Table 2.
PCR markers used to map the Pst resistance locus in wild barley
| Gramene IDa | Genbank ID | Locus IDb | Typesc | Forward primers (5′→3′) | Reverse primers (5′→3′) | Enzymesd | Bands in bpe |
|---|---|---|---|---|---|---|---|
| MLOC_36989 | AK358025 | 11_10885 | InDel | TCTGCTCAGCAAGAAGAACG | AGCAATATTTACGCCGAACC | – | 268 (431) |
| MLOC_51298 | AK376744 | 11_20847 | CAP | AACGTTGTGGCCTTTTATGG | TTCCAGTGTCGACGGAAGAT | HhaI | 764 (465) |
| MLOC_39511 | AK359663 | – | InDel | GCTACAACAGTTGGCAAGTCTG | GAAAAGTGATCCGCGTGTTT | – | 140 (131) |
| MLOC_26380 | AK374153 | – | CAP | CCACCTAACCTTGTGCCTTG | TGCTGCATTCCCATGTAAAC | AflII | 793 (1191) |
| MLOC_26380 f | Tamalpais | CAP | ATCTTTGGCCTGTTTGGTGT | TTAAGTGTCGACGGTGAACG | TaqI | 698 (857) | |
| MLOC_16765 | AK366838 | 11_10687 | CAP | TCGGTGAATCTGGGCTATTC | TCAGTGCACCAGTTCTTTCC | DdeI | 326 (507) |
| MLOC_52705 | AK374563 | – | CAP | GTGCAAGCTGTCGTATGCTC | CCAACCGGCAAATGTTGAT | FokI | 578 (446) |
| MLOC_18254 | CB880323 | – | InDel | CCCCAAAACACCCTCAGGTCT | GAGGGACGCGGGGAAGCAAA | – | 101 (107) |
| Mx-contig_58199 | CAJW010058199 | – | CAP | GGGGCTTCAGAGCATATCAG | GCCGGTGAAGTTACATTGCT | NheI | 1180 (1327) |
| MLOC_37425 | – | – | dCAP | CAGCCTTGTCACCGGAGAAGTAGTA | CATGTTTTTGGCCTTCACACA | RsaI | 269 (295) |
| MLOC_65262 | – | – | CAP | TTTCAATAGAAACACGCTCACA | CACACGCTTTCATCATCACC | TaqI | 812 (510) |
| MLOC_52532 | AK361699 | dCAP | TGATTTAGCAGAGGAGGTTAC | GAACATACTCGCAAAGACTTGGT | BsrI | 193(217) | |
| MLOC_37646 | AK362947 | – | CAP | CTTGCACTTGTAAGGGCTGA | CTGGTTTTCAAACAGCAGCA | AluI | 366 (471) |
| MLOC_37646 f | Tamalpais | dCAP | ATCTGTCAAAGCCAAGTATTTGGTGATT | TCCAAAGCAATCACAGACG | HinfI | 293 (259) | |
| MLOC_22197 | AK250823 | – | CAP | GAGACAGTCATCCCGGAGAG | CCGACAACCAGTTCAAGGTC | PvuII | 777 (1265) |
| MLOC_24177 | AK363137 | – | InDel | TGATGTGTCCACTTGCAAAAA | TAAGTGTGTGGTGCCTGGTG | – | 190 (178) |
| MLOC_6480 | AB032839 | – | dCAP | GTAGTTGCTGTAATCAACATGGT | CAATGGCAAGACCAGTAGCA | HphI | 243 (263) |
| MLOC_4670 | AK359069 | 11_20139 | InDel | AGCTTGATGACCTTTCTGCAA | CACGAAGCGCTCAACACTAC | – | 190 (179) |
| MLOC_13779 | AK360979 | 11_21223 | InDel | GACAACGTGGTGTTCCACAA | AACACGACGTCAGAACACAAGAGC | – | 175 (144) |
| MLOC_55101 | AK355501 | 12_30593 | CAP | TGAGACTTTGTAATGGTGCCAA | TCTGTGAAACGCCTGCTAGAT | TaqI | 460 (784) |
| MLOC_71862 | AK250063 | 11_20414 | CAP | ATTTGGGAACGGAGGGAATA | ATCTGCAGCGCGTAGTTGT | AvaII | 861 (607) |
| MLOC_75180 | AK252062 | 11_11012 | InDel | TCGCCCAGGACAGCGACGTAA | GTTGAACCCGCTCTCCATC | – | 166 (180) |
| MLOC_36989 | AK358025 | 11_10885 | CAP | CAGGAAGAGGCTCTCCAAGA | CAGAAACTCAGTGGCGATCA | AvaII | 928 (782) |
| MLOC_75180 | AK252062 | 11_11012 | CAP | GAAGATCATGCAGGCACAGA | ATCACATTTCCAGTCCAACA | Hpy99I | 545 (318) |
aThe first 20 markers were used for POP366 and the last 2 for POP371
bThe locus ID in the 9 K barley iSelect chip (Comadran et al. 2012)
c CAP cleavage amplification polymorphism, dCAP degenerate cleavage amplification polymorphism, InDel insertion/deletion
dRestriction enzymes used to digest the PCR product
eSize of PCR bands: the first number indicates the product from the resistant parent and the second number in parenthesis the product of the susceptible parent
fDifferent, SNP, PCR primers and restriction enzymes used in the Tamalpais-derived populations