V. MAIZE GENOME DATABASE
http://www.agron.missouri.edu

MaizeDB currently presents 14,000 loci, including quantitative trait loci and gene candidates; 2,227 references; 3,618 colleague addresses; 486 traits; 2,479 genetic stocks; 5,449 elite germplasm pedigrees; 21,399 variations with 3000 images and 763 phenotypes; 46,000 links to external databases from 10,000 records; SwissProt and GenBank (Entrez format) link reciprocally to MaizeDB pages. The WWW page 'Previous What's New' provides an historical listing of data and design changes. Since Jan 1995 there have been 1,455,677 accesses, with 108,658 in Feb 1997. A more detailed usage analysis is accessible from the database homepage.

 Of Loci, Probes and Maps
MaizeDB maintains information on 1109 mapped genes (to chromosome or better) and 2839 probed sites (RFLP, SSR). There are 1627 public EST's (partially sequenced cDNA's or expressed sequence tags), and 288 have been placed, as probed sites and/or genes, onto public maps. Of 1284 designated genes, there are 794 with some map data, 601 with described phenotypes, and 429 with sequence information, including 160 EST's and 33 simple sequence repeats (SSR). Of the probed sites that do not include designated genes, 462 have probes with sequence information and there are 312 where the sequence is an EST; 160 probed sites have SSRs.

FINDING MAP INFORMATION -- or "why are there so many maps?"

Loci may be initially placed onto any of the following: classical genetic maps (837 loci), the cytogenetic maps (2307 loci), and genetic maps derived from individually defined mapping populations (2614 loci on either/or the UMC and BNL mapping populations (see Table 1). The 1935 genetic map has expanded from 718 centimorgans to some 1800, and is in agreement with the total centimorgans for the maps based on map score data from defined mapping populations (see Table 2).

Integration. The bins maps were first presented in in MNL 66:127 (1992) and currently represent some 6750 loci that have been placed on public maps. However, within a bin, order needs to be ascertained by examining other maps; most loci have not been ordered on more than one map. For example, of 2614 loci placed on either the BNL or UMC map populations, only 371 are on both maps. Of these 371, only 53 are on the genetic map, although some 195 loci on the genetic maps are on either a BNL or a UMC map. See Table 1 for more details.

Other maps in MaizeDB. (1) mitochondrial; (2) maps for tropical or mixed subspecies germplasm; (3) Early releases of maps (BNL, UMC, genetic) for historical and data tracking. To see a full list of the maps in MaizeDB, type a % in the Map Name field and then retrieve.

 Retrieval of map score data. Complete sets of map scores for a population may be retrieved using the WWW focussed query form called "Map Score Tables". Subsets, constrained by a range of bins, may be retrieved from "[Map Scores].By Bins" focussed query page. Alternatively, individual locus pages list all the map scores for a locus, distinguished from the recombination data used for the genetic map.

 TABLE 1. NUMBERS OF LOCI SHARED BY DIFFERENT MAPS
MAP Bin1
Bin 6750 Cyt2
Cyt 2305 2307 Gen3
Gen 836 96 837 BNL4
BNL 1816 2 114 1897 UMC5
UMC 1087 1 132 371 1088 BxM6
BxM 200 0 24 143 119 204 MxH7
MxH 212 212 0 25 116 92 307
1Bin, bins map, coordinates are bins numbers, styled chr#.bin#. A bin is an interval between two fixed Core Marker loci (MNL 69:230, 1995) and includes the beginning (leftmost or top) Marker. It is statistically defined (rather than absolute) only in the sense that chance can lead to inaccurate left-right placement of loci: Some placement to bins is dependent only on the Core Markers, for example, and order may be determined only by 3-point data. That is just the classical mapping order problem. In the case of multipoint data, order can be called with increasing certainty as markers increase in number or populations increase.
2Cyt, cytogenetic map, coordinates vary from -1.0 (short arm) to 1.0 (long chromosome arm) and represent proportional physical distances along a chromosome arm.
3Gen, classical genetic maps.
4BNL recombinant inbreds(RI) from CO159 x Tx303 and/or T232 x Cm37.
5UMC immortal F2 from Tx303 x CO159.
6BxM B73 x Mo17 RI.
7MxH Mo17 x H99 RI 3,4,5,6,7centimorgan coordinates.

TABLE 2. COMPARISON OF LINKAGE GROUP SIZES FOR SELECTED MAPS.
Map: Bins Genetic 1997 Genetic 1935 BNL 95/96 UMC 1995 UMC 1996
Chr bins cm cm cm cm cm
1 12 258 128 284 260 218
2 10 224 71 203 219 181
3 10 216 103 182 215 148
4 11 172 111 196 212 164
5 09 185 72 220 183 166
6 08 144 61 159 151 144
7 06 128 52 180 122 145
8 09 177 18 171 171 154
9 08 178 70 145 174 151
10 07 174 32 140 177 137
Total 79 1856 718 1880 1884 1608

Mary Polacco


Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors

Return to the MNL 71 On-Line Index
Return to the Maize Genome Database Page