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Table 4 Physical and genetic locations of BAC clones hybridized to potato chromosome 5

From: Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin

Chromosomal arm (a) BAC clone Figure Color Physical location (FL) (b) MTP Haplotype (e) AFLP marker (number/name) Genetic position (bin number) (f)
5 L (EC) RH042N03 1,2 Yellow 0.40 ± 0.06 4846 0 20179 EAAGMACC_272 4
5 L (EC) RH201A02 1,2 Blue 1.14 ± 0.30 1070 0    (4)
5 L (EC) RH081B09 1,2 Green 2.70 ± 0.42 2129 0 7241 EAACMCAG_149.7 4
5 L (EC) RH199B23 1,2 Yellow 3.20 ± 0.66 3171 -    
5 L (EC) RH202I20 1,2 Red 5.00 ± 0.42 6457 0 7202 EAGGMAGA_385 1-4
5 L (EC) RH133F12 1,2 Magenta 5.88 ± 0.35 25 0 7235 EATCMCTC_236.2 4
5 L (EC) RH043P07 1,2 Green 7.01 ± 0.33 941 1    (12)
5 L (EC) RH133I18 1,2 Blue 8.52 ± 0.37 382 0 7260 PGA/MATG_101.5 12
5 L (EC) RH085N22 1,2 Magenta 8.66 ± 0.76 1015 1 7265 EACAMACC_361.6 16
5 L (EC) RH052G17 1,2 Red 10.07 ± 0.85 2478 0 20145 EAACMCTT_435H 16-17
5 L (EC) RH095I08 1,2,3 Green/Blue 12.71 ± 1.15 1015 1 7280 EAACMAGG_167 21
5 L (EC) RH052M07 1,2 Yellow 13.46 ± 1.13 903 0 7287 CAAGMCAT_174.6 26-27
5 L (EC) RH035K21 1,2 Blue 16.64 ± 2.34 (c)     
5 L (EC) RH082N16 1,2 Magenta 16.64 ± 2.34 1382 M    
5 L (EC) RH196F10 1,2 Red 19.51 ± 1.25 178 M    
5 L (EC) RH076O08 1,2 Blue 20.66 ± 1.32 799 1 20640 EAGAMACC_230 37
5 L (EC) RH103P18 1,2 Green 21.76 ± 1.04 1841 M    
5 L (EC) RH078E16 1,2 Red 23.02 ± 1.27 1800 1 7296 EAGGMACA_500 37
5 L (EC) RH085C18 1,2 Blue 25.21 ± 2.02 1114 0    (37)
5 L (HC) RH167O23 1,2 Yellow 24.76 ± 0.51 3004 1 11894 EATCMCAG_17H 37
5 L (HC) RH176P24 1,2 Magenta 25.21 ± 2.02 672 0    (46–47)
5 L (HC) RH017I02 1,2 Red 25.67 ± 2.33 672 0    (46–47)
5 L (HC) RH048J07 1,2 Yellow 35.34 ± 2.78 1685 1 12427 EAGGMAAG_2H 47
Centromere   1,2,3 Asterisk 41.67      
5S (HC) RH056O13 1,2 Magenta 45.11 ± 2.68 5325 1 11936 EACAMACC_270.9H 46-47
5S (HC) RH071D16 1,2 Green 46.78 ± 2.45 3424 0 7590 EAGTMAGC_997 46
5S (HC) RH102K09 3 Green 47.86 ± 2.38 1645 1 12129 EAGAMCCT_586.0H 46
5S (HC) RH138C23 3 Magenta 47.93 ± 2.00 1645 1    (46–47)
5S (HC) RH095M08 3 Yellow 51.94 ± 2.13 1054 0 7392 EAAGMCAT_15 45
5S (HC) RH193O24 3 Red 52.03 ± 2.45 1054 0    (47)
5S (HC) RH013O07 1,2 Red 57.28 ± 1.74 (d)     (46–47)
5S (EC) RH089A21 1,2 Blue 60.68 ± 1.87 6472 1 12520 EACTMCTA_188.9H 55
5S (EC) RH044A21 1,2 Magenta 68.57 ± 1.80 4210 0 7626 EAACMCTC_205 60
5S (EC) RH136O01 1,2 Green 70.33 ± 1.47 6915 0 7629 EAAGMCTT_144.9 65
5S (EC) RH028L14 1,2 Blue 71.12 ± 1.98 6915 0    
5S (EC) RH144F10 1,2 Yellow 72.16 ± 1.14 6915 0 7631 CATAMCCA_322.3 66-69
5S (EC) RH060F21 1,2 Green 73.51 ± 0.84 6844 M    
5S (EC) RH093O07 1,2 Yellow 74.36 ± 1.14 429 0    
5S (EC) RH089M16 1,2 Magenta 75.42 ± 1.17 6844 1 12569 EATCMCTC_27H 78
5S (EC) RH075N11 1,2 Red 76.70 ± 0.93 648 0 7651 EAGTMCCA_208.5 78
  1. (a) 5 L = long arm; 5S = short arm; EC = euchromatin; HC = heterochromatin.
  2. (b) Physical location (= fraction length) was calculated as (S/T)binT, where S = the distance in μm from the FISH hybridization site to the north end of Chr-5, T = the total length of Chr-5 in micrometer, binT = the total bin value (78) of Chr-5.
  3. (c) Unsequenced BAC clone aligning to DM superscaffold PGSC0003DMB000000210.
  4. (d) Unsequenced BAC clone with marker GP188 and aligning to DM superscaffold PGSC0003DMB000000328.
  5. (e) ‘-’ = haplotype undetermined; M = monomorphic region (i.e. no difference between haplotypes).
  6. (f) Bin numbers in brackets are from AFLP anchors in adjacent BAC clones in the RH physical map. Bin values for AFLP markers can deviate slightly from the true bin value due to missing scores, e.g. in practice markers mapped to the bin 45–47 region all belong to the bin 46 segment of the genetic map.