Supplementary Table 2. Genes Located Within 100 Kbp Atthe Qtls Detected for Tissue Culture

Supplementary Table 2. Genes located within 100 Kbp atthe QTLs detected for tissue culture ability in VCS3M-DH population of B.rapa.

QTL / Closed marker / Genetic position (cM) / Physical
position(bp) / Gene name* / Gene position (bp) / Gene funtion
Start / Stop
Callus induction
qCi2 / KS51030 / 29.96 / 5,924,807 – 5,925,516 / Bra020242* / 5825685 / 5826793 / AGL62 (Agamous-like 62); DNA binding / transcription factor
Bra020243* / 5832331 / 5832979 / ARF4 (AUXIN RESPONSE FACTOR 4); transcription factor
Bra020244* / 5833577 / 5834193 / AGL62; AGL62 (Agamous-like 62); DNA binding / transcription factor
Bra020245* / 5836853 / 5837275 / AGL62 (Agamous-like 62); DNA binding / transcription factor
Bra020246* / 5841468 / 5843146 / AGL62 (Agamous-like 62); DNA binding / transcription factor
Bra020247* / 5849108 / 5850154 / AGL62 (Agamous-like 62); DNA binding / transcription factor
Bra020248 / 5858311 / 5858490 / HB25 (HOMEOBOX PROTEIN 25); DNA binding
Bra020249 / 5862809 / 5867479 / SIZ1; DNA binding / SUMO ligase
Bra020250 / 5871008 / 5871396 / unknown protein
Bra020251 / 5871963 / 5873402 / elongation factor 1-alpha / EF-1-alpha
Bra020252 / 5878247 / 5878644 / unknown protein
Bra020253 / 5879246 / 5880682 / elongation factor 1-alpha / EF-1-alpha
Bra020254 / 5881794 / 5883655 / unknown protein
Bra020255 / 5884564 / 5886663 / AALP (Arabidopsis aleurain-like protease
Bra020256 / 5887741 / 5888890 / unknown protein
Bra020257 / 5889859 / 5890311 / unknown protein
Bra020258 / 5891175 / 5893145 / lectin protein kinase family protein
Bra020259 / 5894623 / 5896616 / lectin protein kinase family protein
Bra020260 / 5898922 / 5901041 / LOCATED IN: plasma membrane; BEST Arabidopsis thaliana protein match
Bra020261 / 5902800 / 5903516 / Dof-type zinc finger domain-containing protein
Bra020262 / 5919105 / 5921100 / TOE2; TOE2; DNA binding / transcription factor
Bra020263 / 5924090 / 5925610 / APRR3 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 3
Bra020264 / 5926216 / 5927984 / protein kinase family protein
Bra020265 / 5929219 / 5931198 / protein kinase family protein
Bra020266 / 5933828 / 5935315 / PRLI-interacting factor-related
Bra020267 / 5935521 / 5943658 / NRPC1; DNA binding / DNA-directed RNA polymerase
Bra020268 / 5944100 / 5944657 / unknown protein
Bra020269 / 5947074 / 5949101 / ATLAC17; LAC17 (laccase 17); laccase
Bra020270 / 5952716 / 5957860 / FAD binding / calcium ion binding / electron carrier/ iron ion binding etc
Bra020271 / 5974845 / 5976567 / FUNCTIONS IN: molecular_function unknown
Bra020272 / 5978481 / 5983007 / RNase P subunit p30 family protein
Bra020273 / 5983423 / 5984482 / RNA and export factor-binding protein, putative
Bra020274 / 5987278 / 5989158 / ULI3; ULI3; diacylglycerol binding / heme binding
Bra020275 / 5990876 / 5991304 / "H2B, HTB2; HTB2; DNA binding
Bra020276 / 5992170 / 5992778 / ADF4 (ACTIN DEPOLYMERIZING FACTOR 4);
Bra020277 / 5993837 / 5994530 / ADF1 (ACTIN DEPOLYMERIZING FACTOR 1);
Bra020278 / 6002097 / 6002631 / HTA6; HTA6; DNA binding
Bra020279 / 6003352 / 6004158 / RNA-binding protein, putative
Bra020280 / 6004798 / 6006263 / 40S ribosomal protein S15A (RPS15aF)
Bra020281* / 6005864 / 6006226 / gibberellin-regulated family protein
