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Published online 16 July 2007
Published in Crop Sci 47:S-83-S-95 (2007)
© 2007 Crop Science Society of America
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Distribution of Genes, Recombination, and Repetitive Elements in the Maize Genome

Kevin Fengler*, Stephen M. Allen, Bailin Li and Antoni Rafalski

DuPont Crop Genetics Research, DuPont Experimental Station Building E353, Wilmington, DE 19880-0353


Figure 1
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  		Figure 1. Distribution of genes and recombination along the chromosomes. The cumulative gene count (small black squares) and centimorgan counts (empty diamonds) were plotted against the physical length, expressed as number of fingerprinted bands for each chromosome. On average, 1000 fingerprinted contig (FPC) bands corresponds to 4.9 megabases. Large black squares on the physical distance axi correspond to the location of the centromeres identified on the physical map. For chromosomes 6 and 8, the centromere cores could not be placed in the integrated physical–genetic map, and their genetic positions are based on the IBM2 map and indicated by large black square on this axis.

 

Figure 2
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  		Figure 2. Distribution of Mu-flanking sequences, recombination, and genic similarity along the chromosomes. Genetic similarity is defined here as the ratio between the count of shared overgo positives to inbred-specific overgo positives (see also Fig. S-1). The number of shared and inbred-specific overgo positives was counted in each of 10 bins, defined by physical size, along the maize chromosomes. The percentages of total recombination (cM) and the percentages of the total number of Mu-flanking sequences per chromosome were tallied in the physical distance bins.

 

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  		Figure 3. Distribution of retrotransposons along chromosome 1. Relative abundance of each retrotransposon on chromosome 1 in physical distance bins (10% chromosome each). Bin1 and bin10 constitute the subtelomere region and bin5 contains the centromere. (A) centromere-preferred distribution, (B) centromere-depleted distribution, (C) uniform distribution.

 

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  		Figure 4. Distribution of seven major retrotransposons. Percentage of each retrotransposon type localized to the subtelomere or centromere regions. Values represent the pooled average for chromosomes 1, 3, 4, 7, and 10. Subtelomere values are the average of physical distance bin1 and bin10. Centromere values are taken from the physical distance bin that contains the centromere.

 

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  		Figure 5. Distribution Of genes, transposons, and recombination. Values represent the pooled average for chromosomes 1, 3, 4, 7, and 10. Subtelomere values are the average of physical distance bin1 and bin10. Centromere values are taken from the physical distance bin that contains the centromere.

 




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