Table 6 Differential expression of gene transcripts associated with QTLs detected using RNA-seq

Sb01g032875

1

55828932

6.3

Translation elongation factor EF1B

qMC2-1a

qMC2-1, qBY-1

Sb01g032880

1

55840286

4

SPX domain-3

qMC2-1a

qMC2-1, qBY-1

Sb01g032920

1

55885605

6.84

Frigida putative expressed

qMC2-1a

qMC2-1, qBY-1

Sb01g033010

1

56047918

9.1

Retrotransposon protein,

qMC2-1a

qMC2-1, qBY-1

Sb01g033090

1

56202769

3.98

Mannose-binding lectin superfamily

qMC2-1a

qMC2-1, qBY-1

Sb01g033360

1

56595053

−5.2

Acetoacetyl-CoA thiolase 2

qMC2-1a

qMC2-1, qBY-1

Sb01g033410

1

56731990

4.27

Cation/carnitine transporter 3

qMC2-1a

qMC2-1, qBY-1

Sb01g033620

1

56944250

2.77

Metacaspase 1

qMC2-1a

qMC2-1, qBY-1

Sb01g034190

1

57636134

2.49

O-Glycosyl hydrolases

qMC2-1a

qMC2-1, qBY-1

Sb01g035910

1

59529076

9.28

Glutathione S-transferase

qMC2-1b

Sb01g036330

1

59936853

−3.38

Ribosomal protein L16p/L10e family

qTW1

Sb01g036790

1

60395728

2.56

Late embryogenesis abundant protein 1

qTW1

Sb01g037480

1

61031332

4.1

Nicotianamine synthase 4

qTW1

Sb01g038720

1

62214256

−7.69

LHT1 lysine histidine transporter 1

qAD-1

Sb01g041180

1

64497962

−3.32

HSP21 Heat shock protein 21

qGY-1b

Sb01g041350

1

64653444

2.63

Subtilisin-like serine protease 2

qGY-1b

Sb01g041390

1

64692370

−2.39

Senescence associated protein

qGY-1b

Sb01g041640

1

64933485

2.04

Oxidoreductase superfamily protein

qGY-1b

Sb01g041810

1

65045823

3.75

STRUBBELIG-RECEPTOR FAMILY 7

qGY-1b

Sb01g042500

1

65775142

1.99

Caleosin-related family protein

qGY-1b

Sb01g042530

1

65792345

2.89

MA3 domain-containing protein

qGY-1b

Sb01g044230

1

67360823

2.26

Polyamine oxidase 1

qGY-1b

Sb01g044810

1

67970813

3.04

MADS-box transcription factor family

qGY-1b

Sb01g045620

1

68676107

2.29

Lectin protein kinase family protein

qGY-1b

Sb01g047250

1

70350087

2.412

Leucine-rich repeat transmembrane protein kinase

qGY-1b

Sb01g047550

1

70645925

2.215

Tetratricopeptide repeat (TPR)-like superfamily protein

qGY-1b

Sb01g047650

1

70741548

−3.156

CCT motif family protein

qGY-1b

Sb01g047780

1

70919577

−8.348

Magnesium transporter 6

qGY-1b

Sb01g048000

1

71075448

1.861

Glutathione S-transferase

qGY-1b

Sb01g048030

1

71101357

3.126

Cytochrome P450, family 78,

qGY-1b

Sb01g048100

1

71159986

−4.194

LYM2 lysm domain GPI-anchored protein 2 precursor

qGY-1b

Sb01g048640

1

71596638

6.418

Leucine-rich repeat family protein

qGY-1b

Sb06g002090

6

3921155

3.276

F-box/RNI-like/FBD-like domains-containing protein

qGY-6a

Sb06g002180

6

4089379

−2.511

UDP-glucosyltransferase

qGY-6a

Sb06g003180

6

6636307

3.018

CAP (Cysteine-rich secretory proteins

qGY-6a

Sb06g005420

6

13588101

6.889

expressed protein

Sb06g006920

6

16373350

−2.546

purple acid phosphatase 27

qGY-6b

Sb06g008990

6

26359064

2.375

Oxidoreductase, zinc-binding dehydrogenase family protein

qGY-6b

Sb06g010870

6

30379011

3.616

Cytochrome P450, family 71

qGY-6b

Sb06g011767

6

32144416

6.478

auxin response factor 2

qGY-6b

Sb06g011770

6

32145882

6.844

C2H2-like zinc finger protein

qGY-6b

Sb06g012040

6

32755618

2.708

Minichromosome maintenance (MCM2/3/5) family protein

qGY-6b

Sb06g012280

6

33774679

2.815

UDP-Glycosyltransferase superfamily

qGY-6b

Sb06g012290

6

33921889

4.708

Galactose oxidase/kelch repeat superfamily protein

qGY-6b

Sb06g014250

6

39313831

4.128

multidrug resistance-associated protein 9

qGY-6b

Sb06g014400

6

39867816

−3.085

HSP70 Heat shock protein 70

Sb06g015520

6

43082617

3.501

B-block binding subunit of TFIIIC

qPH-6, qGY-6c

Sb06g016160

6

44576681

2.202

seed storage 2S albumin superfamily

qPH-6, qGY-6c

Sb06g016230

6

44708205

2.164

Late embryogenesis abundant hydroxyproline-rich glycoprotein

qPH-6, qGY-6c

Sb06g016260

6

44735351

2.5

Aluminium activated malate transporter

qPH-6, qGY-6c

Sb06g019470

6

49032854

1.3

Copper transport protein family

qMC1-6a

Sb06g019600

6

49168975

4.279

Cytochrome P450 superfamily protein

qMC1-6a

Sb06g019610

6

49174004

2.452

phosphofructokinase 2

qMC1-6a

Sb06g024400

6

53535970

1.683

NUDIX family, domain containing protein

qMC1-6b

qMC1-6b

Sb06g024590

6

53686490

1.958

tonoplast intrinsic protein

qMC1-6b

qMC1-6b

Sb06g024650

6

