Skip to main content

Table 2 The number of wheat SNP genotyping primers designed from 1,527 gene loci containing one or more SNPs.

From: BatchPrimer3: A high throughput web application for PCR and sequencing primer design

Primer type

Genome

Chromosome

Total

  

1

2

3

4

5

6

7

 

SBE primer

A

51

57

43

63

53

55

54

376

 

B

52

51

47

66

54

53

59

382

 

D

58

57

56

56

60

84

57

428

 

Total

161

165

146

185

167

192

170

1186

AS primer

A

62

69

49

69

63

62

62

436

 

B

64

55

54

65

60

65

68

431

 

D

67

63

61

67

66

90

64

479

 

Total

193

187

164

201

189

217

194

1346

Tetra- primer

A

17

19

16

25

22

22

20

141

 

B

20

25

14

19

25

26

27

156

 

D

23

23

23

27

30

42

20

188

 

Total

60

67

53

71

77

90

67

485

  1. Note: The same parameters were applied to SBE primer and AS primer design: primer length of 25 to 30 bases with the optimum 27 bases, Tm of 50 to 65°C with the optimum 60°C. All three types of primers shared the same GC content (20% to 80%), primer complementarity (≤ 8) and 3' complementarity (≤ 3). Tetra primer design required a primer of 28 bases in length, ranging from 26 to 30 bases, and a broader Tm range (50 to 80°C) with the optimum 65°C. The optimum inner product size was 120 bases ranging from 100 to 200 bases with a proper size ratio range of two products (from 1.1 to1.5).