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Table 1 Genes that were included in the expression analysis

From: The mQTL hotspot on linkage group 16 for phenolic compounds in apple fruits is probably the result of a leucoanthocyanidin reductase gene at that locus

Group

Gene name

Gene ID

Forward primer (5’→ 3’)

Reverse primer (5’→ 3’)

LG on “Golden Delicious”

Gene position on LG (kbp)

Structural genes

MdLAR1pair1

MDP0000171928

GTGGTTAACGGAGGCACAGT

CCGAGGAGAAAGGACTACCC

LG16

1536

MdLAR1pair2

AY830131

GTGCTTCGATGGCTTTCTTC

TAACAAGCTCACCCCCAAAC

LG16

1530

MdLAR2

AY830132

ATGCCACAATCGTGTCAAAA

GGCTGGCTTCAGCTACAAAC

LG13

2860

MdPAL

ES790093

CGAGGAGTGTGACAAGGTGTTCCA

AGGAATGCAGCATGTAAACCGTGAC

LG4

8075

MdC4H

EB135197

GGACGTTTAGTCCAGAACTTCGAGCT

ACTTCATCACAATGGTGGAATGCTTC

LG11

4614

Md4CL

EB122629

CATAAACAGTGTCCCCAAGTCAGCAT

AGTGTTCCTACAAGCCTTCCCGATAA

LG11

5126

MdCHS

CN944824

GGAGACAACTGGAGAAGGACTGGAA

CGACATTGATACTGGTGTCTTCA

LG9

15948

MdCHI

CN946541

GGGATAACCTCGCGGCCAAA

GCATCCATGCCGGAAGCTACAA

LG1

16132

MdF3H

CN491664

TGGAAGCTTGTGAGGACTGGGGT

CTCCTCCGATGGCAAATCAAAGA

LG5

20985

MdDFR

AF117268

GATAGGGTTTGAGTTCAAGTA

TCTCCTCAGCAGCCTCAGTTTTCT

LG12

21890

MdANS

AF117269

GATGAAGGGAGGCTGGAGAAAG

GTGGAGGATGAAGGTGAGTGC

LG6

13776

MdFLS

EB137300

TCAGATGGAGATAATGAGCAATGGAAA

ATTAACGGGGTTCACAAGCTGTGG

LG8

15333

MdANR

EB125405

TCGCTGGCTTATGATCCTCCTGTT

CCGTTTGCCAAACTCAGCAAATTA

LG5

2243

MdHCTchr9

MDP0000851389

CGATGCTGTTTTCAGAACCA

GCAGCAGACGAGGATGATTA

LG9

24590

MdC3Hchr8

MDP0000466557

CAAAGGAGGTGCTCAAGGAG

TGGACTCGACCATAGCAGTG

LG8

29024

MdF3’Hchr6

MDP0000539956

ACTCTCTTCATGCGCTTGGT

TGCCTATCCTCACCCAAAAG

LG6

22805

MdF3’Hchr14

MDP0000370951

ACCATTAAACCCCAACAACG

ATCACGGTTTGGAGCTCTTG

LG14

27562

MdUFGT

AF117267

AAGGTCTCTCCAATGTACGAAT

AGGAGTTTGTTGACTTTGGACT

LG1, LG7

29053, 26292

TF genes at mQTL hotspot

MdMYB1361

MDP0000375685

CTGGGGGTTCAAGTAGTCCA

CTCCGTGGTGGCTTGATAAT

LG16

1361

Mdb-HLH1967

MDP0000261293

GATACGGCATCATTCCTGCT

GCCTGAGGATTTCCAACAAA

LG16

1967

Mdb-HLH1881

MDP0000154272

CTCAACCGGGACTTATCCAA

GCTCATCCTCCCACACATTT

LG16

1881

Mdb-HLH1543

MDP0000319726

GAGCTGAAACGCCAAACTTC

CGGTGATGAACAACACGTTC

LG16

1543

MdAP21480

MDP0000939633

GCACCTTCAACGAAGAGGAC

GACTTGGAGTGGGAGCTCAG

LG16

1475

MdG2L61440

MDP0000202657

AGACCGACTCCAACAATTCG

GGACTGGTGGTGAGACCTGT

LG13

2702

MdbZIP1380

MDP0000250967

CTGTTTCTGGCAAAGGCTTC

CCATCAACATTGCAGTGGAC

LG16

1376

Transcription factor genes outside the mQTL hotspot

MdCOL1220

MDP0000185616

TGATTTTATGGGGTGCCAAT

TAATCACCGCCTCGTAATCC

LG16

1224

Mdb-HLH1080

MDP0000725991

GGCCAATGACACCTCCTTTA

TGAGCTGTGGAATGAGCAAC

LG16

1084

MdMYB1070

MDP0000659260

ACTCCGCAAGAACAGCTCAT

GCTGTTCGACTCGATGTTCA

LG16

1058

MdC2H21020

MDP0000183099

CCTCCTCACCTCCTCTCTCC

CCCGGCTCTGTTGTAGTACC

LG16

1021

MdC2H21000

MDP0000283750

ATTCAGCAAGTTGGGTGTCC

TTTGCTTTGTGCAGTTGAGG

LG16

1003

MdMyb5a.A

MDP0000791870

GGGGAGGAGGAAATGAAGAG

CAGAGTCCCAGCCAAATGTT

LG3

967

Mdb-HLH33

MDP0000309179

GGAGACATCAAAACCCGAAA

TGAAGGACATGCAAAGCAAG

LG15

37144

MdTTG1

MDP0000906307

GACCCGGATACCCTTTCAAT

AAACTCGCTGGTCTTGCTGT

LG1

28763

Mdb-HLH3

MDP0000225680

GTCGCCATTGGTAAGGCTAA

CCACCGTGGTCTCAATTCTT

LG11

32877

MdMyb9

MDP0000210851

GGCCACTAGGTTGACCAAAA

ATCATCGCAGCCAAAGTTCT

LG8

9430

MdMyb11.A

MDP0000437717

TGAAGGTCGCTCATGTTCTG

ATTCACCGCCTGGTTTAGTG

LG13

30373

 

MdGAPDH

CN494000

GCTGCCAAGGCTGTTGGAA

ACAGTCAGGTCAACAACGGAAAC

LG16, LG13

5636, 7648

  1. 17 putative structural genes of the phenylpropanoid pathway, seven putative transcription factor genes in the genetic window of the mQTL hotspot on LG16, and 11 putative transcription factor genes outside this mQTL hotspot were studied. MdGAPDH was used as a reference gene. The last four digits in some transcription factor genes represent their positions on the genome in kbp.
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BMC Research Notes

ISSN: 1756-0500

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