53730735

4.367

expansin B2

qMC1-6b

qMC1-6b

Sb06g025220

6

54190773

−2.114

calcium-dependent protein kinase 29

qMC1-6b

qMC1-6b

Sb06g025250

6

54207289

2.782

Prolyl oligopeptidase family protein

qMC1-6b

qMC1-6b

Sb06g025330

6

54262137

2.362

expressed protein

qMC1-6b

qMC1-6b

Sb06g028210

6

57045616

2.252

Terpenoid cyclases/Protein prenyltransferases superfamily protein

qMC2-6

Sb06g028480

6

57260405

2.019

unknown

qMC2-6

Sb06g028760

6

57496434

1.729

Leucine-rich receptor-like protein kinase

qMC2-6

Sb07g022670

7

57311597

2.956

Glutamate decarboxylase

qChl3-7, qBY-7

Sb07g022800

7

57514740

2.625

aspartyl protease family protein

qChl3-7, qBY-7

Sb07g023140

7

57977647

4.794

Gibberellin receptor GID1L2

qChl3-7, qBY-7

Sb07g023220

7

58087984

−3.707

phospholipase A

qChl3-7

Sb07g023300

7

58178273

2.495

expressed protein

qChl3-7

Sb07g023770

7

58722654

11.097

rotamase

qChl3-7

Sb07g024200

7

59189842

−7.492

Ribosomal protein L1p/L10e family

qChl3-7

Sb07g025190

7

60212195

4.048

MATE efflux family protein

qChl3-7

Sb07g025240

7

60280418

−2.248

hydroxymethylglutaryl-CoA synthase

qChl3-7

Sb07g025843

7

60959427

2.544

ethylene-responsive transcription factor ERF114, putative, expressed

qChl1-7

Sb08g000550

8

482761

−2.111

ferritin-1, chloroplast precursor

qGS-8

Sb08g002590

8

2673615

−2.004

WRKY DNA-binding protein 55

qGS-8

Sb08g002660

8

2779571

2.726

Protease inhibitor/seed storage/LTP

qGS-8

Sb08g003170

8

3513569

3.001

Chalcone and stilbene synthase family

qGS-8

Sb08g003820

8

4423015

−3.008

zinc finger superfamily protein

qGS-8

Sb08g004500

8

5410066

−2.127

fructose-bisphosphate aldolase 2

qGS-8

Sb09g018440

9

46098300

6.288

methyl esterase 3

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g020000

9

49032969

8.222

inosine-uridine preferring nucleoside hydrolase family protein

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g020240

9

49471823

3.041

Major facilitator superfamily protein

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g021016

9

50446536

3.241

ethylene-responsive transcription factor

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g021250

9

50714173

2.158

alpha/beta-Hydrolases superfamily protein

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g021490

9

50944384

4.533

Subtilase family protein

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g021720

9

51194456

−1.869

histone deacetylase 8

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g022390

9

52044973

8.308

Ribosomal protein

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g023150

9

52794183

2.46

ribonuclease P family protein

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g023320

9

52948577

6.593

Major facilitator superfamily protein

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g024840

9

54319624

−2.168

ferredoxin--nitrite reductase

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g025530

9

55006797

2.719

O-methyltransferase family protein

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g025540

9

55018768

2.155

O-methyltransferase family protein

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g025730

9

55141225

3.406

non-symbiotic hemoglobin 2

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g025900

9

55284480

−2.24

HSP101 Heat shock protein 101

qAD-9a, qChl2-9b

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g026590

9

55803666

1.86

RING/U-box superfamily protein

qAD-9a, qChl2-9b

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g027380

9

56449825

−2.508

serine/threonine-protein kinase SNT7, chloroplast precursor

qAD-9a, qChl2-9b

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g027470

9

56561299

7.612

Disease resistance protein

qAD-9a, qChl2-9b

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g027590

9

56662520

2.783

seed storage 2S albumin superfamily

qAD-9a, qChl2-9b

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g028890

9

57684814

2.326

Iron-sulfur cluster, SufE/NifU family protein

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g028960

9

57721281

3.573

ribosomal protein L13

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9

Sb09g029540

9

58186320

5.903

AMP-dependent synthetase

qAD-9a

qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9