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FIGURE S1 (Wu et al)

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FIGURE S1 (Wu et al)

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  1. Figure S1 – The Tomato Genetic Map Used in Comparison with the Pepper Map. The framework of this map is predominantly based on COSII markers. For a reference to the previously published high-density tomato map (Frary et al 2005; Fulton et al 2002; http://www.sgn.cornell.edu/cview/map.pl?map_id=9&show_offsets=1&show_ruler=1), the framework markers of that earlier map were also positioned on the current framework. Approximate centromeric locations are indicated by black dots based on the comparison with the maps by Frary et al 2005. Markers in bold and connected by tick marks are framework markers (LOD>3); marker in bold, italic are internal markers with 2≤LOD<3; others are interval markers with LOD<2; cosegregating markers are denoted by vertical bars beside the marker names.

  2. T1 T2 T3 TG479 C2At1g14810 C2At1g30540 E492334 CT233 C2At3g19800 0cM C2At3g12685 cLEC7P21 C2At4g14570 TG301 C2At5g37260 Hba181H07SP6 5 TG31 TG324 T309C C2At3g51140 CAB3 CT197 C2At2g34860 C2At5g44200 C2At4g18230 10 T343 T1117 C2At5g51970 T888 cLPT5E7 15 CT209 TG276 T1650 T869 20 C2At1g28530 CD15 CT196 C2At1g26940 SSR40 C2At1g61150 T1619 C2At5g19130 25 C2At3g51510 MboI077E18SP6 C2At1g14310 T1959B CT255 TG132 30 C2At1g78690 C2At3g06580 T0525 C2At4g19830 TG517 35 TG554 C2At3g06790 TG130 T0697 CT62 TG585 C2At4g20410 40 C2At4g15790 cLEC37C06B C2At2g34560 T1957 T677 T1256 C2At5g18590 C2At1g51160 45 T1516 C2At4g01880 CT171 SSR356 T1704 C2At1g65720 50 U223436 SSR51 C2At1g72030 TG451 C2At2g38780 C2At5g23880 C2At4g18060 55 C2At3g23590 C2At3g63530 T1665 C2At5g13700 TG520 TG14 C2At3g12630 T0753 60 C2At5g45760 C2At5g13450 cTOF10H7 cLEW17M24 T1241 T1751 65 C2At3g56210 CT231 C2At1g02140 C2At5g45950 cLEG27F13 C2At1g64770 cLET1I09 70 TG273 C2At3g03100 C2At4g21710 C2At3g60300 C2At5g41040 C2At4g04955 cLET5J13 C2At5g62390 75 CT38 TG224 C2At5g17170 C2At1g10580 SSR135 TG247 80 C2At1g11380 T1284 CT90A C2At1g11600 C2At4g00090 T1260 85 C2At1g11430 T1162 C2At4g39630 T1395 TG59 C2At5g60160 CT244 90 C2At4g00740 T1278 T0702 C2At3g61140 T1659 TM20 cLES5J1 T0772 95 cLET1A5 P51 C2At3g48330 C2At4g35560 C2At2g45620 T1511 100 TG469 C2At4g00560 T518 T0759 C2At2g45910 TG246 C2At5g66090 105 TG460 T196 TG463 T1409 C2At5g52820 cLEC7H4 TM21 C2At5g49970 110 C2At3g51130 T767 C2At5g23060 CT232 cLET7E12 T1130 115 Ovate SSR29 T0781 TG645R T0852 C2At5g08050 TG48 120 C2At2g38730 TG134 T0628 C2At3g06730 T0794 C2At3g01480 TG607 C2At1g18660 125 TG518 T1963 C2At1g74470 C2At2g04700 TM40 C2At1g80170 130 C2At2g04690 TG83 TG284 cLED19B24A C2At3g47640 C2At1g54520 CT9 135 T1935 cLPT5M7 T1480 C2At1g79720 TG19 C2At3g02220 C2At1g16080 140 T1488 T0347 T0761 CT267 cLPT1A21 C2At1g16180 C2At1g02560 145 C2At2g23750 T0482 U217757 C2At4g37130 T1621 TG142 150 ORFX3 TG152 C2At3g53010 T1400 C2At1g18270 C2At5g26680 TG140 CT243 155 T276 cLEZ17J15A C2At3g18520 TG161 T0706 C2At1g79910 TG528 160 C2At5g67370 cLET5F17 CT163 T0634 T1143 T141 165 C2At4g37300 C2At3g13700 T1669 cLEX2I9 SSR601 TG245 CT59 170 T0879B T1084 C2At4g37280 TG549 C2At5g64350 C2At3g27310 SSR300 SSR117 175 C2At5g40530 T1109 C2At5g49830 C2At3g27200 TG244 C2At5g09580 180 CT24 TG17 C2At3g14075 T1096 T896 C2At3g20240 185 SSR156 C2At3g26900 C2At3g19630 TG154 190 TG474 C2At1g67730 CT137 T646A 195 C2At4g34350 T1782 C2At3g18860 TG158 C2At4g34700 TM22 T0283A CT190 C2At2g16920 FIGURE S1 (Wu et al)

  3. T0707 CT119 T4 T5 T6 GP180 C2At2g29630 C2At5g41270 CT101 CT216 CD59 C2At1g60440 T1928 0cM T1181 T0687 T1252 CD14 5 T1440 C2At2g01770 C2At1g07080 C2At2g30100 C2At1g23890 T0529 C2At3g46780 TG623 CT229 C2At3g25120 10 C2At1g70160 T1198 SSR43 cTOS7C13 C2At2g39690 T0564 T0506 C2At4g01900 T876 15 T0208 TG178 C2At1g24340 T0741 T892 U227536 TG370 C2At3g10920 T1592 C2At3g51010 C2At3g56130 20 CT242 C2At3g17040 T0774 C2At1g26945 TG483 C2At1g14790 C2At3g56040 C2At1g60560 TG590 C2At2g39580 25 C2At3g11210 C2At1g08630 T0507 T0703 T1079 T1068 C2At1g30110 C2At1g06110 CT175 30 C2At2g01410 TG182 C2At4g25650 CT167 C2At3g52155 T0834 35 T0891 T0635 CT83 SSR115 CT157 C2At2g01110 C2At1g21640 40 C2At1g27385 C2At1g44760 C2At1g13380 C2At3g62940 TM43 C2At1g03150 T1335 C2At4g39660 T805 45 CD64 T0725 TG240 C2At4g10030 C2At1g05055 C2At1g79810 CT258 C2At3g25690 50 cLET5C8 C2At4g39870 C2At1g73885 C2At1g65230 TG365 C2At1g77250 C2At5g07960 CT93 55 T0877 T0570 C2At4g24830 CT204 T883 cLET7N9 TG253 CD55 60 C2At1g26520 C2At1g71810 T1640 T1556 T1050 C2At1g28140 TG264 C2At1g24360 65 T1405 TG96 cTOA4O17B T0737 TG292 C2At1g69420 TG62 C2At1g78230 T0040 T1169 70 C2At4g09010 C2At1g27980 T1232 C2At2g43360 TG379 T1975 CT146 C2At1g67325 TG574 75 T1049 C2At1g67700 TM19 T405 C2At2g46580 P56 cLET19J2 C2At1g09920 TG318 C2At5g22820 80 C2At1g27530 TG555 CT109 T730 T1955 CT118 T0769 85 T0708 cLEX13G5 CT50 U221402 TG548 TG345 C2At3g16150 90 C2At1g18640 C2At1g46480 T1746 cLEX2F13 C2At5g25900 CD39 C2At3g55800 TG443 95 T974 C2At2g39950 cLES1K3 C2At1g19340 CT172 CT206 100 TM13 TG23 C2At1g16870 cLED19B12 TG581 C2At3g06440 TG115 105 TG351 TG482 C2At1g19600 T1053 C2At5g49510 C2At1g75350 C2At4g28530 TG60 SSR350 110 CT173 C2At4g12590 T0861 T0739 C2At1g20050 115 C2At3g55360 C2At1g47830 T360 TG69 120 C2At1g20575 C2At1g63610 T1584 C2At1g42990 TG163 CD74 125 CT51 T1933 C2At3g54860 C2At1g76080 C2At5g04270 C2At1g79790 130 T0633 TG185 CT138 FIGURE S1 (Wu et al)

