THE FULL LENGTH INSERT SEQUENCE PROJECT FOR MAIZE MARKER RFLP PROBES
collaboration between PlantGDB and the Cytogenetic Map of Maize Project
(led by Dr. Hank Bass, Florida State University; informatics by Dr. Carolyn Lawrence, USDA-ARS)
The maize genome is divided among 10 chromosomes, and gene locations can be charted as genetic, physical, or cytological maps. The maize cytogenetic map is based on the pachytene stage chromosome karyotype that has been ruled by a fractional arm length unit currently referred to as centiMcClintocks (cMC). The cytogenetic map has many translocation breakpoint loci, but relatively few genetic markers (RFLP loci) to define those breakpoints. The mapping of markers that are shared among the three different maps will enhance the integrated view of the maize genome structure while creating new genetic and molecular tools for genome research and improvement. The Cytogenetic Map of Maize Project aims to produce a cytogenetic map of the entire maize genome (NSF-DBI-0321639) using sorghum BACs as fluorescence in situ hybridization (FISH) probes on pachytene spreads. The goals of the project all involve using FISH to determine the cytogenetic locations of genetically mapped maize marker sequences. Current specific aims are (1) to develop a framework cytogenetic map with markers (CBMs) distributed at 10-20 cM intervals, (2) to develop a detailed map of maize chromosome 9, and (3) to map centromeric loci as an indirect method of locating the centromeres more precisely within the current linkage maps. The results will be integrated with other genome maps and released immediately into GenBank and MaizeGDB for public access.
The RFLP Full Length Insert Sequencing (FLIS) Project is an endeavor ancillary to the Cytogenetic Map of Maize Project. The goals of this undertaking are to determine and submit to GenBank a hiqh-quality (both strands) full length insert sequence for maize RFLP markers including the CBMs (~ 90 total) and potentially as many as ~ 500 other markers from the UMC 98 map. In addition to being useful for the Cytogenetic Map of Maize Project, these sequences are useful in that they can anchor assemblies of the maize genome to the genetic and cytogenetic maps.
The following table summarizes the RFLP-FLIS and provides links to the best B73 sequence match as well as off-site resources.
| Bin | Locus | CBM? | Probe | Probe Type | Probe Length | Probe FLIS (GI) |
Best Sequence Match in B73 (GI) 
|
Exemplar?
|
% ID Between Probe and B73 Match
|
|---|---|---|---|---|---|---|---|---|---|
| 1.2 | umc157(chn) | Y | p-umc157 | genomic | 1250 | 75853388 | 33981684 | N | 99 (915/919) |
| 1.3 | umc76a | Y | p-umc76 | genomic | 710 | 54402363 | 30846486 | N | 95 (691/723) |
| 1.4 | asg45(ptk) | Y | p-asg45 | genomic | 332 | 54111436 | 28418938 | Y | 100 (332/332) |
| 1.5 | csu3 | Y | p-csu3 | cDNA | 1064 | 75853389 | 30882360 | N | 100 (420/420) |
| 1.6 | umc67a | Y | p-umc67 | genomic | 644 | 54111437 | 34208050 | N | 97 (628/646) |
| 1.7 | asg62 | Y | p-asg62 | genomic | 465 | 66912523 | 34294752 | Y | 100 (465/465) |
| 1.8 | umc128 | Y | p-umc128 | genomic | 755 | 75853390 | 29233336 | N | 90 (450/469) |
| 1.11 | umc161a | Y | p-umc161 | genomic | 723 | 54111438 | 34110208 | N | 99 (721/723) |
| 2.2 | umc53a | Y | p-umc53 | genomic | 608 | 54111439 | 28104363 | N | 98 (550/559) |
| 2.3 | umc6a | Y | p-umc6 | genomic | 604 | 54111440 | 32046909 | N | 95 (495/517) |
| 2.4 | umc34 | Y | p-umc34 | genomic | 934 | 66912524 | 34250206 | N | 95 (561/589) |
| 2.5 | umc131 | Y | p-umc131 | genomic | 859 | 54111441 | 28982391 | N | 100 (802/802) |
| 2.6 | umc255a | Y | p-umc255 | genomic | 1013 | 75853391 | 30850573 | N | 96 (656/677) |
