Table 1 Details of the RAPD primers, Microsatellite markers and SNP markers used.
RAPD Primers | |||||
|---|---|---|---|---|---|
Serial no. | RAPD Primer ID | Sequence (5'-3') | GC content (%age) | Annealing temp. | MgCl2 (mM) |
1. | 80/07 | GCACGCCGGA | 80 | 38°C | 3.0 |
2. | 80/01 | GCACCCGACG | 80 | 35°C | 3.0 |
3. | 70/04 | CGCATTCCGC | 80 | 35°C | 3.0 |
4. | 70/01 | CATCCCGAAC | 70 | 38°C | 3.0 |
5. | 60/31 | TGCGCGATCG | 70 | 38°C | 3.0 |
Microsatellite markers | |||||
Serial no. | Microsatellite marker ID | Primer sequences (5'-3') | Annealing temp. | Product size (bp) | |
1. | D4S3173 | Left Primer: TTGGAGTCCCTGAAGGACC Right primer: TACAAACACCAAGCCCCTTC | 57°C | 103–104 | |
2. | D4S2827 | Left Primer: GACGGGAGAGAAAATGCATT Right primer: TCAATAAGCACCAAAACTACTCAG | 55°C | 132–133 | |
3. | D4S1295 | Left Primer:TAACAAAACCATCTCCAAACTTCTC Right primer: GTGGACAGTACAACACAGTTGAC | 57°C | 170 | |
4. | D4S2643 | Left Primer:TTGTCCAATAACTCTTTTCCTAACA Right primer: CTGATTCCTATATCAATCTTGGCC | 57°C | 179–180 | |
5. | D4S2672 | Left Primer: TAAAGATGTGATTTGTATTGCATTG Right primer: AGTTTCAGCCTCTCAAAATTTCA | 57°C | 199–200 | |
SNP markers | |||||
Serial no. | SNP Cluster ID | Primer sequences (5'-3') | Annealing temp. | Product size (bp) | Restriction endonucleases |
1. | rs2276930 | Left primer: GCCGTAACTAACCTCGGCATC Right primer: GCCTCACGCTCCCCGAGCGCA | 61°C | 270 | BstN1 |
2. | rs3733414 | Left primer: CGCCCCAGTTCTCTTCTGT Right primer: TGTTGTTACTTCAAGTTCAAAATGG | 60.8°C | 290 | Rsa1 |
3. | rs455600 | Left primer: TCATTGACTTTTGCTTTTCCTAA Right primer: CCAACGAATCAGCAAAGAAC | 60.8°C | 299 | Acc1 |
4. | rs213090 | Left primer: GGCAGTTGAAATTTACTTTATAGTTCT Right primer: AGACTGCAGTGTGCAATTCTG | 61°C | 394 | HaeIII |
5. | rs450320 | Left primer: CGAAATCCTACTCCTGGCTTT Right primer: GCATCACTCCTGCTCCTCAT | 60.8°C | 349 | Hpy1881 |
6. | rs7663350 | Left primer: TGGTTTTGGTGAAGCATAAGAA Right primer: AAGTTATCCAGGATTTCAATCTCA | 60.8°C | 400 | Sau3A1 |
7. | rs1193110 | Left primer: AGACCCTTTCAGCCAGTTCA Right primer: AGTGAGATGAGGCCAGTGCT | 61°C | 369 | Msp1 |
8. | rs1298865 | Left primer: TTGTCATCCTTCCTTTTAGCAA Right primer: GATCCTTCAATGAATATGTTCTTCTC | 60.8°C | 400 | Dde1 |