  4. T7 T8 T9 C2At1g29320 C2At5g45680 SSR241 GP39 0cM C2At2g24270 CT156B cLPT4C24 C2At2g18710 TG176 C2At2g37240 C2At5g34850 C2At4g17380 TG254 CT52 C2At3g52860 5 CP52 C2At1g31410 C2At4g30580 C2At4g31130 C2At5g22010 C2At2g24390 T1641 10 SSR52 cLPT2K10 C2At2g16060 CD40 cLED21J7 T0721 TG61 TG18 15 C2At5g56940 T1328 C2At1g18480 cLEX11K1B C2At3g09920 cTOA21D4 20 C2At4g32280 T0720 TG9 T1428 C2At1g30360 CD57 25 T1673 C2At5g27390 C2At5g20520 CT92 C2At3g09925 CT135 CT228 CT143A T1962 T1435 T0532 30 T0671 T1352 TG223 C2At4g33250 CT283 cLED22K8 CT77 T0880 TG252 35 C2At3g10070 T643 TG349 T837A C2At5g11480 Brix9-2-5 T676 C2At5g11490 C2At5g06130 C2At5g14520 TG513 40 C2At4g26680 C2At2g37500 C2At2g04842 C2At2g32970 T1617 CT287 45 T1510 TG302 TG183 cTOB1K3 C2At5g25630 CT84 C2At5g02020 C2At2g35610 TG217 C2At3g45900 T1212 50 C2At2g42750 C2At4g19003 cLET2D4 C2At4g03210 C2At1g32220 C2At5g58410 C2At2g20860 cLET5O24 T1267 C2At3g58790 55 CT88 C2At2g29210 TG639 CT257 C2At3g63190 C2At1g17200 cTOF16B6 CD3 TG572 T0556 T1341 C2At2g38020 60 TG390 C2At1g32410 C2At1g53670 T431 T1624 SSR38 C2At1g03360 C2At1g78620 C2At5g47010 C2At4g03200 65 TG510 T1421 SSR45 C2At5g13200 C2At2g47580 U230185 TG348 C2At3g14910 CT111 70 T0732 TG216 cLPT1J10 C2At1g05385 C2At3g15290 T1581 CT177 C2At3g15430 CT74 75 cLET7D17 C2At4g12230 cTOA4O17A cLES17G6 CT148 TG199 80 C2At1g07310 CT265 TG421 85 T966 C2At3g23400 C2At1g63260 C2At4g26750 TG424 T0487 T1255 90 T0608 T0337 T1519 cLEX13I15 C2At4g11560 GP101 95 T1522 C2At1g04530 C2At4g16450 C2At5g41350 C2At1g55880 C2At3g24050 C2At1g55870 100 T0848 T1558 C2At3g24010 CD61 TG499 C2At1g64150 T0156 CT223 105 T1433 C2At4g23840 C2At1g56050 SSR599 CT252 110 TG328 C2At5g56130 CT68 C2At1g32900 115 C2At1g63980 C2At1g55670 C2At1g16590 120 T0463 T1065 125 C2At5g06360 FIGURE S1 (Wu et al)

  5. T10 T11 T12 C2At5g09880 P47 C2At3g13235 TM14B 0cM TG313 C2At5g64730 TG230 5 cTOA5G7 TG629 cLEC5E20 TG497 TG180 TG395 T1968 T659 10 CT269 CT16 C2At4g03280 CD19 C2At1g53000 CT19 T1657 15 T1551 cLPT6E9 C2At4g15010 TG303 C2At4g28830 C2At2g28600 C2At5g60990 SSR136 C2At3g52180 20 C2At5g04420 T1391 TG651 TG68 C2At3g54840 T787 25 C2At3g25910 C2At4g03400 C2At3g60830 CT234 U216669 T1125 T0637 C2At5g19690 TG508 30 U228331 T0408 CT79 C2At2g46340 TM26 U217183 TG523 35 TG560 C2At5g16630 C2At2g06530 C2At5g16710 T0028 TG386 C2At4g22260 40 T989 cLED11F6 CP58 C2At3g52640 T0283B CT211 CT182 T55 C2At4g16710 CT217 C2At1g79260 cLET8K4 45 C2At5g01990 C2At5g57970 C2At3g02870 C2At3g08760 C2At1g21690 T1263 TG280 SSR46 C2At5g48300 TG408 50 C2At4g08230 C2At4g11120 C2At1g67740 C2At4g08280 TG360 TG285 T0675 CT99 T0571 C2At5g42740 C2At3g17590 55 T0246 C2At3g13180 TG420 cLET5M3B C2At3g57270 TG283 T0173 60 TG565 cTOB8M7 C2At4g18593 TG47 CT20 C2At3g24490 CD72 C2At1g33970 T1185 T0615 65 cSTA37E18 cLPT1F6 C2At4g30220 cLEG37H17 cLEG24B23 U241351 C2At4g12340 T1684 TG400 C2At1g17410 70 CT124 C2At1g51350 T0567B TG241 C2At5g04590 TG394 C2At2g28800 C2At3g09740 TG367 75 T1648 P68 C2At3g44890 T1266 C2At3g51840 T1071 80 T0801 T1521 C2At3g44600 TG63 P64 85 T1014 TG46 TG233 cLET10O11 CD32 90 C2At2g27450 C2At5g01350 C2At5g60540 T1483 T0142 C2At4g16580 95 C2At5g60600 C2At4g33360 C2At2g28250 TG36 C2At1g76150 100 TG468 C2At5g11550 C2At5g38530 TG296 TG105A 105 C2At4g31150 TG26 CT156 cLET24J2A T0770 C2At5g58490 110 C2At2g28490 CT80B C2At1g48300 115 CT120A 120 cTOA22C23 TG393 CT276 C2At5g59960 T814 125 T0800 CD2 C2At5g21170 TG350 TG473 FIGURE S1 (Wu et al)

  6. T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 Figure S2 – Comparative Map of Pepper and Tomato (Close-up of Figure 3). Pepper chromosomes are designated as P1 - P12, and tomato chromosomes as T1 – T12. Each tomato chromosomes is assigned one color (see color code below) and the corresponding pepper chromosome segment(s) are painted with the same color. Approximate centromeric locations are indicated by while dots based on the comparison with the maps by Frary et al 2005 and Linvingstone et al 1999 (regions of AFLP/RAPD marker clusters) respectively. The pepper map includes all framework markers and synteny markers; the tomato map includes synteny markers only. Markers in bold are framework markers (LOD>3); marker in bold, italic are internal markers with 2≤LOD<3; others are interval markers with LOD<2; interval markers are connected by tick marks to their approximate positions, which were estimated from that of flanking framework markers (see Materials and Methods); markers mapped beyond either of the end framework markers have no tick mark connected; cosegregating markers are denoted by vertical bars beside the marker names. “~Tx” following the name of a marker indicates its chromosome location on the tomato map. Similary, “~Px” indicates the chromosome location on the pepper map. Synteny Marker Pairs (SMPs, see Results & Discussion) are highlighted in red, and numbered according to their map locations (in square parenthesis), e.g. P1.1.1 represents P1, Conserved Synteny Segments (CSS) one, Synteny Marker Pair (SMP) one.

