Supplementary Table S1 Map positions (cM) of SNP loci in chromosome 3D of consensus 90K SNP map (Wang et al. 2014) and corresponding KASP primer sequences

SNP / cM / Primer sequence
Allele 1* / Allele 2** / Reverse
KASP_72555 / 134.802 / gaagaaattgatgacgtccaagt / ctgaagaaattgatgacgtccaagc / ccgacattctcacggagctttctt
KASP_22532 / 142.3175 / cgctcaggtttctcggttgatga / gctcaggtttctcggttgatgc / caggccgcgataaggatacaatgaa
KASP_41228 / 142.3175 / cgcccaccaccatgagtat / ctcgcccaccaccatgagtac / gcagcgggcggcgagcaat
KASP_47097 / 142.3175 / gtaccagcactagctagcaatatgt / accagcactagctagcaatatgc / ttggtgagtgggggctccgat
ǂKASP_57983 / 142.3175 / gatattactgttgtggtattattcatggaa / atattactgttgtggtattattcatggac / caccgtagagcctcctgctgat
KASP_7538 / 142.3175 / tcttgtcgatggatcaaatcggct / cttgtcgatggatcaaatcggcc / acttaagtccagggcagctgcataa
KASP_8306 / 142.3175 / gccacgttgatatccagagcaca / ccacgttgatatccagagcacg / gcatccttcgttgcgcgctacat
KASP_10989 / 142.3175 / cgatactgggctgtgcagagtat / gatactgggctgtgcagagtag / gaaaggaatcgatctgtcaccgctt
KASP_11519 / 142.3175 / catgttccgagagatcgcctct / atgttccgagagatcgcctcc / cctcgtcgctaagcacctcgta
KASP_151 / 143.0073 / ggatctgaatgatcaacatctcttctta / gatctgaatgatcaacatctcttcttg / ttgtcattagcaggatttgacccaatgta
KASP_2371 / 143.0073 / ccgcacttgcagtctgagcca / cgcacttgcagtctgagccg / atgtcttgcaactgtggatccggtt
KASP_12802 / 143.0073 / gcctgcccaagcatcgttaat / gcctgcccaagcatcgttaac / gaagatggcaggccgagttgctt
KASP_14491 / 143.0073 / cacaatcaacagtccgtatgcca / cacaatcaacagtccgtatgccg / ctcaactatcggtcccatacttgctt
KASP_14550 / 143.0073 / agcatctggtcggacaagctca / gcatctggtcggacaagctcg / tgtacttgtactcgaacccctcctt
KASP_16434 / 143.0073 / caacatgccattacatctgccacat / aacatgccattacatctgccacag / cttgagactgaaagccgttagtcctt
KASP_16761 / 143.0073 / ggatctcgtagtagtccaccga / gatctcgtagtagtccaccgg / tcatgcatcttcattacggttcacgat
KASP_17207 / 143.0073 / catgttgtgcaaatgctcgctctt / atgttgtgcaaatgctcgctctc / gccaattggtggtttgttgatgccat
KASP_23073 / 143.0073 / tctccaaaccgtgttcagagt / cttctccaaaccgtgttcagagc / cgtttcgaaaagagaatgaacagaaccat
KASP_23615 / 143.0073 / gaaacttgccgaaacaccatcttgat / aaacttgccgaaacaccatcttgac / ggactagatggaaaagacgagtcgat
KASP_28497 / 143.0073 / ataaaggagttggctgatcagctaatt / aaaggagttggctgatcagctaatc / cgtacatttgaaggctgagtgccaa
KASP_28840 / 143.0073 / cctcattccttcttttagtaaagtaagga / ctcattccttcttttagtaaagtaaggc / atgttgtgccaaggccaactgtcat
KASP_29396 / 143.0073 / gtatcagtgcaacccaacatgcaat / atcagtgcaacccaacatgcaac / aacatcccgtggaggcggcaaa
KASP_34814 / 143.0073 / actagtgttcagtagctaatttattcatgt / ctagtgttcagtagctaatttattcatgc / atgaagatccatacaagtaccgtccaa
KASP_37975 / 143.0073 / atacgagtgtgcgacattgctct / acgagtgtgcgacattgctcc / gtacccccaagcaaggagccat
KASP_43136 / 143.0073 / gtttgtataactggacttgttacaagtca / gtataactggacttgttacaagtcg / caagcaggtccgcattccgcaa
KASP_43814 / 143.0073 / gagatgtttggcattactggactgat / agatgtttggcattactggactgac / ctgaagaaactcataatatccaaggccat
KASP_44062 / 143.0073 / aaacatcaaaggtgatgatcatctgca / acatcaaaggtgatgatcatctgcg / ctctttccggatcttgagggcatta
KASP_45955 / 143.0073 / aatccttccatgagacgaataatgtga / ccttccatgagacgaataatgtgc / aattacttcgtgaaggagatcgaccaaa
KASP_63833 / 143.0073 / aagaggaagttgaagaagttgaggat / agaggaagttgaagaagttgaggac / gacaaggacaggctcgacctctt
KASP_72414 / 143.0073 / ccatacatacaggtagaattttccgt / ccatacatacaggtagaattttccgc / gtaaacctgttgcggctgcccaa
KASP_8886 / 143.0073 / tgttaatatagtcagaacggtacgtt / gttaatatagtcagaacggtacgtc / cgacgatgtgcacagcgtcctt
KASP_8928 / 143.0073 / gtcttataatctccaataaatggtccatttt / cttataatctccaataaatggtccatttg / ccgatgatagacatactgctacaaatcaa
KASP_9142 / 143.0073 / caagaatgctgcaatccctctaataaa / aagaatgctgcaatccctctaataac / ccccaaattgtggggtaatttcccat
KASP_10437 / 143.0073 / ccacgagttcatggacgcggt / cacgagttcatggacgcggc / aagagtgatcacgcaggaagtggaa
KASP_10438 / 143.0073 / cccaggggcctcccccat / ccaggggcctcccccac / gttcgacgtcttcgggaacgactt
KASP_10689 / 143.0073 / ctaggcaaagcagagccacca / ctaggcaaagcagagccaccg / aagtgtgatggaattgtacactagctgtt
KASP_2022 / 145.6738 / tgagaaggacggcagtgagtta / gagaaggacggcagtgagttg / ctgctaacgacaacactacatttgttgaa
KASP_40709 / 145.9723 / cagggagtgtttcacagagcca / agggagtgtttcacagagccg / caaattgtttagcgctgatagcaaagcat
KASP_58813 / 147.3416 / cgggtgaagtttggctggatga / gggtgaagtttggctggatgc / cagtcactgtcctttgcaatgggaa
KASP_1494 / 148.4089 / acaggaaagagtagctatctggact / aggaaagagtagctatctggacc / ctgagcagcttcattggcagcattt
KASP_26400 / 148.4089 / gggtggtcaatcttgatggagca / ggtggtcaatcttgatggagcg / gctgaagtttgttcagaaacaacttcaaat
KASP_26909 / 148.4089 / catcttgttgaatcgtccctctact / atcttgttgaatcgtccctctacc / ggccattactctggttgacaaggaa
KASP_63653 / 148.4089 / cgccgcgtgcatcatatctatga / gccgcgtgcatcatatctatgg / agcgttacatggtagtagatggtagata
KASP_4163 / 149.0025 / gatgcttcttaaacctcctggaca / atgcttcttaaacctcctggacg / agtccctccccccaggtttgaa
KASP_14087 / 149.0025 / atttcaggacacagcactcattacta / tcaggacacagcactcattactg / gttagtttccgttgtatacaattgtgggtt
KASP_16679 / 149.0025 / catatcccatactgcataaaagtcaacat / atcccatactgcataaaagtcaacac / ctggccttatgatgccatttatcaaacaa
KASP_45351 / 149.0025 / aaggtaccgaccttctcgcca / ggtaccgaccttctcgccg / acactggaaacatcgcgaaagccat
KASP_48314 / 149.0025 / gacattgaatacctatcatctagagaca / acattgaatacctatcatctagagacg / gcccgttgcggctccccat
KASP_19457 / 151.4082 / actctgtgtacatgcatgatacca / actctgtgtacatgcatgataccg / gcgggaactcggaggaaaatgaata
KASP_36035 / 152.8358 / acaaggaaactccatgcgatgca / caaggaaactccatgcgatgcg / gtcttaacagctagcgctttgcctt
KASP_59163 / 152.8358 / aaattagctgatggacaaggagatgta / agctgatggacaaggagatgtg / gcagaatgcctcgatagtaagctcta
IWA7388 / - / caacaagaataattgataaccacgaagca / acaagaataattgataaccacgaagcg / cttcactcgccttctttttcaagtttctt
KASP_16737 / - / catcatgaagcttccgagttcatca / atcatgaagcttccgagttcatcg / tgtccacaaagttgacatctatggcaat
KASP_17243 / - / ataatcaagccttgtggtcatcttgt / aatcaagccttgtggtcatcttgc / ctggtattcaaattttagagaagtgcaaaa
KASP_20836 / - / gtggtatctcctgctcctgct / gtggtatctcctgctcctgcc / cagtcgtgacaggcagctggtt
KASP_23518 / - / ccaccgtgcaaccccgaca / caccgtgcaaccccgacg / cagttatacaaacagcagtaacacctgtt
KASP_37813 / - / agctgacgtccatcgataaagct / gctgacgtccatcgataaagcc / agccaggaggggtcgaaaggat
KASP_40719 / - / aaccagcagatgtgttgaaccca / accagcagatgtgttgaacccg / gtctcttccactgcaatttgcgctt
KASP_57328 / - / ccctggaactcttgctgctca / ccctggaactcttgctgctcg / tggcactccaagtacgagaggaaa
KASP_59022 / - / ggagcaacttgccgctgtacttt / gagcaacttgccgctgtacttc / cgaggaagatgagattgactgggaa

*Allele 1 Fam sequence gaaggtgaccaagttcatgct

**Allele 2 Hex sequence gaaggtcggagtcaacggatt

ǂ markers mapped in the SA65/SA67 population