Table 2 Chromosome localization of the identified wheat carotenoid biosynthetic/catabolic genes on the durum [29] and bread wheat [28] consensus maps and allele frequency in the tetraploid wheat collection of 233 genotypes

PSY1

Phytoene synthase 1

BS00022137_51

IWB6923

A/G

7AL

203.2

-

0.26–0.74

0.12–0.88

BobWhite_c4483_603

IWB3406

A/G

7AL

-

226.1

monomorphic

monomorphic

CAP7_c12398_110

IWB13781

T/G

7BL

200.1

164.2

failed

failed

BS00010747_51

IWB6281

T/G

7BL

200.1

164.2

failed

failed

BS00084631_51

IWB11376

T/G

7DL

-

-

Kukri_rep_c105287_311

IWB49080^aa

T/C

7DL

208.1

PSY2

Phytoene synthase 2

BobWhite_c339_247

IWB2660

G/T

5AS

-

15.6

0.83–0.17

0.84–0.16

RAC875_c51670_117

IWB58766

C/T

5AS

-

15.6

0.77–0.23

0.87–0.13

Excalibur_c2922_3416

IWB24805^a

C/T

5AS

46.6

15.6

monomorphic

monomorphic

Excalibur_c30273_138

IWB24947

C/T

5BS

-

19.7

0.29–0.71

0.13–0.87

Kukri_c23694_370

IWB42850

A/G

5BS

-

19.7

0.75–0.25

0.87–0.13

GENE-3207_610

IWB33289

C/T

5BS

-

19.7

0.72–0.28

0.87–0.13

GENE-3207_134

IWB33287

A/G

5BS

-

19.7

failed

failed

Excalibur_c3948_1315

IWB26051^a

C/T

5BS

15.8

19.7

0.43–0.57

0.48–0.52

GENE-3207_174

IWB33288

A/G

5DS

-

-

PSY3

Phytoene synthase 3

CAP7_c7840_316

IWB14264

A/G

5 L

-

-

monomorphic

monomorphic

BS00077855_51

IWB10965^a

C/T

5AL

126.8

82.0

0.74–0.26

0.88–0.12

PDS

Phytoene desaturase

BobWhite_c3609_361

IWB2819

A/G

4AS

-

-

0.01-0.99

monomorphic

Tdurum_contig11560_383

IWB67151

C/T

4BL

-

-

monomorphic

monomorphic

IACX725

IWB36188

A/G

4BL

-

-

monomorphic

monomorphic

Kukri_c20125_281

IWB42264^a

C/T

4BL

83.1

75.6

0.81–0.19

0.90–0.10

Ra_c72128_236

IWB52568

A/G

4DL

-

-

Z-ISO

cis-zeta-carotene isomerase

-

-

ZDS

Zeta-carotene desaturase

CAP11_c754_335

IWB13046

A/G

2AS

-

-

monomorphic

monomorphic

JD_c52783_234

IWB37604

C/T

2BS

-

-

monomorphic

monomorphic

Kukri_c23475_1485

IWB42817

A/G

2BS

-

-

monomorphic

monomorphic

RFL_Contig3540_283

IWB64386

A/C

2BS

-

-

monomorphic

monomorphic

Ra_c5594_569

IWB52265

A/G

2DS

-

-

D_contig22022_580

IWB16076

T/G

2DS

-

-

CRTISO (CISO)

Carotenoid isomerase

IAAV5931

IWB35115

A/G

1AS

-

66.9

0.98–0.02

monomorphic

IAAV2888

IWB34631^a

A/G

1AS

43.3

66.3

0.12–0.88

monomorphic

CAP11_c292_249

IWB12814

T/C

1BS

-

-

monomorphic

monomorphic

LYCB (LCYB)

Lycopene beta-cyclase

CAP7_rep_c12997_415

IWB14395

A/G

6S

-

-

monomorphic

monomorphic

Excalibur_c9273_1271

IWB29407^a

T/C

6DS

-

-

LYCE (LCYE)

Lycopene epsilon-cyclase

wsnp_Ex_c48136_53140385

IWA4009

T/C

3AL

-

85.4

monomorphic

monomorphic

RAC875_c2375_132

IWB55558

A/G

3AL

-

-

monomorphic

IAAV4785

IWB34923^a

G/T

3AL

65.9

85.4

0.29–0.71

0.35–0.65

Excalibur_c34554_312

IWB25473^a

C/T

3BL

67.2

64.4

0.31–0.69

0.16–0.84

D_contig37716_635

IWB16739

A/G

3DL

-

-

Kukri_c196_184

IWB42160

AC

3DL

-

-

BCH1 (CHYB1, HYD1)

Carotenoid β-ring hydroxylase (β-hydroxylase 1)

