S1. List of PCR-based markers developed in this study
Marker / ForwardPrimer / RiversePrimer / Chr. / PCR / Enzyme / AgaroseC161 ALP / ctactgccagatagatgatgctcc / tagccatcactcaggaagcacaag / 1 / 2 b / - / 3% TypeII
PLD HaeIII / atggcgcagatgctgctccatggg / cttggtactgcggacacccctcgc / 1 / 1 a / HaeIII / 3% Agarose21
AP002746 / agtattccttgctgctgctgatgg / aacctaattctgggcgagcaaagt / 1 / 3 c / - / 3% Agarose21
R2151S BsrGI / ctcaagttcgacagcggtttgtac / cgatgcgtcccatcttcttcatgg / 1 / 2 / BsrGI / 3% Agarose21
AP003350 / accgagtcaaattaaccatgtagg / agtatgaaaggaacaaacgaagcc / 1 / 4 d / - / 3% Agarose21
AP003449 / acacaacagaacaatgcctaaagc / aatgtgtggtggcgatgatgtttg / 1 / 5 e / - / 3% Agarose21
AP004225 / aaatcgctacctcccccaagaacc / gggtacgcacttcttgacgacatc / 1 / 6 f / - / 3% Agarose21
S13994 EcoRI / ctgtccagaggaccatacatacag / gctgttgttgaggctatatgcggt / 1 / 2 / EcoRI / 3% Agarose21
S15001A SalI / gcatcaactagtttgtccaagagc / cgacgagatgagctccaccaggtc / 1 / 2 / SalI / 3% Agarose21
AP003286 / tgctgcttttggtggaacattgcc / tgccattagaacagagcgtgatac / 1 / 4 / - / 3% Agarose21
AP004187 / gatgaatgtatgtgttagttgggc / taagagatgagaagagcaatgagc / 2 / 5 / - / 3% Agarose21
AP004112 / gttgatgtgatggaaaaggactga / aaacgagagggtgtgagagtgctt / 2 / 4 / - / 3% Agarose21
AP004066 / gctgatgataattctccgtagtag / atcaatcctacaaacatacccacc / 2 / 4 / - / 3% Agarose21
RA1843BslI / taggtaagaaatcaaatccaccaaccg / gacttgcccattatttgataccgctag / 2 / 2 / BslI / 3% Agarose21
p-SINE-r7 DdeI / tggtacactgattactgaagtagc / cagaagacctctactgaatcctaa / 2 / 2 / DdeI / 3% Agarose21
p-SINE-r4 BslI / tcttagttatgtagaggttgagaaccg / gatacaaccgtactaagaacactc / 2 / 2 / BslI / 4% MetaPhor
AP004092 / gaatgttagactcggttttacggt / ccgaaaagcaaagaaaaacggtag / 2 / 4 / - / 3% Agarose21
S10844 ApaI / cgccatccttgacttgaacagaag / gtttactcctatcaaacaccatcc / 2 / 2 / ApaI / 3% Agarose21
R480 HaeIII / tctggtgttgggaaatcgtgc / ggtatcaagggcgttcaaatg / 2 / 7 g / HaeIII / 2% TypeII
AP004096 / acaagtggaagtagaggttagagt / actattgtacctgctcttatcgtg / 2 / 4 / - / 3% Agarose21
p-SINE-r5 BfaI / ttaaatgccaacaatgtcagccat / gctgaaaatgttactcattcagt / 2 / 2 / BfaI / 3% Agarose21
G1234 MboI / ctcaagctcacgtcgccactg / atatgttgctcgtggtttgtcagg / 2 / 8 h / MboI / 2% TypeII
R2218 EcoRI / gagcccaaaacgagtcgataatcgaat / cttacgaaggaggaaaggctgatg / 3 / 2 / EcoRI / 3% Agarose21
AP000615 / ttagctgtgttgtggtgggcttag / acaagcggttttttcgtttcgcct / 3 / 4 / - / 3% TypeII
R3126 SalI / cccattcaatacttcatcatagcc / tcatagccaatccaagcaatagag / 3 / 4 / SalI / 3% Agarose21
D83726 BstZ17I / tcaaaacttgccaacttcctccga / taccacctataatcaaccgtaggc / 3 / 2 / BstZ17I / 2% TypeII
AL607101 / tactccttccattcccttccatag / atttaggagtatttttaggccacg / 3 / 4 / - / 3% Agarose21
S1466 HhaI / gtgctggaaacaggagtaag / tgggttgaggacctttgtg / 3 / 9 i / HhaI / 2%TypeII
C50029S MboI / ggaccacgatgttaggtatattgg / gatatttggtgctgtcatagaccga / 3 / 2 / MboI / 3% Agarose21
AC096855 / cacaccttatttcctcatggctag / catatcactgccgtccatctgtcc / 3 / 10 j / - / 2%TypeII
