Table 2 Evaluation of the amplification efficiency and polymorphic potential of 47 fluorescent dye labeled primers

P/M ^B

PIC

1

CA297715

UGSuM2a

(AT)43

CDS

CTGTGTATATGTTCGTAGTTTG

CACTTAGTCACACTCTCACACAC

Sucrose phosphate synthase

55

2

20

206-302

Step-wise

1

P

P

0.86

UGSuM2b

4

481-512

Mixed

2

CA278792

UGSuM5

(TA)28

CDS

TCACATCCATCATCCACAGC

TCCAATGCAAGCAAACTCAC

Maize-Cyclin III

55

1

23

80-170

Step-wise

0

P

P

0.84

3

AY596609

UGSuM11

(TA)21

3'UTRs

TGGTAACCCTAGGCAGGTGA

GTGCACCAGATTTGGATGGT

Fructose-bisphosphate aldolase

56

1

23

92-190

Step-wise

0

P

P

0.83

4

CA279221

UGSuM15a

(CCTCGC)6

CDS

GTTTAAGACAAGATGGTGTAGATG

TACATATTTACATTGTTACTCCGC

Hypothetical protein

56

2

17

170-247

Mixed

1

P

P

0.80

UGSuM15b

3

360-378

Step-wise

5

CA278282

UGSuM16

(AT)18

CDS

GCGTCTTCATCATCTGCAAC

GCGTCTTCATCATCTGCAAC

Pathogenesis-related PRMS protein

55

1

22

150-244

Step-wise

0

P

P

0.82

6

CA253277

UGSuM17

(AG)18

CDS

TTTCCATTCTTCCATTCAACTG

GGCAGGCTGAGAGACTGTTC

Abcisic acid-protein kinase

55

1

10

90-188

Step-wise

1

P

P

0.78

7

CA227482

UGSuM18a

(GA)18

CDS

GGCGAGAGAGAGAGAGAGAGAG

AGGTGGAGATCTTGAGGTAGGC

Glycine decarboxylase

56

2

20

96-193

Mixed

1

P

P

0.81

UGSuM18b

2

326-348

Step-wise

8

CA126180

UGSuM20a

(TCA)12

CDS

ATCCCTTATGCTACAGAAATGT

TTAGCCTAGAGGTTTGATTGAT

Acetyl-CoA synthetase

54

2

16

190-259

Step-wise

1

P

P

0.83

UGSuM20b

4

392-428

Step-wise

9

CA177414

UGSuM21

(AGGA)9

CDS

CGCTCCCTCACCGTCATT

CTCCGCATCCTCGTCACC

Transcription regulator protein

62

1

20

160-252

Step-wise

0

P

P

0.81

10

CA223153

UGSuM22a

(GCG)12

3'UTRs

CTCCCTCCTCCTCCCGTTG

CTCTTGGGTGTGAACCAG

Polyadenylate-binding protein

64

2

19

96-187

Mixed

1

P

P

0.85

UGSuM22b

3

322-358

Step-wise

11

CA122659^A

UGSuM24a

(TTTTC)7

5'UTRs

CTGTACAACAGCAATTATGAATCT

CTCGACTACGAGAGGATATGAT

Hypothetical protein

55

3

12

240-294

Mixed

1

P

P

0.86

UGSuM24b

4

398-428

Step-wise

UGSuM24c

5

531-571

Step-wise

12

BU103692^A

UGSuM26

(CT)17

5'UTRs

CTCGATCCCAGAGAGCTCCACAG

AGTACCGAATTCATTAAACTCCT

Beta-amylase

55

1

21

250-346

Step-wise

0

P

P

0.85

13

CA073284

UGSuM27a

(GGC)11

CDS

CTGCAGTACGGTCCGGAATC

GTACCACCATGGCTCTAGCTTC

30 S ribosomal protein S16

60

2

2

50-54

Mixed

1

P

P

0.84

UGSuM27b

22

154-288

Mixed

14

AY596606

UGSuM33a

(AGC)10

CDS

CGAGGCACTGAACCCATATC

TGTTTGAACTGGATGGCGTA

Hypothetical protein

58

3

17

92-189

Mixed

1

P

P

0.84

UGSuM33b

2

293-305

Step-wise

UGSuM33c

2

431-491

Step-wise

15

CA268640

UGSuM34a

(AAG)10

CDS

