Outline of Barley CAP Approach

Breeding lines from 10 breeding programs are phenotyped (over 40 traits) in collaborative trials and individual breeder trialsBreeding lines from 10 breeding programs are genotyped at the Cereal Crops Research (USDA-ARS) with two Oligo Pool Assays (OPAs) consisting of 3,072 SNPs.

PHENOTYPING & GENOTYPING

BREEDING LINES

THE HORDEUM TOOLBOX

All genotype and phenotype data gathered by Barley CAP breeders is uploaded to The Hordeum Toolbox (THT) webportal. THT consolidates information from ten breeding programs into one and uses it to map genes controlling yield, malt and food quality, and disease tolerance.

QTL MINER(LINKAGE DISEQUILIBRIUM MAPPING)

QTL Miner software is used to identify SNP markers associated with loci controlling traits of interest. Traditional mapping uses populations of progenies from two parents, whereas QTL miner uses trait and genotype data from breeding programs.

Overall approach: 96 lines from each of 10 breeding programs from each year of the project are used for SNP genotyping (3,072 SNPs) and phenotyping for over 40 traits. Association mapping is used to detect QTL. MAS strategies will be developed from the QTL information.

NORTH DAKOTA STATE UNIVERSITYRichard Horsley

OREGON STATE UNIVERSITYPatrick Hayes

UTAH STATE UNIVERSITYDave Hole

VIRGINIA TECHCarl Griffey

WASHINGTON STATE UNIVERSITYSteven Ullrich

* Denotes breeding programs

10 BREEDING PROGRAMS COLORADOBlake Cooper(Busch Agricultural Resources, Inc)

USDA-ARS, IDAHODonald Obert

UNIVERSITY OF MINNESOTAKevin Smith

MONTANA STATE UNIVERSITYTom Blake

Ten breeding programs each contribute 96 lines per year to the project.

MAS, USDA GENOTYPING LAB

USDA regional genotyping centers service small grain breeding programs by increasing efficiency of generating marker data and by eliminating the need for individual researchers to do genotyping.

Oregon Wolfe Barley Genetic Map

bPb-631802_0275 BCD1434 bPb-711211_1311 1_04607DsT-66 1_0410 bPb-018181_063691_1011 3_093311bPb-9608 bPb-7137 Act8A bPb-1318 bPb-7043122_1226143_0919 [222208] 3_0817 3_0950 [220835]3_1533 3_0952 RbgMD [105102]18

[222789]19bPb-7889 MWG837B22scind00046 ABC165C 3_095526[223986]27Bmac039929GBM1007 3_087630bPb-2166 1_0186 [105118] 2_0712 3_024133[221879] BCD098353_127638bPb-3217 bPb-4813 bPb-9418421_0760 [104834] [104921]47GBM1042 [221425] 1_081448bPb-1586 bPb-1231 1_0238 bPb-5672 bPb-1398bPb-9388 bPb-1535 3_0336 1_1357 bPb-86621_1498

51

bPb-0482 2_0514 bPb-5164 [222328] 3_02681_1266 bPb-2175 [221108] bPb-1604 bPb-035752

1_0294572_0810 3_1191 2_0427 [221321] 1_04383_0436 1_1287 bPb-9360 1_1169 2_06983_0258 [223055] 1_0938 2_1312 1_12092_0757 3_1381 1_1336 2_1357 2_14083_1134 Bmag0211 3_0762 3_0562 2_10003_0498 bPb-0579 3_0462 2_0047 2_09121_1036 1_1301

58

3_0774 1_1107 3_0522591_1359 2_1217 1_121761bPb-1791 bPb-3382 3_0243 3_0741 1_0198bPb-1193 3_0710 BG369940 1_0293 1_12563_0348

62

3_0343642_1333 1_1444 1_076865bPb-1723 bPb-9005 1_0201 3_1532 2_1463681_1049 3_0744 1_0617 3_0304692_1131 1_0302703_1179 3_140171bPb-8183 2_0642 bPb-1133 [222086] 2_1431723_0295 1_1367 bPb-5339 bPb-3389 1_10621_000276

ABC160783_0505 1_0166 2_0696 3_0298 1_0463791_1075 3_0742 2_1176 bPb-6117 bPb-8713801_1267811_0279 2_0121 1_089083[224235]841_046690bPb-8477 3_0072941_1463983_0204 1_1144991_05351012_0475 JS10C 1_1008 1_1439 bPb-79632_0769 3_1192102

1_12771032_0754 bPb-2007 2_01691061_0111 1_1173 2_0187 MWG706A 2_09092_1020 [221687] bPb-9180 2_0613 bPb-1419bPb-7429