AC079887 / ctgctaacgaaatctggaagttgg / aatgctaaatgaatgtgggcaatg / 3 / 4 / - / 3% Agarose21
S2516 TaqI / caaggagcggtatatggatgcttg / tcaatagcatccatcaccgttcag / 3 / 2 / TaqI / 3% Agarose21
AC084748 / agaacctaacccgagtcttcatag / tgacataactagccgaggtgatat / 3 / 4 / - / 3% Agarose21
C1484 ApaLI / gagtcattctgatgaggctggaac / ttctgtccgaatcagccgtgtgct / 3 / 2 / ApaLI / 3% Agarose21
AC092557 / gactcactttacaggatgggcacg / caaggagatactaggttgctgggc / 3 / 4 / - / 3% Agarose21
AL606589 / ggtgacttgtggggtggtttttgt / gcaagagacataaaaaaccgaggc / 4 / 5 / - / 3% TypeII
S10628 BstUI / agaagagccccgtgaggctgttgc / tgacgaggaacctggagaggaacg / 4 / 11 k / BstUI / 3% Agarose21
AL606460 / gacggctgttgagaggtagagaaa / tggtgtttggtttgttggttggac / 4 / 4 / - / 3% Agarose21
AL606688 / tcgacctctctctctcctcgatgg / aatttacggtgctcgggggtgtac / 4 / 4 / - / 3% Agarose21
C600 AfaI / cagtgggagcttgatcgattcgtc / cagatcagaaagcctggtgaacta / 4 / 13 m / AfaI / 2% TypeII
G177 HinfI / accttgactgatcggacatggt / gccacaacacttcctactccta / 4 / 12 l / HinfI / 2% TypeII
C597 HincII / cgttctcctcttcccctctacctc / tacaggatttgggcggcggtgttc / 5 / 14 n / HincII / 2% TypeII
RPC175 MboI / gtgacatcgaatcccaggaa / cttcatggccacctgcaggtttgc / 5 / 15 o / MboI / 3% MetaPhor
AC093919 / tcgtgtttttgtttgacttttggc / gacaacatcatcaggaatagttgc / 5 / 4 / - / 2% TypeII
AC098573 / cgagtagtgcagacgcgaggaacc / tccaacgcaagaacaggagagagg / 5 / 6 / - / 3% Agarose21
S1515 ALP / ggaaatggaagccaatgaagagtg / tatagggtagaaacttacgcttgg / 6 / 4 / - / 3% Agarose21
C226 ALP / tcaagctcctcctcagcagcagac / gctgaaagcctgaaactgaaagcaac / 6 / 2 / - / 3% Agarose21
R2349 AluI / gccaagaagtgcctcccgtag / gacacccccggcatctggac / 6 / 8 / AluI / 3% Agarose21
R2171 ALP / gtgaaggtactgctgttgatgtg / cgctgctatcaattttatcgtccg / 6 / 16 p / - / 0.7% TypeII
C133 NsiI / gaaaggaccagtcaggtgacaaac / ggtcgctattagctatgacttatatgc / 6 / 2 / NsiI / 3% Agarose21
S10324 NsiI / gcatgaaactagaatggtacactg / gctaacgcagctgcaactccatgc / 6 / 2 / NsiI / 3% Agarose21
C358 NsiI / gacaaatagctcaacccattcagatgca / ctcactcccttgtgcaaatgtagc / 6 / 2 / NsiI / 3% Agarose21
R2614 ApaLI / ctcatcaatcatttctgcgtgctg / agttaatcttctgcatggggtgca / 6 / 2 / ApaLI / 3% Agarose21
S14082S NsiI / gagatggacttctacagcaagacg / taaagcaagctaggtagcgatatg / 7 / 2 / NsiI / 3% Agarose21
AP003702 / tgttttccagcatacgaccaagat / ttttgtgcagtgtgttcgttctac / 7 / 4 / - / 3% Agarose21
AP003829 / ttgaattgaactggggccgtggtg / gtccacgagagcaagcaaagcaac / 7 / 4 / - / 3% Agarose21
AP003955 / tgttggccggtgatctgtccatgc / ccagatacatagccagaagttagc / 7 / 4 / - / 3% Agarose21
C1023 EcoRV / gaagcatgccgctcagctttgcgt / tccagcacagtaaacataaagttc / 7 / 17 q / EcoRV / 2% TypeII
AP003932 / cttcgtggacttcatttcaactcg / aaagatgggaggtgggattttctg / 7 / 5 / - / 3% Agarose21
AP003804 / ggtcattttggttattaggctcgg / tttaacagcacttcccctcttttg / 7 / 5 / - / 3% Agarose21
AP003747 / ctaacttgagatgagagatagact / tctttaggtagcgtcatcttccaa / 7 / 5 / - / 3% Agarose21
