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GrainGenes Reference Report: BMG-10-582

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Reference	BMG-10-582
Title	Development and implementation of high-throughput SNP genotyping in barley.
Journal	BMC Genomics
Year	2009
Volume	10
Pages	582
Remark	As of December 7, 2009 this publication is in production and is available as a provisional .pdf at BMC Genomics
Author	Close TJ [ Show all 28 ]
Abstract	ABSTRACT: BACKGROUND: High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. RESULTS: Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. CONCLUSIONS: The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.
External Databases	http://www.biomedcentral.com/1471-2164/10/582 http://dx.doi.org/10.1186/1471-2164-10-582
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POPA1_1467 POPA1_1471 POPA1_1474 POPA1_1476 POPA1_1491 POPA1_1514 POPA1_1519 POPA1_1520 POPA1_1523 POPA1_1531 POPA2_0004 POPA2_0019 POPA2_0024 POPA2_0025 POPA2_0026 POPA2_0028 POPA2_0030 POPA2_0033 POPA2_0034 POPA2_0035 POPA2_0038 POPA2_0040 POPA2_0041 POPA2_0043 POPA2_0046 POPA2_0048 POPA2_0049 POPA2_0050 POPA2_0051 POPA2_0054 POPA2_0055 POPA2_0056 POPA2_0061 POPA2_0065 POPA2_0066 POPA2_0067 POPA2_0068 POPA2_0069 POPA2_0070 POPA2_0071 POPA2_0073 POPA2_0075 POPA2_0077 POPA2_0081 POPA2_0082 POPA2_0084 POPA2_0087 POPA2_0088 POPA2_0091 POPA2_0094 POPA2_0098 POPA2_0106 POPA2_0110 POPA2_0111 POPA2_0116 POPA2_0120 POPA2_0122 POPA2_0123 POPA2_0128 POPA2_0137 POPA2_0140 POPA2_0152 POPA2_0154 POPA2_0161 POPA2_0163 POPA2_0164 POPA2_0165 POPA2_0166 POPA2_0167 POPA2_0171 POPA2_0174 POPA2_0175 POPA2_0177 POPA2_0190 POPA2_0191 POPA2_0194 POPA2_0199 POPA2_0202 POPA2_0203 POPA2_0204 POPA2_0208 POPA2_0209 POPA2_0213 POPA2_0214 POPA2_0216 POPA2_0218 POPA2_0221 POPA2_0223 POPA2_0228 POPA2_0231 POPA2_0233 POPA2_0238 POPA2_0243 POPA2_0244 POPA2_0248 POPA2_0250 POPA2_0253 POPA2_0254 POPA2_0255 POPA2_0256 POPA2_0258 POPA2_0261 POPA2_0263 POPA2_0268 POPA2_0270 POPA2_0271 POPA2_0275 POPA2_0277 POPA2_0279 POPA2_0280 POPA2_0282 POPA2_0284 POPA2_0286 POPA2_0296 POPA2_0299 POPA2_0301 POPA2_0304 POPA2_0305 POPA2_0308 POPA2_0310 POPA2_0312 POPA2_0313 POPA2_0316 POPA2_0318 POPA2_0319 POPA2_0321 POPA2_0322 