Table 2.
COS and microsatellite markers used to genotype the Aegilops
| Marker | Forward primer (5′-3′) | Reverse primer (5′-3′) | Source sequence | Wheat homologue (EST or EST assembly) | B. distachyon homologue (E value) |
| TR119 a, c | GCAGCAGGAATTCTACATCAG | TGACGTGGAAGAGGTTCAC | Os03g52780 | Ta32373_4565 | Bradi1g68120 (1e−114) |
| TR129a | TTTGTAAGGGCATCCAACATG | CTGAGTAGTACCGAAGCAC | Os03g49230 | CD865921 | Bradi1g11700 (5e−42) |
| Psp3078a | TTATTTTGCAGCTTGACATA | TTAGGGCTCATAAGGGTCTA | Microsatellite | – | – |
| 4Ga, c | GCAATCACGAACGGCTCGATCA | ATCTGGCAGCTTGCCAAGGCT | BE442666 | BE442666 | Bradi1g11670 (1e−60) |
| TR113b | TCCTACAATCAAGGCTCTGTG | TTCTCTGAAAGCCTCTTCCAG | Os03g03470 | CV768642 | Bradi1g76790 (1e−51) |
| TR126b, c | CCGGATGCTGTTTGTATCCTG | TCATTCTTGGAGAACAGCGAG | Os03g42810 | CA735797 | Bradi1g07410 (1e−148), Bradi5g24240 (1e−135) |
| TR132 b, c | GTTCCATTCCCTAAGAAGATC | GTCCTGGTCAAAGTGTTGAG | Os03g50230 | CD906287 | Bradi4g00230 (3e−21) |
| TR133b | CATTGAACAGCCTTGGCAATG | TCTGCCAGATACTGTTCAGAC | Os03g51830 | TA25917_4565 | Bradi1g10000 (7e−81) |
| TR151b | GGTATAAGCCAGAGGTTGGTG | AACCGCCAGCGCTTTGGAG | Os04g43922 | TA38377_4565 | Bradi1g04570 (1e−107) |
The COS markers were designed to span one or more introns in a rice gene or were designed against a wheat transcript. All markers are available via www.modelcrops.org. The Brachypodium homologs were identified by BLASTn using the wheat sequences (www.brachybase.org).
a
Markers used for Bulked Segregant Analysis.
b
Additional markers used for linkage analysis.
c
Markers shown by analysis of Chinese spring–Ae. peregrina addition lines to be located on chromosome 4S.