosed by examining the mGWAS data from rice grain.

From: Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals

Metabolite

Associated SNP

M-P value*

P-trait

P-P value†

Cor‡

Candidate gene

Description

Cystathionine

sf0218685490

1.20E-07

   

Os02g31200

Esterase

Asparagine

sf0310123005

5.70E-07

   

Os03g18130

Asparagine synthetase

LPC (1-acyl16:1)

vf0131875915

4.44E-07

   

Os01g55360

Cytidylyltransferase

Sinapoylcholine

sf0629727750

1.89E-09

   

Os06g49050

hAT

Trigonelline

sf0235364705§

2.78E-32

GW

1.2E-08

0.40

Os02g57760

O-methyltransferase

Trigonelline

sf0314995948

5.63E-08

GW

7.5E-08

0.40

Os03g26200

O-methyltransferase

Trigonelline

sf0630519510

1.63E-16

GW

1.3E-08

0.40

Os06g50400

Expansin precursor

Trigonelline

sf0707312584

8.93E-11

GW

6.6E-06

0.40

Os07g12780

Cyclin

Trigonelline

sf0523433859

2.59E-16

GT

9.8E-11

0.38

Os05g39990

Expansin precursor

Trigonelline

sf0721002801

5.94E-08

GT

6.3E-06

0.38

Os07g35060

OsFBX238

Trigonelline

sf1108644317

9.84E-18

   

Os11g15300

O-methyltransferase

C-hex-chr O-hex

sf0224981507§

2.39E-08

HC

2.2E-06

0.33

Os02g41650

PAL

Cya O-rut

sf0424349335

8.17E-12

HC

6.2E-07

0.50

Os04g41350

Amino acid transporter

Del O-hex der

sf0424523684

1.69E-10

HC

4.0E-09

0.61

Os04g41680

Endochitinase A

Peo O-hex

sf1005351606

1.65E-10

HC

1.7E-07

0.40

Os10g09860

Chalcone synthase

Catechin

sf0405211891

6.25E-10

SC

8.8E-09

0.91

Os04g09720

OsSCP22

Peo O-rut

sf0423865941

9.05E-10

SC

9.4E-07

0.60

Os04g40470

Cytochrome P450

Peo O-hex

sf0428130219

1.97E-12

SC

3.5E-08

0.31

Os04g47720

UGT

Di-catechin

sf0519583338

1.43E-18

SC

6.8E-15

0.86

Os05g33430

Xyloglucanase inhibitor

C-pen-api O-rut

sf0520731687

1.73E-07

SC

2.3E-09

−0.37

Os05g35010

Cytochrome P450

Catechin

sf0706686370

2.26E-13

SC

1.9E-13

0.91

Os07g11440

Chalcone synthase

Catechin

sf1223103558

1.15E-10

SC

2.1E-07

0.91

Os12g37690

MYB

Eri O-mhex

sf0129468555

3.39E-08

   

Os01g51260

MYB

Pel O-hex

sf0132150258

2.10E-12

   

Os01g55830

GST

Peo O-hex

vf0235263818

1.21E-12

   

Os02g57580

Anthocyanin permease

Del O-rut

sf0304428849

2.63E-07

   

Os03g08600

UGT

O-methylapi-C-hex

vf0406561691||

6.74E-47

   

Os04g11970

O-methyltransferase

C-pen-api O-rut

sf0524320092

3.25E-52

   

Os05g41645

Chalcone synthase

Tri O-hex-hex

sf0526155386

9.84E-19

   

Os05g45150

UGT

C-hex-lut O-couhex

sf1008424002

6.59E-08

   

Os10g16974

Cytochrome P450

Chr O-hex-rut

sf1111581156

3.90E-13

   

Os11g20080

O-methyltransferase

Tri O-gluc-O-hex

sf1222982501

3.87E-18

   

Os12g37510

UGT

  1. Metabolites abbreviations: Cya O-rut, cyanidin O-rutinoside; C-hex-chr O-hex, C-hexosyl-chrysoeriol O-hexoside; Chr O-ferhex-O-hex, chrysoeriol O-feruloylhexosyl-O-hexoside; Chr O-hex-rut, chrysoeriol O-hexosyl-O-rutinoside; Del O-rut, delphinidin O-rutinoside; Del O-hex der, delphinidin O-hexoside derivative; Eri O-mhex, eriodictyol O-malonylhexoside; C-hex-api O-couhex, C-hexosyl-apigenin O-p-coumaroylhexoside; O-methylapi-C-hex, O-methylapigenin-C-hexoside; Peo O-rut, peonidin O-rutinoside; C-pen-api O-rut, C-pentosyl-apigenin O-rutinoside; Peo O-hex, peonidin O-hexoside; C-pen-api O-rut, C-pentosyl-apigenin O-rutinoside; Pel O-hex, pelargonidin O-hexoside; Tri O-hex-hex, tricin O-hexosyl-O-hexoside; Tri O-gluc-O-hex, tricin O-glucuronide-O-hexoside. Phenotype abbreviations: GW, grain width; GT, grain thickness; GST, glutathione S-transferase; HC, hull colour; LPC, lysophosphatidylcholine; hAT, hAT transposon superfamily protein; PAL, phenylalanine ammonia lyase; SC, seed colour.
  2. *P value of the corresponding metabolic trait calculated by LMM.
  3. †P value of the corresponding phenotypic trait calculated by LMM.
  4. ‡The correlation between metabotype and phenotype.
  5. §SNP introducing initiation codon.
  6. ||2-bp deletion.
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