TTACAAATGTAGCCTTGCCTTG

ATCTTTCCTTGCTTGCCTCTC

Soluble acid invertase

61

2

19

99-178

Mixed

1

P

P

0.83

UGSuM34b

4

333-351

Step-wise

16

CA131350

UGSuM41

(CCG)10

CDS

ATCATTCTCCATCATTTCTCA

AGGCTCTTCAACCGTGCT

Unknown protein

54

1

20

120-210

Step-wise

0

P

P

0.80

17

CA133924

UGSuM42a

(CTCTCC)5

5'UTRs

TTCATACAGAAGAACCTCCAC

TCCATCAGAGACAAGCAGA

Auxin-independent growth promoter

54

3

12

130-212

Mixed

1

P

P

0.83

UGSuM42b

8

325-367

Step-wise

UGSuM42c

2

475-487

Step-wise

18

CA136599

UGSuM43a

(CCG)10

3'UTRs

CAAAGTGCTGTAGGGCTG

TTCAATGGGTGATAAGTGTGT

Ribose-phosphate pyrophosphokinase 1

55

2

17

90-187

Mixed

1

P

P

0.85

UGSuM43b

2

332-368

Step-wise

19

CA139800

UGSuM44a

(CT)15

5'UTRs

TCCATCAAGCCGTTCCTC

GCCAAGCAGATAAAGAAGTG

Rudimentary enhancer

55

2

16

220-308

Step-wise

1

P

P

0.84

UGSuM44b

1

419

-

20

CA171090

UGSuM45a

(AAAAG)6

CDS

ATCTCCTCTTATTCGTTCTGG

AGCAGCGTCTTATCTGGG

PAP fibrillin

56

3

5

91-141

Step-wise

1

P

P

0.79

UGSuM45b

2

267-287

Step-wise

UGSuM45c

2

368-393

Step-wise

21

CA196477

UGSuM46a

(GAC)10

CDS

ACTCCTCCCGCCTCCACTAC

CTCACCGAAGCAATCAAG

Hypothetical protein

60

2

15

101-188

Mixed

1

P

P

0.81

UGSuM46b

3

341-377

Step-wise

22

CA228772

UGSuM47a

(GCC)10

CDS

ATTTATGGAGGAAGAAACGG

ATTACAAACAAGAAGAGCGG

Transport protein particle component

55

2

3

82-97

Step-wise

1

P

P

0.80

UGSuM47b

14

215-270

Mixed

23

CA161416

UGSuM50

(TC)14

CDS

CTACTGCCGAGGAAAGATCG

GGAAAAGTTTGTGGCAAGGA

Hypothetical protein

58

1

16

94-188

Step-wise

0

P

P

0.80

24

CA228375

UGSuM73a

(CGC)8

5'UTRs

CTTTCAACCTCTACACCTCCAC

ACTAGAAGACTGAGAAGAACCAGT

40 S ribosomal protein S11

55

2

13

101-186

Mixed

1

P

P

0.82

UGSuM73b

5

354-375

Step-wise

25

CA261182

UGSuM74

(ACA)8

CDS

TCAGCAGCTGTGAAGTTTCATT

CGTCTCTTTTGGGTTTCATCTC

Transcription regulator protein

55

1

18

190-271

Step-wise

0

P

P

0.81

26

CA219230

UGSuM75a

(TA)12

CDS

TTGTGCTGATGTTTCCTGCT

CAAGAGAAGATGCCATTAGCC

Patatin-like protein

55

2

13

94-176

Step-wise

1

P

P

0.83

UGSuM75b

4

333-351

Step-wise

27

CA093071

UGSuM96a

(AT)11

CDS

TCAAACCAGGATCTAAGCTCAC

GGTAGTGCCATTGAGGTTGC

Putative apyrase

57

2

11

205-290

Mixed

1

P

P

0.81

UGSuM96b

5

408-458

Step-wise

28

CA229840

UGSuM97a

(GA)11

5'UTRs

GCGAGAGAGATAGAGGGAGAGA

AGGTGCCGTTCATGAGGTAGT

Glycine decarboxylase

56

2

19

240-334

Step-wise

1

P

P

0.85

UGSuM97b

2

453-469

Step-wise

29

CA112979

UGSuM149a

(AGC)7

CDS

GTTCAATCAAATCCCTCTCCTC

AGCTTGGTCAGCTCCTCATCGTT

Ubiquitin-specific protease 4 (UBP4)

