a01-p

Myb2MSE1M142.20E32M19M204.4 P21M47M78.514P14M51M88.719E32M19M138.2 P23M50M66.922Myb2MSE1M490.823E32M19M439.227E32M19M435.529P21M47M164.6 P21M47M178.140Myb2HaeIIIM329.441E32M47M133.543BR384(DA04) BR325(DA04)44BrSVPP2d49P23M50M127.651BrPHYAP3c59E32M47M136.064

A04

BrCCA1P3b0BrSPA1P1a19BrSPA1P2a23BRMS-034(A05)39E32M19M221.842Myb2MSE1M88.846P14M51M182.051BrFES1P3b55BrFES1P2c60Myb2RSAIM232.862P23M48M63.664BrSPL5P3a68BrTCTPP2b70P23M48M-36.673E32M47M460.0 Myb2HaeIIIM-605.380P14M51M121.982P23M50M241.183P21M47M339.0 E32M47M113.6E32M47M118.184BrVRN1P1b87Myb2HaeIIIM263.789E34M15M420.891Myb2HaeIIIM295.293E32M47M462.396BrSPL5P2b112P23M50M132.9113MADsHaeIIIM373.0114E32M47xM81.7118Myb2RSAIM-714.5123MADsHaeIIIM392.7135BRMS-007(A05)145E32M47M-43.3146E32M19M258.3150BR378(DA05)158

A05

P21M47M384.10BrCBFsP2b2Myb2MSE1M70.04E34M15M464.08E37M47M175.4 P14M51M386.910E34M15M60.512BrDRB1P1d15P21M47M134.719P21M47M386.121BrFPF1P1d25BrPHYEP1b30P13M48M288.631P13M48M286.633E32M47M106.135P14M51M279.438P13M48M102.439E32M19M325.841Myb2RSAIM-742.7 P21M47M287.442E34M15M249.643P13M48M71.5 E34M15M228.8E37M47M343.3 P21M47M224.1P21M47M409.8

44

BrELF5P1a BrHUA2P1bBrCDP2e BrCDF1P2eE34M15M386.3 P14M51M302.2

45

P14M51M114.146P23M50M64.3 P23M48M102.147P23M48M254.348Na12H07(A06) ENA23l(A06)51Br450P1a53BrFPF1P2a56BrESD4P1a60BrBCAT3-1MiA0661BrST5cMiA0663BrCYP79F1MiA0664

A06

BrAP2P1d0BrFDP1g4Myb2RSAIM114.612P23M48M93.217E37M47M266.921BrPHYEP2c26BrSLY1P1b28Myb2RSAIM91.131P14M51M213.333BrEBSP1b36E32M47M77.937Myb2MSE1M276.941P23M50M87.242P14M51M298.047P14M51M174.348P14M51M243.350MADsHaeIIIM-503.052P23M50M317.9 P23M50M312.3E34M15M238.653

P13M48M247.254BrBCAT3-2MiA0155Myb2AluIM357.3 Myb2AluIM488.556E34M15M83.059P23M48M219.263E32M47M179.866P13M48M218.670E32M47M123.174BrSPL5P1a79P13M48M221.588E32M19M239.3 P13M48M384.891BrMYB51-2bMiA0196BrCOL2P3a106P23M50xM326.7114E32M47M212.2116Myb2HaeIIIM475.9120BrCOL2P4a126BrATVGT1P1a130

A01

BrMAF2P1b0BrAGL15P2a5BrBFTP1a9Myb2MSE1M480.811BrFLC2(XA0)18BrFLC2-221BrFLMP2d22P13M48M137.123BRH04D11flc2 P23M50M179.624Br323(DXA02)29BrFYP1a32ENA13l(DA02)37BrVIN3P2b44BrEBSP2d45BrPIP1b48E34M15M142.850BrCOL1P1f51E37M47M115.452BrPIP2a57E32M19M308.564BrFTP1c68BrTSFP2c69BrCALP2a(XA02)70Myb2RSAIM315.3 E32M19M266.4Myb2RSAIM320.075

BrCALP1g79P14M51M219.482Na12H09(A02)84P14M51M76.590P23M50M230.5 P23M48M115.691Myb2RSAIM475.092Myb2RSAIM341.0 P21M47M166.793Myb2MSE1M-614.595P21M47M168.597E32M19M76.7101P23M48M176.7106P21M47M94.9109P23M48M273.5 P13M48M157.8Br333(DA02)110

Myb2HaeIIIM270.6111E34M15M461.1113Myb2HaeIIIM-550.5117BrFULP1b118BrMYB28-3MiA02120E37M47M153.4121ENA23h125Myb2RSAIM496.0128Myb2MSE1M125.7129BrFLMP1b131Myb2RSAIM146.8133BrMAF4P1d137BrMAF4P2a139

A02

P23M48M291.70BRMS-008(A03)1P23M48M293.82Myb2HaeIIIM-586.15BrFLCP5a(XA0)8BrFLCP5b(XA0)9Myb2AluIM377.311Myb2AluIM381.013Myb2MSE1M355.0 Myb2MSE1M321.814Myb2AluIM-589.120BrMYB29-1MiA0322E37M47M128.129P13M48M381.0 Br360(DA03)35E32M47M252.438E32M47M255.139BrVIN3P3a Myb2HaeIIIM390.248Myb2AluIM138.849P13M48M244.750P21M47M198.655E37M47M134.560BRMS-04362BrAS1P1c BrAS1P2a66OlB05(DA03) P21M47M190.4P23M48M149.067

BrGSL-OHMiA0370P23M48M159.673BR356(DA03)75BrATBRMP1d78Myb2RSAIM183.981BrSNZP3b85BrAS1P3b SOC1P1d-SSR89P14M51M168.793E32M47M85.799BrGA1P2c100BrFLKP2b102BrIQD1-1MiA03105BrFLDP1c108Myb2HaeIIIM-601.3110P23M48M439.2114P23M48M321.5115BrVRN1P3b116P21M47M171.0117P14M51M135.1118Myb2MSE1M67.4 Myb2RSAIM69.3119BrTCTPP1b120BrBCAT4-1MiA03121BrELF8P1b(XA03)124Myb2MSE1M222.2125BrMAM3-1MiA03126BrMYB28-1MiA03127MAM-4(DA0) BrTOC1P1b129MAM-1(DA0) P23M50M273.1Bac130(DA03) BRMS-050-1(A03)F3H-ssr3

131

P23M48M99.5133E34M15M383.9135E32M47M382.4140E32M47M384.5141BrNS1P2c142BrAGL24P2c146BrAGL24P1b147Myb2RSAIM-734.9151P23M50M284.3154E34M15M495.3157P14M51M64.2 Myb2MSE1M253.7172E32M19M420.2174E37M47M397.6176E37M47M426.1 E34M15M255.7177P23M50M53.6180Myb2HaeIIIM86.2192

A03

Title: The Brassica rapa FLC homolog BrFLC2 is a key regulator of flowering time, identified through transcriptional co-expression networks