112

3_01911182_0780 KFP170 [223108] 2_0921119bPb-9108 2_0625 [221039]1202_00211223_1526 bPb-5198 bPb-5014 bPb-20631241_09051271_14091281_0338 3_0257 1_0854 [221902]1302_11721341_0339 3_11051351_1457136MWG2028 1_0207141ABC261 1_0808 3_1387 bPb-50901421_0693 bPb-9552 bPb-6065 KFP257B 3_06491431_0903 bPb-65021452_03831483_0803 1_12711492_1105 WMC1E81511_1509 MWG912 1_0041 1_13201532_05941543_1081 3_0048 bPb-1487 bPb-2260 2_0840ABG387A bPb-5550 scssr04163 bPb-3756156

1H

[223556]0bPb-3598 bPb-3608 bPb-7892 bPb-0611 [222367][220862] bPb-0485 bPb-5191 1_1407 bPb-0516bPb-8959 1_0970 3_1446 bPb-7151

1

2_1466 ABG05831_0718 scind02622 [222211]42_14155bPb-5900 bPb-7969 bPb-0471 bPb-0205 1_1030bPb-5033 [223937]7

bPb-7557 bPb-0615 [223539] [221144] bPb-7024bPb-5688 bPb-55199

1_1059 1_023012[223312]143_0775 bPb-6128 bPb-8399 3_0402 bPb-0715ABG008 [220974] bPb-1708 bPb-5444 bPb-44813_0155 bPb-9220 bPb-4295 bPb-6897 3_0631[221686]

15

[104949] bPb-6494 bPb-6879 bPb-8374 [222296]bPb-2355 bPb-2782 2_1423 [221518] bPb-2108bPb-4715 [222714] bPb-8986

18

2_0724 bPb-8292201_104022bPb-9682 bPb-4261 bPb-4875 scssr10226 2_1261462_059349scssr07759 1_0307 bPb-2501 1_0891 2_0368bPb-3190 bPb-790650

2_104951GBM1066 1_1304521_0847531_0919 1_1057 Pox 3_0420 2_03262_1461 3_0657 bPb-2230 bPb-0722 1_03421_0837 1_0296 1_0178 1_0525

55

1_1493 1_0084563_0379 3_0029 1_0715573_0491 1_0486581_1340 2_0281 1_0204601_0498 bPb-9925 1_1505 bPb-5057632_0688 1_0156 [223952] bPb-0220 2_06743_0691 3_0604 1_1428 2_100565

[221628] 1_1302 1_1131 scssr03381 [222438]1_0422 2_0929 1_063866

1_1400 3_1474 1_1522682_0748 2_0234 2_0917 bPb-6438 1_0147bPb-6881 1_0927 3_0195 3_0251 2_02352_0602 2_0387 bPb-3056

71

Hot1 2_0643 1_0558 3_0557 2_00043_0209 3_048772

2_0032 3_1189 2_0378 2_0181 bPb-18361_0154 1_0485 [220842] 2_0196 1_13691_1211 3_0772 3_0206 2_1286 [222433]1_0947 3_0634 1_0330 [220925] 3_08531_0883 1_0099 1_1288 2_0417 scssr022361_0948 3_0068 Ebmac0684 2_1337 2_14342_0500 2_0039 3_1218 1_1155 2_08781_0474 2_0458

73

1_1384742_0335753_0245 scssr00334761_0640 1_0436 1_0632772_1476 2_0374 2_0442 3_1252 ABG3561_1430 1_1316 3_125678

bPb-4837 1_1347 bPb-7256 2_1094 bPb-64373_1307 1_1072 GBM1023 bPb-088580

bPb-5440 [222771] bPb-4040 1_1096 bPb-6088bPb-975483

bPb-8100 3_0205 1_0407 2_0833 bPb-72433_102186

2_0528 2_0667871_1402883_1394893_017891scsnp03343 [222968]941_1388 3_1445951_0859 1_0786971_110099vrs1 3_0901 2_0340 3_0897 3_09001_1533100

1_09361032_1351 1_0969105Bmag0125 2_0793106DsT-41109MWG503113bPb-4835 2_1007 bPb-7991 bPb-6194 1_1307bPb-1926 GBM1062 1_1285 3_0216 bPb-3563115

KFP2031161_0398 3_0200 2_0923 MWG882A1191_0900 1_1466 2_15271203_0480 3_0095121bPb-3653 bPb-4577 3_0555 bPb-8737 1_1323bPb-1772 3_0049125

1_1094 bPb-6822128[223776] 1_0128 2_0064 bPb-8274 bPb-3870ABG072 1_0990 1_0263 1_0989 2_0955bPb-2481 1_1043 2_1238 3_1402

135

1_0429 2_0989 1_1236 1_0707 3_04591361_07391401_0780 3_1406143bPb-1266 bPb-89491443_0097 bPb-0541 bPb-6688 [221435] 2_01412_1315 1_1365 bPb-7992 3_0152147

2_1406 3_0041 2_1459 1_1486 3_11001_0109 Ebmc0415 1_0446 3_0695 3_0310[222960]

149

bPb-5412 cnx1 bPb-2971151[222464]1523_0678 2_1125 1_0472 1_0383 2_13361_0065 bPb-3858 2_0215156