  7. T1 P1-wild T8(reversed) C2At1g63980~P1 C2At1g14810~P1 C2At1g63980~T8 0cM C2At1g32900~P1 5 C2At4g23840~P1 C2At5g41350~T8 10 C2At3g12685~P1 C2At1g32900~T8 15 C2At2g34860~P1 C2At5g41350~P1 C2At5g51970~P1 C2At4g23840~T8 20 25 C2At1g63260~P1 30 C2At1g63260~T8 35 C2At1g14310~P1 C2At4g12230~P1 40 C2At4g12230~T8 C2At3g06790~P1 C2At5g13200~P1 45 C2At5g18590~P1 TG510~T8 TG510~P1 C2At4g01880~P1 C2At5g13200~T8 50 C2At5g47010~P1 C2At5g47010~T8 C2At1g32410~P1 C2At3g23590~P1 C2At3g18860~T1 55 C2At5g13450~P1 C2At1g32410~T8 C2At4g19003~P1 60 C2At3g45900~P1 65 C2At2g35610~P1 C2At4g19003~T8 C2At5g25630~P1 70 C2At2g35610~T8 C2At3g45900~T8 C2At5g11490~P1 75 C2At2g45620~T1 C2At4g00740~P1 C2At5g11480~P1 C2At3g61140~P1 80 CT77~P1 C2At2g45620~P1 85 C2At4g00560~P1 C2At3g61140~T1 C2At2g45910~P1 90 C2At1g30360~P2 C2At4g00740~T1 C2At4g32280~P6 95 C2At5g51970~T1 100 C2At2g24390~P8 105 C2At2g34860~T1 C2At4g31130~P8 C2At1g31410~P8 110 C2At3g12685~T1 C2At3g52860~P8 C2At3g06730~P1 C2At4g17380~P8 115 C2At3g06790~T1 C2At5g45680~P1 C2At1g14310~T1 120 TG83~P1 C2At4g10030~T6 125 C2At5g13450~T1 130 TG19~P1 C2At1g05055~T4 135 C2At4g01880~T1 C2At3g23590~T1 140 C2At5g18590~T1 C2At1g02560~P1 145 GP1049 C2At1g14810~T1 150 C2At3g11210~T6 C2At5g45680~T8 155 CP10020 160 GP20095 C2At5g11490~T8 165 C2At5g64350~P1 GP20062 170 C2At5g11480~T8 C2At5g25630~T8 C2At3g19630~P1 175 C2At4g00560~T1 CT77~T8 180 C2At4g34350~P1 C2At2g45910~T1 C2At3g18860~P1 185 C2At4g34700~P1 190 C2At3g06730~T1 195 TG83~T1 C2At2g16920~P1 200 TG19~T1 205 CP10060 C2At1g02560~T1 210 CP10061 215 NN1 220 225 C2At5g64350~T1 C2At3g19630~T1 230 235 C2At4g34350~T1 240 245 C2At4g34700~T1 250 C2At2g16920~T1 FIGURE S2 (Wu et al) [P1.1.1] [P1.2.1] [P1.3.1] [P1.4.1] [P1.4.2] [P1.5.1] [P1.5.2] [P1.5.3] [P1.5.4] [P1.5.5] [P1.5.6]

  8. P1-wild T8(reversed) C2At1g63980~P1 C2At1g63980~T8 C2At1g32900~P1 0cM 5 C2At4g23840~P1 C2At5g41350~T8 10 C2At1g32900~T8 15 C2At5g41350~P1 C2At4g23840~T8 20 25 C2At1g63260~P1 30 C2At1g63260~T8 35 C2At4g12230~P1 40 C2At4g12230~T8 C2At5g13200~P1 45 TG510~T8 TG510~P1 C2At5g13200~T8 50 C2At5g47010~P1 C2At5g47010~T8 C2At1g32410~P1 C2At3g18860~T1 55 C2At1g32410~T8 C2At4g19003~P1 60 C2At3g45900~P1 65 C2At2g35610~P1 C2At4g19003~T8 P8-wild C2At5g25630~P1 70 C2At2g35610~T8 C2At3g45900~T8 C2At5g11490~P1 75 C2At2g45620~T1 C2At5g11480~P1 R45S-C 80 CT77~P1 85 C2At4g31130~T8 C2At3g61140~T1 C2At2g24390~T8 90 C2At1g30360~P2 C2At4g00740~T1 C2At1g31410~T8 C2At4g32280~P6 95 C2At3g52860~T8 C2At5g51970~T1 100 C2At2g24390~P8 [P8.1.1] NN8 105 C2At2g34860~T1 C2At4g31130~P8 NN9 C2At1g31410~P8 110 C2At3g12685~T1 C2At3g52860~P8 C2At4g17380~T8 C2At4g17380~P8 115 C2At3g06790~T1 C2At5g45680~P1 C2At1g14310~T1 120 C2At4g10030~T6 125 C2At5g13450~T1 130 C2At1g05055~T4 135 C2At4g01880~T1 C2At3g23590~T1 140 C2At5g18590~T1 145 GP1049 C2At1g14810~T1 150 C2At3g11210~T6 C2At5g45680~T8 155 CP10020 160 GP20095 C2At5g11490~T8 165 GP20062 170 C2At5g11480~T8 C2At5g25630~T8 175 C2At4g00560~T1 CT77~T8 180 C2At2g45910~T1 185 190 C2At3g06730~T1 195 TG83~T1 200 TG19~T1 205 CP10060 C2At1g02560~T1 210 CP10061 215 NN1 220 225 C2At5g64350~T1 C2At3g19630~T1 230 235 C2At4g34350~T1 240 245 C2At4g34700~T1 250 C2At2g16920~T1 FIGURE S2 continued (Wu et al)

  9. P2 T2 C2At1g30540~P2 C2At5g44200~T2 0cM C2At3g19800~P2 [P2.1.1] C2At5g37260~P2 5 C2At3g51140~P2 C2At3g51140~T2 [P2.1.2] C2At5g44200~P2 C2At1g30540~T2 10 C2At1g02140~T3 C2At3g19800~T2 15 20 C2At5g19130~P2 25 C2At3g51510~P2 C2At5g19130~T2 30 C2At1g78690~P2 [P2.2.1] 35 C2At3g51510~T2 C2At4g20410~P2 C2At2g34560~P2 40 C2At1g78690~T2 [P2.2.2] CT232~T2 45 GP20031 U223436~P2 C2At4g20410~T2 C2At4g18060~P2 C2At1g30360~T8 50 55 C2At2g34560~T2 CT128 60 C2At4g21710~P2 C2At4g18060~T2 C2At4g04955~P2 [P2.3.1] 65 U223436~T2 C2At1g10580~P2 70 C2At4g21710~T2 C2At1g11380~P9 [P2.4.1] C2At1g10580~T2 C2At1g11430~P2 75 C2At4g04955~T2 C2At1g11430~T2 80 C2At4g35560~P2 C2At5g66090~P2 85 BD076366 C2At5g37260~T2 C2At3g51130~P2 90 CT232~P2 C2At4g35560~T2 Ovate~P2 C2At5g66090~T2 95 CP10081 C2At3g51130~T2 C2At3g01480~P2 [P2.5.1] 100 C2At2g04700~P2 Ovate~T2 C2At2g04690~P2 105 C2At4g37280~T2 110 [P2.6.1] C2At5g67370~T2 115 C2At3g02220~P2 C2At4g37130~T2 120 [P2.6.2] C2At3g02220~T2 C2At4g37130~P2 125 C2At2g04690~T2 [P2.6.3] C2At2g04700~T2 130 C2At3g01480~T2 135 C2At5g40530~T2 C2At3g27200~T2 C2At5g67370~P2 140 C2At1g67730~T2 145 C2At4g37280~P2 150 C2At5g40530~P2 C2At3g27200~P2 155 C2At1g67730~P2 FIGURE S2 continued (Wu et al)