Myb2MSE1M142.20E32M19M204.4 P21M47M78.514P14M51M88.719E32M19M138.2 P23M50M66.922Myb2MSE1M490.823E32M19M439.227E32M19M435.529P21M47M164.6 P21M47M178.140Myb2HaeIIIM329.441E32M47M133.543BR384(DA04) BR325(DA04)44BrSVPP2d49P23M50M127.651BrPHYAP3c59E32M47M136.064

A04

BrCCA1P3b0BrSPA1P1a19BrSPA1P2a23BRMS-034(A05)39E32M19M221.842Myb2MSE1M88.846P14M51M182.051BrFES1P3b55BrFES1P2c60Myb2RSAIM232.862P23M48M63.664BrSPL5P3a68BrTCTPP2b70P23M48M-36.673E32M47M460.0 Myb2HaeIIIM-605.380P14M51M121.982P23M50M241.183P21M47M339.0 E32M47M113.6E32M47M118.184

BrVRN1P1b87Myb2HaeIIIM263.789E34M15M420.891Myb2HaeIIIM295.293E32M47M462.396BrSPL5P2b112P23M50M132.9113MADsHaeIIIM373.0114E32M47xM81.7118Myb2RSAIM-714.5123MADsHaeIIIM392.7135BRMS-007(A05)145E32M47M-43.3146E32M19M258.3150BR378(DA05)158

A05

P21M47M384.10BrCBFsP2b2Myb2MSE1M70.04E34M15M464.08E37M47M175.4 P14M51M386.910E34M15M60.512BrDRB1P1d15P21M47M134.719P21M47M386.121BrFPF1P1d25BrPHYEP1b30P13M48M288.631P13M48M286.633E32M47M106.135P14M51M279.438P13M48M102.439E32M19M325.841Myb2RSAIM-742.7 P21M47M287.442E34M15M249.643P13M48M71.5 E34M15M228.8E37M47M343.3 P21M47M224.1P21M47M409.8

44

BrELF5P1a BrHUA2P1bBrCDP2e BrCDF1P2eE34M15M386.3 P14M51M302.2

45

P14M51M114.146P23M50M64.3 P23M48M102.147P23M48M254.348Na12H07(A06) ENA23l(A06)51Br450P1a53BrFPF1P2a56BrESD4P1a60BrBCAT3-1MiA0661BrST5cMiA0663BrCYP79F1MiA0664

A06

BrAP3P1b0E34M15M398.911Myb2MSE1M-575.514E32M47M426.117Myb2RSAIM230.619Myb2RSAIM-549.330P23M48M221.9 BRMS-018(A07)32Myb2RSAIM387.635BRMS-040-1(A07) P23M50M168.436P23M50M106.037BrFDPP1a BrSEP3P2aE37M47M123.438

P14M51M355.039Myb2HaeIIIM373.940Myb2MSE1M213.642P13M48M242.843Br372(DA07)48Myb2RSAIM-796.849P13M48M64.050E32M47M467.251E34M15M-504.052BrFKF1P2d53BrFKF1P3c55BrFVEP2a56BrLKP2P1a58BrFKF1P1c65BrSEP3P1a67

A07

E32M47M413.10P23M48M88.96P23M50M86.422BrVRN2P4b23P13M48M456.439Br307(DXA08) P23M50M335.345BrESD4P2b49E32M47M222.651P23M48M289.2 P23M48M276.553P23M48M-34.357Ra2E12t61P23M50M72.864E34M15M312.5 P13M48M174.468BrVEL1P1e73BrBIN1P2c77BRH80C09flc3(DA08)79BrEDF1P2c80BrCUL3P1a82BrPFT1P3b87Myb2RSAIM405.988P21M47M358.894Myb2RSAIM-541.1 Myb2MSE1M257.4103BrMFTP1b105Myb2AluIM123.6106Myb2MSE1M405.1110BrDRL1P3b BrDRL1P2b115Myb2RSAIM414.9122Myb2AluIM190.6124Myb2AluIM263.6127BrMFTP2b131Myb2RSAIM-589.3135Myb2RSAIM238.7139BrCRY2P2c140BrCRY2P3a143

A08

BrVIP4P2b0P23M50M-40.98P14M51M177.011BC105(DA09)12Br308(DXA09)14Ol10D08(DA09)19MADsHaeIIIM-576.424P23M48M212.830BrMYB28-2MiA0931BrT1N6-2P1c34MADsHaeIIIM-573.036BrAPRR5P1b39BrFRY1P1b42BrVIP4P1b45BrCCA1P1c48P13M48M155.449BrFDPP2a51BrST5b-9MiA09 BrCSlyase2MiA0954BrST5b-3MiA0957P13M48M214.958BrTOC1P2b61Myb2MSE1M-596.763E34M15M260.665E32M47M56.067P23M50M115.969E37M47M169.8 MADsHaeIIIM296.570BrRGAP2c71P14M51M397.672E32M19M418.373E32M19M404.0 E32M19M95.0BrCRY1P2d74

BrFRL2P1b75P21M47M328.3 P14M51M153.9P14M51M147.276

BrUGT74B1-1MiA0978BrPFT1P2c BrPFT1P4f80P23M48M200.2 MADsHaeIIIM363.381MADsHaeIIIM243.282BrGIP1d84BrGIP3b85BrGIP2b87BrCRY1P1c90P13M48M110.694BRMS-051(A09) BR321(DXA09)95Myb2AluIM450.899Myb2AluIM454.0100BrSNZP2b102BR343(DA09)105CAPS5107P14M51M126.2108BrFPAP1c110BrELF3P1c115E32M19M175.8116BrGAr3P1a117BrVIM3P3b120BrSVPP1c126E32M19M328.9 MADsHaeIIIM249.4127BrFVEP3a P14M51M321.6128BrDRL1P1 BrMYB51-1MiA09130BrFMO-GS-OX5MiA09137BrDDF1P2b142BrPHYAP1g146BrGAr3P2b150P14M51M110.5154P14M51M209.8158P14M51M206.7159

A09

BrCRY2P1a0BrPHYEP1a5P13M48M153.716P23M50M264.317P23M50M252.718P23M48M168.819E32M47M344.220P23M48M165.8 E32M47M166.0E32M19M392.9 Myb2RSAIM268.821E34M15M212.9 P23M48M244.623BrFRIP2c24chsssr13(DA10)27E37M47M69.528E32M19M323.333E32M19M310.435BrVIN3P1a41P23M48M314.751BrVIN3P1a55BrTFL2P4b BrTFL2P2a58BrFRL1P2a59P13M48M342.961BrTFL2P1d BrTFL2P1c73BrCOL1P1c76BRH80A08flc1(DA10)84P21M47M444.386EJU6R10(DA10)88BrCPDP1a105BrTFL1P2b-SSR118

A10

Supplementary Fig. S1. An updated genetic linkage map constructed with 125 Ft

candidate gene target markers (GT) based on DH68 population (YS-143×PC-175). The

flowering time candidate gene markers were marked by red colour.

