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GrainGenes Reference Report: HER-103-110

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Reference
HER-103-110
Title
A high-density transcript linkage map of barley derived from a single population.
Journal
Heredity
Year
2009
Volume
103
Pages
110-117
Author
Sato K
Nankaku N
Takeda K
Abstract
A high-resolution transcript linkage map of barley was created using a single doubled haploid (DH) mapping population, only 3'-end expressed sequence tags (ESTs) and only PCR-based assays. Cultivar 'Haruna Nijo' and an ancestral wild-form accession 'H602' were used as EST donors and crossing parents of the mapping population. Of the 10,366 primer sets developed from a non-redundant set of 3'EST sequences, 7700 sets generated useful amplicons and 3975 (52%) showed polymorphisms between the mapping parents. Of these, 2890 (28% of the total) were mapped by single nucleotide polymorphisms (1717), cleaved amplified polymorphic sequence (933) and INDELs (240). The present work involves an estimated 9% of the genes of barley. Of the mapped ESTs, 2689 (93%) are formatted in the Affymetrix Barley 1 GeneChip and full-length cDNA sequences are available for 1039 (36%). Mapped ESTs show highest similarity with sequences in the wheat gene index (93%) and moderate similarity with rice (50%). Comparison of mapped EST positions and the rice pseudomolecule indicated collinear regions between two species; these are particularly conserved for the entire barley chromosome 3H and rice chromosome 1. These mapped genes, together with a systematically developed set of genetic resources, will make it easier to directly clone genes showing simple inheritance and to determine the genetic basis of complex traits. The information will contribute to the development of a framework for the physical mapping of barley, which is necessary for genome sequencing.
External Databases
http://dx.doi.org/10.1038/hdy.2009.57
Germplasm
H602 (barley)
Locus
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HvLTPPB
HvLOX
Bmac0064
cMWG682
MWG502
MWG2077
cMWG699
MWG2076
MWG975
MWG848
MWG2033
MWG620
MWG897
MWG2031
MWG511
cMWG704
MWG2062
HVM20
HVM36
HVM27
HVM33
HVM60
HVM62
HVM40
HVM3
HVM68
HVM67
HVM30
HVM31
HVM4
HVCMA
HVM49
cMWG694
MWG058
MWG2249
MWG2218
HVM5
HVM6
HVM9
EBmac764
Bmag120
Bmag211
Bmag125
EBmac415
Bmac67
Bmag136
Bmac209
Bmag225
Bmag13
Bmag353
Bmac113
Bmac316
Bmac40
k04435
k02872
k00440
k06268
k05172
k04699
k08237
k11140
k08190
k04713
k06117
k11311
k09634
k00751
k03512
k11098
k10023
k01023
k00712
k09019
k02195
k09766
k08433
k05258
k04277
k06586
k08509
k01431
k08302
k04425
k10955
k03671
k06257
k04230
k04261
k06326
k07043
k00936
k09804
k09483
k04620
k09401
k06727
k08050
k03878
k06308
k06031
k09197
k08197
k07130
k11402
k00320
k07810
k01252
k07273
k10261
k11123
k01005
k05094
k00256
k00321
k11207
k08590
k07686
k08747
k00647
k00894
k03235
k02948
k11309
k01339
k00690
k08186
k04911
k02167
k08548
k08567
k09469
k01042
k04311
k02276
k06611
k03373
k03338
k06847
k00464
k00654
k08165
k07147
k09850
k08526
k07951
k06232
k03631
k08546
k01492
k05211
k06058
k04927
k06908
k02563
k00782
k06493
k05001
k08173
k00681
k10124
k10219
k07511
k04899
k02235
k00216
k00070
k00341
k09680
k08483
k08939
k00548
k02459
k02993
k02190
k02301
k02306
k06814
k03070
k04031
k07909
k04280
k00079
k07464
k07676
k07187
k03861
k06450
k09605
k03667
k01126
k03661
k04596
k04224
k03514
k04290
k03045
k03111
k00072
k00526
k08877
k06481
k09588
k03555
k06916
k02151
k11133
k04050
k02787
k07706
k07510
k09911
k02177
k09704
k08853
k03293
k00856
k03591
k00527
k01268
k02585
k09241
k04778
k05079
k03009
k01344
k02023
k03806
k07365
k02068
k09761
k08257
k01527
k08348
k04310
k02939
k00297
k09384
k06372
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k07988
k02456
k03006
k04476
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k00304
k01388
k06478
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k03269
k09981
k00347
k02318
k10833
k09166
k00270
k09541
k00661
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k05000