  10. FIGURE S2 continued (Wu et al) T3 T9(reversed) E492334~P4 0cM Hba181H07SP6~P4 5 C2At4g18230~P4 C2At1g16590~P3 10 cLPT5E7~P4 15 20 C2At1g28530~P4 T0156~P3 25 C2At3g24010~P3 MboI077E188P6~P4 C2At3g24050~P3 TG132~P4 30 C2At1g04530~P3 35 T1519~P3 TG517~P3 40 TG130~P3 C2At3g23400~P3 45 C2At1g07310~P3 C2At1g51160~P3 50 C2At1g65720~P4 C2At1g72030~P6 55 C2At5g23880~P3 C2At3g63530~P3 C2At1g05385~P3 60 C2At2g47580~P3 C2At1g02140~P2 65 C2At4g03200~P3 C2At1g64770~P3 C2At3g03100~P3 70 C2At5g41040~P3 C2At2g29210~P9 C2At5g62390~P3 C2At5g58410~P9 C2At5g17170~P3 75 80 85 C2At5g06130~P9 90 95 C2At5g52820~P3 100 C2At3g09925~P9 C2At5g49970~P3 C2At5g23060~P3 105 C2At3g09920~P9 110 115 120 C2At2g37240~P9 C2At1g18660~P3 125 GP39 C2At1g80170~P3 130 C2At3g47640~P3 135 140 C2At1g16180~P3 C2At1g18270~P3 145 150 155 160 C2At3g13700~P3 165 170 175 180 C2At3g14075~P3 C2At3g20240~P3 P3 P3 C2At1g16590~T9 [P3.1.1] T0156~T9 [P3.1.2] C2At3g24050~T9 C2At3g24010~T9 [P3.1.3] T1519~T9 C2At1g04530~T9 [P3.1.4] C2At3g23400~T9 [P3.1.5] C2At1g07310~T9 [P3.1.6] C2At1g05385~T9 C2At2g47580~T9 [P3.1.7] C2At4g03200~T9 C2At5g42740~T12 TG517~T3 C2At4g18593~T12 C2At3g13180~T12 C2At1g64770~T3 C2At5g62390~T3 TG130~T3 C2At3g63530~T3 C2At5g23880~T3 C2At1g51160~T3 C2At5g17170~T3 C2At3g03100~T3 C2At5g41040~T3 [P3.2.1] C2At5g52820~T3 C2At5g49970~T3 C2At5g23060~T3 [P3.2.2] C2At1g18660~T3 [P3.2.3] C2At1g80170~T3 [P3.2.4] C2At3g47640~T3 C2At1g16180~T3 C2At1g18270~T3 [P3.2.5] C2At3g13700~T3 [P3.2.6] C2At3g14075~T3 C2At3g20240~T3

  11. FIGURE S2 continued (Wu et al) T3 T4 P4 T0707~P5 E492334~P4 C2At4g18230~T3 0cM CD59 E492334~T3 Hba181H07SP6~P4 5 Hba181H07SP6~T3 C2At4g18230~P4 C2At2g01770~P5 TG135~T3 10 cLPT5E7~P4 15 cLPT5E7~T3 C2At3g51010~P5 20 C2At1g28530~P4 [P4.1.1] C2At3g17040~P5 C2At1g60560~P5 25 C2At2g39580~P5 C2At1g28530~T3 MboI077E18SP6~P4 C2At1g08630~P5 [P4.1.2] TG132~P4 30 MboI077E18SP6~T3 C2At4g25650~P5 [P4.1.3] 35 TG517~P3 C2At3g52155~P5 TG132~T3 T0635~P5 40 TG130~P3 C2At1g27385~P5 45 C2At4g39660~P12 C2At1g51160~P3 C2At1g05055~P1 50 C2At4g39870~P12 C2At1g65720~P4 C2At1g65720~T3 C2At1g65230~P12 C2At1g72030~P6 55 C2At1g77250~P4 C2At5g23880~P3 C2At3g63530~P3 60 C2At1g71810~P4 C2At1g02140~P2 65 C2At1g64770~P3 GPMS203 TG62~P4 C2At3g03100~P3 C2At1g78230~P4 NN11 70 C2At5g41040~P3 C2At4g09010~P4 C2At1g77250~T4 C2At5g62390~P3 C2At5g17170~P3 75 C2At1g09920~P4 C2At1g27530~P4 80 [P4.2.1] NN7 85 C2At3g16150~P4 90 C2At1g46480~P4 C2At1g71810~T4 C2At5g25900~P4 [P4.2.2] 95 TG62~T4 C2At5g52820~P3 100 C2At5g49970~P3 [P4.2.3] C2At5g23060~P3 105 C2At1g78230~T4 BM061461 C2At1g75350~P4 C2At4g09010~T4 110 [P4.2.4] C2At1g09920~T4 [P4.2.5] 115 C2At1g27530~T4 120 C2At1g20575~P4 [P4.2.6] C2At1g63610~P4 C2At1g18660~P3 C2At3g16150~T4 C2At1g42990~P4 125 T1933 C2At1g46480~T4 C2At1g80170~P3 130 C2At1g76080~P4 [P4.2.7] C2At3g47640~P3 135 C2At5g25900~T4 [P4.2.8] 140 C2At1g16180~P3 C2At1g75350~T4 [P4.2.9] C2At1g63610~T4 [P4.2.10] C2At1g18270~P3 145 C2At1g20575~T4 C2At1g42990~T4 CA523715 150 155 160 C2At1g76080~T4 C2At3g13700~P3 165 170 175 180 C2At3g14075~P3 C2At3g20240~P3