BobWhite_c34273_67

IWB2683

A/nulli

2AL

133.3

-

0.81–0.19

monomorphic

Tdurum_contig5114_319

IWB72154^a

C/T

2AL

-

112.1

0.51–0.49

0.30–0.70

RFL_Contig329_957

IWB64290

T/nulli

2BL

-

-

0.90–0.10

monomorphic

RFL_Contig329_877

IWB64289

A/G

2BL

-

-

monomorphic

monomorphic

BCH2 (CHYB2, HYD2)

Carotenoid β-ring hydroxylase (β-hydroxylase 2)

Tdurum_contig12547_293

IWB67643

T/C

4BL, 4DL, 5AL

-

-

monomorphic

monomorphic

CYP97A3 (LUT5)

Carotenoid β-ring hydroxylase (Cytochrome P450-type monooxygenase CYP97A3)

wsnp_JD_c7795_8868122

IWA6182

C/T

6AL

-

138.3

0.04–0.96

0.01–0.99

wsnp_BF291974A_Ta_2_1

IWA441^a

C/T

6AL

122.7

138.0

0.58–0.42

0.55–0.45

Tdurum_contig569_263

IWB72540

A/G

6BL

145.3

108.9

0.77–0.23

0.75–0.25

CAP11_c816_470

IWB13062^a

A/G

6BL

145.3

-

0.54–0.46

0.33–0.67

GENE-3988_631

IWB33711

A/G

6BL

145.8

-

0.04–0.96

monomorphic

BobWhite_c12032_371

IWB293

T/C

6DL

-

133.54

CYP97C1 (LUT1)

Carotenoid ε ring -hydroxylase (Cytochrome P450-type monooxygenase CYP97C1)

Kukri_rep_c111979_282

IWB49532

T/C

1AL

-

Excalibur_c29401_543

IWB24832

A/G

1BL

-

CCD7 (MAX3)

Carotene (9,10) cleavage dioxygenase

-

-

CCD8 (MAX4)

(13,14) cleavage dioxygenase

-

-

CCD1 (NC5)

(5,6) (5′,6′) (9,10) (9′,10′) carotenoid cleavage dioxygenase

wsnp_Ex_c6209_10838456

IWB4445

A/G

5AS

-

-

CAP11_c2357_97

IWB12774

T/C

5BS

-

-

TA004832-0873

IWB65889

A/G

5BS

0.7

8.7

BobWhite_rep_c53718_103

IWB5053

T/C

5DS

-

-

CYP711A1 (MAX1)

Cytochrome P450-type monooxygenase CYP711A1

-

-

-

-

ZEP (ABA1)

Zeaxanthin epoxidase

RAC875_c856_92

IWB60810

A/C

2DL

-

-

CAP7_c4349_243

IWB14103

A/G

2DL

-

-

D_GBF1XID01ASYXD_209

IWB18346

A/G

2DL

-

-

VDE

Violaxanthin de-epoxidase

wsnp_Ex_c11728_18862431

IWA1533

A/G

2AL

-

-

0.87–0.13

monomorphic

wsnp_Ex_rep_c69465_68405569

IWA5610

C/T

2BL

-

99.8

0.08–0.92

0.02–0.98

wsnp_Ex_c39862_47046812

IWA3696

C/T

2BL

-

99.6

0.01–0.99

monomorphic

wsnp_Ex_c9805_16183499

IWA4965^a

C/T

2BL

94.2

99.8

0.07–0.93

0.02–0.98

Kukri_c52435_163

IWB46254

A/G

2BL

-

-

monomorphic

monomorphic

NXS

Neoxanthin synthase

-

-

NCED4 (CCD4)

9-cis-epoxycarotenoid dioxigenase 4

wsnp_RFL_Contig4424_5193532

IWA8592^a

C/T

6AL

62.8

82.4

0.24–0.76

0.07–0.93

CAP11_c4654_171

IWB12893

A/G

6DL

-

-

NCED9 (NC2; CCD9)

9-cis-epoxycarotenoid dioxigenase

CAP11_c5699_107

IWB12966

T/C

6DL

-

-

CAP7_c6372_329

IWB14194

A/G

6DL

-

-

ABA2 (SDR)

Short-chain alcohol dehydrogenase

Tdurum_contig13608_72

IWB68029

T/G

5AL

-

-

failed

failed

RFL_Contig4520_749

IWB64707

A/G

5BL

157.5

137.1

0.70–0.30

0.54–0.46

Tdurum_contig13608_195

IWB68027

T/C

5DL

-

-

AAO3

Abscisic aldehyde oxidase

RAC875_c64451_465

IWB59875

C/T

7AL

180.3

-

0.76–0.24

0.70–0.30

Kukri_c5789_1029

IWB46699

T/C

7AL

180.3

-

failed

failed

Ku_c5789_1180

IWB39660

G/T

7BL

155.7

120.8

0.37–0.63

0.24–0.76

Excalibur_rep_c112889_341

IWB30603

A/G

7DL

-

184.18