Maize
Genetics Cooperation Newsletter 78. 2004.
V. COMMUNITY IBM (cIBM2004) MAPS
Map
score data for the community IBM maps were supplied by various cooperators
(Table 1) and are based on the IBM-94 panel of 94 stocks. These lines are a subset of the high
resolution IBM-302 mapping population used to anchor the physical map (Cone et
al., Plant Physiol 130:1686-1696, 2002). The IBM recombinant inbreds were
developed from the Syn 5 generation, following 4 inter-matings of B73xMo17
(Lee, M et al., Plant Mol Biol 48:453-461,
2002). Seed for the IBM-94 (Table
2) is distributed by the Maize Genetics Cooperation Stock Center <http://maizegdb.org/cgi-bin/stockcatalog.cgi?id=1>. DNA samples of the IBM-94 and
the parent lines, along with protocols, are distributed at the University of
Missouri-Columbia (<http://www.maizemap.org/dna_kits.htm>. Map score data submitted over the web
<http://www.maizemap.org/CIMDE/cimde.html
> will return map results within a week after submission; loci are
placed based on a framework of 250 loci, also previously placed on the high
resolution IBM maps. Each new marker is assigned to chromosome and mapped on the
individual chromosomes using the build and place commands of Mapmaker.
With
permission of individual cooperators, the community map will be published
annually to MaizeGDB. Loci submitted to MaizeGDB are vetted, in consultation with
the contributors, for nomenclature, and probe details, including relationships
of probes to physical map probes.
The first community map was provided to MaizeGDB Dec 2003 and is called
cIBM2003. Information about associations
to the physical map are additionally provided to Cari Soderland via the IBM
neighbors (Polacco, M et al., Plant and Animal Genomes XII Conference, 2004,
Maize Workshop < http://63.141.253.172/12/abstracts/W34_PAG12_159.html>
for inclusion in the maize FPC product <http://www.genome.arizona.edu/fpc/maize/>
and to the Maize Mapping Project iMap representation <http://www.
maizemap.org/imap.htm>.
Table
1. Cooperators providing raw map
data include:
Ivan Acosta, Yale University, New Haven, CT: hlm2, tip1
Hank Bass, University of
Georgia, Athens, GA: fsu1b(smh2), smh1.
Tom Brutnell, Cornell University, Ithaca, NY <http://bti.cornell.edu/Brutnell_lab2/Projects/Tagging/BMGG_pro_tagging.html>: bti00191a::Ac, bti00191b::Ac, bti03525::Ac, bti03526::Ac, bti03545::Ac, bti03557::Ac, bti03616::Ac, bti03702::Ac, bti03811::Ac, bti31132a::Ac, bti31132b::Ac, bti31192::Ac, bti99224::Ac, btilc175::Ac, mon00004::Ac, mon00030::Ac, mon00038::Ac, mon00044::Ac, mon00060::Ac, mon00072::Ac, mon00084::Ac, mon00088::Ac, mon00092::Ac, mon00106::Ac, mon00108::Ac, mon00122::Ac, mon00128::Ac, mon00150::Ac, mon00152::Ac, mon00178::Ac, mon00186::Ac, mon00192::Ac, mon00200::Ac, mon00218::Ac, mon00236::Ac, mon03068::Ac, mon03077::Ac, mon03078::Ac, mon03080::Ac.
