Supplemental Table 1. Markers used for mapping.

Sequence / Map1 / Rice ortholog2 / Similarity / Notes / Forward primer / Reverse primer
k04468 / 6H3 / none / TaqI CAPS / AACGCTGATCTCGGTTTACCC / GCCGAAGATGTGACACCAGAG
U32_2219 / 6H:57.95 / LOC_Os02g10070 / 1.4e-96 / NlaIII CAPS / GGACCCACTTTTCCAACTGGT / TGCTTCAGTTAATCCGAAGTGG
U32_3656 / 6H:60.10 / LOC_Os02g40514 / 5.8e-30 / NlaIII CAPS / TGAAAGTCACACAGAGAGCACA / TGAAGCACTGAATGGGTCCTC
U32_1965 / 6H:62.14 / LOC_Os07g08200 / 2.0e-147 / HpaII CAPS / TTTTGGCTATCTCGCTTCTTCG / CACGTAGTACGACGCGCATATC
U32_7770 / 6H:64.07 / none / TaqI CAPS / GCCAAGGGAAAACATTCTGGA / CATCACAAGACACCATTGATGA
U32_832 / 6H:64.70 / LOC_Os01g22010 / 9.1e-135 / RsaI CAPS / GCTCAGGTACACCGATTGCG / CTCATCTCCACCCAGCATGAC
U32_2298 / 6H:64.07 / LOC_Os02g43020 / 9.1e-190 / NlaIII CAPS / CCCAACCTTCTCCAAAGGGTA / ATGGTTGCATGGCGTAACTTC
U32_5873 / 6H:57.95 / LOC_Os06g41590 / 4.1e-118 / DdeI CAPS / GGTCGATTCACGTTACCATACGA / GCCATGGTTCTGTCTCTGCAC
U32_2437 / 6HS4 / LOC_Os02g17390 / 0.0 / AciI CAPS / ATGAGGCACTAGGCACGGTTT / GCGCATTAAGCAGCAAACATC
TC2145145 / 6H:57.95 / LOC_Os02g10300 / 3.8e-62 / TaqI CAPS / GACATCCAGGTCACCAACTGC / GTGCCGGTGTACTTGAGGTTG
U32_3803 / 6H:52.38 / LOC_Os02g24354 / 4.1e-210 / BamHI CAPS / TGGCTTCGACCTACAACCTGA / ACAACAAGCCGGTAGGTCCAT
U32_4488 / 6H:58.72 / LOC_Os02g11840 / 1.5e-18 / NlaIII CAPS / CGAAGATGACGGAGCAGAAGA / GCAGGTTGCTGTTCCACTATCC
U32_9863 / 6H:58.72 / LOC_Os02g13960 / 2.5e-268 / BstUI CAPS / AGCAGCCTTCTGTTGTGCATC / ATCAACCGCCCTCAAGCTAGT
U32_810 / 6H:58.72 / LOC_Os02g37862 / 3.6e-109 / HindIII CAPS / GCCGCATGAGATGACCTTCTA / CTTGCAGCACGAACAGAACAA
U32_6593 / 6H:58.72 / LOC_Os02g33730 / 2.1e-35 / HpyAV CAPS / GCGGATGAGGAGGTATCTGA / CTGATATTCATACCACAGGTAGACACA
U32_6909 / 6H:58.72 / LOC_Os02g38240 / 1.8e-126 / BfuCI CAPS / GATCGATTCCGAGGAAGATGC / TATCCTGTTTGGCCCGAATTT
MWG2231 / 6H:bin0066 / LOC_Os02g39870 / 7.9e-28 / Fnu4HI CAPS / GCGATCACTGTGTAGTTTGAAGTTTG / TGCAATTTTTGCTTCATCATCA
MOC1-like7 / LOC_Os02g10360 / 5.0e-104 / Steptoe allele / AACTTCCCCCTCCAATAAATATTTTG / AAAAACACCAAGGGGAGCAAG
MOC1-like7 / LOC_Os02g10360 / 5.0e-104 / cul2 allele / CAACTTCCCCCTCCAATAAATATTG / AAAAACACCAAGGGGAGCAAG
HvIpk2b 8 / LOC_Os02g32370 / 6.7e-101 / Map di-Telo / GCCTCTGCTCCCTCATCAAGT / TGTAATCAAACAGGGGCCAAA

1 Unless indicated map coordinates are from the updated barley SNP map (Muñoz-Amatriaín et al. 2011)

2 Rice orthologs obtained from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/)

3 Mapped in Sato et al. 2009

4 Mapped to 6HS (Cho et al. 2006). This contig was mapped to 3H using a different SNP probe (Close et al., 2009),

5 TC214514 is a barley EST contig from The Gene Index Project (http://compbio.dfci.harvard.edu/tgi/)

6 Mapped in RFLP bin map (http://barleygenomics.wsu.edu/)

7 Allele specific primers for the barley MOC1-like sequence (JF710617) target a two-basepair indel downstream of the gene. Gradient PCR was used to establish the specificity of the primers, and an annealing temperature of 57 ˚C was used.

8 The EST contig U32_7775 sequence was used for HvIpk2b.