  12. P5 T5 P5 CT101~P11 C2At4g25650~T4 0cM C2At1g60440~P11 5 C2At3g52155~T4 C2At1g23890~P11 10 T0635~T4 C2At1g70160~P11 C2At2g39580~T4 15 C2At1g08630~T4 C2At1g60560~T4 20 C2At1g14790~P11 25 30 NN2 T0707~T4 35 C2At3g17040~T4 C2At2g01110~P11 C2At3g51010~T4 40 C2At1g13380~P11 C2At1g33970~T11 45 C2At2g01770~T4 50 C2At1g27385~T4 55 C2At2g46580~T5 Hpms2-45 60 C2At1g26520~P11 NN6 65 C2At1g69420~P11 70 C2At3g10920~T6 C2At1g27980~P11 U221402~T5 C2At1g67325~P11 C2At3g55800~T5 75 C2At2g46580~P5 C2At3g06440~T5 80 C2At4g12590~T5 85 6B11 U221402~P5 90 C2At3g55800~P5 95 C2At3g55360~T5 100 C2At3g06440~P5 105 CD74~T5 110 C2At4g12590~P5 C2At3g54860~T5 C2At5g04270~T5 115 C2At3g55360~P5 T0633~T5 120 CD74~P5 125 C2At3g54860~P5 C2At5g04270~P5 130 C2At1g79790~P12 T0633~P5 FIGURE S2 continued (Wu et al) T4 (partial, reversed) C2At1g27385~P5 [P5.1.1] T0635~P5 C2At3g52155~P5 C2At4g25650~P5 C2At1g08630~P5 C2At2g39580~P5 C2At1g60560~P5 C2At3g17040~P5 [P5.2.1] C2At3g51010~P5 C2At2g01770~P5 CD59 T0707~P5 [P5.3.1] [P5.3.2] [P5.3.3] [P5.3.4]

  13. T6 P6 C2At2g29630~P6 T1928 C2At4g01900~T6 0cM C2At1g07080~P6 C2At2g30100~P6 C2At1g72030~T3 C2At3g46780~P6 5 C2At3g25120~P6 C2At2g39690~T6 C2At2g39690~P6 10 C2At4g01900~P6 C2At3g10920~P5 15 C2At3g56130~P6 20 C2At3g56040~P6 25 C2At3g11210~P1 [P6.1.1] C2At1g06110~P6 30 35 C2At3g25120~T6 40 C2At1g44760~P6 C2At2g30100~T6 C2At1g03150~P6 C2At4g10030~P1 C2At3g46780~T6 45 C2At2g29630~T6 C2At1g79810~P6 C2At3g56130~T6 C2At1g73885~P6 50 C2At3g56040~T6 C2At5g07960~P6 55 C2At1g06110~T6 [P6.2.1] 60 C2At1g44760~T6 C2At1g24360~P6 65 70 CA516334 C2At2g43360~P6 75 80 C2At1g03150~T6 85 90 C2At1g18640~P6 C2At1g79810~T6 C2At1g73885~T6 95 C2At5g07960~T6 100 C2At1g16870~P6 C2At1g24360~T6 [P6.3.1] 105 C2At4g28530~P6 110 C2At2g43360~T6 C2At1g20050~P6 115 CA523558 120 125 C2At1g18640~T6 130 C2At1g07080~T6 C2At1g16870~T6 C2At4g28530~T6 135 C2At4g32280~T8 C2At1g20050~T6 140 FIGURE S2 continued (Wu et al)

  14. P7 T7 SSR241 C2At2g24270~P7 C2At2g18710~T7 0cM C2At2g18710~P7 C2At5g34850~P7 C2At4g30580~P7 5 C2At5g22010~T7 C2At5g22010~P7 C2At2g16060~P7 10 C2At4g30580~T7 15 20 C2At2g24270~T7 25 C2At5g20520~P7 CT135~P7 NN4 30 C2At4g33250~P7 35 CT135~T7 40 C2At5g14520~P7 C2At5g34850~T7 C2At4g26680~P7 C2At2g04842~P7 45 C2At2g16060~T7 C2At2g32970~P7 C2At4g33250~T7 C2At2g42750~P7 C2At5g20520~T7 50 C2At4g03210~P7 C2At2g32970~T7 C2At2g20860~P7 C2At4g26680~T7 55 C2At3g58790~P7 C2At5g14520~T7 C2At2g38020~P7 C2At2g04842~T7 C2At1g53670~P7 60 C2At1g78620~P7 65 C2At4g03210~T7 C2At3g14910~P7 70 C2At3g15290~P7 75 C2At2g20860~T7 C2At3g15430~P7 TG199~P7 80 85 C2At2g42750~T7 C2At4g26750~P7 90 95 C2At3g58790~T7 C2At1g55880~P7 100 C2At2g38020~T7 C2At1g78620~T7 105 C2At3g15290~T7 C2At3g14910~T7 C2At1g53670~T7 110 C2At1g55880~T7 C2At3g15430~T7 C2At1g55670~P7 115 C2At4g26750~T7 C2At1g55670~T7 120 T0463~P7 T0463~T7 TG199~T7 C2At5g48300~T12 FIGURE S2 continued (Wu et al) [P7.1.1] [P7.1.2] [P7.1.3] [P7.1.4] [P7.1.5] [P7.1.6] [P7.1.7] [P7.1.8] [P7.1.9] [P7.1.10] [P7.1.11]

  15. T9 P9 P9 T12 C2At5g06130~T9 GP39 0cM TM14B C2At2g37240~P9 5 C2At3g09920~T9 10 TG180~P9 C2At4g03280~P9 C2At3g09925~T9 15 C2At4g28830~P9 C2At3g09920~P9 20 25 C2At2g37240~T9 C2At3g09925~P9 C2At3g25910~P9 30 C2At5g19690~P9 35 C2At2g06530~P9 C2At5g06130~P9 C2At2g29210~T9 40 C2At5g58410~T9 GPMS163 C2At4g16710~P9 45 C2At1g11380~T2 C2At5g57970~P9 TG180~T12 50 C2At5g48300~P7 C2At4g03280~T12 C2At5g58410~P9 C2At4g11120~P9 55 C2At2g29210~P9 C2At5g42740~P3 60 C2At3g13180~P3 C2At4g03200~P3 C2At4g28830~T12 C2At4g18593~P3 65 C2At2g47580~P3 C2At3g24490~P12 C2At1g05385~P3 70 C2At1g17410~P12 C2At3g25910~T12 75 C2At1g07310~P3 80 T0801~P12 85 C2At3g23400~P3 90 T1519~P3 C2At5g19690~T12 95 C2At1g04530~P3 C2At4g16580~P12 C2At3g24050~P3 C2At4g33360~P12 100 C2At1g76150~P12 C2At3g24010~P3 T0156~P3 C2At5g38530~P12 105 C2At2g06530~T12 C2At4g31150~P12 110 115 C2At1g48300~P12 C2At1g16590~P3 120 C2At5g57970~T12 125 C2At4g16710~T12 T0800~P12 TG350~P12 130 135 140 C2At4g11120~T12 FIGURE S2 continued (Wu et al) [P9.1.1] [P9.1.2] [P9.2.1] [P9.2.2] [P9.2.3] [P9.2.4] [P9.2.5]

  16. P10 T10 C2At3g13235~T10 C2At3g13235~P10 0cM TG395~T10 [P10.1.1] 5 TG619 TG395~P10 10 C2At5g60990~T10 15 C2At5g60990~P10 20 25 C2At4g03400~P10 [P10.1.2] 30 NN5 C2At2g46340~P10 U217183~P10 35 40 C2At5g01990~P10 C2At4g03400~T10 C2At3g08760~P10 45 C2At1g67740~P10 50 [P10.1.3] C2At5g01990~T10 55 C2At3g57270~P10 C2At2g46340~T10 C2At3g08760~T10 60 U217183~T10 GPMS159 65 C2At4g30220~P10 C2At3g51840~T10 70 C2At5g01350~T10 75 CD32~T10 C2At3g51840~P10 80 85 CD32~P10 90 C2At5g01350~P10 GP1078 [P10.2.1] 95 100 CT57 105 C2At4g30220~T10 110 [P10.2.2] 115 C2At3g57270~T10 120 125 130 C2At1g67740~T10 FIGURE S2 continued (Wu et al)