POPA2_0330 POPA2_0331 POPA2_0337 POPA2_0338 POPA2_0341 POPA2_0344 POPA2_0348 POPA2_0352 POPA2_0353 POPA2_0360 POPA2_0364 POPA2_0376 POPA2_0377 POPA2_0378 POPA2_0380 POPA2_0382 POPA2_0389 POPA2_0391 POPA2_0393 POPA2_0395 POPA2_0397 POPA2_0398 POPA2_0399 POPA2_0400 POPA2_0401 POPA2_0404 POPA2_0405 POPA2_0408 POPA2_0418 POPA2_0420 POPA2_0423 POPA2_0425 POPA2_0426 POPA2_0430 POPA2_0431 POPA2_0433 POPA2_0435 POPA2_0437 POPA2_0445 POPA2_0446 POPA2_0447 POPA2_0456 POPA2_0457 POPA2_0459 POPA2_0462 POPA2_0464 POPA2_0469 POPA2_0470 POPA2_0471 POPA2_0473 POPA2_0474 POPA2_0477 POPA2_0478 POPA2_0481 POPA2_0483 POPA2_0484 POPA2_0490 POPA2_0491 POPA2_0492 POPA2_0499 POPA2_0503 POPA2_0506 POPA2_0508 POPA2_0510 POPA2_0512 POPA2_0516 POPA2_0517 POPA2_0519 POPA2_0520 POPA2_0522 POPA2_0530 POPA2_0535 POPA2_0538 POPA2_0539 POPA2_0540 POPA2_0541 POPA2_0542 POPA2_0543 POPA2_0544 POPA2_0547 POPA2_0548 POPA2_0554 POPA2_0555 POPA2_0556 POPA2_0559 POPA2_0564 POPA2_0565 POPA2_0569 POPA2_0575 POPA2_0578 POPA2_0579 POPA2_0581 POPA2_0587 POPA2_0588 POPA2_0589 POPA2_0592 POPA2_0596 POPA2_0598 POPA2_0604 POPA2_0614 POPA2_0615 POPA2_0616 POPA2_0619 POPA2_0621 POPA2_0622 POPA2_0624 POPA2_0627 POPA2_0630 POPA2_0633 POPA2_0634 POPA2_0635 POPA2_0638 POPA2_0655 POPA2_0658 POPA2_0661 POPA2_0663 POPA2_0664 POPA2_0665 POPA2_0672 POPA2_0677 POPA2_0678 POPA2_0679 POPA2_0683 POPA2_0692 POPA2_0693 POPA2_0702 POPA2_0703 POPA2_0705 POPA2_0706 POPA2_0716 POPA2_0717 POPA2_0726 POPA2_0727 POPA2_0735 POPA2_0738 POPA2_0739 POPA2_0741 POPA2_0747 POPA2_0751 POPA2_0752 POPA2_0753 POPA2_0756 POPA2_0759 POPA2_0763 POPA2_0764 POPA2_0767 POPA2_0768 POPA2_0773 POPA2_0774 POPA2_0776 POPA2_0779 POPA2_0787 POPA2_0788 POPA2_0789 POPA2_0800 POPA2_0802 POPA2_0804 POPA2_0806 POPA2_0809 POPA2_0811 POPA2_0812 POPA2_0813 POPA2_0814 POPA2_0819 POPA2_0821 POPA2_0822 POPA2_0823 POPA2_0834 POPA2_0836 POPA2_0837 POPA2_0842 POPA2_0843 POPA2_0846 POPA2_0852 POPA2_0857 POPA2_0859 POPA2_0860 POPA2_0865 POPA2_0869 POPA2_0870 POPA2_0871 POPA2_0872 POPA2_0874 POPA2_0875 POPA2_0888 POPA2_0899 POPA2_0900 POPA2_0901 POPA2_0902 POPA2_0910 POPA2_0913 POPA2_0914 POPA2_0916 POPA2_0918 POPA2_0919 POPA2_0925 POPA2_0927 POPA2_0928 POPA2_0930 POPA2_0932 POPA2_0933 POPA2_0935 POPA2_0937 POPA2_0938 