1_1227158[221983] 3_0396 bPb-1505 3_0106159Zeo11603_02481632_0590 2_1181165[223553]171bPb-1184 bPb-4092 GBM1019 1_1023 bPb-72081_0566 [221407] bPb-1815 1_0315 bPb-0303bPb-8530 bPb-5619 bPb-1986 bPb-5460 bPb-1566

173

2_0943174Aglu5 3_0823 Aglu4175MWG720 3_1300 1_09371772_0957178bPb-4601 bPb-7212 bPb-1181 bPb-4232 bPb-16111801_0329 GBM10121821_1050 bPb-6048 bPb-1085 bPb-9419 bPb-3102[223337] bPb-0305 bPb-6296 1_0085 bPb-8698185

2_14141872_1496188MWG949A scssr08447 3_0102190

2H2_0090 2_0858 bPb-4022 3_14280[221259]2bPb-3815 bPb-4895 bPb-2553 [224140] [223116]2_07973

1_143452_0252 3_1409 bPb-1264 2_0953 1_14539bPb-368911bPb-9945 2_1027 2_1398 3_0297 1_1005131_1310 2_0976 3_0910 1_088614[221362] 3_091515[220882] [223877] [223396] [221142]163_011319bPb-9745 2_0172 2_141020[221552] bPb-7448 2_0742 bPb-0654 [221551]1_056521

bPb-3865 bPb-0548 bPb-0663 bPb-3229 bPb-482423GBM1074 2_0982263_0192272_0552292_0794 3_0920 1_0691 1_0559301_1237 [220909] MWG798B 2_0455 [221274]2_0968 3_0284 2_140232

bPb-2929 bPb-5289 bPb-9903 [105024] bPb-9961331_1527 2_1268 2_0607 3_0431 1_0026bPb-3030 Dst-27 3_057135

bPb-2324 bPb-9129 bPb-2993 bPb-5892 1_0081[222411] bPb-7938 [221166] 1_0968 [222615]bPb-2910 BCD706 1_0598 [222320] bPb-6275[220886]

38

3_1298 3_1159 3_095341bPb-0158 bPb-3332432_1506 2_1259 1_1117 3_0913493_0609 2_118954bPb-4407 3_0467 2_0264 1_1069553_0583 1_1102 3_0721563_0922 bPb-6771 1_1387 3_0923 [223843]3_1015 bPb-0068 [224015]57

1_1511 1_0233 alm 3_0680592_0866603_0262 1_1265 3_1008 1_0391611_1099 1_0784 2_1062 3_1502 2_07213_0039 2_0408 1_1283 2_1435 1_11253_0130 1_0925 2_0591 bPb-8666 1_12952_0583 2_1411 1_1337 2_0439 2_11472_0801 Bmac0209 2_0486 1_1530 1_14822_1472

63

2_0444 1_001164bPb-6491652_1511 ABC325 1_0653 1_0850 1_06781_1429 2_1064 2_0325 2_010866

DsT-67701_1191 bPb-4757 2_0863711_1152 2_0608 2_1502 1_1342 bPb-38051_1284 bPb-6923 bPb-004072

2_1305 3_1153751_1314 1_1394 bPb-0079 bPb-3317 1_0200bPb-841076

3_0754771_0452 2_0694 3_1529783_0743 2_0695 3_0399 1_0609 2_01242_0521 1_068379

3_1346801_0047 2_0362 bPb-7872 scssr25691 [223370]1_1454 2_0597 2_119483

ABG377 1_1524 2_0115 2_0849 2_1163851_1517882_0063 1_113892Bmag0225933_0663983_03251012_0659 1_05831021_0747 1_10211043_1367108ABG499 3_0090113bPb-6722 3_0640 2_01301141_0184 [221404]1152_1083 2_13811161_0662 2_1495 3_03421222_14931232_0009 [223016] 3_01191251_1392 bPb-9336 2_0023 2_1161 2_10811262_12771293_03751313_13291321_05841341_0680 3_0928 scsnp00940135bPb-4209 bPb-36301361_1330141bPb-1579 bPb-7695 2_0944 3_1269 bPb-1961bPb-9110142

1_0918 [223788] 2_1405144bPb-4386 3_0274 bPb-77851451_1338 3_1525 3_0924 1_0754 1_08213_0084149

3_1238 2_04131503_05071523_00811531_1196 2_0369 2_0343 2_0662 1_1141ABG004 1_0505155

2_0612 1_08421563_09731582_0527 3_0092159scind02281166bPb-5796 3_0860 bPb-8506 2_0085 1_1328bPb-8894167

bPb-4830 3_1496169MWG883 3_0137172bPb-7833 bPb-3109 bPb-5129 bPb-0049 2_1386bPb-2737 bPb-8021177

bPb-2420 bPb-3899 bPb-3843 bPb-6228 bPb-47481_1297 bPb-4739 bPb-1253179

3_1161 bPb-07891822_1531 bPb-7413 [222583]1832_0421186HVM62 3_0370 2_1345 bPb-1829 bPb-4456bPb-0302 1_1436 bPb-6631187

bPb-02001893_0271 2_1237 3_0767 3_0960 2_10081_0935 1_0702193

2_0605 ABC8051951_0893 bPb-1411 1_0681 1_0629196bPb-4387 bPb-41691973_1388198[222593] [222092] 1_0014199bPb-0164 1_15162013_0229 2_01762033_13412042_15002053_0055206bPb-5256 3_1296 bPb-5346 2_1387 [223314]1_0343 ABC172 [221355] 1_0215 bPb-71203_0135 bPb-8962 [221492] bPb-7724 bPb-3295bPb-0136 [221662]

