Combined F2 and IF2 RFLP map
--Oscar Heredia-Díaz, Jack Gardiner, Dave Hoisington, Shiaoman Chao, Ed Coe, Theresa Musket and Guilin Xu

Our initial RFLP mapping research was reported in MNL 63:141-151 in 1989. The first UMC maize RFLP map was generated using an F2 population derived from Tx303 x CO159. The map included 256 RFLP loci, scored in 46 individuals, and the linkage analysis was done using Mapmaker v2.0 (Unix). In order to be able to continue mapping after the F2 tissue was exhausted, a new immortalized F2 (IF2), consisting of 56 individuals, was generated during the spring of 1989 (MNL64:47). The latest count of loci mapped on the IF2 is 404, which includes 389 RFLP-defined loci (268 genomic, 78 leaf cDNA, 43 cloned gene candidates), and 15 isozymes.

Toward our effort to integrate available information on RFLP and morphological loci into a consensus map, we have combined segregation data from both populations (current IF2 and previous F2) to generate a combined map, which consists of segregation data for 616 loci scored on 102 individuals in total.

We used SAS (Statistical Analysis System) to concatenate both data sets (see program below). Whenever no segregation information was available for any marker in one of the two populations, it was filled with missing data ("-" in Mapmaker). The combined data set was subjected to linkage analysis using Mapmaker v3.0 (Unix). After identifying linkage groups (LOD=6.0 and -=0.4), a framework was set identical to the IF2 map order, and thereafter all remaining loci (those mapped on the first F2 , but not on the IF2), were placed by implementing the command "try". The "try" command places a given marker into a known framework of markers by determining the interval into which it can be inserted to give the highest likelihood map. Mapmaker computes the maximum likelihood maps for the given framework and the trial locus inserted into each interval, and will display each map's likelihoods relative to the best likelihood found. All map distances are recomputed for each map calculation. By repeating this procedure, 112 additional RFLP loci were mapped. Whenever a marker was inconsistently placed, i.e. more than one possible placement, it was re-tried after all other loci with solid placement were incorporated into the map sequence. Graphic representation of the combined map is shown in the accompanying figure. Markers with Id number out of sequential order are the newly incorporated loci. Loci with php and a 4-digit number are new, detected with recently defined Pioneer probes. Loci with csu and a number are ones detected with cDNA sequences isolated by Chris Baysdorfer. These loci were given umc numbers in the 300 range on last year's maps, but our consensus (among the Baysdorfer, Helentjaris, Burr, and Missouri labs) is now to use the csu designation, with the sequential numbers assigned by Baysdorfer. The mapping data, and the identities and parameters for the probes, are being incorporated into the Maize Genome Database (Maizedb). Please refer to the item on Maizedb, in this issue, for criteria that are being used to define and designate loci and genes (examples: cDNA csu77 shows 68% identity to a bacterial malate dehydrogenase, probes a site matching mdh4, mapped as an isozyme; the site is designated mdh4).

Incorporation of more data sets with the already existing ones, linkage analysis, and refinement of the integrated maps will provide useful and powerful tools for mapping of complete genomes, genetic studies, gene tagging, gene cloning, and integration of more complex traits.

The SAS program used to merge the segregation data sets from both populations follows:

FILEDEF POP1 DISK POP1 DATA A1;
FILEDEF POP2 DISK POP2 DATA A1;
FILEDEF POPn DISK POPn DATA A1;

DATA POP1;
INFILE POP1;
INPUT LOCUS $ 1-14 @ 15 (IND1-56) ($1.);
PROC SORT; BY LOCUS;

DATA POP2;
INFILE POP2;
INPUT LOCUS $ 1-14 @ 15 (IND57-102) ($1.);
PROC SORT; BY LOCUS;

DATA POPn;
INFILE POPn;
INPUT LOCUS $ 1-14 @ 15 (IND103-n) ($1.);
PROC SORT; BY LOCUS;

FILEDEF OUT DISK MERGED DAT A1 (LRECL 200 BLOCK 200 RECFM F;

DATA ALL;
MERGE POP1 POP2 POPn;
BY LOCUS;
ARRAY CHANGE IND1-INDn;
DO OVER CHANGE;
IF CHANGE= ' ' THEN CHANGE='-';
END;
FILE OUT;
PUT LOCUS $ 1-14 @ 15 (IND1-INDn) ($1.); 


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

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