Table 2 Positions in the sorghum genome and primer sequence of the 16 single nucleotide polymorphisms (SNPs) chosen for PCR amplification and subsequent Sanger sequencing validation (Chr = Chromosome)
From: Mining sequence variations in representative polyploid sugarcane germplasm accessions
Code | SNP type | Callera | Chr. | Forward sequence | Reverse sequence |
|---|---|---|---|---|---|
SNP1 | T/A | F, G, Sa, St, T | 2 | ACGTCAAAAGCTTCGCAGGA | GGCAAAGAAAGCACTGAAGG |
SNP2 | C/T | F, G, Sa, St, T | 2 | GCCTGAGATGGCACAAAAAT | CACTGTTTTGCATCCTTTGC |
SNP3 | G/A | F, G, Sa, St, T | 3 | CACCACCCACCAACCTAAGC | TTCTTTGCAGTGACCCAGTG |
SNP4 | A/T | T | 3 | GGAAGGGCAAGGACTCCTAC | GAAGCCCAGGGACATTGTTA |
SNP5 | T/C | F, G, Sa, St, T | 3 | GCTCGCTACAGGGCATAAAG | ACCGTGGTGCTTTTAGAGCT |
SNP6 | T/C | F, G, Sa, St, T | 3 | GGGAACCAAAAAGGAGGGTA | GCATACCCTCAAAGGAGTTG |
SNP7 | C/T | F, G, Sa, St, T | 4 | GCTCCCAAAGACCATGACAG | TGTCGTGCAGAAGCCAATTA |
SNP8 | G/A | F, G, Sa, St, T | 4 | GCTCCCAAAGACCATGACAG | TGTCGTGCAGAAGCCAATTA |
SNP9 | G/A | F, G, T | 4 | CATCCTGGTTTTCAGGGGTA | TTGCGGAGGATATGCAGAGT |
SNP10 | A/G | F, G, Sa, St, T | 5 | ATGAACGCTTTCCAGATGCT | TCTCACCTGGTGCTCCTTCT |
SNP11 | C/T | G, Sa, St, T | 5 | TCAGCCTGGTGAGTTTCCTT | TGTAAACTGGGGAGGACCAG |
SNP12 | C/T | T | 5 | TGCAGGTGCTTGCTGAGTAT | AAGCAAGATTGTGCCCTTCA |
SNP13 | C/A | F, G, Sa, St, T | 5 | TCTGGATGGGGTACTGGGTA | CCCGGCTAAAGACAATACGA |
SNP14 | A/G | F | 6 | CCTGTCCTTAGTGTCTGCAT | CAAGCAAGCAAGTTCCCATT |
SNP15 | C/T | F, G, Sa, St, T | 6 | CCTGTCCTTAGTGTCTGCAT | CAAGCAAGCAAGTTCCCATT |
SNP16 | G/A | F, G, T | 6 | AAAACATTGAAAGCAGATGC | GCATGTGGCATGTAATGAGG |