5 012346

A01-P

BrAP2P1d(XSA01)0.0BrFDP1g(XSA01)4.1Myb2RSAIM114.611.9P23M48M93.217.5E37M47M266.920.5BrPHYEP2c(XSA01)26.1BrSLY1P1b(XSA01)28.1Myb2RSAIM91.131.3P14M51M213.332.9BrEBSP1b(XXA01)35.9E32M47M77.937.0Myb2MSE1M276.940.9P23M50M87.241.5P14M51M298.047.4P14M51M174.348.4P14M51M243.350.5MADsHaeIIIM-503.052.2P23M50M317.953.0P23M50M312.353.2E34M15M238.653.3P13M48M247.253.7BrBCAT3-2MiA0155.0Myb2AluIM357.355.8Myb2AluIM488.556.4E34M15M83.058.8P23M48M219.262.7E32M47M179.865.9P13M48M218.670.4E32M47M123.173.6BrSPL5P1a(XSA01)78.8P13M48M221.587.8E32M19M239.390.7P13M48M384.891.2BrMYB51-2bMiA0196.3BrCOL2P3a(XSA01)106.2P23M50xM326.7113.7E32M47M212.2115.5Myb2HaeIIIM475.9119.8BrCOL2P4a(XSA01)125.7BrATVGT1P1a(XSA01)129.9

A01

A01

eQTL fQTL

LODBra0110240.0FVE0.6VIP30.7VEL10.9FLP11.4KNAT51.6ATH12.1AGL162.5CIB12.6FDP FD3.1AP23.6COP33.8T28I19.160 AGL17AGL213.9

BIN14.2CKB2 CKB14.5PHYE4.8JMJ145.8PDF26.3EBS6.5AGL14 AGL196.9AT4G233407.1SLY17.7AGL24 PGI7.9GA20OX1 GA20OX28.3FWA8.4CIP79.6DFL19.7TOR19.8HAT410.6FIP2 FCA10.7CKL1311.2FAR112.0ELIP212.2LUX/PCL113.5ARP413.8

VIP516.6GA20OX4 YAP16916.7GA20OX1 GA20OX2PGM17.4

A01 [1]

CKL1318.7TIC19.5AT3G2132020.0FIS320.4ATFYPP320.8HAF2 RTV1VRN121.0

SPL521.6SPA4 SPA321.7NFYB3/HAP3C21.9TCTP22.2

ATVGT124.2GASA524.4COL2 SEPALLATA224.6LDL224.8LCL126.0DFL226.6ICE126.8COL926.9ELS127.3LSH2 LSH1SEC27.6

MBD9 Bra04052027.7

A01 [2]

Bra0283860.0CDF20.3BNQ10.4XPB20.7CIP10.8FLC FLM/MAF1MAF21.2

TCP111.5GA20OX4 YAP1691.7CPD1.9TFL1 LMI12.2PRR72.4PNY2.5LAC82.6HY52.8EMF12.9NFYA1/HAP2A3.1FY3.3BNQ2 GASA43.7COL13.9TFL24.3AAT24.8PI5.0NPH45.1CAM15.3MIR172(EAT) TOE25.9AT1G10588 AT5G59845ZAT126.0

VIP2 FDPSRR16.1

COL56.7VIN36.8FT TSF7.7RGL17.8EMF28.1GA20OX1 GA20OX28.3CAL AP19.0TEM29.2DFL19.5XAL110.1CSTF6410.2TFIIIA10.4HAP2C10.8GASA611.5GA2OX113.0PRE13.6GA3ox2 GA3OX413.8CUL416.5LBA117.1CKB2 CKB117.2NFYB2 RAV117.6HSP88.117.8SEPALLATA418.0

A02 [1]

ICU218.1PKS118.2UBC118.3ICE1 FUS319.3TEL120.6LSH2 LSH121.9PRMT4B PRMT4a22.3PAT122.6BR6OX222.8K19B1.17 CDF123.4LFY23.7VIP423.8FUL23.9HUA224.0APRR524.3FLM/MAF1 MAF4MAF5 FLM/MAF1MAF2 MAF3MAF5

25.0

RGL225.5ATVGT125.6Bra03202825.7

A02 [2]

Bra0056570.0LAC8 PNY0.2LCL10.4TFL10.6CPD1.0GA20OX4 YAP1691.3CHE1.5FLC1.8EMF12.0NFYA1/HAP2A2.3FY2.5AGL152.6AT5G149202.8BNQ2 GASA42.9SEPALLATA23.0PI4.0CAM14.2ZAT12 VIP24.7SEF5.0VIN35.2DFL15.9FRI6.8CBF2 CBF3CBF1 FLC7.1

SPL3 FES18.1GA2OX38.2NFYB19.4ELF49.8CAM110.1COR15b COR15a10.4PIF410.5CKB4 AGL6CKB310.9

SOC111.0ATBRM11.1SPA111.2protein_coding11.3ELF4-L111.4TOE111.5ATC11.6pEARLI13.1PDF213.4GA113.7CRP14.3COL214.6ATVGT114.7LSH2 LSH1FLK14.9

CLPS3 WNK115.0HAP2B15.2COL915.7FLD16.1SPY16.4FADB NFYB3/HAP3C17.5TCTP17.8

A03 [1]

Bra0110240.0FVE0.6VIP30.7VEL10.9FLP11.4KNAT51.6ATH12.1AGL162.5CIB12.6FDP FD3.1AP23.6COP33.8T28I19.160 AGL17AGL213.9



A01 [1]




MBD9 Bra04052027.7

A01 [2]



VIP2 FDPSRR16.1


A02 [1]


25.0

RGL225.5ATVGT125.6Bra03202825.7

A02 [2]





A03 [1]





A01 [1]




MBD9 Bra04052027.7

A01 [2]



VIP2 FDPSRR16.1


A02 [1]


25.0

RGL225.5ATVGT125.6Bra03202825.7

A02 [2]





A03 [1]




A01 [1]




MBD9 Bra04052027.7

A01 [2]



VIP2 FDPSRR16.1


A02 [1]


25.0

RGL225.5ATVGT125.6Bra03202825.7

A02 [2]





