Table 4.
Allele-specific primers
| Marker allele | Primer sequence (5′–3′) | T A (°C) | PCR product size (bp) |
|---|---|---|---|
| Pain1-8c |
f-cacataatcaacgtgatgtttaagta r-ggtaatagtaattgcttctaaccg |
68-63a | 703 |
| Pain1 prom-d/e |
f-ctcatcataacttattccatcg r-tggaccacgcataagaaat |
63 | 551 |
| Stp23-8b |
f-cgcatcagaaaaaacctcgg r-acctcctcctgaccatcttt |
65-60a | 348 |
| StpL-3e |
f-ggaccctttgtattttcaggat r-aaagctcttccctgaaagaac |
65-60a | 360 |
| StpL-3b |
f-gaagaagtttctctgttagccac r-cgagtgacgtctgtagttatactagt |
65-60a | 1236 |
| AGPsS-9a |
f-ctgctttcttgcttagttttacc r-catttttcagaaattatatcaggtg |
63 | 210 |
| AGPsS-10a |
f-gaaaatttatcctgaacaaacaccca r-gttaataggaagctaacctcctct |
65-60a | 449 |
aTouch down PCR: the annealing temperature in the initial cycle was set 5 °C above the optimal T A of the primers. In subsequent cycles, T A was decreased in steps of 1 °C/cycle for five cycles and maintained for 30 cycles