| 2.7 | umc5a | Y | p-umc5 | genomic | 830 | 54111442 | 61709054 | N | 97 (668/686) |
| 2.8 | asg20 | Y | p-asg20 | genomic | 337 | 75853392 | 34241793 | N | 98 (176/179) |
| 2.9 | umc49a | Y | p-umc49 | genomic | 627 | 75853393 | 28707822 | N | 93 (321/342) |
| 3.1 | umc32a | Y | p-umc32a | genomic | 1019 | 66912525 | 34265073 | N | 97 (795/819) |
| 3.2 | csu32 | Y | p-csu32 | genomic | 411 | 75853394 | 32121444 | N | 100 (391/391) |
| 3.3 | asg24(gts) | Y | p-asg24 | genomic | 372 | 54111443 | 34081732 | Y | 100 (372/372) |
| 3.4 | asg48 | Y | p-asg48 | genomic | 1617 | 66912526 | 40353248 | N | 99 (1594/1600) |
| 3.5 | umc102 | Y | p-umc102 | genomic | 1023 | 66866465 | 34232762 | N | 99 (684/689) |
| 3.8 | umc17a | Y | p-umc17 | genomic | 840 | 54111444 | 34126092 | N | 98 (823/835) |
| 3.9 | umc63 | Y | p-umc63 | genomic | 881 | 75853395 | 32080365 | N | 96 (646/667) |
| 3.10 | cyp1 | Y | p-csu25 | cDNA | 960 | 66866466 | 26036071 | N | 100 (773/773) |
| 4.3 | umc31a | Y | p-umc31a | genomic | 582 | 75853396 | 33972000 | N | 96 (515/531) |
| 4.4 | npi386(eks) | Y | p-npi386 | genomic | 1180 | 66866403 | 34152395 | N | 98 (432/437) |
| 4.6 | umc156a | Y | p-umc156 | genomic | 533 | 54111445 | 31968852 | N | 98 (527/533) |
| 4.7 | umc66a(lcr) | Y | p-umc66 | genomic | 1036 | 66866404 | 34093427 | N | 98 (833/844) |
| 4.9 | umc52 | Y | p-umc52 | genomic | 824 | 75853397 | 31969394 | N | 100 (465/465) |
| 4.10 | php20608a | Y | p-php20608 | genomic | 1451 | 66866405 | 34262399 | N | 99 (897/898) |
| 4.11 | umc169 | Y | p-umc169 | genomic | 813 | 75853398 | 34243235 | N | 99 (521/525) |
| 5.3 | tub4 | Y | p-tub4 | cDNA | 230 | 66866406 | 28104588 | N | 100 (201/201 |
| 5.5 | csu93b | Y | p-csu93 | cDNA | 677 | 66803523 | 33968473 | N | 99 (456/459) |
| 5.6 | umc126a | Y | p-umc126 | genomic | 663 | 54111446 | 34064726 | N | 98 (660/673) |
| 5.9 | php10017 | Y | p-php10017 | genomic | 526 | 54111447 | 34848572 | Y | 100 (526/526) |
| 6.1 | umc85a | Y | p-umc85 | genomic | 561 | 54111448 | 34044414 | N | 99 (560/561) |
| 6.4 | umc65a | Y | p-umc65 | genomic | 691 | 54111449 | 33975136 | N | 99 (690/691) |
| 6.5 | umc21 | Y | p-umc21 | genomic | 1062 | 75853399 | 30825795 | N | 96 (894/930) |
| 6.6 | umc38a | Y | p-umc38 | genomic | 1022 | 66803535 | 32145547 | N | 96 (752/776) |
| 6.7 | umc132a(chk) | Y | p-umc132 | genomic | 472 | 75853400 | 42507358 | Y | 100 (472/472) |
| 7.3 | asg49 | Y | p-asg49 | genomic | 400 | 66803540 | 28705091 | N | 98 (223/227) |
| 7.5 | umc245 | Y | p-umc245 | genomic | 665 | 54111450 | 34240514 | N | 96 (241/251) |
| 7.6 | umc168 | Y | p-umc168 | genomic | 1072 | 66803547 | 34074260 | N | 97 (708/724) |
| 8.1 | npi220a | Y | p-G10F-01 | genomic | 406 | 66803556 | 28701338 | N | 99 (403/406) |
| 8.3 | umc124a(chk) | Y | p-umc124 | genomic | 1162 | 66803561 | 34245591 | N | 99 (893/894) |
| 8.7 | npi268a | Y | p-npi268 | genomic | 688 | 75853401 | 71930338 | N | 93 (164/175) |
| 8.8 | npi414a | Y | p-npi414 | genomic | 893 | 54111451 | 42499303 | N | 96 (370/385) |
| 9.1 | umc109 | Y | p-umc109 | genomic | 797 | 54111452 | 25462797 | N | 98 (678/688) |
| 9.1 | umc148 | N | p-umc148 | genomic | 529 | 49359174 | 34242738 | Y | 100 (529/529) |
| 9.5 | umc95 | Y | p-umc95 | genomic | 660 | 54111453 | 34149385 | Y | 100 (660/660) |
| 9.7 | asg12 | Y | p-asg12 | genomic | 647 | 75853402 | 34130652 | N | 98 (559/567) |
| 10.1 | php20075a(gast) | Y | p-php20075 | genomic | 1311 | 66803566 | 34133222 | N | 99 (909/911) |
| 10.3 | umc130 | Y | p-umc130 | genomic | 634 | 66803573 | 32007214 | N | 99 (631/634) |
| 10.5 | umc259a | Y | p-umc259 | genomic | 579 | 75853403 | 34250114 | N | 98 (316/320) |