k05155
k02839
k02374
k02568
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k01952
k04015
k08390
k03340
k10509
k07862
k05194
k03277
k02313
k06536
k09901
k08376
k05061
k08740
k07562
k09874
k02810
k02550
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k04662
k03612
k00680
k09502
k09710
k08132
k03935
k07693
k07944
k06515
k06239
k00462
k03220
k04982
k06614
k02145
k06378
k08204
k07351
k07785
k03756
k09130
k11042
k08304
k07215
k01953
k02923
k02438
k03251
k05204
k07819
k00033
k08810
k02163
k10026
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k02898
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k00227
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k07741
k02371
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k02176
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k10689
k08206
k07622
k07807
k08695
k00944
k02132
k03058
k00200
k01199
k03663
k08647
k10258
k08529
k10726
k00097
k09402
k07639
k02120
k03430
k08440
k04252
k10813
k02936
k05358
k01125
k05362
k00727
k02395
k08585
k03575
k02796
k02435
k00521
k01506
k09225
k07385
k08339
k08459
k10568
k08497
k00222
k08960
k03766
k00240
k03988
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k00219
k08820
k09533
k00067
k09230
k02387
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k01478
k08564
k10843
k09450
k02217
WMCIE8
k08117
k09496
k03450
k06485
k06225
k07543
k07062
k08642
k06512
k10493
k06939
Bmac134
k02996
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k06124
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k07110
k00214
k09976
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k06153
k00951
k09841
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k03558
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k02062
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k00556
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k07774
k00600
k03344
k07607
k04152
k06350
k02937
k04629
k09008
k09899
k05065
k03679
k11260
k04830
k08436
k00535
k04752
k09016
k01188
k07732
k09066
k00083
k00477
k03625
k10972
k07430
k07640
k10406
k06922
k10592
k09044
k01941
k03771
k08866
k00677
k07715
k06715
k09617
k07476
k06774
k00150
k08449
k04773
k02487
k05056
k05160
k07301
k03405
k04612
k02521
k09720
k03031
k04386
k09298
k10154
k02566
k04390
k00223
k02630
k08673
k06869
k02578
k09481
k01091
k03737
k04440
k03182
k07384
k07170
k08446
k09926
k00942
k03931
k05251
k05163
k03651
k08829
k09184
k03886
k08565
k04721
k01990
k03341
k01965
k03333
k02291
k00855
k03068
k07616
k04788
k09520
k03169
k09209
k10569
k02083
k08650
k10967
k01999
k08384
k09891
k08391
k05343
k08149
k03662
k02429
k03033
k04464
k03098
k06107
k03467
k02552
k11203
k10579
k00086
k08589
k08177
k04110
k06975
k03231
k03695
k07128
k08887
k09188
k02279
k07663
k09499
k09407
k02793
k00291
k02415
k10101
k09448
k09373
k09201
k05364
k08849
k06318
k04231
k00168
k07455
k08534
k07452
k08628
k02889
k10295
k10091
k09072
k08369
k06863
k04415
k04531
k09178
k04332
k09593
k03300
k10394
k02469
k09371
k03897
k02425
k02875
k06287
k01031
k02561
k00926
k00371
k03636
k06991
k06332
k02887
k04469
k00186
k00818
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k01338
k00862
k00776
k06725
k07924
k01407
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k01421
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k00871
k02551
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k11393
k00883
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k06560
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k05333
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k09845
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k02455
k00878
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k07702
k07948
k03244
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k09649
k10041
k09307
k01370
k01369
k08968
k10559
k07433
k01088
k03138
k00575
k06872
k08738
k05302
k06608
k06334
k07113
k06687
k01076
k11229
k08563
k04429
k10808
k08692
k10673
k01276
k01387
k00563
k09517
k10752
k00939
k09446
k00504
k10439
k03859
k10743
k04121
k03316
k03443
k08552
k05451
k04939
k05195
k08982