Bra020282 / 6008250 / 6010076 / ATRABE1C, ATRAB8A; ATRAB8A; GTP binding
Bra020283 / 6010362 / 6010960 / unknown protein
Bra020284 / 6021867 / 6022205 / RHL41 (RESPONSIVE TO HIGH LIGHT 41); nucleic acid binding
Bra020285 / 6024276 / 6027342 / SBT5.4; identical protein binding / serine-type endopeptidase
qCi7 / KS31190 / 32.48 / 13,421,530 – 13,421,966 / Bra003463 / 13324457 / 13325230 / unknown protein
Bra003464 / 13329076 / 13334568 / unknown protein
Bra003465 / 13339233 / 13341286 / unknown protein
Bra003466 / 13341926 / 13348290 / ATATG6; autophagy protein Apg6 family
Bra003467 / 13348911 / 13354350 / SDG14 (SET DOMAIN PROTEIN 14); DNA binding
Bra003468* / 13358371 / 13360260 / auxin-responsive protein -related
Bra003469 / 13362020 / 13365465 / ADL1B (ARABIDOPSIS DYNAMIN-LIKE 1B); GTP binding
Bra003470 / 13367351 / 13367625 / nucleobase:cationsymporter
Bra003471 / 13369645 / 13370990 / FUNCTIONS IN: molecular_function unknown
Bra003472 / 13371316 / 13374835 / emb1703 (embryo defective 1703)
Bra003473 / 13375627 / 13377296 / seven in absentia (SINA) family protein
Bra003474 / 13378434 / 13380540 / FUNCTIONS IN: molecular_function unknown
Bra003475 / 13380961 / 13382330 / glycosyl hydrolase family 17 protein
Bra003476 / 13383834 / 13385291 / aspartyl protease family protein
Bra003477 / 13387548 / 13388159 / unknown protein
Bra003478 / 13390768 / 13392155 / ANAC066 (ARABIDOPSIS NAC DOMAIN PROTEIN 66
Bra003479 / 13398050 / 13399822 / zinc knuckle (CCHC-type) family protein
Bra003480 / 13405379 / 13406734 / unknown protein
Bra003481 / 13409020 / 13411841 / protein kinase family protein
Bra003482 / 13421623 / 13422483 / NGA2 (NGATHA2); transcription factor
Bra003483 / 13425645 / 13427002 / PIL2 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 2
Bra003484* / 13438652 / 13439656 / IAA30 (INDOLE-3-ACETIC ACID INDUCIBLE 30); transcription factor
Bra003485 / 13440691 / 13442816 / glycoside hydrolase family 28 protein / polygalacturonase (pectinase)
Bra003486 / 13444437 / 13446511 / tRNAsynthetase class II (G, H, P and S) family protein
Bra003487 / 13448116 / 13450597 / tRNAsynthetase class II (G, H, P and S) family protein"
Bra003488 / 13454709 / 13455659 / epimerase-related
Bra003489 / 13456326 / 13457576 / unknown protein
Bra003490 / 13457705 / 13462900 / PGP21 (P-GLYCOPROTEIN 21)
Bra003491 / 13466232 / 13468217 / VGDH2 (Vanguard 1 homolog 2); enzyme inhibitor/
Bra003492 / 13469519 / 13470166 / invertase/pectin methylesterase inhibitor family protein
Bra003493 / 13471209 / 13474107 / zinc finger (C2H2 type) family protein
Bra003494 / 13478180 / 13479640 / carboxylesterase/ hydrolase, acting on ester bonds
Bra003495 / 13479889 / 13482230 / agenet domain-containing protein
Bra003496 / 13484174 / 13486043 / agenet domain-containing protein
Bra003497 / 13486782 / 13489338 / unknown protein
Bra003498 / 13491560 / 13491754 / cytochrome c oxidase subunit Vc family protein / COX5C family protein
Bra003499 / 13492176 / 13492565 / CP12-2, CP12; CP12-2; protein binding"
Bra003500 / 13492943 / 13493347 / ATBZIP53; ATBZIP53 (BASIC REGION/LEUCINE ZIPPER MOTIF 53
Bra003501 / 13496323 / 13498647 / ATERDJ3B; heat shock protein binding
Bra003502 / 13501723 / 13502820 / FUNCTIONS IN: molecular_function unknown
Bra003503 / 13505979 / 13506416 / unknown protein
Bra003504 / 13509304 / 13510365 / GATL7 (Galacturonosyltransferase-like 7)
