View Full Table | Close Full ViewTable 1.

Information on the individual mapping population data used for consensus map construction.

 
Population Abbreviation Growth habit† Type‡ No. of lines (before curation) No. of lines (after curation) No. of SNPs§ assayed No. and percentage of polymorphic SNPs Reference
Oregon Wolfe Barley created with the Hordeum bulbosum L.-based approach OWBH.b. S × S DH 93 82 4596 1469 (32%) Costa et al., 2001; BarleyWorld. 2006
Steptoe × Morex 1 SM1¶ S × S DH 93 92 4596 1215 (26%) Kleinhofs et al., 1993; USDA-ARS, 2011b
Morex × Barke MB S × S DH 94 93 4596 1574 (34%) N. Stein, personal communication, 2010
Haruna Nijo × OHU602 HO S × W DH 100 94 1536 759 (49%) Sato and Takeda, 2009
Steptoe × Morex 2 SM2 S × S DH 150 146 3060 835 (27%) Kleinhofs et al., 1993; USDA-ARS, 2011b
Anther culture-derived Oregon Wolfe Barley OWBA.C. S × S DH 94 93 3072 1271 (41%) Cistué et al., 2011
Haruna Nijo × Akashinriki HA S × S DH 68 54 1536 734 (48%) Sato et al., 2011a
Mikamo Golden × Harrington MH S × S DH 95 91 1536 491 (32%) Zhou et al., 2011
Vlamingh × Buloke VB S × S DH 347 289 1536 440 (29%) D. Moody, unpublished data, 2010
Foster × CIho 4196 FC S × S F8–9 RIL 94 89 1524 409 (27%) Horsley et al., 2006
Igri × Dobla ID W × F DH 106 102 1536 446 (29%) M.P. Vallés, unpublished data, 2010
Total 1250 1133
Growth habit of the parental genotypes used for the cross (S, spring barley; W, winter barley; F, facultative).
DH, doubled haploid; RIL, recombinant inbred line.
§SNP, single nucleotide polymorphism.
SM1 is subset of SM2.



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Distribution of single nucleotide polymorphism loci in the individual component maps and the consensus map.

 
Chromosome
Map† Characteristic 1H 2H 3H 4H 5H 6H 7H All
OWBH.b. Markers 153 225 240 206 262 191 191 1468
Bins 64 71 89 57 86 59 64 490
cM‡ 154.0 179.3 199.3 123.4 229.0 150.8 195.3 1231.1
SM1 Markers 139 211 233 125 217 119 171 1215
Bins 46 57 62 48 78 41 56 388
cM 138.9 146.6 154.7 141.5 187.3 151.5 140.8 1061.3
MB Markers 208 259 236 142 285 205 238 1573
Bins 60 72 77 41 74 51 64 439
cM 133.7 151.9 178.0 138.2 194.7 133.8 158.9 1089.2
HO Markers 97 135 128 97 116 98 88 759
Bins 47 63 59 48 63 44 47 371
cM 141.4 166.5 158.0 126.9 182.6 122.0 185.4 1082.8
SM2 Markers 99 154 162 84 149 75 112 835
Bins 50 61 69 49 80 36 59 404
cM 133.8 136.9 151.2 127.3 179.9 158.3 134.8 1022.2
OWBA.C. Markers 134 189 207 179 224 174 164 1271
Bins 70 78 76 65 72 51 73 485
cM 178.1 185.1 198.9 151.1 189.9 139.5 215.2 1257.8
HA Markers 86 125 120 100 127 88 88 734
Bins 34 46 35 26 52 31 35 259
cM 155.6 180.6 149.4 100.4 190.1 132.4 157.0 1065.5
MH Markers 49 82 99 55 65 76 65 491
Bins 26 39 34 26 35 28 33 221
cM 122.1 152.9 154.0 117.9 161.8 103.6 150.1 962.4
VB Markers 32 94 41 76 89 42 66 440
Bins 26 72 34 55 58 29 56 330
cM 145.0 197.8 180.7 145.3 207.5 137.9 198.7 1212.9
FC Markers 51 86 65 48 52 50 57 409
Bins 33 45 38 33 30 29 33 241
cM 126.2 167.3 146.2 113.6 139.8 102.4 161.0 956.6
ID Markers 50 71 95 49 73 68 40 446
Bins 27 39 38 30 39 35 22 230
cM 147.5 191.3 148.4 136.2 165.1 132.4 199.6 1120.5
Mean cM 143.3 167.7 165.4 129.2 184.3 133.1 172.4 1095.5
Consensus Markers 345 491 487 359 540 357 415 2994
Bins 145 191 180 155 198 126 168 1163
cM 143.2 172.9 180.1 146.5 189.9 142.2 162.5 1137.3
FC, Foster × CIho 4196; HA, Haruna Nijo × Akashinriki; HO, Haruna Nijo × OHU602; ID, Igri × Dobla; MB, Morex × Barke; MH, Mikamo Golden × Harrington; OWBA.C., anther culture-derived Oregon Wolfe Barley; OWBH.b., Oregon Wolfe Barley created with the Hordeum bulbosum-based approach; SM1, Steptoe × Morex 1; SM2, Steptoe × Morex 2; VB, Vlamingh × Buloke.
Centimorgans estimated using the Kosambi function.