POPA2_0941 POPA2_0942 POPA2_0945 POPA2_0948 POPA2_0950 POPA2_0957 POPA2_0963 POPA2_0964 POPA2_0965 POPA2_0966 POPA2_0967 POPA2_0973 POPA2_0977 POPA2_0978 POPA2_0979 POPA2_0983 POPA2_0984 POPA2_0986 POPA2_0991 POPA2_0992 POPA2_1002 POPA2_1004 POPA2_1006 POPA2_1013 POPA2_1021 POPA2_1022 POPA2_1023 POPA2_1026 POPA2_1028 POPA2_1031 POPA2_1033 POPA2_1034 POPA2_1039 POPA2_1042 POPA2_1043 POPA2_1044 POPA2_1045 POPA2_1046 POPA2_1047 POPA2_1051 POPA2_1054 POPA2_1055 POPA2_1058 POPA2_1059 POPA2_1060 POPA2_1063 POPA2_1066 POPA2_1074 POPA2_1075 POPA2_1076 POPA2_1080 POPA2_1082 POPA2_1084 POPA2_1085 POPA2_1089 POPA2_1090 POPA2_1091 POPA2_1092 POPA2_1097 POPA2_1100 POPA2_1102 POPA2_1106 POPA2_1107 POPA2_1113 POPA2_1118 POPA2_1119 POPA2_1123 POPA2_1127 POPA2_1132 POPA2_1139 POPA2_1143 POPA2_1146 POPA2_1149 POPA2_1152 POPA2_1154 POPA2_1159 POPA2_1164 POPA2_1165 POPA2_1169 POPA2_1170 POPA2_1171 POPA2_1179 POPA2_1180 POPA2_1182 POPA2_1183 POPA2_1185 POPA2_1195 POPA2_1196 POPA2_1198 POPA2_1199 POPA2_1206 POPA2_1211 POPA2_1214 POPA2_1218 POPA2_1222 POPA2_1227 POPA2_1230 POPA2_1231 POPA2_1232 POPA2_1233 POPA2_1235 POPA2_1236 POPA2_1237 POPA2_1240 POPA2_1248 POPA2_1249 POPA2_1252 POPA2_1255 POPA2_1257 POPA2_1262 POPA2_1263 POPA2_1264 POPA2_1269 POPA2_1276 POPA2_1278 POPA2_1279 POPA2_1282 POPA2_1283 POPA2_1284 POPA2_1285 POPA2_1287 POPA2_1292 POPA2_1295 POPA2_1301 POPA2_1306 POPA2_1311 POPA2_1313 POPA2_1316 POPA2_1317 POPA2_1320 POPA2_1322 POPA2_1323 POPA2_1327 POPA2_1329 POPA2_1331 POPA2_1334 POPA2_1336 POPA2_1341 POPA2_1342 POPA2_1343 POPA2_1347 POPA2_1349 POPA2_1352 POPA2_1364 POPA2_1367 POPA2_1368 POPA2_1369 POPA2_1371 POPA2_1375 POPA2_1378 POPA2_1379 POPA2_1380 POPA2_1382 POPA2_1383 POPA2_1387 POPA2_1394 POPA2_1403 POPA2_1407 POPA2_1410 POPA2_1412 POPA2_1413 POPA2_1417 POPA2_1420 POPA2_1424 POPA2_1429 POPA2_1430 POPA2_1432 POPA2_1433 POPA2_1434 POPA2_1439 POPA2_1441 POPA2_1444 POPA2_1451 POPA2_1454 POPA2_1456 POPA2_1457 POPA2_1460 POPA2_1465 POPA2_1466 POPA2_1468 POPA2_1474 POPA2_1478 POPA2_1483 POPA2_1484 POPA2_1485 POPA2_1486 POPA2_1487 POPA2_1488 POPA2_1489 POPA2_1498 POPA2_1499 POPA2_1501 POPA2_1503 POPA2_1510 POPA2_1512 POPA2_1515 POPA2_1518 POPA2_1519 POPA2_1524 POPA2_1525 POPA2_1526 POPA2_1529 POPA2_1530 