The integrated mapping project: Chromosome nine

--Casey Howell, Ed Coe, Jack Gardiner, Susan Melia-Hancock and Shiaoman Chao

The 1990 News Letter reported, by chromosome, projected naked-eye polymorphisms (NEPs) to be mapped in this project. Mapping of chromosome nine is nearly complete, and work is in progress on the other chromosomes.

The F1 that was selfed to produce an F2 mapping population was heterozygous for the following ten NEPs: yg2, c1, sh1, wx1, d3, gl15, bk2, Wc1, Bf1, bm4. All alleles were in a cis arrangement in the F1. We selected 116 individuals among a family of 185 F2 plants (excluding 69 phenotypically normal plants). Typing was carried out on 110 plants showing various recessive phenotypes, and on 6 normal plants. Hetero-fertilization appears likely in a few individual plants, for traits that were characterized by endosperm classification (c1, sh1, wx1, Wc1), but progeny tests that would check the classifications were not available for these specific individuals. Probing with clones of known function (e.g., C1, Sh1, Bz1, Wx1) has not yet been completed. Of the RFLP markers tested 16 were polymorphic. The data were analyzed using Mapmaker Macintosh V1.0. The accompanying map was constructed using a maximum recombination fraction of 0.40, a minimum LOD of 3.0, and applying the Haldane function.

The distal three NEPs on 9L, Wc1, Bf1, bm4, mapped with unexpectedly large intervals and with a "best fit" order for Bf1 and bm4 that conflicts with previous data. The individual-plant data for Wc1, while placing it in the established region, indicate far too many double crossovers, and the classifications for this marker, which is famously difficult, must be considered suspect. This marker has been excluded pending new tests. The classical order of Bf1 and bm4 is rather firmly defined by earlier data (MNL 38:10), and the present data are confounded by the Wc1 situation. In addition we suspect that the conflict may be related to the skewed ratios that occurred in this region. These ratios were: Wc1 76:40; Bf1 105:11; and bm4 113:19. Unfortunately NPI97 segregates with presence-absence (also in cis) rather than codominant alleles, meaning that the data for all 4 distal markers are not robust statistically in any case. A current analysis of new F2 and testcross individuals with the distal 9L markers, verified (and completely classified) by progeny tests, should clarify the orders and interval distances in this region.

Figure. Map of 9 NEPs and 16 RFLP loci in chromosome 9 (recombination percentages and distances in cM), derived with F2 data from 110 plants showing one or more recessives and 6 all-dominant plants.

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