View Full Table | Close Full ViewTable 3.

Comparison of the new single nucleotide polymorphism (SNP)-based consensus genetic map with the Close et al. (2009) consensus map.

 
Close et al. (2009) New consensus map
Number of individuals 373 1133
Number of SNPs 1H 341 345
2H 485 491
3H 475 487
4H 338 359
5H 535 540
6H 352 357
7H 417 415
Total 2943 2994
Number of bins 1H 125 145
2H 161 191
3H 152 180
4H 113 155
5H 180 198
6H 111 126
7H 133 168
Total 975 1163



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Leave-one-out population analysis for the consensus genetic map.

 
Population left out† Consensus genetic map Percent reduction in the number of bins Percent reduction in marker inclusion
Bins Markers
FC 1135 2953 2.4 1.4
HA 1174 2977 –0.9 0.6
HO 1140 2983 2.0 0.4
ID 1151 2987 1.0 0.2
MB 1121 2726 3.6 9.0
MH 1153 2989 0.9 0.2
OWBA.C 1103 2990 5.2 0.1
OWBH.b. 1087 2880 6.5 3.8
SM1 1150 2891 1.1 3.4
SM2 1139 2994 2.1 0.0
VB 1118 2989 3.9 0.2
None 1163 2994 NA NA
Population left out of the construction of the consensus genetic map. FC, Foster × CIho 4196; HA, Haruna Nijo × Akashinriki; HO, Haruna Nijo × OHU602; ID, Igri × Dobla; MB, Morex × Barke; MH, Mikamo Golden × Harrington; OWBA.C., anther culture-derived Oregon Wolfe Barley; OWBH.b., Oregon Wolfe Barley created with the Hordeum bulbosum-based approach; SM1, Steptoe × Morex 1; SM2, Steptoe × Morex 2; VB, Vlamingh × Buloke.



View Full Table | Close Full ViewTable 5.

Genes mapped using flow-sorted chromosome or arms and genetic maps.

 
Method of mapping
Chromosome Arm Flow-sorted chromosomes or arms Genetic map Unique to flow-sorted chromosome or arms Correspondence between flow sorting and genetic mapping
1H NA 432 345 116 316
2H 2HS 153 157 21 129
2HC† 32 38 NA 32
2HL 275 296 27 248
2HB‡ 3 NA 1 2
3H 3HS 118 128 12 102
3HC† 62 69 0 62
3HL 270 290 28 243
4H 4HS 116 104 18 97
4HC† 25 30 0 25
4HL 202 225 15 186
5H 5HS 95 85 12 81
5HC† 34 43 NA 34
5HL 370 412 45 325
5HB‡ 14 NA 1 11
6H 6HS 113 117 11 101
6HC† 48 56 0 48
6HL 170 184 17 152
6HB‡ 1 NA 0 1
7H 7HS 174 182 24 149
7HC† 51 57 0 51
7HL 168 176 22 146
7HB‡ 4 NA 0 4
Total NA 2930 2994 370 2545
C indicates a gene is located in the pericentromeric region based on information from flow-sorted chromosomes and the consensus genetic map.
B indicates a gene was detected on both the short and long chromosome arm.



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Pericentromeric regions of chromosomes 2H to 7H.

 
Chromosome Bins cM region
1H NA NA
2H 74–76 67.1–68.1
3H 56–59 65.3–67.9
4H 57 56.2
5H 39 42.4
6H 48–50 59.3–60.6
7H 86–88 80.3–81.8