POPA2_1532 POPA2_1535 POPA3_0012 POPA3_0013 POPA3_0015 POPA3_0016 POPA3_0017 POPA3_0018 POPA3_0019 POPA3_0020 POPA3_0022 POPA3_0023 POPA3_0024 POPA3_0027 POPA3_0028 POPA3_0030 POPA3_0031 POPA3_0033 POPA3_0034 POPA3_0035 POPA3_0036 POPA3_0037 POPA3_0038 POPA3_0044 POPA3_0045 POPA3_0047 POPA3_0051 POPA3_0052 POPA3_0058 POPA3_0061 POPA3_0066 POPA3_0069 POPA3_0070 POPA3_0071 POPA3_0073 POPA3_0074 POPA3_0075 POPA3_0076 POPA3_0077 POPA3_0078 POPA3_0079 POPA3_0082 POPA3_0085 POPA3_0086 POPA3_0089 POPA3_0091 POPA3_0093 POPA3_0094 POPA3_0099 POPA3_0100 POPA3_0101 POPA3_0103 POPA3_0104 POPA3_0107 POPA3_0112 POPA3_0121 POPA3_0123 POPA3_0124 POPA3_0127 POPA3_0128 POPA3_0131 POPA3_0134 POPA3_0139 POPA3_0156 POPA3_0157 POPA3_0159 POPA3_0160 POPA3_0161 POPA3_0171 POPA3_0172 POPA3_0173 POPA3_0174 POPA3_0175 POPA3_0176 POPA3_0177 POPA3_0180 POPA3_0184 POPA3_0185 POPA3_0188 POPA3_0189 POPA3_0190 POPA3_0194 POPA3_0196 POPA3_0198 POPA3_0201 POPA3_0202 POPA3_0207 POPA3_0208 POPA3_0210 POPA3_0211 POPA3_0212 POPA3_0215 POPA3_0217 POPA3_0218 POPA3_0220 POPA3_0225 POPA3_0227 POPA3_0228 POPA3_0233 POPA3_0234 POPA3_0235 POPA3_0245 POPA3_0246 POPA3_0247 POPA3_0249 POPA3_0252 POPA3_0253 POPA3_0255 POPA3_0256 POPA3_0258 POPA3_0261 POPA3_0263 POPA3_0264 POPA3_0266 POPA3_0267 POPA3_0269 POPA3_0270 POPA3_0272 POPA3_0273 POPA3_0279 POPA3_0280 POPA3_0281 POPA3_0282 POPA3_0286 POPA3_0287 POPA3_0288 POPA3_0289 POPA3_0291 POPA3_0292 POPA3_0293 POPA3_0294 POPA3_0300 POPA3_0302 POPA3_0303 POPA3_0307 POPA3_0309 POPA3_0312 POPA3_0313 POPA3_0315 POPA3_0320 POPA3_0321 POPA3_0322 POPA3_0324 POPA3_0326 POPA3_0327 POPA3_0330 POPA3_0332 POPA3_0333 POPA3_0334 POPA3_0339 POPA3_0340 POPA3_0345 POPA3_0347 POPA3_0349 POPA3_0356 POPA3_0357 POPA3_0359 POPA3_0364 POPA3_0365 POPA3_0366 POPA3_0369 POPA3_0372 POPA3_0373 POPA3_0374 POPA3_0376 POPA3_0381 POPA3_0383 POPA3_0384 POPA3_0386 POPA3_0387 POPA3_0391 POPA3_0392 POPA3_0393 POPA3_0397 POPA3_0398 POPA3_0401 POPA3_0405 POPA3_0407 POPA3_0412 POPA3_0413 POPA3_0415 POPA3_0416 POPA3_0417 POPA3_0418 POPA3_0421 POPA3_0422 POPA3_0426 POPA3_0428 POPA3_0429 POPA3_0433 POPA3_0434 POPA3_0435 POPA3_0437 POPA3_0439 POPA3_0440 POPA3_0442 POPA3_0443 POPA3_0446 POPA3_0447 POPA3_0448 POPA3_0451 POPA3_0452 POPA3_0453 