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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).