Table 3.
Optimized annealing temperature (Tm), Polymorphism information content (PIC), product size and a total number of bands observed for the SSR markers used to check the presence genetic diversity among S. sclerotiorum isolates.
| Primer ID | Primer sequence (5′-3′) | Locus* | Repeat motif # | Tm (°C) | PIC | Amplicon size range | Allele frequency |
|---|---|---|---|---|---|---|---|
| SS 1A | CCGAGCATAATATACATCC | 41-1 | (TA)5 and (CA)10 | 50 | 0.663 | 494–504 | 1 |
| AAGGTTATATTTCCCTCGC | |||||||
| SS 2B | GTAACACCGAAATGACGGC | 5-2 | (GT)8 | 55 | 0.467 | 318–325 | 1 |
| GATCACATGTTTATCCCTGGC | |||||||
| SS 3C | GGGGGAAAGGGATAAAGAAAAG | 6-2 | (TTTTTC)2(TTTTTG)2(TTTTTC) | 55 | 0.564 | 479–484 | 1 |
| CAGACAGGATTATAAGCTTGGTCAC | |||||||
| SS 4D | TTTGCGTATTATGGTGGGC | 7-2 | (GA)14 | 50 | 0.345 | 160–172 | 1 |
| ATGGCGCAACTCTCAATAGG | |||||||
| SS 5E | GCCGATATGGACAATGTACACC | 9-2 | (CA)9(CT)9 | 50 | 0.243 | 358–382 | 1 |
| TCTTCGCAGCTCGACAAGG | |||||||
| SS 6F | CTTTCCTTTCGTTTGAGGG | 11-2 | (GA)6GG(GA)6(GGGA)2 | 47 | 0.806 | 276–284 | 1 |
| GGCAGGTAATGTTGCTTGG | |||||||
| SS 7G | CGATAATTTCCCCTCACTTGC | 12-2 | (CA)9 | 55 | 0.260 | 215–225 | 1 |
| GGAAGTCCTGATATCGTTGAGG | |||||||
| SS 8H | TCTACCCAAGCTTCAGTATTCC | 13-2 | (GTGGT)6 | 50 | 0.391 | 284–304 | 1 |
| GAACTGGTTAATTGTCTCGG | |||||||
| SS 9I | CAGACGAATGAGAAGCGAAC | 5-3 | [(GT)2GAT]3(GT)14GAT(GT)5[GAT(GT)4]3(GAT)3 | 55 | 0.343 | 245–320 | 2 |
| TTCAAAACAACGCTCCTGG | |||||||
| SS 10J | CCTGATATCGTTGAGGTCG | 7-3 | GT10 | 55 | 0.207 | 202–212 | 1 |
| ATTTCCCCTCACTTGCTCC | |||||||
| SS 11K | CACTCGCTTCTCCATCTCC | 8-3 | CA12 | 55 | 0.190 | 251–271 | 1 |
| GCTTGATTAGTTGGTTGGCA | |||||||
| SS 12L | TCATAGTGAGTGCATGATGCC | 17-3 | (TTA)9 | 55 | 0.603 | 345–390 | 4 |
| CAGGGATGACTTTGGAATGG | |||||||
| SS 13M | GACGCCTTGAAGTTCTCTTCC | 20-4 | (GT)7GG(GT)5 | 50 | 0.030 | 268–278 | 1 |
| CGAACAAGTATCCTCGTACCG | |||||||
| SS 14N | CTTCTAGAGGACTTGGTTTTGG | 23-4 | (TG)10 | 60 | 0.360 | 384–388 | 4 |
| CGGAGGTCATTGGGAGTACG | |||||||
| SS 15O | GAATCTCTGTCCCACCATCG | 36-4 | CA6(CGCA)2CAT2 | 50 | 0.097 | 415–429 | 1 |
| AGCCCATGTTTGGTTGTACG | |||||||
| SS 16P | GGTCTCATACAGTCTACACACA | 42-4 | GA9 | 60 | 0.360 | 410–414 | 1 |
| CTCTAGAGGATCTGCTGACA | |||||||
| SS 17Q | CCCTACAATATCCCATGGAGTC | 50-4 | CA7(TACA)2 | 50 | 0.243 | 419–527 | 2 |
| CCTCGTCTATCCGTCCATC | |||||||
| SS 18R | GTTTTCGGTTGTGTGCTGG | 55-4 | TACA10 | 50 | 0.153 | 173–221 | 1 |
| GCTCGTTCAAGCTCAGCAAG | |||||||
| SS 19S | TCGCCTCAGAAGAATGTGC | 92-4 | (CT)12 | 50 | 0.153 | 374–378 | 1 |
| AGCGGGTTACAAGGAGATGG | |||||||
| SS 20T | CTCATTTCATCCCATCTCTCC | 99-4 | (GTAA)2(GCAA)(GTAA)3 | 50 | 0.243 | 402–422 | 1 |
| AATTCAAGCCTTCCTCAGCC | |||||||
| SS 21 U | TGCATCTCGATGCTTGAATC | 106-4 | (CATA)25 | 55 | 0.391 | 491–571 | 1 |
| CCTGCAGGGAGAAACATCAC | |||||||
| SS 22V | ATCCCTAACATCCCTAACGC | 110-4 | (TATG)9 | 50 | 0.294 | 362–378 | 1 |
| GGAGAATTGAAGAATTGAATGC | |||||||
| SS 23W | GCTCCTGTATACCATGTCTTG | 114-4 | (AGAT)14(AAGC)4 | 50 | 0.294 | 351–391 | 1 |
| GGACTTTCGGACATGATGAT | |||||||
| SS 24X | TCAAGTACAGCATTTGC | 117-4 | (TAC)6C(TAC)3 | 55 | 0.564 | 376–388 | 1 |
| TTCCAGTCATTACCTACTAC | |||||||
| SS 25Y | GTAACAAGAGACCAAAATTCGG | 119-4 | (GTAT)6 and (TACA)5 | 50 | 0.135 | 369–391 | 1 |
| TGAACGAGCTGTCATTCCC |
*
Locus names;
#
Repeat motifs as mentioned by Sirjusingh and Kohn (2001).