In the pre-screen images, lane 1 is Chinese Spring, lane 6 is Opata, and
lane 7 is Synthetic 6x.


gpw93005
GCAAAGGGGGCAAGCACAGGCCAAGGCATCAGGCAAAGGTTACAGTTTCGGTGCAACAAG
ACCCAGACCAGCAGAGCGGAATGATAGAGGTCATCGTGGAGCCCAAGACGGTGTCGTCGT
CAGAGCCTTTGGCAGCCGAAGACCAACTTTAGTCAGGATAAGTGTACTAGATGTTCCCCT
TAGAAATGGCCAATTGTTGGCGCCCTTCCCGCTCATTATTTGGGAAGAGGCCCAGGGCCT
CCCTCTATAAATAGGACTAGCCACCACAGAGTAGGGGCATCTTGGAGACGGATTAATCAA
AGAGAGAGAGAGAGAGAGAGAGGCGACTGAATTCACCCCCGCAGTTCATCGCACCAGCTC
AAGAACAGCACTCGCGAGGCTGTTCTCCCTTTGTATTGTTCATCATCAGCCCCTGAGGCA
ATCCACCACACCACACTGGAGTAAGGTATTACACCGCAATGGTGGCCTGAACCAGTATAA
ATCTCGTGTCCCTTGTGTGTTCTTCTTTCTAGCCTAGATCCTTTGTGAGACT

Forward: AGCCACCACAGAGTAGGGG
Reverse: GTGTCTTCGAGTGCTGTTCTTGAGCTG
SSR motif:(AG)11
Annealing temperature: 60°C
Allele size: 
Chinese Spring – 119 bp
Opata – 119 bp
Synthetic 6x – 119 bp
Chromosome NT analysis:
Comments: Very strong amplification with a lot of non-specific
background.  Impossible to map on nulli-tetra’s.