207

[221563]208

3H

2_11170bPb-6938 3_1324 bPb-7534 bPb-94061MWG63473_1486 2_0274 3_014091_1485161_0490 3_1458173_054023MWG077 3_0150 [222436]242_0557 [104902] 1_0574 HVM40 1_0223261_0221 3_1291271_1199281_1136292_1458302_0422 1_1060 1_0626 1_1175 3_03941_0562 [222526] 2_138531

2_0109 2_0777 2_1418 2_0680 CDO54232scsnp01648333_0907 1_0031 CDO12234[222439]363_116437hvknox3 3_1439 1_0810 3_1524 2_1389383_0992 1_0347 1_017140bPb-6611 2_0180 1_0371 bPb-6404 2_0240[223373] 2_0011 1_006341

3_0187 scssr20569 ABC303 1_0048431_0668 1_0793 CDO795472_1490 1_1112 2_0939492_0269 1_0946 3_0525 1_1332 2_13032_0525 3_1382 DST-46 3_0331 3_10263_1360 2_0831 1_0432 2_1442 3_0450[223751] 2_0289 1_0261 scind04312a 1_06073_0488 1_0492 [220846] 1_0667 3_11562_1071 2_0426 1_1042 bPb-9504 1_04111_0942 1_0756 3_0866 2_1073 1_11902_0853 scind03751 1_0577 2_1137 [222294]2_0496 2_1029 3_0777

52

3_0427532_1213 3_0060 1_0088 1_0527 scind017283_0839 1_0262 2_0898 2_1481 Tef21_1108 2_0412 [105086] 1_1232 1_08813_0034 1_0426 3_1297 1_0568 2_06101_0637 2_0363

54

2_1400 2_0151 1_0086 2_1010 2_0361592_1273 bPb-6872 1_1207 3_0706 2_12961_1427 bPb-9907 bPb-6949 2_0453 bPb-230561

bPb-4290 2_0820 bPb-7987 GBM1020 bPb-625962Bmag0353 2_0924 1_0639 2_0062 1_00522_0723 [224001] 2_0098 1_0053 1_143163

1_1070 3_0455641_060665[221608] bPb-4214 scind10455701_0467 2_1504 1_1513713_0994 bPb-0098 bPb-8013723_1258 3_1362732_0143 1_0309 2_1499 2_0207 bPb-35561_131975

2_1332793_0787 scssr14079 1_1500 1_0170 3_022681bPb-9998 bPb-7719 ABG472 1_1526 bPb-6096bPb-373982

1_0723 1_1213 1_0670 2_019783bPb-4750 1_1398 bPb-0018 bPb-0610 bPb-1999GBM1059 2_076584

3_0138882_0732913_0142 3_0232 1_1168921_0785 bPb-5245 KFP22193Ebmac0701953_0114 3_0046 2_0838 1_1292 3_05843_0117 1_0666 3_0158 MWG652B 2_076296

2_0454 3_0990 1_1139 3_1139 1_03342_111199

bPb-1166 bPb-9859 [223032] GBM10481021_11941043_0385105bPb-2677 2_0237 1_1233 1_07121092_0701 bPb-1040 1_1235 [220875]1102_1035 1_1066 2_0883111[223550] Hsh 2_1130 3_0146 1_0697112HVM67 2_02241132_07601143_0888 2_0007 2_1450 3_0884 3_08922_0272 3_0808 bPb-3468 3_0476 3_08873_0886 3_0889 VRN-H2 1_0610 3_0873

115

[223334] KFP241.1 2_0932 3_0239 3_00201163_1422117bPb-5265 3_0824 3_0825 ABG601 bPb-9668125

4H3_0163 bPb-017002_0553 bPb-6051 bPb-648523_098443_0001 3_0979 3_0975 3_0977 3_10223_10235

2_122111scssr0230615MWG618212_0533243_109425ABC483 2_001026ABG610 3_071427bPb-2872 2_1365283_0167 2_0873 bPb-3830 bPb-0351 bPb-1807bPb-8072 bPb-0091 bPb-2460 bPb-6568 2_1065bPb-7407