A03 [1]

eQTL fQTL

LOD

A02-P

BrMAF2P1b(XXA02)0.0BrAGL15P2a(XSA02)4.9BrBFTP1a(XXA02)9.0Myb2MSE1M480.811.3BrFLC2(XA0)17.6BrFLC2-2(XSA02)21.1BrFLMP2d(XSA02)21.5P13M48M137.123.3BRH04D11flc2(DXA02)24.1P23M50M179.624.2Br323(DXA02)28.8BrFYP1a(XSA02)32.0ENA13l(DA02)36.9BrVIN3P2b(XSA02)44.3BrEBSP2d(XXA02)44.7BrPIP1b(XSA02)48.3E34M15M142.849.8BrCOP1f(XXA02)50.6E37M47M115.452.4BrPIP2a(XXA02)56.7E32M19M308.563.8BrFTP1c(XXA02)67.7BrTSFP2c(XXA02)69.0BrCALP2a(XA02)70.4Myb2RSAIM315.374.6E32M19M266.474.8Myb2RSAIM320.075.2BrCALP1g(XXA02)79.4P14M51M219.482.3Na12H09(A02)84.2P14M51M76.589.8P23M50M230.590.5P23M48M115.691.5Myb2RSAIM475.092.0Myb2RSAIM341.093.1P21M47M166.793.5Myb2MSE1M-614.594.5P21M47M168.596.9E32M19M76.7100.7P23M48M176.7106.3P21M47M94.9108.9P23M48M273.5 P13M48M157.8110.1Br333(DA02)110.2Myb2HaeIIIM270.6111.1E34M15M461.1112.8Myb2HaeIIIM-550.5117.2BrFULP1b(XXA02)118.1BrMYB28-3MiA02120.2E37M47M153.4121.3ENA23h125.0Myb2RSAIM496.0128.3Myb2MSE1M125.7129.4BrFLMP1b(XSA02)131.2Myb2RSAIM146.8133.0BrMAF4P1d(XXA02)137.4BrMAF4P2a(XSA02)139.1

A02

A02

0361215 9

012345A03-P

P23M48M291.70.0BRMS-008(A03)1.2P23M48M293.82.0Myb2HaeIIIM-586.15.5BrFLCP5a(XA0)8.3BrFLCP5b(XA0)9.2Myb2AluIM377.311.4Myb2AluIM381.013.2Myb2MSE1M355.013.5Myb2MSE1M321.814.3Myb2AluIM-589.119.6BrMYB29-1MiA0322.4E37M47M128.129.2P13M48M381.034.5Br360(DA03)35.2E32M47M252.438.4E32M47M255.138.6BrVIN3P3a(XXA03)48.1Myb2HaeIIIM390.248.4Myb2AluIM138.849.1P13M48M244.749.6P21M47M198.655.3E37M47M134.560.2BRMS-043(XA03)62.1BrAS1P1c(XXA03)66.1BrAS1P2a(1)(XA03)66.5OlB05(DA03)66.6P21M47M190.467.0P23M48M149.067.4BrGSL-OHMiA0370.4P23M48M159.673.1BR356(DA03)75.4BrATBRMP1d(XSA03)77.5Myb2RSAIM183.981.3BrSNZP3b(XA0)84.8BrAS1P3b(XA03)88.9SOC1P1d-SSR89.2P14M51M168.792.6E32M47M85.798.6BrGA1P2c(XSA03)99.7BrFLKP2b(XSA03)101.6BrIQD1-1MiA03105.1BrFLDP1c(XXA03)107.9Myb2HaeIIIM-601.3110.4P23M48M439.2114.4P23M48M321.5115.3BrVRN1P3b(XSA03)116.4P21M47M171.0117.5P14M51M135.1118.0Myb2MSE1M67.4118.6Myb2RSAIM69.3118.7BrTCTPP1b(XXA03)120.1BrBCAT4-1MiA03121.1BrELF8P1b(XA03)124.3Myb2MSE1M222.2125.3BrMAM3-1MiA03126.0BrMYB28-1MiA03127.2MAM-4(DA0)129.1BrTOC1P1b(XXA03)129.4MAM-1(DA0)130.6P23M50M273.1130.7Bac130(DA03)131.1BRMS-050-1(A03)131.2F3H-ssr3131.5P23M48M99.5133.5E34M15M383.9134.7E32M47M382.4139.7E32M47M384.5140.7BrNS1P2c(XXA03)142.1BrAGL24P2c(XSA03)145.8BrAGL24P1b(XXA03)147.2Myb2RSAIM-734.9150.8P23M50M284.3153.7E34M15M495.3157.3P14M51M64.2171.5Myb2MSE1M253.7172.2E32M19M420.2174.3E37M47M397.6176.3E37M47M426.1176.6E34M15M255.7176.8P23M50M53.6179.7Myb2HaeIIIM86.2192.2

A03A03

eQTL fQTL

LOD6




A01 [1]




MBD9 Bra04052027.7

A01 [2]



VIP2 FDPSRR16.1


A02 [1]


25.0

RGL225.5ATVGT125.6Bra03202825.7

A02 [2]





A03 [1]

RTV1 VRN118.2ATFYPP318.5DDL18.6AT3G2132018.8TIC19.2CKB2 CKB120.7ESD421.2TOC122.3FUL22.5HUA222.7DFL223.1ENS23.4ELF823.5PDF224.1GA2OX824.3DFL124.7CBF2 CBF3CBF1 GA20OX1GA20OX2

25.2

PGI AGL2425.5AT4G2334026.1AGL14 AGL1926.4EBS26.7KNAT527.0FLP1 ELF927.3SKB127.4VEL127.8AT4G33280 AGL1629.0ATH129.2FDP FD29.7SNZ AP230.2COP330.4Bra01790531.2

A03 [2]

Bra0404310.0CAM1 CML24SPL9 GAr3AT5G28450

0.1

CIP1 CKB1COL3 AGL170.2

SVP ELF3XPB2 SHP20.3

ELF4 PMI15HOS1 ATX10.4

CAM10.5ATBRM CAM10.6FHY1 COP1AGL13 PRR90.7

ATC HUB1FIO1 CLFSOC1

0.8

GA2OX30.9CDF2 PIF41.0SHP11.4SPL151.7AGL18 INO801.9AMP13.2AP33.4COP95.5BR6OX27.1CKB27.3CKB27.7AGL219.1CBFs9.6COP311.3

FRI12.8

A04 [1]

Bra04048618.8

A04 [2]

Bra0044090.0RFI20.1CCA1 PRR90.5SPA10.7SPL30.9SPL91.3SHP2 SHP11.5FPA1.7CKB4 CKB32.2HUB12.3SAP18 AGL6SOC12.5

ELF42.9NFYB13.3FHY13.8NFYA45.2GA2OX35.4FES1 SPL35.7COP16.1

ARR38.2

LD9.1PHYC9.3CIR19.6SPA4 SPA3SPL410.2

GA2ox711.5VIP111.9GA2OX412.4RTV1 VRN113.0

TIC15.2AT3G2132015.8

FIS3 FIS316.8ATFYPP317.3TCTP17.5PHYB PHYD17.6

A05 [1]

RTV1 VRN118.7NFYB3/HAP3C FADB19.5SPA4 SPA319.8SPL519.9PIE121.0SPY MYB65MYB3321.5

PRMT4B PRMT4a21.9COL922.1LCL122.6GAr223.3MBD923.5SEPALLATA223.7Bra03918323.8

A05 [2]