POPA3_0457 POPA3_0458 POPA3_0460 POPA3_0461 POPA3_0463 POPA3_0464 POPA3_0466 POPA3_0468 POPA3_0469 POPA3_0470 POPA3_0471 POPA3_0479 POPA3_0483 POPA3_0484 POPA3_0485 POPA3_0489 POPA3_0490 POPA3_0493 POPA3_0495 POPA3_0497 POPA3_0500 POPA3_0501 POPA3_0507 POPA3_0512 POPA3_0513 POPA3_0518 POPA3_0519 POPA3_0520 POPA3_0523 POPA3_0526 POPA3_0527 POPA3_0529 POPA3_0534 POPA3_0535 POPA3_0536 POPA3_0537 POPA3_0541 POPA3_0542 POPA3_0547 POPA3_0548 POPA3_0549 POPA3_0551 POPA3_0552 POPA3_0553 POPA3_0558 POPA3_0559 POPA3_0560 POPA3_0568 POPA3_0570 POPA3_0572 POPA3_0578 POPA3_0579 POPA3_0585 POPA3_0586 POPA3_0587 POPA3_0599 POPA3_0601 POPA3_0607 POPA3_0608 POPA3_0610 POPA3_0612 POPA3_0613 POPA3_0614 POPA3_0615 POPA3_0617 POPA3_0623 POPA3_0624 POPA3_0628 POPA3_0629 POPA3_0632 POPA3_0633 POPA3_0638 POPA3_0641 POPA3_0643 POPA3_0647 POPA3_0648 POPA3_0650 POPA3_0652 POPA3_0659 POPA3_0660 POPA3_0661 POPA3_0662 POPA3_0664 POPA3_0667 POPA3_0669 POPA3_0670 POPA3_0671 POPA3_0675 POPA3_0676 POPA3_0679 POPA3_0682 POPA3_0686 POPA3_0687 POPA3_0688 POPA3_0689 POPA3_0692 POPA3_0699 POPA3_0701 POPA3_0704 POPA3_0706 POPA3_0708 POPA3_0711 POPA3_0712 POPA3_0713 POPA3_0720 POPA3_0722 POPA3_0725 POPA3_0726 POPA3_0727 POPA3_0730 POPA3_0731 POPA3_0733 POPA3_0735 POPA3_0738 POPA3_0739 POPA3_0740 POPA3_0741 POPA3_0746 POPA3_0756 POPA3_0757 POPA3_0758 POPA3_0763 POPA3_0766 POPA3_0770 POPA3_0771 POPA3_0773 POPA3_0776 POPA3_0778 POPA3_0784 POPA3_0789 POPA3_0791 POPA3_0798 POPA3_0800 POPA3_0801 POPA3_0803 POPA3_0805 POPA3_0807 POPA3_0808 POPA3_0810 POPA3_0811 POPA3_0812 POPA3_0813 POPA3_0814 POPA3_0815 POPA3_0816 POPA3_0862 POPA3_0874 POPA3_0875 POPA3_0881 POPA3_0885 POPA3_0887 POPA3_0888 POPA3_0890 POPA3_0898 POPA3_0903 POPA3_0911 POPA3_0912 POPA3_0928 POPA3_0932 POPA3_0936 POPA3_0937 POPA3_0938 POPA3_0943 POPA3_0946 POPA3_0947 POPA3_0954 POPA3_0961 POPA3_0964 POPA3_0970 POPA3_0971 POPA3_0986 POPA3_1001 POPA3_1013 POPA3_1024 POPA3_1025 POPA3_1027 POPA3_1028 POPA3_1030 POPA3_1031 POPA3_1036 POPA3_1037 POPA3_1038 POPA3_1039 POPA3_1040 POPA3_1045 POPA3_1047 POPA3_1051 POPA3_1052 POPA3_1056 POPA3_1057 POPA3_1058 POPA3_1060 POPA3_1061 POPA3_1063 POPA3_1067 POPA3_1068 POPA3_1069 POPA3_1070 POPA3_1073 POPA3_1078 POPA3_1079 POPA3_1080 POPA3_1082 