GENELIST: A table of the defined and designated gene loci of maize, derived by extraction from the Maize Genome Database, follows. Included are the symbol for the locus; the chromosome (L=long arm, S=short arm) and map location ("+-" denotes a map location near the position listed); the name and a brief description of the phenotype; and references to original descriptions. Stocks of variants may be obtained from the Maize Genetics Stock Center (preceding section); many variations (e.g., isozymes and RFLPs) occur naturally among generally available strains. The gene list was compiled by Ed Coe and Mary Polacco. Georgia Davis and Pat Byrne participated in collection and refining of the data and descriptions; Stan Letovsky and Denis Hancock aided in deriving the output.
NOMENCLATURE: New definitions of standards and criteria are presented in the following section. Oliver Nelson chaired the committee that has carefully developed this standard.
MAPS: Working maps follow the table. The traditional linkage map is in the center, showing recombination distances in centimorgans. Each chromosome begins at the top with the most distal locus known in the short arm. Locations of the centromeres are indicated according to the best available data from cytogenetic studies. To the right are shown genes (alphabetically in groups) for which a "rough" placement has been defined, either near a gene already on the map or to a region of the map. Furthest to the right are shown genes placed only to chromosome (vertical line with arrows) or to one arm (vertical line from near the centromere to the end of the arm). Substantive changes in the maps this year include a general revision for chromosome 8, and local revisions in 6S and in 1L near adh1.
The cytological map of each chromosome, immediately to the left of the linkage map, shows the arms in proportion and locations of selected aberrations. B-A translocations, which generate hemizygous segments, are shown as TB-..., and A-A translocations as T with chromosome numbers and identifiers (see MNL 55:140ff.); placements on the linkage map are in relation to cytogenetic mapping data (see MNL 52:129ff., 59:159ff., 60:149ff., et seq.). The vertical line associated with simple B-A translocations represents the segment within which the breakpoint is located (genes distal to the line on that arm should be uncovered; genes spanned by the line may or may not). In the case of compound translocations, the associated vertical line on the linkage map for the first arm involved (e.g., 1L of TB-1La-5S8041) defines the segment within which the second breakpoint is located (genes distal to the line are not uncovered). On the map of the second arm involved (5S in the example), genes distal to the line are uncovered.
To the left are RFLP and isozyme loci on the Core Map derived at the University of Missouri. Maximum likelihood treatment of multipoint data (Mapmaker) has until now only been suitable for F2 data, providing a map on which statistical qualifiers can be stated. Loci for which the order is uncertain (LOD scores do not differ by 3) are marked with a dotted line. Highlighted with boxes are Core Markers, a spaced set of widely used, informative markers (Gardiner et al., Genetics, in press) available from the laboratory of Shiaoman Chao. Loci new to the Core Map include ones probed by sequenced cDNAs (table below). Accompanying the Core Map is a parallel list of markers mapped at Brookhaven National Laboratory, in map order and matched to the Core Map; cooperation of Ben Burr in providing the large and complex current data set for this parallel representation is greatly appreciated. Tools for analysis of these data by maximum likelihood have just become available and are being applied to the data at Brookhaven. These and the several other available RFLP maps are largely consistent with each other, and plans for merging of the accumulated data to produce a consolidated map are in progress. Dashed cross-lines show interrelated locations; these are mutually interdependent (i.e., derived from information from each source by circular logic).
Construction of a map that integrates the locations of genes, cytogenetic variants, and molecular markers requires systematic compilations of data (which are in progress under the Maizedb program), but further requires new mapping engines under development.
The maps were compiled and prepared by Ed Coe with participation by Gerry Neuffer, Jack Gardiner, and Shiaoman Chao; technical help of Susan Melia-Hancock, Oscar Heredia-Diaz, Theresa Musket, and Guilin Xu is appreciated.
The current Plastid Chromosome Genetic Map, prepared by Steve Rodermel, follows the nuclear working maps. For the Mitochondrial Map, see MNL 64:165.
MAP IT: The value of mapping with probes of known function cannot be overstressed. This gives functional significance to particular places in the genome, important as additional studies (particularly in quantitative genetics) progress. IF YOU HAVE A CLONE for a known function and know or believe that it hybridizes to a maize genomic sequence, please attempt to map the locus (or loci). This can be accomplished in a couple of ways (and we recommend doing both). The Brookhaven set of recombinant inbreds can be probed and the data sent to Ben Burr for inclusion in the data resource. The probe can be sent to Missouri for mapping in the Immortal F2 population and inclusion in the Core Map resource. We would also use the probe in correlation to physical and conventional markers. Included in this Newsletter is a sample form with the desired information for each clone you provide. If you have any questions regarding mapping of RFLP loci (both old and new), please call or write.
QUALITY of these resources is enhanced each year by corrections, clarifications, and suggestions provided by Cooperators; your input is welcome and needed.
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