Bra0379540.0SPL40.5HAP5C NFYC9(NF-YC3)0.8CBFs1.2

F14G24.73.1DDF1 DDF24.2ICE14.3RAV14.5AT1G105884.9OTS2 OTS1ARR35.0

DRB15.3PHYA PIF35.4GA3OX16.6UBC17.1NPH47.4

UBP269.2NFYC1/HAP5A9.7REF69.9BNQ310.3CDF310.5LUX/PCL1 BOA11.0

CAM112.2

UBP2613.9LFY14.0NFYC1/HAP5A14.3ALX814.5LIP115.0FLM/MAF1 MAF2MAF3 MAF5MAF4

15.1

AT5G6554015.4APRR517.1FKF1 FPF117.3TNY GA317.7

A06 [1]

012345

A04-P

Myb2MSE1M142.20.0E32M19M204.414.2P21M47M78.514.5P14M51M88.719.4E32M19M138.221.7P23M50M66.922.4Myb2MSE1M490.823.5E32M19M439.226.7E32M19M435.529.2P21M47M164.6 P21M47M178.139.8Myb2HaeIIIM329.441.5E32M47M133.543.0BR384(DA04)43.7BR325(DA04)44.2BrSVPP2d(XSA04)48.6P23M50M127.651.3BrPHYAP3c(XSA04)59.0E32M47M136.063.6

A04

A04

eQTL fQTL

LOD

6 RTV1 VRN118.2ATFYPP318.5DDL18.6AT3G2132018.8TIC19.2CKB2 CKB120.7ESD421.2TOC122.3FUL22.5HUA222.7DFL223.1ENS23.4ELF823.5PDF224.1GA2OX824.3DFL124.7CBF2 CBF3CBF1 GA20OX1GA20OX2

25.2


A03 [2]


0.1






0.8


FRI12.8

A04 [1]

Bra04048618.8

A04 [2]



ARR38.2



TIC15.2AT3G2132015.8


A05 [1]



A05 [2]





CAM112.2


15.1


A06 [1]


25.2


A03 [2]


0.1






0.8


FRI12.8

A04 [1]

Bra04048618.8

A04 [2]



ARR38.2



TIC15.2AT3G2132015.8


A05 [1]



A05 [2]





CAM112.2


15.1


A06 [1]

A05-P

BrCCA1P3b(XA0)0.0BrSPA1P1a(XXA05)19.2BrSPA1P2a(XSA05)23.1BRMS-034(A05)38.8E32M19M221.842.1Myb2MSE1M88.846.2P14M51M182.051.1BrFES1P3b(XSA05)54.9BrFES1P2c(XSA05)59.8Myb2RSAIM232.861.9P23M48M63.663.8BrSPL5P3a(XSA05)68.4BrTCTPP2b(XSA05)70.4P23M48M-36.673.3E32M47M460.079.9Myb2HaeIIIM-605.380.5P14M51M121.981.9P23M50M241.183.4P21M47M339.083.9E32M47M113.6 E32M47M118.184.0BrVRN1P1b(XSA05)86.8Myb2HaeIIIM263.788.9E34M15M420.890.6Myb2HaeIIIM295.293.5E32M47M462.395.7BrSPL5P2b(XSA05)111.6P23M50M132.9113.2MADsHaeIIIM373.0114.2E32M47xM81.7117.8Myb2RSAIM-714.5122.6MADsHaeIIIM392.7134.7BRMS-007(A05)144.6E32M47M-43.3146.2E32M19M258.3149.7BR378(DA05)157.8

A05

A05012345

eQTL fQTL

LOD

6RTV1 VRN118.2ATFYPP318.5DDL18.6AT3G2132018.8TIC19.2CKB2 CKB120.7ESD421.2TOC122.3FUL22.5HUA222.7DFL223.1ENS23.4ELF823.5PDF224.1GA2OX824.3DFL124.7CBF2 CBF3CBF1 GA20OX1GA20OX2

25.2


A03 [2]


0.1






0.8


FRI12.8

A04 [1]

Bra04048618.8

A04 [2]



ARR38.2



TIC15.2AT3G2132015.8


A05 [1]



A05 [2]





CAM112.2


15.1


A06 [1]


25.2


A03 [2]


0.1






0.8


FRI12.8

A04 [1]

Bra04048618.8

A04 [2]



ARR38.2



TIC15.2AT3G2132015.8


A05 [1]



A05 [2]





CAM112.2


15.1


A06 [1]


25.2


A03 [2]


0.1






0.8


FRI12.8

A04 [1]

Bra04048618.8

A04 [2]



ARR38.2



TIC15.2AT3G2132015.8


A05 [1]



A05 [2]





CAM112.2


15.1


A06 [1]

GAr2 GAr1AT5G2723018.3

hst WNK118.4LSH2 LSH118.5BFT18.8YAP16919.0CDF119.2ELF519.4PRMT4B PRMT4a21.1ADG1 PAT121.4SEPALLATA4 HSP88.121.6RAV121.8TEL122.0ICE1 FUS322.2BR6OX223.2PKS123.4UBC123.5GAI RGA23.9RPI224.1CKB124.4CUL424.7DOG124.8BIN125.4Bra03375926.2

A06 [2]

Bra0364110.0

HXK10.9LKP2 FKF11.1

F17F8.152.7

VIN3-L4.1

ADG15.0FIP15.6SEP35.7

GA2OX27.0TOE17.3ATC7.8CAM18.0CYP72B18.1ICU28.6

CAM112.1AGL1812.2SPL1512.4NFYC2/HAP5B12.6SHP2 SHP112.7CKB4 CKB313.0AT5G2845013.2PIL213.3GAr313.5PRE13.8NUA14.0MIF115.0HAP2C15.4TFIIIA15.5CSTF6415.6XAL115.7MMP15.9CDF5 NAP16.1ORTH2 VIM316.6FT TSF16.8CML24 CAM117.1

A07 [1]

CAL AP118.1NAP CDF518.3EFS18.7FT TSF18.9ASHH119.0MIF119.8HAP2C20.4XAL120.8MMP21.4SHW121.5UBC121.6GA2OX121.8NUA22.1GA2/KS22.2Bra03520622.5

A07 [2]

Bra0308070.0ARP60.1HUB20.4MED90.6TFL21.3RGL21.4GA20OX51.8

RTV1 VRN13.6ATFYPP34.1RPI24.7

VIP15.6ATR45.8UFO SUF46.2ESD46.7HAF27.8COP99.0SPA29.5AGL14 AGL1910.0EBS10.2PDF210.4GA2OX810.5GA3OX310.6FIP211.8VRN211.9FLP113.2SKB113.3VEL113.6VIP313.7CBF2 CBF114.5FDP FD14.7COP315.3T28I19.160 AGL17AGL2115.5

BIN115.8CKL1316.1GA2OX216.4SEP317.1PFT1 EDF117.4CAL AP117.5CUL317.6

A08 [1]

