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Table 2 Primer sequences and restriction enzymes of STS and CAPS markers yielding polymorphic bands for tea germplasm

From: Development of STS and CAPS markers for variety identification and genetic diversity analysis of tea germplasm in Taiwan

Marker*

Forward primer

Reverse primer

Size (bp)

Annealing temp.

Nuclease

Size of major bands (bp)

Allele number

PIC§

Reference sequence

Prediction function

C01

GAGGGGAAGGATGGATTGTT

GTGCCACAAATGACCTACGA

677

55°C

Taq I

A: 677 B: 552 + 125

2

0.15

AY741470

photosystem II CP43 protein

C02

GAGGGGAAGGATGGATTGTT

GTGCCACAAATGACCTACGA

677

55°C

Bsr DI

A: 677 B: 483 + 194

2

0.13

AY741470

photosystem II CP43 protein

C03

GAGAGAGAGGGATTCGAACC

GTTTTTGGAGCTGGGATGAA

659

55°C

Sfa NI

A: 659 B: 449 + 210

2

0.27

AY839880

trnS ~ trnfM

M01

TGGTGAGGAGCATTGTTTTG

GAGCAAACACTCGAACGTGA

836

55°C

Eco RI

A: 836 B: 509 + 327

2

0.15

AY839898

NADH dehydrogenase subunit 1

M02

CCAATTTTTGGGCCAATTCC

TCTCTAAAGGGGCGTAAGCA

610

55°C

Hinc II

A: 610 B:385 + 225

2

0.31

AY845285

NADH dehydrogenase subunit 5

M03

GCCGGAAAAATAACAGACGA

AAAAGGAAGGTTGGGTGCTT

458

55°C

Bbs I

A: 458 B: 308 + 149

2

0.28

AY845314

NADH dehydrogenase subunit 7

M04

GATAGGAGCATTCGGTGGAA

CGGTAACCAAAGCGTATCGT

844

55°C

Hph I

A: 805 + 35 B: 492 + 313 + 35

2

0.28

AY845314

NADH dehydrogenase subunit 7

M05

ACAGCACCTTTTTCCCCTCT

CATAACACGGCTCTCCCACT

686

55°C

Xmn I

A: 686 B:443 + 243

2

0.34

AY845314

NADH dehydrogenase subunit 7

M06

TGAATGAATCCCATCCCCTA

GGCATACAACCGAAACGACT

413

55°C

Rsa I

A: 413 B:309 + 104

2

0.35

AY845285

NADH dehydrogenase subunit 5

M07

TAGCTATGCCCTGCTTGGTC

CCTGTCTGTCGTACCGTTGA

667

55°C

Bss SI

A: 667 B: 460 + 207

2

0.28

AY845298

NADH dehydrogenase subunit 7

G01

TGCTTTGCGTCAATAACTGC

TGATACATCCTCGCCAACAA

647

55°C

Hph I

A:647 B:441 + 206

2

0.25

DQ869863

zinc finger protein

G02

GCCTATCTAATCTACTCGGCTTTCT

AGTAACACTAACCCACCCAACAATA

834

55°C

Fsp I

A:834 B:645 + 189

2

0.36

AB117640

ammonium transporter

G03

GCCTATCTAATCTACTCGGCTTTCT

AGTAACACTAACCCACCCAACAATA

834

55°C

Ava I

A:834 B:729 + 105 C:501 + 228 + 105

3

0.55

AB117640

ammonium transporter

G04

GAGACAGAGGACTACTTCGATTCAG

GAATCAGAAATGATACAGAGGAGGA

721

55°C

Mse I

A:721 B:447 + 274

2

0.37

AB247282

cyclin D3-1

G05

GAGACAGAGGACTACTTCGATTCAG

GAATCAGAAATGATACAGAGGAGGA

721

55°C

Rsa I

A:721 B:571 + 150

2

0.30

AB247282

cyclin D3-1

G06

GCCTATCTAATCTACTCGGCTTTCT

AGTAACACTAACCCACCCAACAATA

834

55°C

Nde I

A:834 B:749 + 85

2

0.25

AB117640

ammonium transporter

G07

GCCTATCTAATCTACTCGGCTTTCT

AGTAACACTAACCCACCCAACAATA

834

55°C

Hph I

A:510 + 147 B:468 + 147 + 120 + 57

2

0.31

AB117640

ammonium transporter

G08

GCCTATCTAATCTACTCGGCTTTCT

AGTAACACTAACCCACCCAACAATA

834

55°C

Ava II

A:443 + 190 + 134 + 67 B: 324 + 67

2

0.15

AB117640

ammonium transporter

G09

GCCTATCTAATCTACTCGGCTTTCT

AGTAACACTAACCCACCCAACAATA

834

55°C

Bst UI

A:575 + 204 + 55 B:455 + 204 + 120 + 55

2

0.07

AB117640

ammonium transporter

G10

TGAGACAACATTATGGTCGATAGAA

ATACTCCTTGCAAACTTCTGAATTG

750

55°C

Bst YI

A:750 B:590 + 160

2

0.14

AY641731

