Article Title: Construction of a Genetic Linkage Map Based on RAPD, AFLP, and SSR Markers

Article title: Construction of a genetic linkage map based on RAPD, AFLP, and SSR markers for tea plant (Camellia sinensis); Journal name: Euphytica; Author names: Yali Chang, Eun Ui Oh, Min Seuk Lee, Ho Bang Kim, Doo-Gyung Moon, and Kwan Jeong Song; Corresponding author: Kwan Jeong Song, Research Institute for Subtropical Agriculture & Biotechnology, Jeju National University, Jeju 63243, Korea, and E-mail: [email protected].

Online resource 2. RNA-seq based SSR markers being polymorphic between ‘Fushun’ and ‘Kemsull’. Notes: a, SSR markers with underline were used into mapping analysis; b, the anticipated band size in silico; c, ‘f’ means ‘Fushun’, ‘k’ means ‘Kemsull’; d, illuminate why some SSR markers with admissible genotypes by JoinMap 4.0 could not apply into linkage analysis.

SSR IDa Forward primer (5'-3') Reverse primer (5'-3') unit Band sizeb Genotype (f-k)c Notesd type

(AC TTTCACCAGGACGAA KF0007 CACAGAATGCAGTGCTATGAAA AAT 194 aa-ab TGCACTA A)2

TATAAACCACCTCGC (TC KF0036 GGGGCTGGTGTTCTTCATAGAA 362 ac-bd GAGACTC A)8

(AT TTTGCTCTGCATTTT CA KF0043 ATGCTGCTTGAGAGACCATGAA 260 ab-cd GCTGC AA) 6

ATGTGGTTGGTTCTG (TT KF0055 ACTTGCCGGGTTAAGCGTATTA 249 abc-cc ACTCGAT C)5

KF0073 CTTGTTCCCTCCTAT ATGGCGCAAAATCATCATACGG (CC 192 ab-bcd GCCCTTT ACC T)4

(CA CCTCCTACACAGCAT KF0097 TAATCTCACTCCTTTCGGTGGC CCG 206 cc-ab CACCATT C)2

(AC GTAGAAATCGCCGA KF0112 AACTCTTTGCTCCAGCTCATCA CCG 212 ab-ac AATCACCG G)2

(TT TGGGGCGTTGAACA KF0120 CCTGCCTGAATCACAAAACCAG GAT 194 ab-ab ATCATCTA G)2

(CT TACCAGCGTGTCCTA AG KF0134 CCTAACGAAGCAAAAACGAGCA 250 aa-bb AAACTCC CC) 3

GCATGAAGAGCTCG (AA KF0141 ACCTTCCATGGCATTCGAATCT 208 ab-ab CCTTTAAG G)7

(CA CCTTGGCTACAAAGA AC KF0147 GACCTTGCTAAAGTTGGTGCAG 387 ac-ab GCAGAGA AG) 2

(TC PCR amplicons were unclear and ATCAGCTCGAATCAA KF0166 TTTGGGTTTTGCGGGGTTAATC GCT 189 cd-ab most F1 seedlings were genotype ACCCCTT C)2 ‘abcd’.

GCAGAAAGAAAGGG (AA KF0191 GCTTCATCTACTTCGTCTCCGT 202 abcd-ac GCGAAAAT G)5

AGATGTAACTCTAGC (AC KF0213 GGAAAGGCTAATCGGGATAGGG 279 bb-abc AGTGGC C)7 (TT AGCCTCATGCCCAAA KF0217 GCAACTGGATGATGGTGATGTG TC) 399 aa-ab PCR amplification failure. TCTTGTA 9

AAAACTTCCCGATTC (TC KF0231 TCAGACAATGGACGCTGATGAA 398 ab-aa PCR amplification failure. CTCCTCC T)7

(TA CACTCTCTCTCACAG CG KF0234 ACGTGTTTCTTCGCTAGTGGAT 273 aa-ab AAACCCC AC) 3

TCAAAATCGAGTGCG (AG KF0236 AGGGATGACCAAACAGGATTCC 268 abc-ac CCCTATA G)5

(GG CCAACCCAACCTAGT KF0251 AAAGTGGATGTGTCCCTCTTCC CCA 297 ac-bc PCR amplification failure. CTACCAC T)4

GTGTTCTTCAGTGAT (GG KF0265 TCTGGTTTCGCATCTTGCTAGT 373 aa-bc CCCGAGT T)6

(AA CACCTCCTCCTCAAA PCR amplicons were KF0269 GGGGACACACATGCCTATTACT CAC 398 aa-ab AGGTCTC undistinguishable. A)3