NPH418.7MFT18.9ATCSTF7719.0ICE119.6DDF1 UBC1DDF219.7

LHY20.1GA2OX620.2CRY220.4STO20.7HAP5C NFYC9(NF-YC3)21.2DRB1 Bra03080621.4

A08 [2]

Bra0362260.0GA10.1SDG100.4CRP0.8APRR51.5FKF1 FPF11.6TNY1.7AT5G272302.1WNK1 LSH2LSH12.2

PAT12.5BR6OX22.6K19B1.173.0TOC13.2VIP4 FUL3.3FRY13.4LIP13.6FDP4.6SVP ORTH2VIM35.0

AAT25.4HXK15.8FVE5.9DDF26.0LSD1 AAT2SCO17.6

GA20OX4 YAP1698.5OTS18.9ARR39.0ATFYPP39.9ATXR710.3CRY110.7SEP311.9SEF12.0CKL1313.1HSP88.114.5SEPALLATA414.7PKS1 UBC115.0GAI RGA15.3NFYB215.6AT5G4691015.9CUL416.5DOG116.7AGL14 AGL1916.9pEARLI17.2AGL1517.5PCFS4 PDF217.7

A09 [1]

A06-P

P21M47M384.10.0BrCBFsP2b(XSA06)2.3Myb2MSE1M70.04.5E34M15M464.08.0E37M47M175.49.9P14M51M386.910.1E34M15M60.511.7BrDRB1P1d(XXA06)15.4P21M47M134.718.7P21M47M386.120.7BrFPF1P1d(XSA06)24.9BrPHYEP1b(XXA06)29.7P13M48M288.631.5P13M48M286.633.3E32M47M106.135.5P14M51M279.438.1P13M48M102.439.5E32M19M325.840.6Myb2RSAIM-742.741.6P21M47M287.442.1E34M15M249.643.1P13M48M71.543.8E34M15M228.844.2E37M47M343.3 P21M47M224.144.3P21M47M409.844.4BrELF5P1a(XSA06) BrHUA2P1b(XXA06)44.5BrCDP2e(XA0) BrCDF1P2e(XXA06)44.6E34M15M386.344.8P14M51M302.245.3P14M51M114.145.8P23M50M64.346.8P23M48M102.147.4P23M48M254.348.4Na12H07(A06)50.9ENA23l(A06)51.2Br450P1a(XSA06)53.5BrFPF1P2a(XSA06)56.4BrESD4P1a(XXA06)59.5BrBCAT3-1MiA0661.3BrST5cMiA0662.5BrCYP79F1MiA0663.9

A06

A06012345

eQTL fQTL

LOD

6

A07-P

BrAP3P1b(XSA07)0.0E34M15M398.910.7Myb2MSE1M-575.514.3E32M47M426.117.2Myb2RSAIM230.619.1Myb2RSAIM-549.330.2P23M48M221.931.8BRMS-018(A07)32.5Myb2RSAIM387.635.3BRMS-040-1(A07)35.9P23M50M168.436.2P23M50M106.037.0BrFDPP1a(XSA07)37.6BrSEP3P2a(XXA07)37.7E37M47M123.438.4P14M51M355.039.2Myb2HaeIIIM373.940.1Myb2MSE1M213.641.6P13M48M242.842.6Br372(DA07)48.2Myb2RSAIM-796.848.6P13M48M64.049.7E32M47M467.251.0E34M15M-504.052.1BrFKF1P2d(XSA07)52.8BrFKF1P3c(XSA07)54.8BrFVEP2a(XSA07)56.4BrLKP2P1a(XSA07)58.5BrFKF1P1c(XSA07)64.9BrSEP3P1a(XSA07)66.7

A07

A07012345

eQTL fQTL

LOD

6



A06 [2]

Bra0364110.0

HXK10.9LKP2 FKF11.1

F17F8.152.7

VIN3-L4.1




A07 [1]


A07 [2]





A08 [1]



A08 [2]





A09 [1]



A06 [2]

Bra0364110.0

HXK10.9LKP2 FKF11.1

F17F8.152.7

VIN3-L4.1




A07 [1]


A07 [2]





A08 [1]



A08 [2]





A09 [1]

A08-P

E32M47M413.10.0P23M48M88.96.4P23M50M86.421.7BrVRN2P4b(XXA08)23.2P13M48M456.439.1Br307(DXA08)44.6P23M50M335.345.2BrESD4P2b(XXA08)49.3E32M47M222.651.3P23M48M289.252.7P23M48M276.553.2P23M48M-34.356.9Ra2E12t60.7P23M50M72.863.7E34M15M312.567.5P13M48M174.467.8BrVEL1P1e(XXA08)72.9BrBIN1P2c(XXA08)77.3BRH80C09flc3(DA08)79.1BrEDF1P2c(XSA08)80.3BrCUL3P1a(XXA08)81.6BrPFT1P3b(XSA08)86.5Myb2RSAIM405.987.6P21M47M358.894.1Myb2RSAIM-541.1103.1Myb2MSE1M257.4103.4BrMFTP1b(XSA08)105.0Myb2AluIM123.6106.3Myb2MSE1M405.1109.7BrDRL1P3b(XXA08)114.8BrDRL1P2b(XA0)115.1Myb2RSAIM414.9121.9Myb2AluIM190.6123.7Myb2AluIM263.6126.9BrMFTP2b(XSA08)131.3Myb2RSAIM-589.3135.2Myb2RSAIM238.7139.5BrCRY2P2c(XSA08)139.7BrCRY2P3a(XSA08)142.9

A08

A08012345

eQTL fQTL

LOD

6GAr2 GAr1AT5G2723018.3


A06 [2]

Bra0364110.0

HXK10.9LKP2 FKF11.1

F17F8.152.7

VIN3-L4.1




A07 [1]


A07 [2]





A08 [1]



A08 [2]





A09 [1]



A06 [2]

Bra0364110.0

HXK10.9LKP2 FKF11.1

F17F8.152.7

VIN3-L4.1




A07 [1]


A07 [2]





A08 [1]



A08 [2]





A09 [1]