ChromDB <http://www.chromdb.org>, University of Arizona, Tucson, AZ. Chromatin RFLP: ago108, bnlg182, brd101, brd102, brd103, chb101a, chb101b, chb102, chc101a, chc101b, chr106a, chr106b, chr109a, chr109b, chr110a, chr110b, chr111, chr112a, chr112b, chr113, chr116a, chr116b, chr117a, chr117b, chr117c, chr117d, chr118, chr118, chr119, chr120, chr122, chr124, chr125a, chr125b, chr126a, chr126b, crd101, dmt101, dmt102a, dmt102b, dmt103a, dmt103b, dmt103c, epl101, fie2, gta105, gta106b, gta107a, gta107b, gtb101, gtc101, gtc102, gtd101, gte101, gte102, hac101a, hac101b, haf101, hag101, hag102, hag103a, hag103b, hag105, hda102, hda108, hda109, hda110, hdt102, hdt103, hdt105, hmga101, hon104a, hon104b, hon105, hon106a, hon106b, hon107a, hon107b, hon110, hxa102a, hxa102b, mbd101a, mbd101b, mbd105, mbd106, mbd108, mbd109, mbd116, mbd119, mbd121, mez1, nfa101, nfa102a, nfa102b, nfa104, nfc101, nfc103a, nfc103b, nfc104a, nfc104b, nfc104c, nfc105, nfd101a, nfd101b, nfd102, nfd104a, nfd104c, nfd104d, nfd104e, nfd105, nfd106, nfd107, nfd108, nfd109, nfd110, nfd114, nfe101, sdg101, sdg102a, sdg102b, sdg102c, sdg104, sdg105a, sdg106, sdg107, sdg108a, sdg108b, sdg110, sdg111a, sdg113, sdg115, sdg116a, sdg116b, sdg117a, sdg117b, sdg118, sdg119, sdg123, sdg129, sgb101, sgb103, sgf101, smh4, vef101a, vef101b.
Genoplante, France <http://genoplante-info.infobiogen.fr>. RFLP related to Overgos on the physical
map: gpm1, gpm10, gpm11, gpm12, gpm13, gpm14, gpm15, gpm16, gpm2, gpm3,
gpm4, gpm5, gpm6, gpm7, gpm8, gpm9
Peter Rogowsky, EDP ENS-Lyon, Lyon France: ensl015, ensl016.
Mike McMullen, USDA-ARS
Columbia, MO. SNPs related to
Overgos on the Physical map: AI714808, AI737325, AI861369, AW036917,
AW172071, AW231791, AW258116, AY103622, AY103942, AY103944, AY104188, AY104234,
AY104686, AY105043, AY105132, AY105205, AY105451, AY105479, AY105872, AY106026,
AY106137, AY106170, AY106313, AY106318, AY106439, AY106518, AY106592, AY106674,
AY106825, AY107012, AY107018, AY107034, AY107053, AY107079, AY107121, AY107128,
AY107193, AY107200, AY107292, AY107329, AY107414, AY107489, AY107496, AY107517,
AY107629, AY107682, AY107743, AY107844, AY107881, AY107910, AY107911, AY108545,
AY108825, AY108844, AY109061, AY109096, AY109128, AY109538, AY109804, AY110113,
AY110240, AY110782, AY110827, AY110835, AY110853, AY111089, AY111254, AY111333,
AY111822, AY111877, AY111962, AY112119, AY112175, AY112199, AY112283, AY112355,
BE518809, BG266188
Sahtoh Namiko, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY: shpl1.
Wolfgang Werr, Roman Zimmerman, Institut fŸr Entwicklungsbiologie,Universtaat Kšln, Kšln, Germany: nact11, nact12, nact15, nact16a, ns1
Table 2. The IBM-94 panel includes the below lines:
MO001 MO005 MO007 MO008 MO010 MO012
MO014 MO015 MO016 MO017 MO021 MO022 MO023 MO024 MO025 MO027 MO028 MO029 MO030
MO031 MO032 MO033 MO034 MO035 MO039 MO040 MO043 MO044 MO045 MO046 MO048 MO051
MO052 MO054 MO055 MO057 MO058 MO060 MO061 MO062 MO063 NO066 MO067 MO074 MO075
MO076 MO077 MO079 MO262 MO264 MO265 MO266 MO267 MO269 MO272 MO275 MO276 MO281
MO284 MO287 MO288 MO296 MO297 MO298 MO309 MO310 MO311 MO315 MO317 MO321 MO322
MO323 MO325 MO326 MO328 MO337 MO341 MO344 MO345 MO346 MO352 MO354 MO355 MO357
MO360 MO364 MO365 MO368 MO369 MO378 MO379 MO382 MO383 MO384
These line numbers are identical to the
corresponding line in the larger panel of stocks, IBM 302, where seed is also
maintained at the Stock Center.