AP003803 / gacatgaacaaatataggctgacc / ttaggtacaggaagatgcaggcgg / 7 / 5 / - / 3% Agarose21
AP003927 / cagtgtttgatggtggaattgaag / atcgaagaaacatgcaacggcggc / 7 / 5 / - / 3% Agarose21
S13453 NsiI / tttctctcccttgttccacctcgg / gcctaaaacacaactcacagtgca / 7 / 2 / NsiI / 3% Agarose21
R1789 MwoI / caaccatggcaaccattgccattatt / gagaagcatatccgattgagccag / 7 / 2 / MwoI / 3% Agarose21
S13161 AseI / tcagtttgttgctcacatcatccc / catattcaaatgctgtaacgaaggattaa / 7 / 2 / AseI / 3% Agarose21
AP003910 / tgcaataaagcgaatgagaggacg / cattcagtcccagcttgtatcgag / 8 / 4 / - / 3% Agarose21
AP003940 / ccaccataaaaacaactcaagggg / ctaaagctcaacgtgtaagtgtgc / 8 / 4 / - / 3% Agarose21
R2736 MfeI / gccgagaagaatggacctaac / gggctatgctgatgaggataa / 8 / 18 r / MfeI / 2% TypeII
AP003928 / tactctgattgtgataaaagcggc / ctgtcccacgaaaaaccgatctag / 8 / 4 / - / 3% Agarose21
R1164 NcoI / tatagtccatctccaactggattgg / tcagcagtttatcagaaacctacgac / 9 / 2 / NcoI / 3% Agarose21
R2638 MwoI / aacaagaaactatgtatagtggctacagta / gcttctctcgaaacaacctttggtagc / 9 / 2 / MwoI / 3% Agarose21
E4055 DdeI / ctatgcacctggacaagaagtgag / gttagagaagatagttcttcatggca / 9 / 2 / DdeI / 3% Agarose21
S1456 MfeI / gaacatcaacagtccaagcaaccg / catacttccatggacatgggactg / 9 / 2 / MfeI / 3% Agarose21
AC084884 / ttatggctcgtttgcttccttggc / gggactaaaaaacacttctccacc / 10 / 4 / - / 3% Agarose21
AB007404 SmaI / atatgcttgtgcttgtatctgctg / gaaggcatcagtttttcagtaccc / 10 / 19 s / SmaI / 2% TypeII
R2825 BstUI / ctccattcccctcctcgccta / acaacaagaatcatccatccggtc / 10 / 8 / BstUI / 2% TypeII
AC022457 / ggtacaaaaactaaaagccctatc / atcttgcacttatcagccatgtcg / 10 / 6 / - / 3% Agarose21
XSG7 TaqI / cgtcattgcttcttggactaaccc / cagtcaggtcaagccattgacgac / 10 / 2 / TaqI / 3% Agarose21
C794 NruI / gcgatttcgacattagtgatgtcc / catccttctccactctcttgacgc / 11 / 2 / NruI / 3% Agarose21
AB004648 TaqI / ctgaaagtagtgcttgctaagcattcgtcg / gcacattatgttagtcatgctcctc / 11 / 2 / TaqI / 3% Agarose21
R728 HindIII / cgtcgttgaaacaactccaggaag / caaaaccagtcctccatatgtggc / 11 / 2 / HindIII / 3% Agarose21
G257 ALP / ctgcaggtacgtgaacaatag / gcagctgcacgccattaacca / 11 / 20 t / - / 2% TypeII
E51178 DraI / cttctgtttcatgcttctgcaagggtttaa / tgccaagccttggaactaatacag / 11 / 2 / DraI / 3% Agarose21
S20160 EcoRI / ggctaaaattgatatgcttgaactttgaat / gctatgttaccagaaacacaatgtatg / 11 / 2 / EcoRI / 3% Agarose21
R1506 HhaI / ctccaagaaatcaagctggtggg / gccaaggatgttagcccgtttg / 11 / 9 / HhaI / 2% TypeII
G193 AluI / cggtctctggcgcggcacggcatc / tgtattgcctgctgctttagtgag / 12 / 21 u / AluI / 3% TypeII
R3023 HindIII / tcagccaggacagcagatcaagct / ctccttacatcttcgttggctact / 12 / 2 / HindIII / 3% Agarose21
rbcSa MspI / gcacaatccatcttaatgttttcaagc / agaaaataaatcccacagtttagtacg / 12 / 2 / MspI / 3% Agarose21
C901 PvuII / gagagtgctcctggtgatatacag / cgtggatgatacattcatctcgtg / 12 / 2 / PvuII / 3% Agarose21
a After pre-heating for 2min at 94℃, 35 PCR cycles (0.5min at 94℃and 1.5min at 72℃), followed by 2min at 72℃.