A09-P

BrVIP4P2b(XSA09)0.0P23M50M-40.98.1P14M51M177.010.9BC105(DA09)12.2Br308(DXA09)14.2Ol10D08(DA09)18.7MADsHaeIIIM-576.424.1P23M48M212.829.6BrMYB28-2MiA0930.7BrT1N6-2P1c(XXA09)34.3MADsHaeIIIM-573.036.0BrAPRR5P1b(XXA09)39.3BrFRY1P1b(XXA09)42.4BrVIP4P1b(XXA09)45.2BrCCA1P1c(XXA09)48.3P13M48M155.448.9BrFDPP2a(XXA09)51.3BrST5b-9MiA0953.9BrCSlyase2MiA0954.4BrST5b-3MiA0956.5P13M48M214.957.8BrTOC1P2b(XXA09)60.9Myb2MSE1M-596.762.6E34M15M260.664.5E32M47M56.066.5P23M50M115.968.9E37M47M169.869.9MADsHaeIIIM296.570.1BrRGAP2c(XXA09)70.6P14M51M397.672.1E32M19M418.372.7E32M19M404.073.5E32M19M95.074.0BrCRY1P2d(XXA09)74.2BrFRL2P1b(XSA09)74.8P21M47M328.375.7P14M51M153.975.8P14M51M147.276.3BrUGT74B1-1MiA0977.7BrPFT1P2c(XXA09) BrPFT1P4f(XXA09)79.9P23M48M200.280.5MADsHaeIIIM363.381.2MADsHaeIIIM243.281.8BrGIP1d(XXA09)83.7BrGIP3b(XA09)85.2BrGIP2b(XA09)87.0BrCRY1P1c(XA09)89.8P13M48M110.694.3BRMS-051(A09) BR321(DXA09)95.2Myb2AluIM450.898.8Myb2AluIM454.0100.5BrSNZP2b(XXA09)102.2BR343(DA09)105.4CAPS5106.7P14M51M126.2108.3BrFPAP1c(XSA09)109.8BrELF3P1c(XA09)114.7E32M19M175.8115.8BrGAr3P1a(XXA09)116.9BrVIM3P3b(XXA09)120.4BrSVPP1c(XXA09)125.6E32M19M328.9126.9MADsHaeIIIM249.4127.0BrFVEP3a(XXA09)128.0P14M51M321.6128.2BrDRL1P1 BrMYB51-1MiA09130.2BrFMO-GS-OX5MiA09136.8BrDDF1P2b(XSA09)141.9BrPHYAP1g(XSA09)145.9BrGAr3P2b(XA09)150.4P14M51M110.5154.4P14M51M209.8157.7P14M51M206.7158.7

A09A09

012345

eQTL fQTL

LOD

6

F17F8.15 SUF420.0FRL2 FRL120.5

GA2OX222.0

T22J18.14 GI22.8

CUL323.8EDF1 TEM2PFT124.2

AP327.0AMP127.1SNZ SMZ27.3CAM128.1INO80 AGL1828.4SHP2 SHP128.9PIL629.0FPA29.1CKB4 CKB329.4PIL230.1GAr330.4ELF330.6ORTH2 VIM330.8AGL17 AGL2131.5FVE32.3GA3OX133.4UBC133.7RAV134.1LWD1/ATAN11 LWD2DDF134.3

CBFs34.8HAP5C NFYC9(NF-YC3)PIF3 PHYA35.1

ARR335.3STO35.9

A09 [2]

CKL1336.2PSAT136.3Bra03267036.9

A09 [3]

Bra0379250.0

PSAT11.5CRY2 CKL131.7UBC12.1STO2.6

CO T1N6_23.9LHY SIN14.2GA2OX64.4CCR25.1MYB65 MYB335.7

AAT27.0PI7.2NPH47.4CAM17.7MIR172(EAT) TOE2PRR3 AT5G598458.6

AT1G10588 VIP28.7SRR18.8SEF9.3COL59.6

FRL2 FRL1ELF913.1

COL1 COSEPALLATA213.3

BNQ213.5AGL1513.9NFYA1/HAP2A14.2HY514.7AT5G1062514.8FLC15.0CPD15.3GA20OX4 YAP16915.9HUA2 CHE16.2ELF616.8TFL116.9LMI117.0LCL1 PRR717.2ELF717.3FHL PNY17.4Bra00964617.6

A10



A06 [2]

Bra0364110.0

HXK10.9LKP2 FKF11.1

F17F8.152.7

VIN3-L4.1




A07 [1]


A07 [2]





A08 [1]



A08 [2]





A09 [1]

F17F8.15 SUF420.0FRL2 FRL120.5

GA2OX222.0

T22J18.14 GI22.8




ARR335.3STO35.9

A09 [2]

CKL1336.2PSAT136.3Bra03267036.9

A09 [3]

Bra0379250.0





FRL2 FRL1ELF913.1



A10

Markered col ourLOD l evel3- 44- 66- 88- 10>10

F17F8.15 SUF420.0FRL2 FRL120.5

GA2OX222.0

T22J18.14 GI22.8




ARR335.3STO35.9

A09 [2]

CKL1336.2PSAT136.3Bra03267036.9

A09 [3]

Bra0379250.0





FRL2 FRL1ELF913.1



A10

A10-P

BrCRY2P1a(XXA10)0.0BrPHYEP1a(XSA10)4.5P13M48M153.716.1P23M50M264.317.1P23M50M252.717.8P23M48M168.818.9E32M47M344.220.0P23M48M165.820.5E32M47M166.020.7E32M19M392.9 Myb2RSAIM268.820.8E34M15M212.922.7P23M48M244.623.4BrFRIP2c(XSA10)24.2chsssr13(DA10)27.1E37M47M69.528.4E32M19M323.333.3E32M19M310.434.7BrVIN3P1a(XSA10)41.2P23M48M314.751.1BrVIN3P1a-2(XA0)55.3BrTFL2P4b(XXA10)57.6BrTFL2P2a(XSA10)57.9BrFRL1P2a(XSA10)59.0P13M48M342.961.2BrTFL2P1d(XA0) BrTFL2P1c(XA0)73.3BrCOL1P1c(XSA10)76.2BRH80A08flc1(DA10)83.6P21M47M444.385.6EJU6R10(DA10)88.2BrCPDP1a(XSA10)105.5BrTFL1P2b-SSR118.4

A10

A10012345

eQTL fQTL

LOD

6

Supplementary Fig. S2. Ft genes as anchors between genetic map (YS-143×PC-175) (cM) and physical map

(Mb). A total of 730 Ft candidate genes were included in the physical map. The same Ft candidate genes are

connected with solid lines between genetic and physical maps. P behind linkage group assignment indicates the

physical map. eQTL represented by expression block are shown on the left of the linkage groups, close to their

corresponding genetic markers. Physical maps ends represent Chiffue-401 genome end markers. The displayed

physical and genetic location of all Ft genes with eQTL is included as Supplementary Table S10.

Chromosome

ChromosomeChromosome

LOD

LOD

Chromosome

LOD

LOD


LOD

Chromosome

LOD

Chromosome

LOD

Chromosome

LOD

Chromosome

Chromosome

LOD

Chromosome

LOD

Chromosome

LOD

Chromosome

LOD

LOD

Chromosome

Supplementary Fig. S3. The relative abundance of 13 Ft candidate gene transcripts using RT-qPCR, plotted at 1cM distances along all

linkage groups. X-axis shows the chromosome numbers, A01-A10. Y-axis shows the LOD scores from restricted MQM Mapping in

MapQTL.

A


K

Circadian clock

Photoperiod/circadian clock

Photoperiod

Supplementary Fig. S4. Extraction of functional clusters from the general gene network. Figures present the genes involved in

specific functional pathways with their correlations to genes from other pathways, resulting in a multitude of interactions. Genes from

different pathways are indicated with different coloured dots: gibberellin light blue; floral meristems dark blue; vernalization magenta;

autonomous light pink; red/far red light signaling orange; photoperiod/circadian clock red; regulation of transcription black; light

signaling purple; floral integrators green; development yellow and unknown functional pathways grey.