Acknowledgements. This report would not have been possible without the considerable contributions of Karen Cone, Mike McMullen, Georgia Davis, Seth Haverman and Hector Sanchez-Villeda towards the design and implementation of the CIMDE (Community IBM map data entry) software package (Sanchez-Villeda et al., Bioinformatics 19:2022-2030, 2003) and the encouragement of Ed Coe, PI of the Maize Mapping Project, NSF DBI 9872655, which funded the software resources used for these maps.
Maps Legend.
Bin edges are indicated to the left of each chromosome; asterisks indicate a core marker. Positions of off-frame loci are indicated as an interval value, in parentheses, and refer to the interval ÔdownÕ from the framework locus to their immediate left. Note, due to the inter-matings in this population, these map coordinates are not centiMorgan (cM) units as defined in the classical sense.
Submitted by
Mary Polacco
USDA-ARS
University of Missouri
_________________________________________________
Please
note:
Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only
with consent of the authors.
Return to MNL 78on-line index.
Return to MNL index.
Return to MaizeGDB home page
____________________________________________
|
cIBM2004 CHROMOSOME 1 |
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|
|
|
|
|
BIN |
Position |
Locus |
Locus Off Frame |
|
1.00 |
0 |
umc1354 |
|
|
1.01 |
2.3 |
tub1 |
|
|
|
6.9 |
dmt103b |
|
|
|
10.5 |
umc1566 |
(17.4)mon03077::Ac |
|
|
44.2 |
lim179 |
(7.7)AY107629 |
|
|
68.1 |
umc1977 |
|
|
|
80.4 |
AY110853 |
|
|
1.02 |
90.5 |
umc157a |
|
|
|
107.3 |
csu1171 |
|
|
|
134.6 |
bnlg1953 |
(2.3)mon03080::Ac |
|
|
180.6 |
mon00192::Ac, mon00106::Ac |
|
|
1.03 |
180.7 |
umc76a |
|
|
|
185.9 |
umc1403 |
|
|
|
234.1 |
AY106592 |
|
|
|
243.0 |
asg35b |
|
|
|
254.0 |
AY110240 |
|
|
|
257.1 |
AY107489 |
(4.8)bnlg182 |
|
|
262.5 |
umc1598 |
|
|
|
274.5 |
mmp100 |
|
|
1.04* |
295.7 |
umc1169 |
(0.6)chr125b |
|
|
310.2 |
bnl9.11b |
(3.1)AY103942 |
|
1.05 |
324.6 |
csu3 |
(5.5)btilc175::Ac |
|
|
339.0 |
umc1515 |
|
|
|
342.1 |
nfd104c |
|
|
|
346.1 |
AY106439 |
|
|
|
347.2 |
AY107682 |
|
|
|
358.7 |
hac101b |
|
|
1.06* |
367.4 |
mbd106 |
|
|
|
369.8 |
umc1972 |
(1.1)gpm4 |
|
|
385.5 |
mbd119 |
|
|
|
392.3 |
asg58 |
|
|
|
404.1 |
nact15 |