  17. T5 T11 P11 CT101~P11 C2At1g60440~P11 C2At5g09880~P12 0cM C2At2g01110~T5 C2At5g64730~P12 5 C2At1g23890~P11 C2At1g13380~T5 C2At1g70160~P11 10 [P11.1.1] 15 C2At4g15010~P12 NN3 C2At2g28600~P12 20 C2At1g14790~P11 C2At3g54840~P12 25 C2At1g26520~T5 C2At3g60830~P12 [P11.1.2] C2At1g69420~T5 30 T0408~P12 35 GP20064 C2At5g16630~P12 C2At2g01110~P11 C2At5g16710~P12 C2At1g13380~P11 40 C2At4g22260~P12 C2At1g14790~T5 C2At3g52640~P12 CA519548 [P11.2.1] 45 C2At1g79260~P12 C2At1g21690~P12 GP20087 50 C2At1g70160~T5 [P11.2.2] CT101~T5 C2At1g67325~T5 55 C2At1g23890~T5 C2At1g60440~T5 C2At1g26520~P11 60 C2At1g27980~T5 GP20117 C2At1g33970~P5 65 C2At5g04590~T11 C2At1g69420~P11 C2At5g59960~T11 C2At1g51350~T11 C2At1g51350~P11 70 C2At1g27980~P11 C2At2g28800~T11 C2At5g04590~P11 C2At1g67325~P11 C2At2g28490~T11 C2At2g28800~P11 C2At2g46580~P5 75 C2At3g44890~P11 80 C2At3g44600~P11 85 U221402~P5 90 C2At2g27450~P11 C2At2g27450~T11 C2At5g60540~P11 C2At3g55800~P5 95 C2At2g28250~P11 TG36~P11 C2At3g44600~T11 100 [P11.3.1] C2At3g06440~P5 C2At5g11550~P11 C2At3g44890~T11 105 C2At5g60540~T11 C2At5g11550~T11 C2At4g12590~P5 110 C2At2g28250~T11 C2At2g28490~P11 [P11.4.1] 115 C2At3g55360~P5 TG36~T11 120 C2At5g59960~P11 CD74~P5 C2At3g54860~P5 C2At5g04270~P5 C2At1g79790~P12 T0633~P5 FIGURE S2 continued (Wu et al 2008)

  18. T11(reversed,partial) P12 C2At4g22260~T11 C2At1g21690~P12 0cM C2At1g79260~T11 C2At1g79260~P12 C2At3g52640~T11 5 C2At3g52640~P12 C2At4g22260~P12 C2At5g16630~T11 C2At5g16710~P12 [P12.1.1] 10 C2At5g16630~P12 C2At5g16710~T11 15 T0408~P12 T0408~T11 20 [P12.1.2] C2At3g60830~P12 GP20056 C2At3g54840~P12 25 C2At3g60830~T11 [P12.1.3] C2At3g54840~T11 30 C2At2g28600~P12 NN10 C2At4g15010~P12 [P12.1.4] 35 C2At2g28600~T11 40 C2At4g15010~T11 [P12.1.5] C2At5g64730~P12 45 C2At5g64730~T11 C2At5g09880~P12 C2At5g09880~T11 50 C2At3g24490~T12 C2At4g39660~T4 55 C2At4g39870~T4 C2At1g65230~T4 C2At1g79790~T5 60 T0801~T12 [P12.2.1] CP10131a 65 C2At1g17410~T12 GP1017 70 75 C2At4g33360~T12 80 C2At4g16580~T12 85 [P12.3.1] 90 C2At1g76150~T12 95 C2At1g21690~T11 C2At5g38530~T12 100 C2At4g31150~T12 105 [P12.4.1] 110 C2At1g48300~T12 115 [P12.4.2] T0800~T12 120 TG350~T12 125 FIGURE S2 continued (Wu et al) T12 TM14B TG180~P9 C2At4g03280~P9 C2At4g28830~P9 C2At3g25910~P9 C2At5g19690~P9 C2At2g06530~P9 C2At4g16710~P9 C2At5g57970~P9 C2At5g48300~P7 C2At4g11120~P9 C2At5g42740~P3 C2At3g13180~P3 C2At4g18593~P3 C2At3g24490~P12 C2At1g17410~P12 T0801~P12 C2At4g16580~P12 C2At4g33360~P12 C2At1g76150~P12 C2At5g38530~P12 C2At4g31150~P12 C2At1g48300~P12 T0800~P12 TG350~P12

  19. Figure S3 – Prediction of COSII Markers onto the Pepper Genetic Map based on Pepper-tomato Synteny. Markers on the right were placed by genetic mapping (as shown in Figure 1 and with the same legend); markers in bold or bold italic on the left are Synteny Marker Pairs (SMPs) used for prediction; other markers on the left were mapped on the tomato map and then predicted onto the pepper map based on pepper-tomato synteny (refer to Results & Discussion); Red markers on the left were first predicted and then mapped actually to verify the prediction (see their actual map positions on the right).Tick marks either connect to the actual map positions (for framework markers) or estimated positions (for interval markers; refer to Materials & Methods). Consegregating markers are placed in one line and delimited by comma. Black dots indicate the putative centromeres (refer to Results & Discussion).

  20. Figure S3 (Wu et al) P1 C2At1g63980 0cM CACCEL1i 5 C2At5g41350 10 C2At4g11570, C2At1g32900 C2At1g32900 15 C2At5g60620 TG194 20 C2At4g23840 C2At4g23840 25 30 C2At1g63260 35 40 C2At4g12230 45 TG510 C2At5g13200 50 C2At5g47010 C2At3g18860 C2At1g32410 55 C2At1g32410 BM067271 60 C2At4g19003 65 C2At4g19003 70 C2At2g35610 C2At3g45900 75 C2At2g45620 C2At2g45620 80 C2At2g45670 85 C2At3g61140 C2At3g61140 90 C2At4g00740 95 C2At5g51970 C2At5g51970 C2At5g13030 Hpms1-281 100 C2At3g22660 C2At2g34860 C2At5g53000 C2At3g12685 105 C2At2g34860 Hpms1-41 110 C2At3g12685 C2At3g06790 C2At1g14310 115 C2At4g10030 120 C2At5g13450 C2At1g05055 C2At2g45910 125 CA526211 C2At4g01210 130 C2At4g01880 C2At5g41760 C2At3g23590 C2At3g12300 135 C2At5g18590 ,Skdh-1 C2At2g38730 Pgm-2 140 C2At3g06730 GP1049 C2At5g09860 145 C2At1g14810 ,C2At3g11210 C2At3g04710 Idh-1 C2At1g54460 150 C2At5g45680 C2At3g04780 CP10020 155 TG83 GP20095 C2At1g54520 160 C2At5g11490 ,GP20062 C2At1g54500 C2At5g11480 165 C2At3g04870 C2At5g25630 C2At1g08820 170 C2At4g00560 C2At5g27380 CT77 C2At1g09070 175 C2At2g45910 C2At4g29120 180 C2At5g27720, C2At3g05510 C2At5g27620 185 C2At3g62630 C2At4g11060, C2At3g46940, C2At3g62450 190 C2At3g06730 C2At5g06760 Hpms1-139 195 C2At1g56345 TG83 C2At1g02560 200 TG19 C2At1g56700 CP10060 205 C2At5g26760 C2At1g09070 C2At3g05810 C2At1g02560 210 C2At5g02270 CP10061 C2At1g56500 215 C2At3g53010 NN1 220 C2At5g26680 AF039662 C2At5g49880 225 C2At5g64350 C2At1g10240 C2At3g19630 230 C2At1g09830 C2At4g22200 235 C2At1g33270 C2At1g25260 C2At4g34350 240 C2At4g14110 245 C2At1g12680 C2At4g34700 C2At5g64350 250 C2At5g09580 C2At2g16920 C2At1g50020 C2At3g19630 C2At3g19650 C2At2g14835 C2At3g19230, C2At1g49510, C2At3g19370, C2At3g19260, C2At2g15290 C2At2g15890 C2At2g14910 C2At2g15320 C2At4g34190 C2At4g34350