k08808
k09734
k03160
k02698
k09452
k02590
k05241
k07726
k03524
k10192
k00511
k03026
k07003
k03197
k00749
k04690
k02979
k01219
k06557
k07841
k07470
k09038
k10244
k09037
k00998
k03594
k04755
k04002
k05226
k11237
k07701
k02093
k02687
k07504
k06811
k06035
k04784
k06230
k10735
k00777
k06976
k00161
k08048
k03454
k06712
k04170
k06292
k03257
k08626
k00831
k03762
k11387
k08427
k00314
k07617
k09861
k04771
k08558
k02364
k03880
k10447
k00863
k01053
k03065
k03125
k00957
k06957
k08366
k03825
k03376
k10690
k06970
k05340
k02580
k03388
k10255
k09596
k09505
k03639
k09400
k02356
k09946
k08954
k05037
k04017
k01424
k03697
k00498
k03142
k05269
k00809
k03899
k03741
k00092
k04408
k01161
k10103
k04860
k06342
k07865
k10907
k09612
k10964
k02982
k09397
k09959
k09242
k08168
k00484
k04637
k03047
k06518
k01408
k08894
k01963
k00422
k02390
k00205
k07333
k00917
k06831
k00590
k03044
k04179
k07608
k09212
k06430
k00663
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k08891
k03833
k04545
k02419
k03569
k06489
k00323
k01380
k04655
k02157
k07600
k04190
k08640
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k05038
k04213
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k00932
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k08380
k03869
k07553
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k09344
k07124
k06290
k02080
k07185
k02360
k10050
k05016
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k09088
k04833
k06270
k08012
k00616
k10578
k10765
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k07300
k03624
k00247
k01107
k00778
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k09790
k02515
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k03238
k05014
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k00614
k03021
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k06994
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k07026
k02683
k01008
k07429
k07582
k00069
k08613
k10282
k03841
k06006
k01389
k11250
k00022
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k06718
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k10077
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k06632
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k10548
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k01358
k10084
k07554
k08141
k08490
k06114
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k04296
k10181
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k02309
k04562
k09226
k08180
k10491
k02820
k09337
k04672
k09280
k09032
k02436
k00683
k11014
k02381
k00643
k00243
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k09341
k05214
k06433
k10480
k04176
k07120
k07630
k00904
k01349
k03844
k08323
k00280
k03481
k07424
k03692
k09604
k02524
k03628
k01297
k03001
k06965
k08381
k10105
k03480
k00486
k04656
k08337
k09490
k09489
k10122
k10011
k02506
k02735
k03336
k06778
k06761
k07761
k10771
k03504
k07212
k07179
k02658
k09462
k04307
k03472
k02350
k04654
k04460
k04172
k03670
k00892
k06071
k10978
k10565
k08125
k09142
k00866
k02394
k06620
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k02018
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k00552
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k11168
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k06631
k04916
k08908
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k04427
k04165
k02125
k01141
k08883
k01469
k02445
k06959
k01356
k07237
k10036
k02164
k10659
k06721
k01292
k01055
k03423
k10901
k04127
k07964
k01212
k05292
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k04790
k08907
k07968
k02218
k02715
k08238
k01300
k00824
k06766
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k00595
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k03027
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Bmac156
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k01176
k08540
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k08533
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k04412
k09497
Map Data
Barley, HN x H602, Sato2009
Probe
bah55e06
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