|
|
|
427.2 |
ntf1 |
|
|
|
448.5 |
umc192 |
(56.1)mon00186::Ac |
|
1.07 |
449.1 |
asg62 |
|
|
|
510.4 |
bnlg1556 |
|
|
|
520.3 |
dmt103c |
|
|
|
537.9 |
hon105 |
(8.7)bti03557::Ac |
|
|
547.4 |
bnlg1025 |
|
|
1.08 |
561.1 |
umc128 |
(0.6)AY105132 |
|
|
568.2 |
bnlg2228 |
|
|
|
570.7 |
chr124 |
|
|
|
574.3 |
bti03545::Ac |
|
|
|
577.4 |
sdg123 |
|
|
|
586.5 |
umc1991 |
|
|
|
606.2 |
nfc103a |
|
|
1.09 |
611.1 |
cdj2 |
(3.7)AY106137 |
|
|
625.8 |
umc2047 |
|
|
|
639.7 |
AY112283 |
|
|
1.10 |
644.4 |
umc107a |
|
|
|
650.8 |
chb101b, chr106a |
|
|
|
650.9 |
nfa103a |
|
|
|
656.2 |
AY104234 |
|
|
|
660.6 |
hxa102b |
|
|
|
662.5 |
vef101b |
|
|
1.11* |
671.6 |
lim39 |
(21.7)mon00200::Ac |
|
|
696.7 |
umc1421 |
(2.7)hon110 |
|
|
714.2 |
AY109096 |
|
|
|
727.0 |
AY106825, umc1630 |
|
|
|
730.6 |
AY112175 |
|
|
|
741.5 |
AY109128 |
|
|
|
772.3 |
phi064 |
|
|
1.12 |
790.7 |
bnl6.32 |
|
|
|
792.6 |
umc1605 |
|
|
|
801.7 |
AY104686 |
|
|
cIBM2004 CHROMOSOME 2 |
|||
|
|
|
|
|
|
BIN |
Position |
Locus |
Locus Off Frame |
|
2.00 |
0 |
isu53a |
|
|
2.01* |
22 |
umc1165, bti00191a::Ac |
(42.1)sgb101 |
|
2.02* |
64.7 |
umc1824a |
|
|
|
78.4 |
dmt102b |
|
|
|
84.2 |
eks1 |
(22.0)gpm7 |
|
2.03 |
110.1 |
umc6a |
|
|
|
128.3 |
nfd102 |
|
|
|
139.4 |
mmp33 |
|
|
|
152.2 |
sdg104 |
|
|
|
157.1 |
AY107034 |
|
|
|
159.8 |
sdg107 |
|
|
2.04* |
161.3 |
phi109642 |
|
|
|
169.2 |
AY103944 |
|
|
|
172 |
umc1326 |
|
|
|
174.3 |
hag103a |
|
|
|
192.1 |
AI714808 |
(4.9)bti03811 |
|
|
197.4 |
umc2030 |
(1.0)sdg102a |
|
|
200 |
hda102 |
(0.9)AY112119 |
|
2.05 |
206.1 |
umc131 |
|
|
|
207.4 |
zpu1 |
(0.4)AY107012 |
|
|
212.6 |
ns1 |
|
|
|
214.6 |
AY111877 |
|
|
2.06* |
217.3 |
pbf1 |
|
|
|
226.9 |
umc1080 |
(0.5)sdg119 |
|
2.07* |
238.9 |
umc2129 |
(3.1)AI861369 |
|
|
244 |
umc1890 |
|
|
|
255.7 |
nfc104b |
|
|
|
259.4 |
sdg106, nfd101b |
(11.7)chr119,(9.7)sdg116b |
|
|
271.8 |
umc1560 |
|
|
2.08 |
274.7 |
asg20 |
|
|
|
286.8 |
mon00084::Ac |
|
|
|
296.4 |
hda109, chr122 |
|
|
|
303.1 |
umc1604 |
|
|
|
308 |
hag105 |
|
|
|
312.4 |
chc101b |
|
|
|
326 |
mmc0381 |
|
|
|
336.2 |
gpm16 |
|
|
2.09 |
346 |
umc49a |
|
|
|
355.3 |
umc1252 |
|
|
|
380.9 |
BG266188 |
|
|
|
401.4 |
bnlg469b |
|
|
2.10* |
437.1 |
AY106674 |
|
|
|
446.7 |
lim104 |
(0.9)chr106b |
|
|
452.4 |
| |