Bra003505 / 13511158 / 13512567 / protein transport protein sec61, putative
Bra003506 / 13513825 / 13514967 / PRP3 (PROLINE-RICH PROTEIN 3); structural constituent of cell wall
Bra003507 / 13516953 / 13517663 / ATL5 (ATL5); protein binding / zinc ion binding
Bra003508 / 13521432 / 13524204 / glycosyl hydrolase family 3 protein
Plant regeneration
qPr6-1 / KS51082 / 37.4 / 18,840,509 – 18,841,317 / Bra010032 / 18743149 / 18745198 / WRKY48, ATWRKY48; WRKY48; transcription factor
Bra010033 / 18755490 / 18757161 / PDF3; PDF3 (PREFOLDIN 3); unfolded protein binding
Bra010034 / 18757670 / 18758165 / unknown protein
Bra010035 / 18761970 / 18762398 / AtbZIP1 (Arabidopsis thaliana basic leucine-zipper 1); DNA binding
Bra010036 / 18765824 / 18773780 / transducin family protein / WD-40 repeat family protein
Bra010037 / 18774487 / 18775329 / zinc knuckle (CCHC-type) family protein
Bra010038 / 18787924 / 18792022 / BXL1 (BETA-XYLOSIDASE 1); hydrolase, hydrolyzing O-glycosyl compounds
Bra010039 / 18793200 / 18794803 / unknown protein
Bra010040 / 18799281 / 18799973 / FUNCTIONS IN: molecular_function unknown
Bra010041 / 18800968 / 18804285 / BON1 (BONZAI 1); calcium-dependent phospholipid binding"
Bra010042 / 18806100 / 18806556 / FUNCTIONS IN: molecular_function unknown
Bra010043 / 18807371 / 18808079 / unknown protein
Bra010044 / 18810000 / 18814576 / AML1 (ARABIDOPSIS MEI2-LIKE PROTEIN 1); RNA binding
Bra010045 / 18838529 / 18842401 / signal recognition particle-related / SRP-related
Bra010046* / 18845325 / 18850359 / AGD1 (ARF-GAP domain 1); ARF GTPase activator/ protein binding
Bra010047 / 18851405 / 18854335 / pentatricopeptide (PPR) repeat-containing protein
Bra010048* / 18869274 / 18872992 / ARF2 (AUXIN RESPONSE FACTOR 2); transcription factor
Bra010049 / 18874693 / 18875694 / AT-HSFB2A; DNA binding
Bra010050 / 18877904 / 18878104 / none
Bra010051 / 18886560 / 18887912 / diphthamide synthesis DPH2 family protein
Bra010052 / 18895638 / 18896541 / brother of FT and TFL1 protein (BFT)
Bra010053 / 18896949 / 18900089 / OXA1; P-P-bond-hydrolysis-driven protein transmembrane transporter"
Bra010054 / 18900604 / 18900957 / lipid binding
Bra010055 / 18901294 / 18904463 / IQD23 (IQ-domain 23); calmodulin binding
Bra010056 / 18907258 / 18910684 / mitochondrial transcription termination factor-related / mTERF-related
Bra010057 / 18938983 / 18939989 / unknown protein
qPr6-2 / B007A19-3 / 81.9 / 22,903,559 – 22,904,356 / Bra025165 / 23000942 / 23005268 / protein kinase family protein
Bra025166 / 22998539 / 22998977 / unknown protein
Bra025167 / 22996220 / 22998080 / LTA2; dihydrolipoyllysine-residue acetyltransferase
Bra025168 / 22994820 / 22995320 / unknown protein
Bra025169 / 22976702 / 22977313 / NIMIN-2; NIMIN-2 (NIM1-INTERACTING 2)
Bra025170* / 22970759 / 22971715 / AP2 domain-containing transcription factor, putative
Bra025171 / 22962815 / 22964716 / HMT-1; homocysteine S-methyltransferase
Bra025172 / 22953763 / 22954005 / CLE27 (CLAVATA3/ESR-RELATED 27); protein binding
Bra025173 / 22949989 / 22950945 / zinc ion binding
Bra025174 / 22948704 / 22949804 / RPL15; structural constituent of ribosome
Bra025175 / 22943976 / 22944713 / FUNCTIONS IN: molecular_function unknown
Bra025176 / 22940364 / 22940806 / mitotic spindle checkpoint protein, putative (MAD2)"
Bra025177* / 22937602 / 22938979 / F-box family protein