trans-cinnamate 4-hydroxylase

G11

TGAGACAACATTATGGTCGATAGAA

ATACTCCTTGCAAACTTCTGAATTG

750

55°C

Bst UI

A:750 B:470 + 280

2

0.10

AY641731

trans-cinnamate 4-hydroxylase

G12

ACGACTACAGCTTCTTTCTCTACCA

ATACACCTCGTCGACATACTTCTTC

824

55°C

Ava I

A:824 B: 527 + 297 C:325 + 202

3

0.43

AB114913

ammonium transporter

G13

CCATCAAATCCATTGGGAAC

AAGACGAGCCAGGAGAAACA

580

60°C

Mbo II

A:580 B:449 + 131

2

0.10

EF205149

1-aminocyclopropane-1-carboxylate synthase

G14

CCATCAAATCCATTGGGAAC

AAGACGAGCCAGGAGAAACA

580

60°C

Bsr DI

A:359 + 221 B:455 + 125 C:221 + 218 + 141 D:260 + 195 + 125 E:359 + 125 + 96 F:455 + 320 + 260 + 125 G:260 + 125 + 99 + 96

7

0.52

EF205149

1-aminocyclopropane-1-carboxylate synthase

G15

GCCTATCTAATCTACTCGGCTTTCT

AGTAACACTAACCCACCCAACAATA

834

55°C

Bsa JI

A:546 + 288 B:318 + 288 + 228 C:546 + 183 + 105 D: 318 + 228 + 183 + 105

5

0.58

AB117640

ammonium transporter

G16

CCTACAAAACAGTCATAAGCCAACT

ACGAAAACACTCTTGATCAGTAAGG

572

55°C

Bbv I

A:309 + 263 B:263 + 166 + 143

2

0.04

AB015047

PR-1 like protein

G17

ACGTGTGTGTTTCATTTGCC

AACCCAATGATGTGTAAGTG

556/401

55°C

Mbo II

A:556 B:455 + 101 C:300 + 101

3

0.28

D26596b

phenylalanine ammonia-lyase

G18

CTTACGGCTCTCGCAGAAGA

GAACCGTGATCCAGGTTTTG

1100/930

55°C

Hind III

A:1100 B:930 C:650 + 280

3

0.49

AY641730

flavanone 3-hydroxylase

G19

TGCTTTGCGTCAATAACTGC

TGATACATCCTCGCCAACAA

647

55°C

Hpa II

A:619 + 28 B:463 + 156 + 28

2

0.37

DQ869863

zinc finger protein

G20

ACGTGTGTGTTTCATTTGCC

AACCCAATGATGTGTAAGTG

556/401

55°C

Hph I

A:556 + 401 B:401 C:319 + 237 D:237

4

0.47

D26596a

phenylalanine ammonia-lyase

G21

ACGTGTGTGTTTCATTTGCC

AACCCAATGATGTGTAAGTG

556/401

55°C

Taq I

A:556 B:460 + 96 C:305 + 96

3

0.53

D26596a

phenylalanine ammonia-lyase

G22

CTTACGGCTCTCGCAGAAGA

GAACCGTGATCCAGGTTTTG

1100/930

55°C

Bst YI

A:930 B:680 + 250 C:510 + 420 D:680 + 420

4

0.62

AY641730

flavanone 3-hydroxylase

G23

CTTACGGCTCTCGCAGAAGA

GAACCGTGATCCAGGTTTTG

1100/930

55°C

Bbs I

A:1100 B:930 C:600 + 330

3

0.55

AY641730

flavanone 3-hydroxylase

G24

CCAGGAACACCAACAACCCGT

CCATGCTGCTTTCTCTGCCAA

958

55°C

Hind III

A:958 B:550 + 408

2

0.35

AB018685b

dihydroflavonol 4-reductase

G25

GATCCTTCAGACATGCAGAGC

CACTTCCTCAAGTGATGCAAA

960

55°C

Rsa I

A:960 B:605 + 355

2

0.21

EF526217

caffeine synthase

G26

CGACCATCCTGCAATTTTCT

AACGTCATTAGGACCTTCAATCG

299

55°C

Taq I

A:310 B:299 C:290 D:277

4

0.49

EF205148

leucoanthocyanidin reductase

G27

GGTGCTCAGGACATGGTTTT

CGCTCTATTCCCTGCAAGTC

377

55°C

Hph I

A:377 B:198 + 179

2

0.37

DQ194358

flavonoid 3′,5′-hydroxylase

PAL

ACGTGTGTGTTTCATTTGCC

AACCCAATGATGTGTAAGTG

556/401

55°C

-

A:556 B:401

2

0.27

D26596a

phenylalanine ammonia-lyase

F3H

CTTACGGCTCTCGCAGAAGA

GAACCGTGATCCAGGTTTTG

1100/930

55°C

-

A:1100 B:930

2

0.28

AY641730

flavanone 3-hydroxylase

  1. *Note: “C” represents chloroplast CAPS markers, “M” represents mitochondria CAPS markers, “G” represents nuclear CAPS markers, and “PAL”, “F3H” represents nuclear STS markers.
  2. §PIC Polymorphism Information Content.
  3. The primer pairs were referenced from (a) Kaundun and Matsumoto (2004) and (b) Kaundun and Matsumoto (2003).