(GC TGCAACAGCCTTCAT KF0271 GCCGCATGCTGTTAAAAGCTAA AG) 344 bb-ab ACTGCTA 4

(AA TCATGGGTCATTCAT KF0288 TGGAATTCAAAGTGAGCTCCGA CCC 361 ab-aa CGTTGGT T)2

CCCAAATCCCAAGCA (GT KF0289 TGCTAACAATGGAAGCATCCCT 228 ac-bc PCR amplification failure. GTAGAGT A)6 (GA AGAGTGGGCTTTGAT KF0290 CCACCCCTTCGAAAATTATAACCA GAT 212 bb-ac PCR amplification failure. GATTCGT )3

CTGGAGGCTGAATTG (CG KF0304 TTCTTCACAGGACAAGCACAGT 356 ab-bb PCR amplification failure. AGGAAGT A)5

(TG AGACAAAGCTATGA KF0305 CTCCAGAAAACCCATCCACAGA AGT 260 ab-aa CCCTGGTT )3

(AA GCGTTGACAATGCTA TGA KF0311 ACCTGTCCATGTTCCCTTTTGT 214 aa-ab PCR amplification failure. ACTTGGT ACT )2

CTCTCCCTGGGCTTG (TT KF0320 GAACTCACAGCAACAACATCCC 303 ac-ab PCR amplification failure. AATGAAT G)7

(TA CAAAGTGGAATGCA KF0340 ATTGGCTTTCAATCCAGCTATGG TTA 207 ac-bb CCGATTGT C)3

TTTTTCATCTTCCGA (CG KF0350 GGCTATTTGCTGGGTTCCAAAG 228 aa-ab ATGGCGC G)5

(AG AATTCCCACCACGAC Most F1 seedlings were ‘abcd’ KF0353 TGATTCCAACTCCGACAACGAT GGT 233 cd-ab TCTCTTC genotypes. T)4

(TG GTGACTCCGTAGATG KF0365 CTTGGCCCTCTACATCCCTTTT ATG 420 ab-cc GTGATCC T)8

KF0382 AGCTCAAGGATTGGT CACCCAGAGAGTGCAGTAAAGT (TT 388 aa-ab TTCCGAT TCT )5

(CT GGTTTCCCCCTTGTA KF0387 AGGCCTAAACTTCAAACCCTGT GAT 398 ac-ab PCR amplification failure. TGGCTTA G)2

TCTACCTCCTTAGAA (CC KF0391 GTCGTCGTAGTTCTCGAAGTCA 319 bb-ab PCR amplification failure. CCCTGCA A)5

AAGGTGGCCATCATG (CA KF0403 GCTGAGACTCTGTCGCAATTTC 187 abcd-abcd TTCATCT A)7

TTACCATCCTCCTCC (TC KF0411 CACTCAAGCAAACAGAGCAGTC 380 aa-bb ACCTGAT C)10

(GT GCATCTACTGACATT KF0413 TGCACATTTCTTGAGATGTTTACT TGA 191 abcd-cde GCACGTC TT)2

(AA AGCAAAGAGTCAGC KF0416 AGAGAGACAGAGAGATGGGCAA TCC 261 bb-ab TGGATCAA T)4

(CC GGAAATTCTGTTGTT KF0434 ACCAGCTGAGGATGTTGAGAAG CTA 344 bc-aa GACCGCA A)4

(TG TTCCCACCACCATAC KF0453 CTGAGGAGACCCAAACTGTAGG CCC 187 ab-bc TCTTTCG T)4

(AT CTAAATCGGCTTCGT CA KF0468 TCTTACTGTTCTTCGGTTCCGG 315 bb-ab CGTTGTC GA) 4 (GA TGAGGTTCAATCGGC KF0502 GGAGGTTCCCCAAATGGAGAAT GTG 231 ab-bcd TACACAA G)4

AACAATCACTGAGGT (GG KF0503 AACCCATCCCAGAAACAGATCC 365 ab-ac PCR amplification failure. CGATGCT T)9

(GG TGCACCTCCAAACCC AG KF0512 CCTCCCCAAGCTCATACTTGTT 436 bb-ab AATTACT GT) 2

ATTCCCCATGTTTGC (GT Most F1 seedlings were ‘abcd’ KF0515 AGCTCTACATGTCACCATCGTC 305 ac-bd ATACCCT C)5 genotypes.