POPA3_1083 POPA3_1085 POPA3_1087 POPA3_1089 POPA3_1090 POPA3_1091 POPA3_1093 POPA3_1097 POPA3_1098 POPA3_1102 POPA3_1103 POPA3_1104 POPA3_1106 POPA3_1107 POPA3_1108 POPA3_1112 POPA3_1114 POPA3_1116 POPA3_1118 POPA3_1119 POPA3_1121 POPA3_1125 POPA3_1129 POPA3_1130 POPA3_1131 POPA3_1132 POPA3_1133 POPA3_1135 POPA3_1136 POPA3_1141 POPA3_1142 POPA3_1143 POPA3_1145 POPA3_1146 POPA3_1147 POPA3_1150 POPA3_1154 POPA3_1157 POPA3_1158 POPA3_1162 POPA3_1168 POPA3_1171 POPA3_1172 POPA3_1176 POPA3_1184 POPA3_1185 POPA3_1190 POPA3_1191 POPA3_1193 POPA3_1195 POPA3_1196 POPA3_1197 POPA3_1201 POPA3_1204 POPA3_1212 POPA3_1213 POPA3_1216 POPA3_1223 POPA3_1226 POPA3_1228 POPA3_1243 POPA3_1244 POPA3_1245 POPA3_1247 POPA3_1248 POPA3_1255 POPA3_1260 POPA3_1263 POPA3_1265 POPA3_1266 POPA3_1273 POPA3_1287 POPA3_1290 POPA3_1296 POPA3_1301 POPA3_1302 POPA3_1304 POPA3_1306 POPA3_1307 POPA3_1309 POPA3_1311 POPA3_1314 POPA3_1316 POPA3_1318 POPA3_1320 POPA3_1321 POPA3_1322 POPA3_1328 POPA3_1330 POPA3_1331 POPA3_1332 POPA3_1334 POPA3_1335 POPA3_1336 POPA3_1337 POPA3_1338 POPA3_1339 POPA3_1341 POPA3_1343 POPA3_1344 POPA3_1347 POPA3_1348 POPA3_1349 POPA3_1354 POPA3_1355 POPA3_1358 POPA3_1364 POPA3_1365 POPA3_1369 POPA3_1370 POPA3_1371 POPA3_1373 POPA3_1376 POPA3_1378 POPA3_1379 POPA3_1384 POPA3_1386 POPA3_1389 POPA3_1391 POPA3_1397 POPA3_1399 POPA3_1400 POPA3_1403 POPA3_1405 POPA3_1407 POPA3_1412 POPA3_1413 POPA3_1415 POPA3_1416 POPA3_1419 POPA3_1421 POPA3_1425 POPA3_1426 POPA3_1429 POPA3_1430 POPA3_1434 POPA3_1435 POPA3_1436 POPA3_1437 POPA3_1438 POPA3_1439 POPA3_1442 POPA3_1447 POPA3_1449 POPA3_1453 POPA3_1454 POPA3_1455 POPA3_1456 POPA3_1457 POPA3_1459 POPA3_1460 POPA3_1465 POPA3_1466 POPA3_1468 POPA3_1470 POPA3_1471 POPA3_1472 POPA3_1476 POPA3_1478 POPA3_1480 POPA3_1482 POPA3_1483 POPA3_1488 POPA3_1489 POPA3_1494 POPA3_1501 POPA3_1504 POPA3_1505 POPA3_1507 POPA3_1508 POPA3_1510 POPA3_1514 POPA3_1516 POPA3_1518 POPA3_1522 POPA3_1530 POPA3_1531 POPA3_1532 POPA3_1533 POPA3_1534 JS074 DAK123B PSR330 BCD1930 Bgq60 Tel3S JS195F BCD1532 JS103.3 Ole1 KFP221 Tel4M DAK133 Tel7L Tel6S DD1.1C Ldh1 Tef1 DAK213C
Map Data	Barley, OPA 2009, Consensus

GrainGenes is a product of the Agricultural Research Service of the US Department of Agriculture.