A list of defined genes for maize follows. The table includes the symbol for the locus, the chromosome (L=long arm, S=short arm) and map location, name and phenotype, availability from the Stock Center (S), photograph (P) in Mutants of Maize (Neuffer et al. 1968), and references to original descriptions. Stocks may be obtained from the Maize Genetics Stock Center (see the preceding section); in many instances variants (e.g., isozymes) exist inherently among generally available strains.
Following the gene list is a new table of mapped RFLP loci. The locations given ARE NOT DIRECTLY cross-referrable between maps. Locations were taken from the BNL and UMC maps beginning with 0 at the most distal marker on the short arm and summing shortest intervals; for others, recent available maps were measured or approximated and subjective judgments were applied when necessary (probe availability was not considered). The BNL and NPI locations were derived with data from one set of 89 recombinant inbreds (RIs) from 2 pedigrees (49 from CM37/T202, 41 from Tx303/CO159; see MNL65 article by Burr et al.); UMC '89 locations with 46 mortal F2 individuals from Tx303/CO159; UMC'91 locations with an Immortal F2 (IF2) of 56 individuals from Tx303/CO159 (see MNL65 article by Gardiner et al.); PIO locations with combined F2s from four hybrids; AGR locations with F2s from A619/Mangelsdorf's Tester. This table was prepared on a short time scale (with little consultation) to simplify "lookups" of potential markers by us and other Cooperators, and to help us in compiling the integrated maps of genes; please treat it as TENTATIVE, pending availability of explicit supporting data.
NOMENCLATURE: New definitions of standards and criteria are needed, but meanwhile every attempt has been made to avoid ambiguities, to honor the Rules of Nomenclature (MNL 49:3-4; see also MNL 61:49), and to retain the distinction between genes defined by genetic vs.molecular criteria. Please inform us of any errors, inconsistencies, or potential flaws in the specific symbols or the standards applied. The terms "homolog" or "candidate" are used whenever a conservative designation appears appropriate.
The working maps follow the lists. The traditional linkage map, based on recombinational analyses of Mendelizing variations in an expression or a gene product, is in the center. Each map represents the order and distances in centimorgans (1% recombination = 1 cM), for loci for which sufficient information is available to make a reasonable judgment of location. 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. The physical map of each chromosome, immediately to the left of each linkage map, is drawn with the length of each arm in proportion to the ratio of the length of that arm to the length on chromosome 1. Locations of B-A translocations, which generate hemizygous segments, are shown as TB-..., and A-A translocations as T with chromosome numbers and identifiers (see MNL 52:129ff., 55:140ff., 59:159ff., 60:149ff.); placement on the physical map is in accordance with observed breakpoints; placement on the linkage map is in relation to cytogenetic mapping data. 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). 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 associated line are uncovered (as they are with simple B-A translocations). TB's shown spanning one or more genes may or may not uncover the indicated gene or genes. To the right of the linkage map 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 at both ends) or to one arm (vertical line from near the centromere to the end of the arm).
To the left of each physical map are the RFLP maps developed at Brookhaven (left) and at Missouri (right). Preliminary localizations of conventional markers are shown adjacent to the RFLP maps; horizontal ticks indicate the RFLP loci used in mapping these genes.
The Integrated Mapping Project, developed under the encouragement, advice and efforts of the maize community, is in the third year of support from NSF. The priorities under this support are (1) to set a universally usable framework of RFLP markers (see the Core Map in MNL65); (2) to define physical locations with translocations; and (3) to map a selected group of markers (see notes in MNL 64). We emphasize that this effort in no way decreases the need for others to map (either traditionally or with RFLPs). This project provides a means by which data can be assembled and distributed to all interested research workers.
The importance of placing loci defined by probes of known function cannot be overstressed. In a number of cases these give very accurate ties to the conventional map and, in the very least, provide functional significance to a particular region of the genome that will be important as further additional studies (particularly in the area of quantitative genetics) progress. Therefore, 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). First, the set of recombinant inbreds should be probed and the data sent to Ben Burr for analysis. Second, it would be appreciated if the probe could be sent to Missouri for mapping in the Immortal F2 population. We would also use the probe in correlation to physical and conventional markers. We have included in this Newsletter a sample form of 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.
As usual, any comments and/or changes to the maps and lists are greatly appreciated.
Ed Coe, Gerry Neuffer, Dave Hoisington and Shiaoman Chao
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