A, The gibberellin functional pathway. Gibberellin genes integrate a diverse set of functional pathway genes. For example,

GASA4_A02 and T22J18.140_A09 connects with each other and many genes belonging to other functional pathways; GA20OX3_A10,

RGA_A06 and SEC_A01 also show connection with genes from other functional pathways.

B, The floral meristem functional pathway. The COP3_A01, T1N6_2_A10, FRL2_A09, ULP1_A06, CRP_A09, CRP_A03 and

UPF2_A02 genes were connected as core genes with genes from other functional pathways. Especially, PI_A02 was connected with

several important flowering time genes (BrSOC1, BrFT, BrSRR1, BrFLC2, BrPHYA, BrVEL1 and BrGASA4) and flowering time

phenotype.

C, The vernalization functional pathway. The Figure shows that SUF4_A09, COR15B_A03.1, COR15B_A03.2, VIP2_A03, FRI_A04,

VIP4_A02.1, FIE1_A05 and FAF4_A02 are correlated with genes from other functional pathways. BrFLC paralogues are connected

with different sets of genes. BrFLC2 is notably interacting with some floral integrator genes and flowering time phenotype.

D, The autonomous functional pathway. The Figure shows that five autonomous functional pathway genes each are core connected

with different sets of genes from other functional pathways. Only GA20OX3_A10 (gibberellin pathway) is connected to the genes

FLK_A03 and FCA_A01.

E, The red or far red light response signalling functional pathway. Expression of nine out of 16 genes is highly correlated. The genes

COL3_A04 and PAT1_A02 are connected to genes from other functional pathways.

F, The photoperiod/circadian clock functional pathway. Genes are highly inter-connected. Some genes are depicted outside the circle to

better visualize their connections with genes from other functional pathways.

G, The regulation of transcription functional pathway. The Figure shows only four genes from different pathways connected with

TFIIIA_A02 and a single gene connected with SPL15_A07.

H, The light signalling functional pathway. The Figure clearly demonstrates that the CML24_A07 gene is connected with 16 genes,

many from the red/far red signalling pathway; and four from these 16 genes were also connected with the light signalling pathway

gene CIB1_A01.

I, The development functional pathway. A large network connects 27 transcripts from several functional pathways to the central genes

PCFS4_A09 and SDG25_A09.

J, The unknown functional pathway. The Figure shows that CAM1_A07 is clearly correlated to many genes from seven functional

pathways.

K, Visualization of correlation between photoperiod genes, circadian clock genes, and genes assigned to both photoperiod and

circadian clock pathways. Clearly genes from these three sub-clusters are highly connected both within (blue lines) and between

(yellow, red and pink lines) sub-clusters. Seven photoperiod genes (31.8%) are connected with five circadian clock genes through 24

interactions (yellow lines), and 15 photoperiod genes (68.2%) with fifteen genes assigned to both photoperiod and circadian clock

pathways through 45 interactions (red lines). Eight circadian clock genes (88.9%) are connected with 12 photoperiod/circadian clock

genes through 35 interactions (pink lines).

A.th_cDNA : PC-FLC-cDN : FLC2-e4-e6 : FLC2-e4-e6 :

* 20 * 40 * 60 * CTTGTGGGATCAAATGTCAAAAATGTGAGTATCGATGCTCTTGTTCAACTGGAGGAACACCTTGAGACTGCCCTCCTTGTGGAATCAAATTCTGA---TGTAAGCGTCGACTCCCTCGTTCAGCTGGAGGACCACCTTGAGACTGCCCTCCTTGTGGAATCAAATTCTGA---TGTAAGCGTCGACTCCCTCGTTCAGCTGGAGGACCACCTTGAGACTGCCCTCCTTGTGGAATCAAATTCTGA---TGTAAGCGTCGACTCCCTCGTTCAGCTGGAGGACCACCTTGAGACTGCCCTCCTTGTGGaATCAAATtctgA TGTaAGcgTCGActCcCTcGTTCAgCTGGAGGAcCACCTTGAGACTGCCCTC

: 75 : 72 : 72 : 72


80 * 100 * 120 * 140 *TCCGTGACTAGAGCCAAGA--------------------------------------------AGACCGAACTCATCCGTAACTAGAGCTAGGA--------------------------------------------AGACAGAACTAATCCGTAACTAGAGCTAGGAAGGTACGTTCACTACAAAATCTCTTTTTTTTTCTTACTTTCAGAAGACAGAACTAATCC-TAA--------------------------------------------------------ATACAGAACTAATCCgTaActagagc a ga AgACaGAACTaA

: 106 : 103 : 147 : 90


160 * 180 * 200 * 220 TGTTGAAGCTTGTTGAGAATCTTAAAGAAAAGGAGAAAATGCTGAAAGAAGAGAACCAGGTTTTGGCTAGCCAGTGTTGAAGCTTGTTGATAGCCTCAAAGAAAAGGAGAAATTGCTGAAAGAAGAGAACCAGGGTTTGGCTAGCCAGTGTTGAAGCTTGTTGATAGCCTCAAAGAAAAGGAGAAATTGCTGAAAGAAGAGAACCAGGGTTTGGCTAGCCAGTGTTGAAGCTTGTTGATAGCCTCAAAGAAAAGGAGAAATTGCTGAAAGAAGAGAACCAGGGTTTGGCTAGCCAGTGTTGAAGCTTGTTGAtAgcCTcAAAGAAAAGGAGAAAtTGCTGAAAGAAGAGAACCAGGgTTTGGCTAGCCAG

: 180 : 177 : 221 : 164

Arabidopsis thaliana_FLCChiifu_BrFLC2

YS-143_BrFLC2PC-175_BrFLC2

Exon 4



: 75 : 72 : 72 : 72



: 106 : 103 : 147 : 90



: 180 : 177 : 221 : 164



Intron 4 (44bp)





: 75 : 72 : 72 : 72



: 106 : 103 : 147 : 90



: 180 : 177 : 221 : 164

Exon 5

12bp



: 75 : 72 : 72 : 72



: 106 : 103 : 147 : 90



: 180 : 177 : 221 : 164



: 75 : 72 : 72 : 72



: 106 : 103 : 147 : 90



: 180 : 177 : 221 : 164

Supplemental Figure S5

Supplementary Fig. S5. BrFLC2 nucleotide sequence (DNA) analyses within exon 4-exon 5 and comparison to Arabidopsis thaliana

(cDNA) and reference genome Chiifu BrFLC2. The consistent nucleotide sequences are highlighted in black; among them, those difference

nucleotide sequence are highlighted in grey.

a01-p

Documents

ft genes

ft candidate genes

gibberellin genes

functional pathways

specific functional

ft candidate gene transcripts

different pathways

genetic map ys