Bra025178* / 22925050 / 22927068 / serine/threonine protein phosphatase 2A (PP2A) regulatory subunit B'
Bra025179 / 22922586 / 22924078 / ATB' DELTA; protein phosphatase type 2A regulator
Bra025180 / 22920039 / 22921473 / plastid-lipid associated protein PAP / fibrillin family protein
Bra025181 / 22915365 / 22919605 / RGS1 (REGULATOR OF G-PROTEIN SIGNALING 1); G-protein coupled receptor
Bra025182 / 22910340 / 22912236 / regulator of chromosome condensation (RCC1) family protein
Bra025183 / 22909293 / 22909586 / FUNCTIONS IN: molecular_function unknown
Bra025184 / 22907006 / 22908643 / catalytic/ pyridoxal phosphate binding
Bra025185 / 22901921 / 22904535 / TEL1 (TERMINAL EAR1-LIKE 1); RNA binding
Bra025186 / 22896555 / 22899014 / glycosyl hydrolase family 5 protein / cellulase family protein
Bra025187 / 22892669 / 22896069 / glycosyl hydrolase family 5 protein / cellulase family protein
Bra025188 / 22887460 / 22889048 / CYP71B17; CYP71B17; electron carrier/ heme binding / iron ion binding
Bra025189 / 22882230 / 22883834 / CYP71B19; CYP71B19; electron carrier/ heme binding / iron ion binding
Bra025190 / 22875225 / 22876812 / CYP71B20; CYP71B20; electron carrier/ heme binding / iron ion binding
Bra025191 / 22863950 / 22865519 / CYP71B21; CYP71B21; electron carrier/ heme binding / iron ion binding
Bra025192 / 22857506 / 22859110 / CYP71B22; CYP71B22; electron carrier/ heme binding / iron ion binding
Bra025193 / 22843983 / 22847484 / CYP71B23; CYP71B23; electron carrier/ heme binding / iron ion binding
Bra025194 / 22838730 / 22840387 / CYP71B3; CYP71B3; electron carrier/ heme binding / iron ion binding
Bra025195 / 22835866 / 22837647 / CSR1 (CHLORSULFURON/IMIDAZOLINONE RESISTANT 1)
Bra025196 / 22833559 / 22835135 / CYP71B35; CYP71B35; electron carrier/ heme binding /
Bra025197 / 22826641 / 22827688 / FUNCTIONS IN: molecular_function unknown
Bra025198 / 22820865 / 22824955 / CYP71B26; CYP71B26; electron carrier/ heme binding / iron ion binding
Bra025199 / 22818544 / 22819999 / CYP71B34; CYP71B34; electron carrier/ heme binding / iron ion binding
Bra025200 / 22810919 / 22812001 / LOCATED IN: chloroplast
Bra025201 / 22809664 / 22809993 / unknown protein
Bra025202 / 22806296 / 22809026 / unknown protein
Bra025203 / 22802128 / 22804499 / EIF4B1; EIF4B1; translation initiation factor
qPr7 / B085F18-4 / 8 / 6,501,149 – 6,501,925 / Bra030096 / 6599031 / 6601566 / FUNCTIONS IN: molecular_function unknown
Bra030097 / 6594298 / 6595815 / HB-1 (homeobox-1); transcription factor
Bra030098* / 6578511 / 6581703 / HSL1 (HAESA-Like 1); ATP binding / kinase/ protein serine/threonine kinase
Bra030099 / 6571702 / 6573166 / ANAC010 (ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 10)
Bra030100 / 6569792 / 6570511 / trypsin and protease inhibitor family protein
Bra030101 / 6565195 / 6566333 / E2F1, E2FB, ATE2FB; E2F1; DNA binding / protein binding
Bra030102 / 6548814 / 6549224 / GRX480; electron carrier/ protein disulfide oxidoreductase
Bra030103 / 6540011 / 6541001 / FUNCTIONS IN: molecular_function unknown
Bra030104 / 6536840 / 6537175 / unknown protein
Bra030105 / 6535570 / 6536303 / AtRABA1i (Arabidopsis RabGTPase homolog A1i
Bra030106 / 6532961 / 6534728 / GDSL-motif lipase, putative
Bra030107 / 6528875 / 6531967 / GDSL-motif lipase, putative
Bra030108 / 6522991 / 6524634 / GDSL-motif lipase, putative
