Table 5 Details of SSR primers used (http://gramene.org/markers/microsat/all-ssr.html)
From: Rice of Northeast India harbor rich genetic diversity as measured by SSR markers and Zn/Fe content
Sl No | Primer name | Sequences (Forward primer/Reverse primer) | Chr.no. | Marker selection | Ta (°C) | Expected amplicon size (bp) |
|---|---|---|---|---|---|---|
1. | RM1 | Fp – 5′-GCGAAAACACAATGCAAAAA-3′ Rp – 5′-GCGTTGGTTGGACCTGAC-3’ | 1 | Random | 55 | 113 |
2. | RM154 | Fp – 5’-ACCCTCTCCGCCTCGCCTCCTC-3′ Rp – 5′-CTCCTCCTCCTGCGACCGCTCC-3’ | 2 | Random | 61 | 183 |
3. | RM131 | Fp – 5’-TCCTCCCTCCCTTCGCCCACTG-3′ Rp – 5′-CGATGTTCGCCATGGCGTCTCC-3’ | 4 | Random | 61 | 215 |
4. | RM135 | Fp – 5’-CTCTGTCTCCTCCCCCGCGTCG-3′ Rp – 5′-TCAGCTTCTGGCCGGCCTCCTC-3’ | 3 | Random | 55 | 131 |
5. | RM153 | Fp – 5’-GCCTCGAGCATCATCATCAG-3′ Rp – 5′-ATCAACCTGCACTTGCCTGG-3’ | 5 | Random | 55 | 201 |
6. | RM125 | Fp – 5’-ATCAGCAGCCATGGCAGCGACC-3′ Rp – 5′-AGGGGATCATGTGCCGAAGGCC-3’ | 7 | Random | 55 | 127 |
7. | RM72 | Fp – 5’-CCGGCGATAAAACAATGAG-3′ Rp – 5′-GCATCGGTACTAACTAAGGG-3’ | 8 | Random | 55 | 166 |
8. | RM171 | Fp – 5’-CGATCCATTCCTGCTGCTCGCG-3′ Rp – 5′-CGCCCCCATGCATGAGAAGACG-3’ | 10 | Random | 55 | 328 |
9. | RM287 | Fp – 5’-TTCCCTGTTAAGAGAGAAATC-3′ Rp – 5′-GTGTATTTGGTGAAAGCAAC-3’ | 11 | Random | 55 | 118 |
10. | RM302 | Fp – 5’-TCATGTCATCTACCATCACAC-3′ Rp – 5′-ATGGAGAAGATGGAATACTTGC-3’ | 1 | Trait-linked (drought) | 55 | 156 |
11. | RM3825 | Fp – 5’-AAAGCCCCCAAAAGCAGTAC-3′ Rp – 5′-GAGCTCCATCAGCCATTCAG-3’ | 1 | Trait-linked (drought) | 55 | 147 |
12. | RM246 | Fp – 5’-GAGCTCCATCAGCCATTCAG-3′ Rp – 5′-CTGAGTGCTGCTGCGACT-3’ | 1 | Trait-linked (drought) | 55 | 116 |
13. | RM260 | Fp – 5’-ACTCCACTATGACCCAGAG-3′ Rp – 5′-GAACAATCCCTTCTACGATCG-3’ | 12 | Trait-linked (drought) | 55 | 111 |
14. | RM525 | Fp – 5’-GGCCCGTCCAAGAAATATTG-3′ Rp – 5′-CGGTGAGACAGAATCCTTACG-3’ | 2 | Trait-linked (drought) | 55 | 131 |
15. | RM219 | Fp – 5’-CGTCGGATGATGTAAAGCCT-3′ Rp – 5′-CATATCGGCATTCGCCTG-3’ | 9 | Trait-linked (drought) | 55 | 202 |
16. | RM315 | Fp – 5’-GAGGTACTTCCTCCGTTTCAC-3′ Rp – 5′-AGTCAGCTCACTGTGCAGTG-3’ | 1 | Trait-linked (salt) | 55 | 133 |
17. | RM223 | Fp – 5’-GAGTGAGCTGGTGCTGAAAC-3′ Rp – 5′-GAAAGGCAAGTCTTGGCACTG-3’ | 8 | Trait-linked (salt) | 55 | 165 |
18. | RM8094 | Fp – 5’-AAGTTTGTACACATCGTATACA-3′ Rp – 5′-CGCGACCAGTACTACTACTA-3’ | 1 | Trait-linked (salt) | 55 | 209 |
19. | RM493 | Fp – 5’-TAGCTCCAACAGGATCGACC-3′ Rp – 5′-GTACGTAAACGCGGAAGGTG-3’ | 1 | Trait-linked (salt) | 55 | 211 |
20. | RM3412 | Fp – 5’-AAAGCAGGTTTTCCTCCTCC-3′ Rp – 5′-CCCATGTGCAATGTGTCTTC-3’ | 1 | Trait-linked (salt) | 55 | 211 |
21. | RM443 | Fp – 5’-GATGGTTTTCATCGGCTACG-3′ Rp – 5′-AGTCCCAGAATGTCGTTTCG-3’ | 1 | Trait-linked (salt) | 55 | 124 |
22. | RM169 | Fp – 5’-TGGCTGGCTCCGTGGGTAGCTG-3′ Rp – 5′-TCCCGTTGCCGTTCATCCCTC-3’ | 5 | Trait-linked (salt) | 67 | 167 |