35

1_0974363_0531 2_076137bPb-5166 bPb-2266392_0576 bPb-0536401_0580452_0980 2_1391 2_084548ABG395 1_131849bPb-4273 bPb-8589 1_0864 bPb-2273 bPb-413550scssr02503 3_0105 1_1432 3_1492571_0913 [222988] 1_0995 1_0252 3_03542_1350 bPb-5584 2_1308 3_0792 3_15201_0177 3_0728 1_1469 2_0461 2_07001_0318 1_0240 2_0481 bPb-0786 [223293]1_1198 2_0179 1_1462 3_0729 3_1257bPb-4210 1_1399 2_0101 2_1011 2_05241_0481 bPb-8929 bPb-8675 3_1317 1_08562_1116 3_0337 bPb-0949 2_1401 2_10403_0109 [221402] 2_0697 2_0841 3_0768bPb-1046 3_1423 2_1447 1_0157 3_0709

58

1_1204 1_1260 bPb-7881 bPb-2762 bPb-5727bPb-550659

3_0214612_0396 2_0059631_0264 3_1117 2_0105 2_1536 bPb-7933653_1340 1_1240 bPb-0503 1_1512 1_11512_0306 1_0237 [221802] 2_0501 1_13633_0111 3_1062 3_1064 2_0981 3_03123_0538 1_0899 3_1183 3_1451

66

1_1523671_0725 NRG045A 3_1035 3_1034 3_10321_108968

bPb-7627 bPb-6260 [223210] scsnp04260 3_0745692_1036 [224132] Ale bPb-8987703_0080 [223812] 1_0641 1_1249 2_0278[222177] 3_0966 2_0392 1_1438 1_0203[223146]

74

1_0548813_0719 2_0297821_095383bPb-9618 [221220] 2_0330 2_0818 3_0252bPb-4067 bPb-0686 bPb-7763 bPb-214786

1_0305882_1128 1_0183 2_1133 1_0127 ABC302921_0140 2_0246 1_0167 2_0096 scind169911_063395

2_0066 1_1515 2_073696scssr15334973_0314 2_118699scsnp06144 1_11351031_06741071_05241111_09301121_05781131_1134 1_0771 1_0518 2_0097 3_08342_0449 3_0533 srh 1_1473114

[105044] bPb-2869 bPb-5532 bPb-90321153_01821161_13501223_0098 2_04031232_01341241_00241263_0846 3_0854 3_0847 1_0844 HvCBF91_0834 3_0850 3_0852 2_1321127

2_0805 3_0705 3_0807 1_0871 3_12361_0507129

bPb-5596 bPb-7395 3_0056 3_0456 1_0477131RSB001A1323_0619 1_13411331_1245 [222196] scsnp00177 [221888]1410SU-STS11461_12981481_1507150bPb-0710 2_1422 bPb-61351512_0405 2_0045152ABG003B 1_1456 [104960]1533_0169 3_0611 2_0300 1_1535 1_02281541_14721571_0755 2_0551 bPb-4084 [221423] 3_1465[223247] bPb-2960168

bPb-6578 bPb-5845 [222215]175Tef31761_00041773_1182 3_1234 2_0731 2_0676 2_08301_0104178

2_0100 1_1441 3_0062 1_0333 1_0080MWG877 3_1206 3_1050 2_1462 2_0388179

3_0795 3_1221 [223182]1822_0104 3_0830 [105067]1832_01861851_14971861_0902 1_0741 3_0238 1_0901 1_05821_0385 1_0536 2_0317 ABG496 3_0759193

2_0560 2_08761942_0646 1_1325 2_1018 3_0642 1_03361_1464 1_0273 3_1375196

bPb-9147 bPb-6195 [222383] 2_0334208scsnp02109 2_0829 E10757A2123_0666 2_0826213bPb-0618 ABG391 bPb-3138 1_1216 [221131]2161_0769 3_0087 JS10B 2_0546217bPb-4595 bPb-0835 bPb-6179219[104899]2201_07782211_0600 bPb-0877 [223339] [223803] [222906]bPb-4621 [222776] [224041]223

1_1450 1_1010 3_1404 ABC622 1_0254224DsT-33 2_0189 bPb-9132 bPb-7421 3_07691_0736 3_0504 3_0494226

bPb-98682292_1393231bPb-8754 1_03102322_1108 bPb-6239 3_1292 1_1364 bPb-1217[222075]236

1_0732 1_1413 3_1481 1_0020238MWG602A bPb-3973 bPb-2419 bPb-7008 [221531]239bPb-6124 scssr03906 bPb-9244 3_1123 2_13563_0958 bPb-4725 2_0402 bPb-7292 1_0322bPb-5766 bPb-7360

240

[221535]241

5H

[223608] 3_0319 bPb-3780 2_02320[223456] 2_0881 [222141] bPb-7030 Bmac0316bPb-73232

bPb-9768 2_088231_11664[223070] bPb-6511 bPb-8275 bPb-9075 2_1204[221458] bPb-3532 2_0262 bPb-1001 2_02945

bPb-3807 bPb-71937[221961] bPb-3433 [222053] bPb-4778 [222316]bPb-6311 bPb-0572 bPb-5498 3_001020