Bra030109 / 6515120 / 6519233 / unknown protein
Bra030110 / 6500791 / 6501226 / GDSL-motif lipase, putative
Bra030111 / 6493661 / 6495554 / ARAB-1; carboxylesterase/ hydrolase, acting on ester bonds
Bra030112 / 6482118 / 6482906 / nodulin MtN21 family protein
Bra030113 / 6465460 / 6466995 / heavy-metal-associated domain-containing protein
Bra030114 / 6460100 / 6461071 / unknown protein
Bra030115 / 6458487 / 6459014 / unknown protein
Bra030116 / 6446064 / 6457725 / unknown protein
Bra030117 / 6431477 / 6432635 / FUNCTIONS IN: molecular_function unknown
Bra030118 / 6427031 / 6428284 / peptidase C1A papain family protein
Bra030119 / 6416493 / 6417051 / copper-binding family protein
Bra030120 / 6411500 / 6414891 / LOCATED IN: cellular_component unknown
Bra030121 / 6398773 / 6403227 / unknown protein
qPr9 / KS11090 / 69.6 / 7,203,792 – 7,204,582 / Bra027623 / 7302208 / 7303266 / SOT18 (DESULFO-GLUCOSINOLATE SULFOTRANSFERASE 18)
Bra027624 / 7298732 / 7300365 / replication factor C 40 kDa, putative
Bra027625 / 7296687 / 7298191 / zinc finger (C3HC4-type RING finger) family protein
Bra027626 / 7294319 / 7296260 / UGE3; UGE3 (UDP-D-glucose/UDP-D-galactose 4-epimerase 3
Bra027627 / 7287759 / 7288751 / FUNCTIONS IN: molecular_function unknown
Bra027628 / 7284104 / 7285174 / C2 domain-containing protein
Bra027629 / 7281744 / 7282001 / CLE14 (CLAVATA3/ESR-RELATED 14)
Bra027630 / 7276892 / 7278835 / TET10; TET10 (TETRASPANIN10)
Bra027631 / 7272721 / 7275278 / ribulose-phosphate 3-epimerase, cytosolic, putative
Bra027632 / 7261623 / 7262376 / ATRSP40, AT-SRP40, RSP35; ATRSP35; RNA binding / nucleic acid binding
Bra027633 / 7257284 / 7258637 / remorin family protein
Bra027634 / 7255457 / 7256577 / myosin, putative
Bra027635 / 7235866 / 7239415 / unknown protein
Bra027636 / 7231805 / 7232779 / pentatricopeptide (PPR) repeat-containing protein
Bra027637 / 7218761 / 7222656 / pentatricopeptide (PPR) repeat-containing protein
Bra027638 / 7217154 / 7217603 / FUNCTIONS IN: molecular_function unknown
Bra027639 / 7207263 / 7210180 / INVOLVED IN: biological_process unknown; EXPRESSED IN: 22 plant structures
Bra027640 / 7198141 / 7201192 / leucine-rich repeat transmembrane protein kinase, putative
Bra027641 / 7188238 / 7195098 / HMA5; HMA5 (HEAVY METAL ATPASE 5); ATPase
Bra027642 / 7185865 / 7187670 / DNA-binding family protein
Bra027643 / 7182090 / 7183106 / basic helix-loop-helix (bHLH) family protein
Bra027644 / 7171544 / 7178712 / transcription factor jumonji (jmjC) domain-containing protein
Bra027645 / 7168940 / 7170333 / unknown protein
Bra027646 / 7153266 / 7155587 / ATP binding / binding / protein kinase/ protein serine/threonine kinase
Bra027647 / 7150005 / 7151790 / unknown protein
Bra027648 / 7145241 / 7147268 / FUNCTIONS IN: molecular_function unknown
Bra027649 / 7140588 / 7141948 / hydroxyproline-rich glycoprotein family protein
Bra027650 / 7135836 / 7137452 / LOCATED IN: anchored to membrane; EXPRESSED IN: flower, root, carpel, leaf
Bra027651 / 7124905 / 7128446 / transmembrane receptor
Bra027652 / 7118552 / 7124253 / kinesin motor protein-related
Bra027653 / 7107120 / 7110218 / EGL3 (ENHANCER OF GLABra 3); DNA binding
Bra027654 / 7101901 / 7104197 / unknown protein

* Putative candidate genes associated to tissue culture ability on the basis of the previously reported studies