ACAGTCAAGCCTCCA (AT KF0536 GTTAGGGGGTTTGGAATCGCTA 249 ab-ac TTCCTTT C)11

(AA TCCCAAATGCTTTCT CA KF0542 TCATTGGCTTGGATGGTCTCAA 430 abc-ab CTCTCCT AT) 2

(TC CTCTGTTCTTCGATC KF0545 CGAAGAACCAAGAAGCTCGTTC TTC 203 ac-ab CACACCA G)5

PCR amplicons were weak and GTGAGGGAAGTTGA (GA KF0551 GCGGCATGTCAAAGTATTTCGT 361 ac-bd most F1 seedlings were ‘abcd’ CGTTAGGT A)8 genotypes.

(TC AGGACATTGCTTCCT KF0587 ATATGGGTGTCAAGCAAGCAGA GTC 189 bb-aa ACTGGTG A)3

KF0593 AAATTCATCGTCGTT CTGAGAGAGGTGGAGAGACAGA (TC 222 ac-bd most F1 seedlings were ‘abcd’ TTGCGGT T)5 genotypes.

(AA TTGTTCCTCTTCAAC KF0595 AACTGAACTGGAGATTCGGCAT TCC 179 ab-bb CCCAACA G)3

(CT GCAAAAATATCACA KF0606 TGATGAGTACTGCCGTTGTTCA CAT 164 aa-ab PCR amplification failure. AGAGAACTGA C)6

TGAACAACGGCAGT (TC KF0607 CATAAGGCGGCCTTTTGATTGG 166 aa-ab ACTCATCA C)7

CTCCGATAGCTTCCT (CT KF0610 TCAGATTTGGGTGTGAATCGGT 255 ab-abc TTCCCTC C)7

(GC CGCACCTCAAACAGC CGC most F1 seedlings were ‘abcd’ KF0635 GGTTGAGCAGGTTTAGGATGGA 305 ab-cd ATTCATT CAC genotypes. T)2

(GG CCCTCCCTTCTCTTCT KF0638 CATCGATTGCATTGCAGCAGAA CTG 129 cd-ab PCR amplification failure. TTTCCA T)3

(AA CCATTGTTGTCAGCA KF0643 TTCAAGCGGCAAAGGCAATTAA CCC 338 ab-cc GCATCAA T)5

ACCTTCACATGCTGG (CA KF0657 GGGGAGATTGTGTGAACCTCAT 198 bc-ab PCR amplification failure. GAATCAT G)6

(CA TTGGCGTAATTTTTG CA KF0660 TCGTCTTCCTCTTAAGTCGCAC 266 bb-aa TCGCAGT AC) 2 (TG ACT GAAGTTACCTGAGTC PCR amplicons were weak and KF0664 GGTTCAACCCTCTTAGCTTCCA GG 300 aa-ab GTCGAGG unclear. GT) 2

AACGAAACCAAACA (GA KF0665 CTCACCGCCTAATTCCTCCTAC 234 aa-bb GTGTTGGG A)6

GTGTGATCCGGAGAC (AA KF0684 TCCGAAACACACTCTTCTCACG 174 aa-ab PCR amplification failure. AGAAACT C)7

(AG ATCCTGCTGTGTGTG GC KF0685 GTGCTTCGTCTTGTTGCTTTCT 224 ab-ab TCAGATT GG) 3

TGGTACACCAATCCA (CT KF0696 AACATGTTACACTGCTGGGCTA 267 ab-aa GGAACAG G)5

CTGTACCAGTGCCTA (CC PCR amplicons were weak and KF0734 ACTGAACATTTGAGGTGCATGC 194 aa-ab ATCAGGG T)7 unclear.

AGAGTGACTTGGCTA (CA KF0768 GACGTAGGCAGCGAATTTCTTC 358 abcd-ce ATGGTGG A)9

(AC ATATACCACTAGCCG KF0783 AGATGTCGTGGAGTTGCAGAAT CAC 150 abcd-ab AACTCGC T)2

(AT GAGAGGAGCACAAC PCR amplicons were weak and KF0784 CCAAGACCCCTTTCCAATAGCT TGT 132 aa-ab GAAGGTAA unclear. C)3

KF0799 TCAAGTTTTGCCTGC ATAATGGGGAGAAGGGGGAGAA (TT 442 ab-bb GAATGAG CCC A)5

(AC CCCTAGCAGCTGTCT KF0807 GAAGATTTTGCGGTGAGAGACG TCC 254 abc-bcd CAAAGAA G)5

(AG GCAACACGCTTAGG KF0810 AAGTTGAGTAGAGGGCTTCTGC AG 257 aa-ab GTTTGATT A)4