Pre-Screen Image:
gpw93018 ATCTTTCCCACTAATGTTGACTGAACTTCCATTGCTGCAACAAAACCTTTGGGAACAATC TCCAGCCGAAGTTCCCTGAGATCCTCGGCTATCTCCTTTGGCAATCCTCCACTTATGAGG GTATTCGTCCTTGTTTTCTTTATGTTGTGTCCTATTTCTCCACAAAGCTTGTATGCACAA GGTTTCTTCATATCCTTTCCATAAGGCCTCAACTTCTGGGACACAGGACGAGATCTTTGA AGAGTCAACTTAAATTCTTCCCAGGTGGTTACTCTTTGCCACCCATTGATGGTTTGGTAC ATACTCCACCAAGTAGCAGCAACTCTTAAAAAGCACTGAAGAGCATGCTGGGTTATATCC TTTCTGGCTTTAGGGTTATCCTCCATGTTCTGAATCCATCGGTCCGTATCCAAATGACTC ATCGGTCTAGAAAATTACAAGCTCATGTCCATTCATCCTTTATTGGGTCCATGGGTTTTG GGGTGGGATAAGAGAGAGAGAGAGATAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGAT GCACACAATACAAACAATGGTTTTTGAAAAGACAGATTTTATTGTGACTG Forward primer: CAAGCTCATGTCCATTCATCC Reverse primer: GTGTCTTTTGTTTGTATTGTGTGCATCCC SSR motif:(AG)23i Annealing temperature:60°C Allele size: Chinese Spring – 94 bp Opata – 94 bp Synthetic 6x – 94 bp Chromosome NT analysis: Comments: Monomorphic in the 7 varieties screened. Very strong amplification - impossible to map on the nulli-tetra’s. Pre-Screen Image:
gpw95001 TGGTTGTAAAACTATTTTATTAAAGACAATTTCAATTGGGTTGTAAAACTATTTTAATTT TCAGACAAATATTTGGACGTGCAAACTAGTTTTGATGAAAATATGGGCATTTTTGGCCCT GACGGACAGGATGGGGGCAAACGGATGCGGCCGCGCGCTGGGCGCACGATCACCGCATTC CAGGACACGTCCGGACACGACCCCATTGCCCTATCCAAACGGATAGAATCCGGACAAAAC GGACTTCCGTTTAGGGTCGCGCGGTGGTGGGGTTGGCCTTACGACGGCAGCGATGTGAGT GGTGAGAGCATTCGGTTTGGCACCGATGGTGGGAGCGAGACATGGTCCAGGTCGTCCACG CCCAGTGATTTTGTCCCTACGACGGGTGGCTTTCCGTCCGACGTGCGGTGTAATCCATCC ATCGCTTTCCGCTTGCTCAAGAGTCCGGTAAGGCCGCCGTGCAGCCTCGCTCCTTCTTCT CCCCTCCAACCTTTTCCCCCTGTTCTGCAAGCCCTTTCCGTCTCCTTCTGGCTGCTTCCT CGCGCAGGTGCTATTTCTGAGCTTCCGAGGCGACAGAGCTGCACAAGAGCAGAGCAGAGC ATAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATGAGGGAGA TCATAAGCATCCACATCGGGCAGGCGGGCATCCAGGTGGGGAATTCCTGCTGGGAGCTCT ACTGC Forward primer: TTCTTCTCCCCTCCAACCTT Reverse primer: GTGTCTTTGTGGATGCTTATGATCTCCC SSR motif:(GA)23 Annealing temperature:50°C Allele size: Chinese Spring – 182 and 192 bp Opata – 182 and 188 bp Synthetic 6x – 182 and 188 bp Chromosome NT analysis: Upper locus of 192 bp, in Chinese Spring maps to 4DL and the lower locus of 182 bp maps to either 2AL or 4DS. Comments: Two loci, lower locus of 182 bp was monomorphic in the 7 varieties screened. Pre-Screen Image:
gpw95005 AAGTGGTTGTTAATAAGACCTAATCAACCTTATTAATGGATCATTTTTAGTGGTATGAAG TTGATGAATTTAGTAAGCACTACCTTCTGTCCCTACCTTTTGTTTTCTGTTTTGTTAGTT AAATAAAATAAAATGCCATGTTTTGTCTGTTTTCTGAATTTCCCGTGCAATAAGAAATGG CCCAAAAATAAAAGTTCTCAGAATGCTCTGAAAATTTAGTACGATTTTTTTTGAATATTT GAGAACTTCTGGTACAAATAATATCAGAGGGAGGTGCACTAGGTGAGCACAACCCACCTG GGCGTGCCAGGGCCCCCAGGCGCGCCCTGGTGGGTTGTGGTCCCCACGTGGTCCCCTCAC TTATCCCTTCACACCACATCATCACTTACCTCCACAAAAAATTCTCCATTGCTCTCTCTC TCTCTCTCTCTCTCTCTCTCTCTCTCGTGTTCTTGCTCTCAAACCCGCGAATT Forward primer: ACTAGGTGAGCACAACCCAC Reverse primer: GTGTCTTCGGGTTTGAGAGCAAGAACA SSR motif:(TC)17 Annealing temperature: 50°C

Allele size: 2A 3B 6B 7B Unlinked Chinese Spring - - 107 155 163 Opata 157 204 105 155 163 Synthetic 6x 158 - 101 153 -

Chromosome ITMI map: 2A (interval Xbcd152b-Xbdc543), 3B (interval Xabg471b-Xbcd1095), 6B (Xfbb327-Xfbb59c), 7B (interval Xbcd310-Xksud27a) and unlinked Chromosome NT analysis: 144bp on 5AL, 140bp on 3AL, 136bp on 3D and/or 5B, 130bp on 6AS, 115bp on 6AS and 89bp on 2DL. Comments: Complex banding pattern. Pre-Screen Image:
gpw95010 gcactcaacctatttataagttgggatccattccgcaaatgatgatagaatcatgtagaa agagagagagagagagagagagagagagagagagagggagggagggagagagagagagag atcgcctgcgtacctcctggagtgtgaagttggtgatgagatgagaac Forward primer: CCATTCCGCAAATGATGATA Reverse primer: GTGTCTTCACCAACTTCACACTCCAGG SSR motif:(AG)17(AGGG)3(AG)7 Annealing temperature: 50°C

Allele size: 6A 6B 6D Chinese Spring 105 129 125 Opata 92+103 - 127 Synthetic 6x 107 137 134