3_084222bPb-8492 [224154]261_0064 MWG602B30bPb-7165 2_1246 [223374] 1_0023 [223325]31bPb-9749 2_0315 bPb-6661 bPb-525234[222286] [221152]38[220998] [223808]401_0774 2_0745 JS10A bPb-3921413_0697423_0673443_130845GBM1021 1_0799 1_0994 1_093948[223386] 1_0427 bPb-0597 bPb-3927 [221169]bPb-600249

bPb-7324 [220812]503_052154[221710]553_0361571_0129 1_0061 1_1455 3_0783 GBM106858[223273]59[220818] 2_0936 bPb-5379601_0539 1_0817 1_0199 BG299297 1_09101_0461 1_0811 2_0983 3_1092 1_0355bPb-1466 2_0707 1_0575 3_0281 3_12743_0317 bPb-6142

61

1_1205 1_1171 bPb-2592 [223115] bPb-52702_0675 3_078262

2_144963HVM31 3_0569642_0656 3_0120 bPb-1666 1_0497 2_03811_1104 bPb-9114 2_0720 1_1353 bPb-65672_1014 2_0651 3_0021 3_1007 2_0601bPb-3487 2_1158 1_0962 2_1473 rob3_0032 3_1004

66

[223002] 1_0591 2_0567 1_0323 [222814]1_1442 2_0854 3_0305 scssr02093 [223671]3_1509 2_0799 3_0765 [223207] [222899]3_0230 2_0785 1_0659 [223845] bPb-2593[224033] [223262] 1_1153 2_0142 1_11401_1312 3_0567 2_0946 [224253] [221391]1_1487 2_1216 [223825] 3_1249 1_07491_0848 3_0508 1_0954 3_1443 [222912]3_0837 3_1187 [223658] [223028] Bmag00092_0572

67

1_0345 bPb-1657 bPb-5196 bPb-0019 2_0202[222484] 1_1181 [221874] [222527] 2_0835bPb-9702 1_0513 3_1174 2_1114 [221245]1_0278

69

bPb-9082 bPb-9051 bPb-983570bPb-5517 bPb-4229 1_0803 bPb-947975bPb-6721 bPb-4409 bPb-4369 1_0964 bPb-83472_0266 bPb-3230 3_1003 ABG47477

bPb-3068781_0189 bPb-1256 [224127] 1_1321791_0392 2_1293 1_1261 2_1225 2_09042_0148 2_129883

2_0714 ABG388 1_0504862_0468871_0596 2_0673 2_0892 [223211] 3_12892_062092

1_1349 2_0848 2_0784 2_0577 scsnp212263_125093

2_0488 MWG820 3_1111 2_0682 3_0236963_0573973_0148993_12531001_03311021_1246 1_01851032_0346 2_14041043_0452 1_1147106[222895]1111_04001121_0202 2_10251133_12351143_0324 3_0932 3_1225 2_09961151_0595 1_0978 GBM1008 2_09721183_1049 1_0139 3_1044 3_1048 3_13533_1043 [220914] 3_1042 [221783] 1_14943_1115

119

2_0379122bPb-9063 bPb-6477123scind04312b125GBM1022 2_0036128bPb-3470129Bmac0040 2_0355136[221063] [221088] 2_0448 bPb-5587137DsT-32B 2_05581403_1198 2_14771483_00251491_0645 1_0107 2_1467 bPb-9413 2_14553_1277 1_0071 1_0051 3_1392 3_0355bPb-7446

150

3_1126 DsT-28 1_1187 3_0057151bPb-55151521_0748 DsT-74 2_0211 1_1488153bPb-2863 2_0868 bPb-2940 bPb-3760 2_0907bPb-6677154

3_1498 3_1469156MWG514 1_0390 bPb-7146 bPb-1621 bPb-23041_1111 MWG798A bPb-1029158

bPb-9890 [222800] [223186] bPb-2410 bPb-9817159bPb-0649 bPb-4626 bPb-0403160[220848]161

6H

2_1419 1_003603_0472 1_1132 ABG704 1_068212_0201 1_0894 1_01212bPb-3732 bPb-7349 [223392] bPb-8272 bPb-0398[223152] bPb-4457 bPb-8084 bPb-7559 bPb-08443

3_135041_11795[221162] 1_1031 [224158] [222156] 3_1173[221346] bPb-44457

bPb-2595 1_10359bPb-5816 [221786] [223056]10bPb-9202 bPb-5897112_0227 [222301] bPb-4634122_0755133_0902 GBSS-I15bPb-3727 bPb-6453 3_0723 1_1052172_105019bPb-4266222_0495 AW98258023[222485]25MWG089 1_0965 CDO475 bPb-8660 3_07803_0329 3_135130

1_0451 3_0702311_0232 bPb-0324 ABG380 bPb-6156 bPb-96012_0993 3_0242 2_0192 bPb-5074 3_0083bPb-5494 bPb-0678 bPb-2533 bPb-5852 bPb-1360[221832] bPb-8939