b After pre-heating for 2min at 94℃, 35 PCR cycles (0.5min at 94℃, 0.5min at 58℃and 0.5min at 72℃), followed by 2min at 72℃.
c After pre-heating for 2min at 94℃, 35 PCR cycles (0.5min at 94℃, 0.5min at 57℃and 1min at 72℃), followed by 2min at 72℃.
d After pre-heating for 2min at 94℃, 35 PCR cycles (0.5min at 94℃, 0.5min at 58℃and 1min at 72℃), followed by 2min at 72℃.
e After pre-heating for 2min at 94℃, 35 PCR cycles (0.5min at 94℃, 0.5min at 55℃and 1min at 72℃), followed by 2min at 72℃.
f After pre-heating for 2min at 94℃, 35 PCR cycles (0.5min at 94℃, 0.5min at 60℃and 1min at 72℃), followed by 2min at 72℃.
g After pre-heating for 2min at 94℃, 30 PCR cycles (0.5min at 94℃, 0.5min at 60℃and 2min at 72℃), followed by 2min at 72℃.
h After pre-heating for 2min at 94℃, 30 PCR cycles (0.5min at 94℃, 0.5min at 63℃and 1min at 72℃), followed by 2min at 72℃.
i After pre-heating for 2min at 94℃, 30 PCR cycles (0.5min at 94℃, 0.5min at 63℃and 2min at 72℃), followed by 2min at 72℃.
j After pre-heating for 2min at 94℃, 35 PCR cycles (0.5min at 94℃, 0.5min at 60℃and 0.5min at 72℃), followed by 2min at 72℃.
k After pre-heating for 2min at 94℃, 35 PCR cycles (0.5min at 94℃, 0.5min at 65℃and 0.5min at 72℃), followed by 2min at 72℃.
l After pre-heating for 2min at 94℃, 30 PCR cycles (0.5min at 94℃, 0.5min at 61℃and 2min at 72℃), followed by 2min at 72℃.
m After pre-heating for 2min at 94℃, 30 PCR cycles (0.5min at 94℃, 0.5min at 65℃and 1min at 72℃), followed by 2min at 72℃.
n After pre-heating for 2min at 94℃, 33 PCR cycles (0.5min at 94℃and 2.5min at 72℃), followed by 2min at 72℃.
o After pre-heating for 2min at 94℃, 30 PCR cycles (0.5min at 94℃, 0.5min at 60℃and 1min at 72℃), followed by 2min at 72℃.
p After pre-heating for 2min at 94℃, 35 PCR cycles (0.5min at 94℃, 0.5min at 59℃and 3min at 72℃), followed by 2min at 72℃.
q After pre-heating for 2min at 94℃, 35 PCR cycles (0.5min at 94℃, 0.5min at 61℃and 1min at 72℃), followed by 2min at 72℃.
r After pre-heating for 2min at 94℃, 30 PCR cycles (0.5min at 94℃, 0.5min at 64℃and 2min at 72℃), followed by 2min at 72℃.
s After pre-heating for 2min at 94℃, 30 PCR cycles (1min at 94℃, 1min at 58℃and 1min at 72℃), followed by 2min at 72℃.
t After pre-heating for 2min at 94℃, 30 PCR cycles (0.5min at 94℃, 0.5min at 57℃and 1min at 72℃), followed by 2min at 72℃.
u After pre-heating for 2min at 94℃, 35 PCR cycles (0.5min at 94℃, 0.5min at 65℃and 2min at 72℃), followed by 2min at 72℃.