The placements of Naked Eye Polymorphisms at the sr1, zb4, ts2, p1, as1, br1, f1, an1, gs1 and bm2 loci with RFLP markers, shown by dotted connecting lines in the 1992 maps (refined this year after re-analysis), are supported by the linkage data presented in the accompanying tabulations. These are scoring data from 4 F2 families provided from the Stock Center collections by Earl Patterson, detailed in 10 segments. The scores, locus by locus and individual by individual, are identified by letters according to the conventions used in MAPMAKER, as follows: A (homozygous for the allele of parent A), B (homozygous for the allele of parent B), H (heterozygous), C (dominant from parent B), D (dominant from parent A) and - (dash; unscored). The volume of mapping data now developing in this laboratory and in others is very considerable. Data in such volume can be offered in hard copy tables such as this, but they will be best documented in the future in database form, where they can be accessed by any user for any desired purpose, and can be merged with other data to develop composite maps. We present the following as examples of systematically organized form for such data, with information about the approach we use in deriving and analyzing the tabulations.

The loci are first arranged in order according to placements on the UMC Core Map, or other RFLP maps and prior information, to derive the best available skeleton order. The array of scores is then sorted in order according to genotypes in the row of scores for the target locus (e.g., sr1) on a primary sort, and secondarily for 1 or 2 nearby loci. The sorted array facilitates scanning for matches and mismatches of adjacent loci (crossovers). If scanning indicates serious misplacement of a gene locus, we assess alternative placements and rearrange where needed. These steps yield the best-order diagnosis. The array is then analyzed by MAPMAKER to derive percents of recombination for closest markers, and to compare alternative orders mathematically by differences in LOD scores. Because data for dominant-recessive loci inherently are less robust than data for codominants, LOD score differences are often small, so a statistically based decision is not always possible. In such cases we use the conventional "fewest-doubles" criterion, and evaluate for chains of the same constitutions across neighboring loci.(i.e., anticipating that, across short distances, interference means that one crossover is not often followed by another in the same strand). We display up to 3 markers on each side of a target locus when available, to aid visualization of chains of constitutions. Comments are provided where appropriate, following each table. Order of the associated loci is emphasized more than distances in these analyses.

Similar diagnoses provide placements for NEPs on chromosome 3 (g2, cr1, ys3, pm1, ig1, lg2, na1, a3, et1), chromosome 4 (ts5, su1, gl4, o1, tu1, gl3), chromosome 5 (a2, bm1, pr1, ys1), chromosome 6 (y1, pl1, wi1, pb4, sm1, py1), chromosome 7 (ra1, gl1, ij1), chromosome 8 (bif1, j1), and chromosome 9 (yg2, c1, sh1, wx1, d3, gl15, bk2, wc1, bm4, bf1). The data will be available in the maizedb database.

FAMILY 1

LOCUS	SCORES	PCT1
bnl5.62	HABBBBHBBHHABBHBHBHHHAHHHHHAHHAABHHHAHBAHHHAHHAAHHHBBHHBBAHHHBHHAAHHHHBHAA
umc164	HABBBBHBBAHABBHBHBHHHAHHHHAAHHAABBHHAHBHHHHAHAAAHHHBBHHBBAHHHBHHHAHHHHHHAA	4.9
umc115	BBBBBBHBBB--BB-BBB-HHHHH-AHHH--HHHHH------AAB-AHHHHHAHHHHAHHHH-------HHHH-	26.2
sr1	BBBBBBBBBBBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD	2.8
zb4	BBBBBBBBBBBBBDDDDDDBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD	13.2
umc76	BB---B-HBBHAHBHA-BHBBBHHAAHHA-AHHHAHHHH--BAA--H------AHHHABHBHHHHAHHHHHH--	17.2
umc162	BBBBBBHBBBHABBHHHBHBBBBHAAHHAHHHHHAHAHHHHHAAHAHHHHHHAAHHHABHBHHBHAHHHHHBHH	7.5
umc11	BBBBBBHBBBHABBHHHBHBBBBHHAHHAHHHHHAHHHHHBHHAHBHHHHHHAAHHHABBBHHBHABHHBBBHB	7.8

¹The percentage of recombination between the locus on that line and the one above it, derived with MAPMAKER.

Comments:
The order of bnl5.62 and umc164 could be reversed; this order is also uncertain in the Core Map.
sr1 and umc115 could be reversed only at the cost of a double exchange.
zb4 and umc76 could not be reversed without reflecting several more double exchanges.
The placement of umc162 in this experiment is consistent with that for the UMC '89 map.
The distance from sr1 to zb4 may be subject to reduction.

Comments: The placement of bnl7.25 in this experiment is consistent with the BNL map.

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