32

2_1292393_0065 1_0979401_0368441_1339472_1491482_0150 2_1326493_0752 3_0371 2_0031 1_077252bPb-8674 2_0113553_0290563_0181581_0403 ABC255 scsnp00460 3_088061[220928] ABC165D [221740] 1_0721621_0050632_0750 3_0031 3_0639 1_0657 2_12703_146364

bPb-4219 bPb-1952 bPb-7952 bPb-3561672_0060 1_1028 1_124270bPb-1447 bPb-8051731_1045 [221655] bPb-5458 1_1257 1_1103scssr15864 3_0997 3_1452 [221264] bPb-1093[222063] 1_1202 2_1492 2_1234

74

3_1120 2_0885 [222546] 2_1167 1_0983[104913]75

3_0344 GBM1030771_1519 1_0083 3_0581802_0200 1_0581 bPb-2188 3_1140 1_06982_1494 1_0268 3_0492 3_0389 bPb-69753_0475 2_0911 DAK642 bPb-8396 bPb-7915bPb-3227 3_0411 3_0621 2_1319 3_1215bPb-5599 bPb-2097 3_0004 2_0879 bPb-89561_0055 3_0445 3_0449 1_1352 MWG8081_0924 2_1335 bPb-2379 3_1345 3_05742_1178 3_0563 1_0370 1_1145 2_08932_0314 1_0115 bPb-5126 1_1291 1_00733_1227 2_0828 3_0794 3_0550 3_0760bPb-1770 1_0773 2_1302

81

bPb-9825833_0565 1_1461 1_1029871_1445 1_0442 3_0199 2_0349 2_13301_0673 1_0531 scsnp00703 1_1091 3_11372_0896

90

2_0771 MWG2031 1_0143 2_1409 2_008391[221574]92bPb-8439 nud bPb-6233943_0301 2_0685 2_1530 1_1437 3_09962_1501 1_024995

bPb-2561 bPb-6386 bPb-9912 bPb-7399 bPb-1847bPb-5296106

lks2 2_12011093_1188 ABC10241123_0335 2_08081142_0611 [222171] 3_0168 2_0103 bPb-1079115[220920] 3_1294 3_1440 1_10511161_0169 2_1464118bPb-4191119Bmag0120 2_08241201_0362 2_0406 DsT-30121WG380B1221_0563 bPb-0027 bPb-9908 bPb-2433128bPb-4272 [105081]1293_0164 ABC310B 1_1184132bPb-84981333_1232 bPb-6186 1_1243 2_0217 bPb-4389Ris44135

3_1535 3_1483 2_03541392_1209 1_1279 2_1229146[221079]1471_0861 ABC2531503_0831 1_0797 bPb-77391573_03801593_1241 ABG461A bPb-0917 bPb-6167 bPb-1556bPb-8644 bPb-0758 bPb-0889 1_0973 [222159]bPb-5923 bPb-4394 3_1282

161

3_1325 3_1491 bPb-1631 bPb-0981 bPb-7983bPb-3980 2_1280 2_0753 [220949] 1_0550164

1_1440 3_1166 1_0843 2_1363 bPb-88333_0593 WG380A DsT-69 2_1223 2_04142_0452 [222528]

165

2_0640166bPb-3232 bPb-9948 1_0130 [223928] bPb-2121bPb-5898168

[221299] 1_1309 1_1275 2_0962 1_08961693_14891703_0244 GBM1065172[223404]173bPb-0328 bPb-9884 3_1019 KFP255 1_0378195ThA1198

7H

The Oregon Wolfe Barley (OWB) population was genotyped for SNPs using pilot OPA1, 2 and 3 (4,608 SNPs) and the data integrated with DArT and other markers, i.e., NEPs, RFLPs and SSRs, to create an integrated 2383-locus map. An integrated SNP map of 2,943 SNP markers has also been developed from three barley mapping populations (Steptoe x Morex; OWB; and Morex x Barke). HarvEST (http://harvest.ucr.edu/) includes the integrated barley SNP map and rice synteny viewer. We would like to thank Drs. Robbie Waugh (Scottish Crop Research Institute) and Nils Stein (IPK) for their assistance in the development of these SNP maps.

Trait Affectedbeta glucan (malt)

Deoxynivalenolalpha-amylase activity

Diastatic PowerSoluble/Total protein

Trait Affectedalpha-amylase activityGrain protein content

Kernel plumpnessbeta glucan (barley)Kernel plumpness

DeoxynivalenolTest weight1.

6.

4.11

.

2.4.

2.7.

3.2.

4.1.

4.5.

4.6.

Trait AffectedDeoxynivalenol

beta glucan (malt)Diastatic Power

alpha-amylase activityDeoxynivalenolDeoxynivalenol

Grain protein contentGrain protein content

Kernel plumpnessbeta glucanase activity

DeoxynivalenolGrain protein content

4.12

.