  21. P2 C2At5g44200 C2At5g44200 0cM 5 C2At3g51140 C2At3g51140 10 C2At1g02140, C2At1g30540 C2At5g08540, C2At3g28670, C2At5g08580 C2At3g19800 15 C2At1g30540 20 Hpms1-143 25 C2At5g19130 C2At5g19130 30 C2At3g51520 35 C2At3g51510 C2At4g20070 C2At1g78690 C2At1g78690 40 CT232 C2At2g35130 GP20031 45 C2At4g19830 C2At4g20410 C2At5g08420 50 C2At1g30360 C2At4g20410 55 C2At2g34560 CT128 60 C2At4g18060 C2At4g18060 U223436 65 U223436 C2At4g21710 70 C2At4g21710 C2At1g10580 C2At4g04955 75 C2At4g04955 C2At1g11430 80 BD076366 85 C2At5g37260 C2At3g51130 pun1 90 C2At4g36380 C2At5g66530, C2At4g35560 C2At3g54350 95 CP10081, C2At5g66090 C2At4g36530 C2At3g51130 100 Ovate Ovate C2At4g37280 C2At5g67530 105 C2At4g34090 C2At4g37280 C2At4g37300 110 C2At5g67530 C2At5g67370 C2At5g37850 115 C2At4g33985 C2At4g37130 C2At4g37130 C2At1g20770 120 C2At2g23750 C2At3g02220 C2At1g19690 125 C2At2g04690 C2At3g02300 C2At2g04700 130 C2At5g15410 C2At3g01480 C2At3g01180 135 C2At5g40530 C2At1g20770 C2At3g27200 C2At3g28720 140 C2At3g01360 C2At1g67730 C2At3g28050 C2At2g04690 C2At5g02850 C2At2g04700 Figure S3 continued (Wu et al)

  22. P3 C2At1g16590 C2At3g24160 C2At1g16590 0cM C2At2g32760 C2At1g09815 5 T0156 T0156 C2At3g24050 C2At3g24050 10 T1519 C2At3g24010 15 T1519 C2At3g16840 C2At1g04530 C2At3g23490 20 C2At5g35620 C2At3g23400 25 C2At3g23400 C2At1g07310 C2At1g07310 30 C2At5g43650 C2At1g04190 35 C2At2g47590 C2At1g05385 40 C2At2g47580 C2At2g47580 C2At4g03200 45 BM059622 C2At5g57170 C2At4g03200 C2At2g40760 50 C2At5g15240 C2At5g42740 C2At5g05990 55 TG517 C2At5g51110 C2At4g18593 C2At3g49260 60 C2At2g43770, C2At5g38880 C2At3g13180, C2At1g64770 C2At3g17810 C2At5g62390 65 C2At5g06160, C2At1g73820 TG130 C2At1g07020 C2At3g10220 70 C2At3g63530 C2At4g17300, C2At4g39630 C2At5g23880 C2At3g48610 75 C2At1g51160 C2At5g63460, C2At5g63380, C2At5g60160 C2At1g05350 80 C2At3g48330 ComT C2At1g74730 85 C2At5g13050 C2At1g07830 90 C2At5g17170 C2At3g47990 C2At3g03100 C2At5g23060 95 C2At5g41040 C2At5g08050 100 C2At1g61620 C2At1g18660 105 C2At1g74520 C2At5g52820 C2At5g62440 110 C2At1g74470 C2At5g49970 115 C2At3g15760 C2At5g23060 C2At1g80170 C2At1g18660 120 C2At1g52590 C2At1g80170 125 C2At5g24170 C2At3g47640 C2At1g80460 C2At1g16180 130 C2At1g16080 C2At1g79720 C2At1g18270 C2At1g16080 135 C2At3g13700 C2At1g09760 BM062655 140 C2At5g51040 C2At3g14075 C2At3g17970, C2At1g18270 145 C2At3g18270 C2At3g20240 C2At3g18520 C2At1g68660 C2At1g79910 C2At1g80360 C2At1g79840 C2At2g42110 C2At1g55170 C2At3g21360, C2At1g52080, C2At3g21300, C2At1g51730 C2At3g13700 C2At3g13800 C2At1g54050 C2At3g14200 C2At3g21215, C2At5g49830 C2At3g14075 Figure S3 continued (Wu et al)

  23. P4 C2At4g18230 E492334 0cM Hba181H07SP6 5 TG135 10 pvr1 15 cLPT5E7 cLPT5E7 20 C2At1g28530 C2At1g28530 25 30 MboI077E18SP6 MboI077E18SP6 35 TG132 TG132 40 45 50 C2At1g65720 55 Hpms1-165 60 GPMS203 65 NN11 70 C2At1g77250 C2At1g77250 75 C2At1g22860 80 NN7 85 C2At1g71810 90 C2At1g43580 C2At1g71810 TG62 95 TG62 C2At4g09040 100 C2At4g09010 CAN130829 C2At1g78230 C2At1g09700 105 BM061461, C2At4g09010 C2At5g10920, C2At1g27530 110 C2At1g09920 C2At1g10030 115 C2At3g03990 C2At1g27530 C2At1g46480 Bcat 120 C2At4g33350 C2At3g16150 125 C2At2g26540 C2At1g46480 C2At5g25900 130 C2At1g74970 C2At5g25900 C2At1g19340 135 CA847580 C2At5g42950 C2At5g42950 C2At1g75350 140 C2At1g19600 C2At1g63610 C2At1g75350 C2At1g20575 145 C2At2g26350 C2At1g42990 C2At2g45730 150 CA523715 C2At1g30755 155 C2At5g40610 C2At1g20575 C2At1g76080 Figure S3 continued (Wu et al)

  24. P5 C2At4g25650 C2At4g25650 0cM C2At5g50720 5 C2At5g37290 C2At3g52155 C2At3g52155 10 T0635 C2At2g39580 C2At2g39580~T4 15 C2At1g08630 20 C2At1g60560 C2At2g20390 25 CelB004 30 C2At1g08640 NN2 T0707 35 C2At3g17040~T4 C2At3g17040 40 C2At3g51010 C2At1g33970 45 C2At2g01770 50 C2At1g27385 55 Hpms2-45, C2At2g46580 60 NN6 65 C2At3g10920 70 U221402 U221402 C2At5g05270 75 C2At3g55800 C2At2g39950 C2At3g06440 C2At2g38140 80 C2At4g12590 C2At3g06440 85 C2At3g17210 6B11 C2At5g49510 90 C2At2g31970 95 C2At3g55360 C2At3g55360 100 105 CD74 CD74 110 C2At3g54860 C2At3g54860 C2At5g04270 115 T0633 Figure S3 continued (Wu et al)

