Interval mapping of NEP factors on chromosomes 1, 3, 4, 5, 6, 7, 8, and 9
--Ed Coe, Oscar Heredia, Susan Melia-Hancock and Shiaoman Chao

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.
FAMILY 2, part 1
zb4 BBBBBBBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD  
ts2 -BBBBBBBBBBBBBD-BBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 8.9
p1 ----BBBBBBBBBBD-BBBBBD--------DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 1.5
npi401 BBBBHBBBBBBBBBHBHHHBBBHAHHBHBHAHHHHAHAAHHBAAAHAAHHH-H-AHHHHAHHBHHHHHHAHAHH 11.0
npi214 BBBBHBBBBBBBBBHBHHHBBBHAAHBHBAAHHHHAHAAHHBAAAHAAHAH-AAAHHHHAHHBAHHHAHAHAHH 4.2
umc167 BBBBHBBBBBBBBBHBBHHBBBHAAHBHBAAHHHHAHAAHHBAAAHAAHAHHAAAHHHHAHHBAHHHAHAHAHH 0.7
Comments:
One double-crossover case in these data (the 22d individual) suggests that the order of ts2 and p1 could be the reverse of that shown on the conventional genetic map, but the conventional order is strongly supported by mapping data involving translocations on either side of ts2 and p1, reported by Emerson in MNL12:9-10.
The placements of npi401 and npi214 in this experiment are consistent with the BNL map.
FAMILY 2, part 2
php200575 BHBBHHHHAHHBBBBBBHABBBBBBBBHHBHBBHAABBAHHHAHAHHHAAHAAAB-A-AHHHHAHHAAAAHAAH  
php200644 BHBBHBBBAHHBBBBBBHHHBBBBBBHHHBHBBHAABHAHHHAAHHHHAHHAAAB-AAAHHHHAHHAABAHAHH 9.4
php200855 BBBBBBBBAHBBBBBBBBHHHAHBHHHHHHAABHHAHHAHHHAAHHHHAHHHAAB-H-AHHHHAHHAA-AHHHB 15.5
br1 --BBBBBBBBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 10.6
f1 --BBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 9.2
Comments:
The placement of php200575 in this experiment is consistent with the PIO map.
FAMILY 3, part 1
zb4 BBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD  
umc76 BHBBHBBA-BHBHBBHBBBHBBHAAAHABAHHAAAHABAHHBAHAAHHAHBAHHAAAAHHAHBHHHHAHAAHAHBHBHAHHHHA 29.4
npi286 BBBBBBBA-HBBBBBBBBBBBBAAAAHAHAHHAAAHAHAHHHAHAHHHAHHAAAAAAAHHAHAAAHAAHAAHAHHHAHAHHHHA 14.7
p1 -BBBBBB---BBBBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 0.0
npi262 BHBBBBBABHBHBBBBBBABBBAAAABAAAHHAAAHAAAHAHAHHHHBAHHHAAAHAAHHAHAAAHAHHAAHAHHHAAAABHHA 10.0
umc67 BHBBBBBAHHBHBBBBBHABBBAHAABAAHAHAAAHAAABAHHAHAHBABABHAABAAHHHHHHAHHHHAHAHAHHAAAABHHA 13.6
bnl5.59 BHBBBBBAHHBBBBBBHHABBBAHAABAAHHHAAAAAAABAHHHHHHBABABHHHBHAHHHHHHAHHHHAHHHAHH-AAABHHA 6.2
Comments:
The order of zb4 relative to umc76 is accompanied by two doubles (BHB), but reversing them would result in many more doubles.
FAMILY 3, part 2
php200644 HHH-HBBBBBBBBBBBBHHABHAHHHHBAAAAHHHAAAAAHHHAAAAHHHBHABABHHHABHHHHHHAHHBHHHBHHHHBAHHB  
umc58 HHH-HBBBBBBBBBBBBHHABHAHHHHBAAAAHHHAAAAAHHBAAAAHHHBHABABHHHABHHHHHHAHHBHHHBHHBHBAHHB 1.2
php200855 HHBBBBBBBBBBBBBBBHHABHAHHHHHHAAAHHHHAAAAHHHAAAAHHHHHABABHHHAAHHHHHHAHHBHHHHHHBHBAHHH 6.9
br1 BBBBBBBBBBBBBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 10.7
f1 BBBBBBBBBBBBBBBBBBBDDBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 6.2
umc128 BBH-HBBBBBBBBBBHBBHBAHHHHHHBHAAAHHHHAAAAHHHABBAHHHHAAHHHHHHAAHHHHHAHHAHHHHHHHHHHBHAH 11.8
umc83 BBB-BBBBBBBBBBBHHBHBAHHHHHBBAAAAHHHHAAAAHHHAAAAHHHHAAHHHHHHAAHHHHHAHHAHHHHHHHHHHAHAH 3.0
Comments:
The order of php200644 and umc58 is well supported in this experiment (this order is uncertain in the Core Map).