60

2

4

104-141

Mixed

0

P

P

0.78

UGSuM149b

3

276-297

Step-wise

30

CA116368

UGSuM150a

(GGC)7

CDS

ACACTGACCGATGGATCCTCTT

ATCAACGTGGACCAGATCTTCTT

hAT family dimerisation domain protein

60

2

12

90-167

Mixed

1

P

P

0.76

UGSuM150b

2

279-291

Step-wise

31

CA280782

UGSuM177a

(TGC)7

CDS

GGTGCTGTCCCTATCACTAC

GCCCTTGTTTCTTTGTCTACT

Hypothetical protein

55

2

3

150-167

Mixed

0

P

P

0.79

UGSuM177b

3

287-314

Step-wise

32

CA291445

UGSuM178

(GAC)7

5'UTRs

GGACTACTACGACTACTGCGA

ACCTTGCTTACATCTTCCTCT

O-diphenol-O-methyl transferase

54

1

15

100-196

Step-wise

0

P

P

0.80

33

CA244023

UGSuM186

(AG)10

CDS

AACATTTCGGCATTTGAAGC

GGTCTTTCTTGGGGATCTCTC

Ubiquitin C-terminal hydrolase

56

1

4

190-232

Step-wise

0

P

M

0.73

34

CA231668

UGSuM187a

(CT)10

CDS

CAACAATTGTCGAAGCCTCTC

TTTGCTTACCCCCTGTTGAC

ATP synthase

58

2

10

200-264

Step-wise

0

P

M

0.83

UGSuM187b

6

376-418

Step-wise

35

AY596560

UGSuM188

(GA)10

3'UTRs

CCCAAGCGAGCTAGAGAGAG

TCTTCTTTCCTTCGCACAGC

Hypothetical protein

55

1

19

95-186

Mixed

0

P

P

0.81

36

CA241232

UGSuM189a

(CT)10

CDS

CCGCGACTCTCCTCTCTCT

GTTCTTCTCGGCGTTCCTC

Auxin-regulated protein

55

2

15

106-200

Step-wise

1

P

P

0.80

UGSuM189b

3

345-377

Step-wise

37

CA133642

UGSuM196a

(AAAG)5

5'UTRs

GCTACTATGGACAACAGGG

ATGAAGAGACGAGACGAAGA

Cinnamoyl CoA reductase

54

2

18

90-181

Mixed

1

P

P

0.81

UGSuM196b

2

373-393

Step-wise

38

CA134472

UGSuM197

(GA)10

3'UTRs

GAAGGAGCAGCAGCGCCAGT

GATTTGCCGTCCTAGGGTTT

Epsin N-terminal homology domain

56

1

22

200-290

Step-wise

0

P

P

0.84

39

CA297648

UGSuM343a

(CAG)6

5'UTRs

ACTCCTCCTCCTCGCCGT

TCTTGTTGTAGTAGCCCTTGT

SOUL heme-binding family protein

62

2

17

250-320

Mixed

1

P

M

0.87

UGSuM343b

3

438-450

Step-wise

40

CA300679

UGSuM344

(CTC)6

CDS

CTATCCTCTTGTTGGGTCCT

TCCGCACCTCCGTTCACC

Nucleoside diphosphate kinase protein

55

1

1

260

Step-wise

0

M

M

0.0

41

CA084691

UGSuM345

(TC)8

CDS

TATACAAGAATGAAAGGTGAGAGA

AAGCATACTCCCTCTATCTCTATG

DC1 domain-containing protein

55

1

2

210-220

Step-wise

0

M

P

0.70

42

CA093455

UGSuM346

(AG)8

CDS

TATACGTAGTAGTGATGATGACCG

CTCCTTCGTCCAGTACCAGTAG

DNA-binding protein DF1

60

1

4

150-180

Step-wise

1

P

M

0.71

43

CA110745

UGSuM347a

(CT)8

5'UTRs

TCTGGCTTTATCGTAACTTGTAT

GAGCCTCGTTTGGGTGGCTTTC

Expressed protein

55

2

5

230-254

Step-wise

1

P

M

0.74

UGSuM347b

1

365

-

44

CA112979

UGSuM348

(CG)8

CDS

CTACCTCCTCGTCTCCTCCCTCTT

AACAAGGAATATGGTCCCTGAG

Unknown protein

61

1

2

240-261

Mixed

0

M

M

0.0

45

CA116458

UGSuM349a

(TC)8

CDS

CAAGATGTACCCGGACATGGCT

TGCTATACTAGCTATCTCCTTCCT

Unknown protein

55

2

3

220-236

Step-wise

0

P

M

0.73

UGSuM349b

2

385-395

Step-wise

46

CA123971

UGSuM464

(ACA)5

5'UTRs

GGCTACTTCAGACACGCA

TCTACGCATCAACCTCTCA

SNF2-domain-containing protein

55

1

1

220-232

Step-wise

0

M

M

0.0

47

CA125310

UGSuM465

(GCA)5

CDS

GCTAACCAACATCAGCAGT

AGGAGATTGACGAAGAAGAAG

Transducin family protein

53

1

2

260-279

Mixed

0

M

M

0.0