  25. P6 C2At4g01900 0cM C2At1g72030 5 C2At2g39690 C2At2g39690 10 15 20 25 30 35 C2At3g25120 40 C2At2g28690, C2At2g30100 C2At2g30100 C2At3g46780 45 C2At2g29630 50 C2At3g56130 C2At1g06110 C2At3g56040 55 C2At1g21640 C2At1g06110 C2At1g44835 60 C2At1g44760 C2At1g77470 65 C2At1g44575 C2At1g44760 70 CA516334 75 80 C2At1g03150 85 90 C2At1g79810 C2At1g73885 95 C2At5g07960 100 C2At1g24360 C2At1g24360 105 C2At1g12060 110 C2At2g43360 C2At2g43360 115 CA523558 120 GPMS178A C2At1g18640 125 CA516044 130 C2At1g07080 C2At1g16870 135 C2At4g28530 C2At4g32280 140 C2At1g20050 Figure S3 continued (Wu et al)

  26. Figure S3 continued (Wu et al 2008) P7 C2At2g18710 0cM 5 C2At5g22010 C2At5g22010 10 C2At4g30580 C2At4g30580 15 20 C2At2g24270 GP1102 25 C2At1g14850, C2At2g16060, NN4 30 C2At5g20180 asu5 C2At5g56940 35 C2At4g24820 CT135 C2At5g34850 C2At2g26590 40 C2At2g16060 C2At3g43230 45 C2At2g06925 C2At4g33250 C2At4g29490, C2At5g20520, C2At5g20520 50 C2At3g26060 C2At1g19140 C2At2g32970 55 C2At3g13050 C2At4g26680, C2At5g14520 C2At3g26060 C2At2g04842 60 C2At4g31040 C2At2g30520 65 C2At4g26680 C2At4g03210 70 C2At2g04842 C2At2g04780 75 C2At2g20860 C2At2g20690 C2At3g21870 80 C2At2g20830, C2At1g03820, C2At3g21820, 85 C2At1g03600 C2At2g42750 C2At3g58790 90 C2At4g15420 C2At3g58790 95 C2At2g42810 C2At2g38020 C2At1g17200 C2At1g78620 100 C2At2g38020 C2At3g15290 C2At3g14770 105 C2At3g14910 C2At1g78620 C2At1g53670 110 C2At1g16900 C2At1g55880 C2At3g15290 C2At3g15430 115 C2At1g52980 C2At4g26750 120 C2At3g15380 C2At1g55670 C2At1g02180 T0463 C2At5g54310 TG199 C2At1g04970 C2At5g48300 C2At1g50575 C2At4g16450 C2At1g55870 C2At1g55840 C2At1g56050, C2At5g56130, C2At1g55670 T0463

  27. P8 R45S-C C2At4g31130 0cM C2At2g24390 C2At1g31410 5 C2At3g52860 C2At3g52860 10 15 C2At5g19940, C2At2g24580 NN8 NN9 20 25 C2At4g17380 C2At4g17380 Figure S3 continued (Wu et al)

  28. P9 C2At5g06130 C2At5g06130 0cM C2At3g52610 C2At3g10070 5 C2At5g11560 C2At3g09920 10 C2At3g09925 C2At2g36720 C2At3g09925 15 C2At2g32600 C2At2g41680 20 GPMS171 C2At2g37025 25 C2At2g36930 C2At2g37240 C2At2g37240 Hpms1-117, Hpms1-3 30 CelA015 35 Hpms2-41 C2At2g29210 40 C2At5g58410, GPMS163 C2At1g11380 45 TG180 TG180 50 C2At4g03280 C2At4g03280 55 C2At1g78600 60 C2At5g35690, C2At4g28830 C2At4g28830 65 C2At2g32950 70 C2At3g25910 C2At3g25910 75 80 85 90 C2At5g19690 C2At5g19690 95 100 C2At4g29735, C2At4g26180 105 C2At2g06530 C2At2g06530 110 115 120 C2At5g57970 125 C2At4g16710 130 135 140 C2At4g11120 Figure S3 continued (Wu et al)

  29. P10 C2At5g44650, C2At3g21610, C2At2g46820, C2At3g20390, C2At3g13235, C2At3g13235 0cM C2At1g04950 TG395 C2At3g01440 5 TG619 C2At5g06430 10 C2At1g53000 C2At5g60990 C2At5g60990 15 20 25 C2At4g28290 30 NN5 35 40 C2At4g03400 C2At4g03400 45 C2At4g04930 50 C2At2g33990 C2At2g46370 55 GP20068 C2At1g01730 C2At5g01990 60 C2At3g60080 C2At5g04910, C2At1g11750, C2At5g36210, C2At2g46340 C2At3g08760 C2At4g35070 U217183 65 C2At5g01010 GPMS159 C2At3g08760 70 C2At3g51840 C2At5g01350 75 C2At2g37330, CD32 CD32 80 C2At2g37510 85 90 C2At3g09740 GP1078 95 CA516439 100 C2At3g58470 CT57 105 C2At4g30220 C2At4g30220 C2At3g12290 110 C2At5g04200 C2At5g04200 Hpms2-21 115 C2At3g54360 C2At1g67660 C2At3g57270 120 C2At4g37510, C2At3g57270 125 130 C2At1g67740 Figure S3 continued (Wu et al)

  30. P11 C2At2g01110 C2At1g25375 C2At2g01110 0cM C2At1g25580 C2At3g25690 5 C2At1g13380 C2At3g55120 NN3 C2At4g24830 10 C2At1g69210 C2At1g26520 C2At1g69210 C2At1g69420 15 C2At2g03510 CelB147 C2At1g26520 20 GP20064 C2At1g28140 25 C2At1g26670, C2At1g14000, C2At1g14790 C2At1g26660 30 CA519548 C2At1g29150 GP20087 C2At1g69420 35 C2At1g70160 C2At1g14790 40 CT101 C2At1g26945 C2At1g67325 45 C2At1g07040 C2At1g23890 C2At1g27050 C2At1g60440 50 C2At1g24340 C2At1g27980, GP20117 55 C2At1g70160 GP20036 C2At5g14320 C2At5g04590 60 C2At1g60200 C2At5g59960 CT101 65 C2At1g51350 70 C2At2g28800 C2At2g28490 75 80 85 90 C2At2g27450 95 C2At3g44600 C2At3g44600 100 C2At3g44890 C2At3g44890 C2At5g60540 105 C2At5g11550 C2At2g28250 110 C2At2g28250 C2At5g11810 ,C2At1g07960 C2At3g52090 115 TG36 TG36 Figure S3 continued (Wu et al)

  31. P12 C2At4g22260 0cM C2At1g79260 C2At3g52640 5 C2At5g16630 C2At5g16630 C2At5g16710 10 T0408 15 GP20056 T0408 C2At3g60830 20 C2At3g54840 25 GP1127 C2At3g60830 NN10 C2At3g54840 30 C2At2g28600 C2At5g04420 C2At4g15010 35 C2At3g52180 C2At5g64730 C2At3g52220 40 C2At5g09880 C2At4g15010 45 C2At3g24490 50 C2At5g09880 C2At4g39660, C2At4g39870 C2At1g79790, C2At1g65230 55 T0801 T0801 CP10131a 60 CP10023 C2At1g17410 65 C2At1g17410 GP1017 70 75 C2At4g33360 80 C2At4g16580 C2At4g16580 85 90 C2At1g76150 C2At1g76150 95 C2At1g21690 C2At5g38530 100 C2At4g31150 C2At4g31150 105 110 C2At1g48300 C2At1g48300 C2At1g48310 115 C2At3g06610 C2At3g17000 120 T0800 T0800 TG350 Figure S3 continued (Wu et al)

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