FAMILY 3, part 3
umc128 BBH-HBBBBBBBBBBBHHBHBBHAHHHHHAAAHHHHAAAAHHHABBAHHHHAAHHHHHHAAHHHHHAHHAHHHHHHHHHHBHAH rec
umc83 BBB-BBBBBBBBBBBBHBBHHBHAHHHHAAAAHHHHAAAAHHHAAAAHHHHAAHHHHHHAAHHHHHAHHAHHHHHHHHHHAHAH 6.9
an1 --BBBBBBBBBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 3.2
bnl8.10 HBBBBBBBBBBBBBBBHBBHHHHAHHHHHBAAHBHHAHAAHHHAAAAHHHHAAHHHHHHAHHHHBHAHHAAHHHHHHHHHAHAA 5.0
umc184a(glb1) HBBBBBBBHBBBBBBBHBBHHHHAHHAHHBAAHBHHAHAAHHHAAAHHAHHAAAHHHHHAHHHHBHAHBAAHHHHHHHHHAHAA 3.6
umc140 HBB-BBBBHBBBBBBBHBBHHHHAHHAHHBAAHBHHAHAAHHHAAAHHAHHAAAHHHHHAHHHHBHAHBAAHHHHHHHHHAHAA 0.0
umc106 HBBBBBBBHBBBBBBBHBHHHHBAHHHHABAAHBHHAHAAHBHAHAHHAHAAA-HHHHHABHHHBHAHHHAHHHHHHHBHAAAH 8.1
npi255 HHBBBBBHHBBB-HHBHBHHHH-AHHHHABAAHBHHAHAAHBHAHAHHAHAAAAHHHHHABHHHBHAHHHAHHHHHHAHHAAAH 3.7
Comments:
The placements of bnl8.10 and umc106 in this experiment are consistent with the BNL map; the order of umc184a(glb1) and umc140 is well supported (this order is uncertain in the Core Map).
FAMILY 3, part 4
umc140 B-BBBHHBHHBHBBBBBBBHHAAAHHHHABHBBBBHHHAHAHHAAHHHAAHHAAHHAHHAAHHHHHAHHHAHBAAHHHHHHAHA  
umc106 BBBBBBHBBBBHBBBBBBBHHAHAHHHBHBHBBBHHHHAHHHAAAHHHAAHHAAHHAHAA-HHHHHAHHHAHHHAHHHHHHAAA 8.2
npi255 BBBHB-HBBBBHHBB-HBBHHAHAHHHHHBHBHBHHHHAHHHAAAHHHAAHHAAHHAHAAAHHHHHAHHHAHHHAHHHHAHAAA 3.7
gs1 BBBBBBBBBBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 8.9
npi238 BBBBBBBBBBBHHHHBHHBBHHBBBHHBHHHBHHHHAHAHHHAAAHHHAAAHAHHAAHAAHHHBHHAHHAAHHHAHHHHHHAAA 13.3
bm2 BBBBBBBBBBBDDDDDDDBBBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 8.6
umc84 BBB-BABBBBBHHHHHAHBHBBHBBHBBHHAHHHHHAHHHABAAAHHHAAAHAHHAAAAHHHAHHHHHBAAHHHAAHHHHHAHA 8.8
Comments:
The placement of umc106 in this experiment is consistent with the BNL map.
npi255 is placed in this experiment; its location is farther to the right than indicated on the NPI map; this may be npi225, near adh1; npi255 could be to the right of gs1, but on balance the tradeoff favors the above order.
FAMILY 4, part 1
bnl12.06 AAHHBBBHBBBBBBBBBBBAHBHHHABBBHBBAHAHHHHHHHAHABHHHHBHBBAAAAAAAAAAHHHHHHHHHHHHHHHHHHHHHHHHHH  
npi262 AAHHBBBHBBBBBBBBBBBHBBBBHABHHHHHHHAHHHHHHHAHHHHHHHHHHBHAAAHHHAAAHHHHHAHBHHHHHAAHHAHHAHHHHA 14.5
as1 ------BBBBBBBBBBBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 5.4
umc167 AAHHBHBHBBBBBBBHBBBBBBBBBAHHHHHHHHHHHHHHHHAHHHHHHHHHHHHAHAHHHAAAHHHHHAHBHAAHHAAHHAHHAHHHHA 2.8
bnl5.59 AAHHBHBHBBBBHBBBBBBBBBBBBHHHBHHHBBHHHHHHHHAHAHHHHHAHHAHAHAHHHAAAHBHHHAHBHAAHHAAHHAHHAHHAHA 6.3
php200644 AABBBHBBBBBBHBBHHBBBHBHBHBHHBBBBBBBHHHHHBHHHAAHBAHAAHAHAHAHHHAAAHBHAHAHBAAHHHAABHHHHAHHAHA 14.2
Comments:
The placement of bnl12.06 in this experiment is consistent with the BNL map.
FAMILY 4, part 2
php200644 AAAAAAAAAAAHHAAHABBBBBHHBBBBBBBHHHHHBBBBABBHHHHHBBHHBBBHBHBHAAHBHHHHAHHHAAHBHHAHBHHHABHHHH  
php200855 AAAAAAAAAAAAAAAAABBHBBBBBBBBBBBBHBHBBBBBAHHHHHHHHHHHBHHHHHBHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH 16.2
br1 -DDDDDDDDDDDDDDDDBBBBBBBBBBBBBBBBBBBBBBB---DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 3.4
umc33 AAAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH 0.0
f1 -DDDDDDDDDDDDDDDDBBBBBBBBBBBBBBBBBBBBDDDDDD-BBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 6.2
bnl8.10 HHHAHHHHAAAAHHHHHBBBBBBBHBBBBBBBBBHBBAHBHHHHBHHBHHAHAHHAABHHHHBHBBHHHHHBHBHHHHHH-HHHHBHHHH 15.6
umc140 AHBAHHAHAAAAAAAHHBBBHBBBHBBBBBHHBBHBBAABHHHHBHHBAHAHAHHAABBHHHBHBHHHHHHHBBHAHHHHHHHHHBBHAA 11.3
umc107 AHHAHHAHHAAAAAAHHBBBHBBHHBBBBBAHBBHBBAABHHHHBHHBABAHAHHAABHHHHBHBHHHHHHHHBHAHHHHHHHHHBAHAA 5.1
adh1 AHAAHBAHHAAHAAHHHBHBHBBHHBBBBBAHBBHBBAABABHHHHHBABAHHHHAABHBHHBBBHBHHHHHHBHAHHHHHHHBHBAHAA 7.5
Comments:
The placement of umc33 in this experiment is consistent with the UMC '89 and BNL maps.
The placement of bnl8.10 in this experiment is consistent with the BNL map.
FAMILY 4, part 3
adh1 ABBBBBBBBBBBBBHHHHHHHHBAAAAAAAAAAAABHHHHHHHHHHBBBBAAAAAAABBBBBBBBHHHHHHHHHHHHHHHHHHHHHHHHH  
bnl7.25 ABHBHBBBBBBBBBHBBHHHAHBAAAAAAAAAAAAHHHAHHHHAHABBBBAHHAAAAHBAHBHBBHHHAHHHHHHHHBHHHHHHHHHHHH 10.5
npi238 ABBBBBBBBBBBBBBBBHHHHH-AAAAAAAAAAAAAAAAAAAAAAABBBBHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH 17.6
bnl8.29 ABBBBBBBBBBBBBBBBBHHBHBAHAAAAAAAAAAAAAAAAAAAAABHBBHHHHHHHHHHHHHHHHHHHHHHHHHAHHHHHHHHHHHHHH 2.9
bm2 -BBBBBBBBBBBBBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD 11.8
umc84 HBBBBBBBBBBBBBBHBBBBBBHHHAHAAAAAAHAAAAAAHAAAAAHAHHHHHHHHHHHHAHBHHHHAHH-HAHHAHHHAHHHHHHHHHH 2.7
Comments: The placement of bnl7.25 in this experiment is consistent with the BNL map.

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

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