Trait Affectedbeta glucan (barley)

Malt extract Grain protein contentFusarium head blightbeta glucan (barley)

Diastatic PowerDeoxynivalenol

Grain protein content

Marker-Trait Associations forMalting Quality, and Resistance to Fusarium

Head Blight & DON

0 10 20 4030 50 60 70 80 90 100

110

120

130

140

150

160

170

180

190

200

210

220

230

240

250

CHROMOSOME 1H

CHROMOSOME 2H

CHROMOSOME 3H

CHROMOSOME 4H

CHROMOSOME 5H

CHROMOSOME 6H

CHROMOSOME 7H

0 10 20 4030 50 60 70 80 90 100

110

120

130

140

150

160

170

180

190

200

210

220

230

240

250

cM Position12.23422.18835.42877.50277.502

88112.049

Number1.1.1.2.1.3.1.4.1.5.1.6.1.7.

cM Position4.405

15.39746.46950-5666.18172.752

125-132173.642

Number2.1.2.2.2.3.2.4.2.5.2.6.2.7.2.8.

cM Position35.12452-65

112.809154.837166.117

Number3.1.3.2.3.3.3.4.3.5.

cM Position0

14.50644.84757.263

122.722157.379176.129190-192239.081

Number5.1.5.2.5.3.5.4.5.5.5.6.5.7.5.8.5.9.

Trait AffectedGrain protein content

Malt extract alpha-amylase activity

Diastatic Poweralpha-amylase activity

beta glucan (malt)Grain protein content

Deoxynivalenolalpha-amylase activity

cM Position30.07430.07442-6142-6767.41986.393

124-127

Number6.1.6.2.6.3.6.4.6.5.6.6.6.7.

Trait AffectedFine coarse difference

Test weightFusarium head blight

Deoxynivalenolalpha-amylase activity

Diastatic PowerFusarium head blight

cM Position31.83760.87961.96674.094

122.249163.886

Number7.1.7.2.7.3.7.4.7.5.7.6.

Trait AffectedKernel Weight

alpha-amylase activitybeta glucan (malt)Extract viscosity

Grain protein contentalpha-amylase activity

1.1.

1.2.

1.3.

1.4.

1.5.

2.1.

2.2.

2.3.

2.5.

2.6.

2.8.

3.1.

3.3.

3.4.

3.5.

4.2.

4.3.

4.4.

4.7.

4.9.

5.1.

5.2.

5.4.

5.5.

5.6.

5.7.

5.9.

5.3.

6.1.

6.2.

6.6.

6.5.

7.1.

7.2.

7.4.

7.3.

7.5.

7.6.

1.7.

4.8.

4.10

.

cM Position3

6.77523.74325.94121-3624-3643.39943.39946.73454.44140-6196.363

Number4.1.4.2.4.3.4.4.4.5.4.6.4.7.4.8.4.9.

4.10.4.11.4.12.

5.8.

6.3.

6.4.

6.7.

Visualization of Haplotype Structure

• Breeding programs create separate populations within a crop. For example, N2 and N6 programs are primarily subpopulations unto themselves (Panel B).

• Different breeding programs align on basis of shared targets and germplasm exchange. For example, commonalities between MT, BA and AB in first column (Panel B).

• Programs exchange germplasm. For example, row for MN program has a gray bar, indicating introgression from N6. This means MN has used N6 lines as breeding parents.

Data identifying subpopulations across 1816 breeder lines in years 1 & 2 show:

Breeding programs are in rows; populations identified by structure are in columns. Bar lengths proportional to # lines from a program within each population.

A. No Admixture model, k = 10; lines assigned according to posterior probability of belonging to each population. Ten subpopulations line up fairly well with 10 breeding programs. So subpopulations are not explicitly named and number designations remained. k = # optimal subpopulations identified by program structure.

B. Admixture model, k = 7; lines assigned by genome fraction of line originating from each population. Gray bars = genome fraction of line originating from population is < 0.80. Column 8 (“Admix”) contains lines for which no population contributed > 0.50. X-axis = abbreviation for 7 subpopulations are (i) 2- or 6-row, (ii) spring (sp) or winter (wi), (iii) 2-letter abbreviation for breeding program that seemed most dominant. Y-axis: 2-letter abbreviation of breeding program submitting lines. k = # optimal subpopulations identified by program structure.

U.S. BARLEY COORDINATED AGRICULTURAL PROJECT

Barley CAP Consortium

U.S. BARLEY COORDINATED AGRICULTURAL PROJECT

Barley CAP Consortium

Summary• 2,943 SNPs were placed on the barley genetic map.• Ten breeding programs contributed 96 lines over two years (1,920 lines) that

were phenotyped for 40 traits and genotyped with 3,072 SNP markers. • Analysis of haplotype structure showed that breeding programs create

separate populations but commonalities exist because of shared targets and germplasm exchange.

• Association mapping led to QTL identification for malting quality, winter hardiness, and Fusarium head blight and deoxynivalenol resistance – information that is being used for MAS approaches.