Chromosome ITMI map: 6A (interval Xfba111b-Xmwg2053), 6B (interval Xcdo507-Xfba42c) and 6D (interval Xbcd1510-Xksud27a) Comments: Using an annealing temperature of 60°C only the locus on chromosome 6D is amplified. Chromosome 6A – Opata has double-banded allele of 92+103 bp and Synthetic 6x has a single band of 107 bp Chromosome 6B - dominant marker with allele 137 amplified from Synthetic 6x Chromosome 6D – this is the main locus with alleles of 127 bp in Opata and 134 bp in Synthetic 6x Pre-Screen Image:
gpw95016 caccaacaagacatcaacaagacagccacaccgcggccatgcctggccactattgctgca taggcatacactattcatccatcaccatcaacagtgtgcagtaccatcaatagtgtaact tgtcccctgggcactagtatataaagtgacccagggggcaagccattgggccatggccac aaggcctcacacaggctggcaagctaactagctatccatccatccaggatgaacacactc cacgcatacatgctagctagcaagctagctagcacacacacacatccattcatccatcca cccacgtccaagcacacacttgtgctcatatgcatatacgaggctagatgcctatggcat tgacctcagatacagctccaggagcaaccctgtaccagatatacataccagatatactca gacatgcaggagtaggggtattatctctccggagagccctgaacctgggtaaactagcgt gtgctactcgcatacccactcccgggcctatcagcagcagtcttaccctcacactaagcc cttgtggcatcag Forward primer: CAGGATGAACACACTCCACG Reverse primer: GTGTCTTGTGTGAGGGTAAGACTGCTGC SSR motif:(CA)6 Annealing temperature:50°C Allele size: Chinese Spring - 312, 301, 277, 268, and 200 bp Opata - 312, 304, 301, 277, 268, and 200 bp Synthetic 6x - 312, 301, 277, 268, and 200 bp Comments: Monomorphic, but couldn’t assign bands to chromosomes using the nulli-tetra’s. Dominant marker allele of 304 bp wasn’t mapped in the ITMI population. Pre-Screen Image:
gpw95022 cttcaaatgctgaggatgacgacgagaaccaccaaaattattgagacactccggaacaat taagaatagaaaggttgagtgaaaaaaatgaaaagaattttgaaagtgatcttggaataa gcatatgactgatgaaattcattcttacgtcaaacttggaaataattagagaataactgc agaaaaaattagaagagcaggtaagatcctggggataaacctgtcggttagggcccactg aaaagaagcaccgttgaaaatgattcaagaagagagatgatacaccagagaaattgaaag acttgaatgaggtgacaaccttgaattaattagaacacaaacacgaatcttctgagatgt ccttagcactccgaaatgatgaaatggcgagaggtgaacgagcaagaggatacatttgag ccgagggaaagaatatgatcaacactggatacttgaattgaatccactggagaagagaac gagagagagagagagagagagagagagagagagagagagaatgacgaactagaatccacc ggttgaaacaattaaggaaagaatgaagaggcttcacacgaacaaaatgatac Forward primer: GATAAACCTGTCGGTTAGGGC Reverse primer: GTGTCTTCCGGTGGATTCTAGTTCGTC SSR motif:(GA)20 Annealing temperature: 60°C Allele size: Chinese Spring - 312 and 330 bp Opata - 310 and 336 bp Synthetic 6x - 310 and 332 bp Chromosome ITMI map: 7D (interval Xbcd707-Xcdo775) Comments: Two loci – lower locus not polymorphic in ITMI, but wasn’t screened against the nulli-tetra’s. Pre-Screen Image:
gpw95024 CAATTCAGTCCACACGCCCGACACAGATTCAGAAACAAGTTACGGCCGAACGCCACACAC ACACACACACACACACACAGGCTCATTCAGATCCTATGGTTTCGCTTGACGTTGGCTGGG CTGGTGGCTGCGGACATGGAACAACTCTTGGCTGTTACAGAGAGTTCATTTCTGAATATC TCCTAGGTTTCATGACGCTGCCCGCTCTGATGTCTGCTTCTCCTTGTCTTCCTCTCCCAA GAGTTTCCTCCGTTGCTGCATAAAGAACAAGAATTTGAATCTGATAGTGTAGTGTCAGTG TTGGAGTAGATTCTGGTGGCTCATTGAAGTAGTGAACTTCAGTAGACATGCAAGATATCT CTAGAACTTCAACTTCTGCTATTAAAACATGTGAGAACCCAACCTCCGTCCGAAATTACT ACCCGTTTGAGCGACAAGTAATTTCGGATGGAGTACTACATGACCATCAGAAATTCAGAA CCAAACCAATCTTGATCTTAGCTAACTAGTGGATTTGACTGTCATCCAGTTGCTGATTAC CTTGTAATGCAGGAAGCCAATCAGCGAATGTGAATTCGGGGAACGAGCTGAGGTCGCGTA CGGCTACTCGGAAAACGTCGGTGAGCACGGTCTTGGACTGCAGCATCACGGCCTTGAGGA TCTCTTTGCCCTGCAGTTGCACCATCAGATCAAACACGTGACCTGCATCGCTCAGTTCCA AGATGAAAATGGAAACGGAACAGTAGTAATTAAGCCACCTCCTTCAACCCAAGCTGCACG Forward primer: AATTCAGTCCACACGCCC Reverse primer: GTGTCTTAGCAGACATCAGAGCGGG SSR motif:(CA)13 Annealing temperature: 60°C Allele size: Chinese Spring – 250 bp Opata – 252 bp Synthetic 6x – 242 bp Chromosome ITMI map: 3D (interval Xcdo407-Xbcd515) Comments: Single locus ITMI population:
gpw95027 AAAAGTCTACAAACGATCCCCTATACTTGTGGGTTATCAGTATTCAATCCGATAAACGAA ATCTCAAAGGGAAAACTCAATTCATCACAACAAGATAGAAATGGAGGAACACCATATGAT CCAACTATATTGACAAAGCCCGCGATACATCAGGATCGTGACATCTCAAGAACACGAGAG AGAGAGAGAGAGAGAGAGAGAGAGAGATTAAACACATAGCTACTGGTACAAACCCTCAGC CCCGAGGGTGGACTACTCCCTCCTCATCATGGCGGTCAACGGGATGATGAAGATGGCCAC CGGTGATGATTTCCCACTCCGACAGAGTACCAGAATGGGGTCTAGATTGGTTTTTCATGG CTACAGAGGCTTGCGGCGGCGGAACTTCTGATTTAGGGTCATTTCTGATGGTTTTCCTAT TTATAGGATTTTTTGGCG Forward primer: TGACAAAGCCCGCGATAC Reverse primer: GTGTCTTGCCATGATGAGGAGGGAGTA SSR motif:(GA)16 Annealing temperature: 60°C Allele size: Chinese Spring Opata Synthetic 6x Chromosome NT analysis: Comments: Single, monomorphic locus with lots of stutter. Very strong amplification - impossible to map on the nulli-tetra’s. Pre-Screen Image:
gpw95032 acgcgcgcgatgcgactggccgaacgtttcggccggtgcgctggcgtaaaccgtttacct tataattagcgggtctcaccccaatgaaatttagagggaggggtgtgtgtgtgtgtgtta aaacttatataggttaatcgtacatttaggattagtgaaaggggaggggggtaaattaga ggatggacacatacgtgcgcaaggtgcagcctggataggtgctgcatgtaagtttactat ttccgatactataaacgcgtgcagaccgcaactcatgcatcgttctcaaacaataaatct ccaatacacaagaaggtttctgactcagctagcgaaatggctttcgcgctcaatgcatct tgctacccttcgtctttctcgtcgctgctcccgtggcggatggcagcagcggtgatgata ccaaggcggaggaatgttctgcctgtcattaaggcggttgcggtggctccgcccgccccg gcgccggcgaagccagcagccgtgaggagccggcccgtgtcggtcaccatggccaagctc atggctaagggcaaggtgcgtgcttatgtgtgtgcatgtgttgtacattgcatgtaacgg acgtgtggactctgaccggatattgggg Forward primer: GGGTCTCACCCCAATGAAAT Reverse primer: GTGTCTTCATGCAGCACCTATCCAGG SSR motif:(GT)8 Annealing temperature: 60°C Allele size: Chinese Spring – 163 bp Opata – 163 bp Synthetic 6x – 165 bp Chromosome NT analysis: 4D (interval Xksuf8b-Xfbb178b) Comments: Single locus Pre-Screen Image: