SSR and e-PCR provide a bridge between genetic map and genome sequence of potato for marker development in target QTL region.

Am J Potato Res

Jingcai Li • Conghua Xie* • Zhendong Tian • Hannele Lindqvist-Kreuze • Merideth Bonierbale • Jun Liu

*Huazhong Agricultural University, Wuhan, Hubei 430070, People’s Republic of China

Tel.: +86 27 87280969, Fax: +86 27 87286939, e-mail:

Table S1 SSR in pseudo-interval of dPI09c

SSR namea / Seq idb / Polymorphismc / Forward primer / Reverse primer / Fromd / To / Lengthe
STMput157a62813 / PUT-157a-St-62813 / M / TGCATCTTATTGAGCAATTTGG / AGAGAACAATCTAATAATTTCCCATGT / 50367330 / 50367459 / 130
STM400053017 / PGSC0003DMT400053017 / P / AGTGGTGGTTTTCGTTCTGG / ACCTACGAAATTTGCCATGC / 50942557 / 50942705 / 149
STM400053053 / PGSC0003DMT400053053 / P / TGTGGATTGCTGAGAAGCTG / GCGGCAACTTGAAATTCTTC / 50953881 / 50954032 / 152
STM09g029020 / Sotub09g029020.1.1 / P / AGAGGGAGTGGAGTTGAGCA / CATTTGAGCTCCTTGGGAAA / 51099469 / 51099585 / 117
STM400067989 / PGSC0003DMT400067989 / M / GCTTGGTTCCGATCACATTT / AAATCAACGCGAAAAACGAC / 51152800 / 51152905 / 106
STM400067934 / PGSC0003DMT400067934 / P / ATTGGAGCCTGTGAAAGGTG / CTGGCTCAGCTTTTTGTGTG / 51163403 / 51163551 / 149
STM400062291 / PGSC0003DMT400062291 / M / CTCCCTCCGTTTCACAAAGA / TTCCACGTGGCATGTTTAAG / 51271509 / 51271661 / 153
STM400067951 / PGSC0003DMT400067951 / M / TCCGGAAAGAATTGCTATGG / TGGCCTCCACCTATTTGTTC / 51283347 / 51283452 / 106
STMput157a13050 / PUT-157a-St-13050 / M / GAAAGCGAGAGAGAGGAGAGAG / CCCACAGATTTGCTTCTTCG / 51290371 / 51290486 / 116
STM400067922 / PGSC0003DMT400067922 / M / CCACCACCTCAGGCTAAGAG / TAGCCAATGCAGCTTGAGAA / 51318553 / 51318694 / 142
STM09g029290 / Sotub09g029290.1.1 / M / TCCGTGATGTTCAATGGCTA / GGAGCGTTGTCACCAAAAAT / 51325267 / 51325375 / 109
STM400042881 / PGSC0003DMT400042881 / M / CTTAGGTCGCAGGTTCAAGC / CCTTCCAAACTCGGTGGATA / 51379119 / 51379219 / 101
STM400017286 / PGSC0003DMT400017286 / M / CGGCATTCTCTGATGGATTT / GACGTCCCTCGTCTGAACTC / 51479349 / 51479483 / 135
STM09g029480 / Sotub09g029480.1.1 / P / AACACCCTTCTGTTGGTTGC / CGCCATTCTTCCAAACATCT / 51508965 / 51509114 / 150
STM400017286 / PGSC0003DMT400017286 / M / AAAATGGGCATTGAGGTGAC / AGAGAATGCCGCCAAGTTTA / 51515806 / 51515913 / 108
STMb09g029510 / Sotub09g029510.1.1 / M / ATTGGGCAACTCAGTCAAGG / CGCGATTCAATGTTCTCAAA / 51551892 / 51552008 / 117
STM400077026 / PGSC0003DMT400077026 / M / TTCAATCTGAGCCTCGGAAC / GAATGTCGAAACGGGTCTGT / 51559160 / 51559304 / 145
STMput163a52 / PUT-163a-Sc-52 / M / TTAGATGGGTTCAAAAGAATTTCA / AAAACCACAAACACATGAAAAA / 51576987 / 51577133 / 147
STM400056316 / PGSC0003DMT400056316 / M / GCCTTTGGAATGCTGATGAT / GCTTTGGGCCATGTAGTTTC / 51577204 / 51577307 / 104
STMput163a52 / PUT-163a-Solanum_chacoense-52 / M / ACATTTATGCCCAAGGCAAG / TGTTGGGGTTTCCAAATGAT / 51577729 / 51577831 / 103
STM400056290 / PGSC0003DMT400056290 / M / TGCCACTGGTGTCATTTCAT / CCAGTTGGCATCCAAGCTAT / 51587894 / 51588026 / 133
STM400048133 / PGSC0003DMT400048133 / M / AGACTCCAAGCACCTCCAGA / CGACTACCGAAGCCATTCAT / 51591825 / 51591967 / 143
STM400049901 / PGSC0003DMT400049901 / M / ACAAGGTGCCAAGGAATGTC / GTCTTGGCTCCACCGTACAT / 51591927 / 51592026 / 100
STM400056290 / PGSC0003DMT400056290 / P / TCTGCAGGAGATGAATGCAC / CAGAAGCCTCAACAGCATCA / 51612339 / 51612472 / 134
STM400056322 / PGSC0003DMT400056322 / M / GACAGCAGCAGTGTGCATTT / AATCGAAATCCCCCAAAATC / 51652243 / 51652362 / 120
STM400056312 / PGSC0003DMT400056312 / M / CAGGTCAAAAACGCAGGAAT / CTCATTCCCGTTTTGCGTAT / 51656770 / 51656903 / 134
STMput157a27242 / PUT-157a-St-27242 / M / TACGTTCTCCGCAAAGTTCC / GACGAAAATAGATGCTGGAAATG / 51657887 / 51657987 / 101
STM400028911 / PGSC0003DMT400028911 / M / TCCCAAAACCAAAGAACTGC / AGCAACAACTCCCACAGCTT / 51658721 / 51658833 / 113
STM400056312 / PGSC0003DMT400056312 / P / GCCCCTGCTACTCTTCCTCT / AAGCTGTGGGAGTTGTTGCT / 51658814 / 51658954 / 141
STM400080919 / PGSC0003DMT400080919 / M / GGACCAAAGGCATTGTGAAT / TAGGAGTGGAGCTGGTGGAT / 51719580 / 51719680 / 101
STMput157a61247 / PUT-157a-St-61247 / M / AACAAGGCGAGTGGTGATGT / ACAACCATATCGGCAACCTC / 51759224 / 51759361 / 138
STMput157a31026 / PUT-157a-St-31026 / M / AGGAGGAGGATACCCTGGTG / CTCCATAACCTCCACGACCA / 51764215 / 51764333 / 119
STMput157a66991 / PUT-157a-St-66991 / M / TGGAGGGTATCCTGGTGGT / GTATCCACCTCCACCACGTC / 51764241 / 51764354 / 114
STM09g029900 / Sotub09g029900.1.1 / M / CGTGGAGGTTATGGAGGGTA / GTGAGGCTTAGCTTGGGTGA / 51764825 / 51764995 / 171
STM400080936 / PGSC0003DMT400080936 / P / CACTTCATGTGGATGGATGG / GACGCGTTTTATGTGGACCT / 51765103 / 51765221 / 119
STM400080937 / PGSC0003DMT400080937 / M / TTCAGAGGAGGCGAATATGG / ATCCAGGATATCCACCACCA / 51771905 / 51772037 / 133
STMput157a68220 / PUT-157a-St-68220 / M / CTTATCACTCCAACACAACCTTTT / ATCTATGAAGAATATCCATTGTGGT / 51794013 / 51794156 / 144
STMput157a11146 / PUT-157a-St-11146 / M / CTCCAGGTGGCGGATACA / GTCACTTAATCATGGCCTCCA / 51811541 / 51811667 / 127
STMput157a11097 / PUT-157a-St-11097 / M / CAACCCTCCACATGACGAAT / TCACTTAATCATGGCCTCCA / 51811542 / 51811651 / 110
STMput157a23599 / PUT-157a-St-23599 / M / GGATACCCCGGTGGTGGT / CGGGATATCCGCCTCTACC / 51832668 / 51832782 / 115
STMput157a23599 / PUT-157a-St-23599 / M / GATACCCCGGTGGTGGTG / CCGGGATATCCGCCTCTA / 51832669 / 51832783 / 115
STM09g029990 / Sotub09g029990.1.1 / M / ATGGGTTCCAAGGCATTTCT / TGGTGGAAGTCTCAGCCAAC / 51843418 / 51843517 / 100
STMput157a53283 / PUT-157a-St-53283 / M / GTATCCACCACCACCACCAT / GATGCAGCCAAGAAATCCAG / 51844249 / 51844443 / 195
STMput157a53916 / PUT-157a-St-53916 / M / GGGTATCCACCACCACCAC / GAAGTACATGAAGCCGAATATGG / 51844279 / 51844418 / 140
STMput157a37068 / PUT-157a-St-37068 / M / AAGCCGAATATGGCGGGTA / GTATCCACCACCACCACCAT / 51844289 / 51844443 / 155
STMput157a53283 / PUT-157a-St-53283 / M / ACTGGATTTCTTGGCTGCAT / AGGAGTTGCCAAAGAAGGAA / 51850544 / 51850738 / 195
STMput157a37146 / PUT-157a-St-37146 / P / GTGTTGGTGGCGGATACC / CCACGGTTGCCTGAGTATTT / 51850644 / 51850773 / 130
STMput157a57743 / PUT-157a-St-57743 / M / AAGGAGTTGCCAAAGAAGGA / ACTGGATTTCTTGGCTGCAT / 51860451 / 51860600 / 150
STMput157a37066 / PUT-157a-St-37066 / M / ATGGTGGTGGTGGTGGAG / CACGGTTGCCTGAGAATTTAC / 51860610 / 51860712 / 103
STMput157a37067 / PUT-157a-St-37067 / M / AGCCGAATATGGCGGGTA / CACCGCCAGGGTATCCAC / 51860621 / 51860712 / 92
STM400080982 / PGSC0003DMT400080982 / M / GATATGGACACGGTGGTGGT / TGTCCATTGCTTCACCTTTG / 51900843 / 51900977 / 135
STM400046163 / PGSC0003DMT400046163 / M / TGGATCGTTGAATGACCTGA / CAGCATGCAACACTTCCACT / 51924960 / 51925080 / 121
STM09g030130 / Sotub09g030130.1.1 / M / ACCGGTCAATCATGAACCAT / CTTTGAGGACGCGAATTAGG / 51966125 / 51966226 / 102
STM400042791 / PGSC0003DMT400042791 / M / TCAAATGCCAAAAGAAGCAA / GCCTGTCCCCTTCTAGCTCT / 51992275 / 51992423 / 149
STM400042870 / PGSC0003DMT400042870 / M / TTGCAATGACTTGCCACATT / ATTCCCCAAGAAATCCATCC / 52061586 / 52061708 / 123
STM400046794 / PGSC0003DMT400046794 / P / TCGGACCCTTCAAAAATGTC / ATCTTGCTCGGACTCTCCAA / 52086879 / 52086948 / 70
STM400018099 / PGSC0003DMT400018099 / M / CCGCTCCTATGCAATAGCTC / TCAAGTTTGAAACCCCTTGC / 52113598 / 52113722 / 125

aIn SSR name, "STM" indicate Solanum tuberosum microsatelet, and suffix after "STM" was derived from Seq id of cognate transcript

bSSR identifier of Solanaceae Genomics Resource at Michigan State University (http://potato.plantbiology.msu.edu/breeder_ssr.shtml)

c"P" indicates polymorphism in population B3C1HP and "M" monomorphism

dStart and end positions of SSRs mapped by e-PCR on pseudomolecule of chromosome 9

eExpected size (bp) of SSR bands estimated by e-PCR

Table S2 DM candidate gene markers identified between STM09g029480 and STMput157a37146

Marker_name / Forward primer / Reverse primer / Polymorphisma / Startb / End / FPKMc / Annotationd
DMG400021869e / CAATGGAGATAGTGGAGGGC / TGAGTAAGTGGGATAGGAGCAA / M / 51572009 / 51576076 / 0.48673 / Conserved gene of unknown function
DMG400021877 / GGAAATGGGACACCAACTG / CAAGGCAAGGGTAACAAAGA / P / 51576905 / 51579093 / 13.8685 / Xyloglucan endo-transglycosylase
DMG400021878 / CCGACTTGTCAGGATGGC / AAGGTGGCGGTAACAGATTC / M / 51587055 / 51589637 / 0.309353 / Hypothetical salt-inducible protein
DMG400021879 / TACACTTTACCCTCCCCAGAC / TTTCGCCTTTTGATAACTTTG / M / 51590269 / 51597417 / 9.73221 / Chloroplast inner membrane import protein Tic22
DMG401021870 / CAAAAGTCACAAACTGGAGCAC / GAAATAGGAGATAGTCAAAATAGGC / M / 51608738 / 51615367 / 3.1646 / Hypothetical salt-inducible protein
DMG402021870 / CCAGGTCCATTAGGGC / TCAAGCCAACCGAACA / P / 51616972 / 51621960 / 0.42727 / Cytochrome P450 monooxygenase CYP83E9
DMG400021872 / GTGCCACCTGGTCCTTTAG / TCACAACGCCTTTCTTTCC / M / 51625978 / 51627435 / 0.253442 / Cytochrome P450
DMG400021873 / TGAGCAGCATCTTAGTCCCA / AACTCCCAATCAAAAGCGTA / M / 51629844 / 51631662 / 0.16754 / Conserved gene of unknown function
DMG400021874 / CAAGCCGCCACTTCACA / CTCCCAATCAAAAGCGTAAA / M / 51637283 / 51639353 / 1.06047 / Cytochrome P450
DMG400021875 / AACAAATGACCCAGACCCG / TGAGCACAACAGCCAAAGG / M / 51641551 / 51647263 / 0.374668 / Conserved gene of unknown function
DMG400021881 / CTACGCCAGCCCTTTTCT / TCTGCTTTCCGAGACCTGTA / M / 51651976 / 51654943 / 6.31912 / Gene of unknown function
DMG401021876 / GGAACTTTGCGGAGAACG / ATACATACAACACCCAACCCA / N / 51656532 / 51659009 / 1.33524 / Gene of unknown function
DMG400031515 / AGCCAAACCGAATGCCA / CCTCTTCTTCCTGCTCCAAA / M / 51678876 / 51687477 / 4.60981 / Conserved gene of unknown function
DMG400031518 / GCTTTCGGTGTTAGGTTTGA / CAAGGTTGGAAGGTCGTCA / M / 51718209 / 51720171 / 0.293715 / Conserved gene of unknown function
DMG400031519 / TGAGCAACATCAGAATCCCA / TCCCAATCAAACGCATAAAG / N / 51725571 / 51727845 / 32.0296 / Conserved gene of unknown function
DMG401031520 / TGGTGAGGGCGAGGAAG / AAGAAGGCAAATGGAATAACG / M / 51730479 / 51735628 / 10.9893 / Cytochrome P450
DMG400031521 / TATGCCTGATTGTGCTCGTG / GCTTTTCCTCAACTTGTCCG / M / 51737205 / 51741005 / 0.270933 / Tospovirus resistance protein B
DMG402031520 / TTGGACAACAAAATGATGCTC / GATTCTTCGTCATACCTAATACCA / M / 51744657 / 51746584 / 19.6069 / Cytochrome P450
DMG401031533 / CGCTGAAGATGCTGGAAGA / TCGTAGGGTGGGAACTGG / M / 51746695 / 51747757 / 0.195182 / Gene of unknown function
DMG402031533 / CCTTCCCAGTTCCCACCC / CCAGAACCAGCCAGAGCAT / M / 51746695 / 51753889 / 12.9915 / Protein transport protein Sec23
DMG400031522 / GGAGATAGGGAAAACTGGGATA / CTAATAGCAAACCGAAAGCATA / M / 51754155 / 51758638 / 0.145391 / Peptidylprolyl isomerase
DMG400031534 / CACTCGCCTTGTTTTCTTCTA / TTTTGGTCTTTTGCTTGCTAT / M / 51758905 / 51759775 / 0.606088 / Glycine-rich cell wall structural protein
DMG400031523 / AAAAGGTCATAGTGAGAATCGG / TTCAAACTCGCAACAACAAAT / M / 51763184 / 51765255 / 11.9891 / Glycine-rich cell wall structural protein 1.8
DMG400031524 / TCCTTAGTTTCCTCATCCTTCTT / CGTTATCCACTCGGCTTCTC / M / 51771447 / 51772429 / 26.1968 / Glycine-rich protein
DMG400031526 / TTGCTTCAGAGTTCCACCAC / CCTGGGTTTGATATTCGTTTT / N / 51780689 / 51781395 / 0.769334 / Gene of unknown function
DMG400031525 / TTGTTCCGTTCCCTCCTTA / TTTGGCGTCATTTGTCTCAC / M / 51792019 / 51794036 / 2.87261 / Plus agglutinin
DMG400031527 / TTGGGTGGGTTCATTGGC / GGTTTCCTACCTGGGTTTTG / M / 51795488 / 51796684 / 22.1676 / Glycine-rich protein
DMG400031528 / AGCTCCATCACTTCCCTCG / CCTATCAAATAATCCCTAATCCC / N / 51799438 / 51800262 / 50.4606 / Gene of unknown function
DMG400031529 / ATAAACAATCTATTTGTCACCCCTAC / CCTCCATACCAACCACCTCTA / P / 51802191 / 51803677 / 0.087652 / Glycine-rich protein
DMG400031535 / TCCGTCACTGGGTGGTTT / GGGAGTTAGCGGAGACTTGTA / P / 51811358 / 51812157 / 1.74441 / Glycine-rich protein A3

a"P" indicates polymorphism in population B3C1HP, "M" monomorphism and "N" no PCR products

bStart and end positions of DM genes on pseudomolecule of chromosome 9

cThe FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks (v1.3.0), indicating RNA-seq gene expression data for DM P. infestans infected Leaves (24hr/48hr/72hr) (PGSC, http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml)

dFunction annotated by the PGSC (http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml)

eDMG400021869 represents marker derived from DM gene PGSC0003DMG400021869