University of Arizona

Duplicated RFLP loci are abundant in the genome

--Jean Dowty and Tim Helentjaris

Duplicated sequences in the genome are commonly revealed by RFLP detection techniques as first described by Helentjaris et al. in 1988 (Genetics 118:353-363). At that time, using over 200 single copy RFLP genomic and cDNA clones as probes, they estimated that approximately 29% of markers detected a duplicate sequence at another locus in the genome. Section V of the 1991 Maize Genetics Cooperation News Letter currently lists approximately 1,400 markers, 35% of which we estimate are duplicated at least once somewhere else in the maize genome. All ten chromosomes have a number of duplicated sequences, but as noted by Helentjaris et al., the duplications are not necessarily scattered randomly over the entire chromosome, but more often appear to cluster (Figure 1).

Figure 1. Duplicated regions shared between chromosomes. Brackets represent regions with a high concentration of markers which map to another chromosome (listed by number next to the bracket).

There is also a higher order pattern to the duplication-saturated regions of 3 different "sets" of chromosomes: 10-2-7 (Figure 2), 5-1-9, and 3-8-6. 70% of the markers on chromosome 2 are duplicated on either chromosome 10 or 7. The short arm of chromosome 2 contains all the duplications mapped to chromosome 10L, while the long arm of chromosome 2 shares all the duplications mapped to chromosome 7. Similarly, 46% of the duplications on chromosome 1 are shared with either chromosomes 5 or 9. All of the duplications shared by chromosomes 5 and 1 map to the short arm of chromosome 5 and the long arm of chromosome 1 respectively. All but two of the duplications shared by chromosomes 1 and 9 map to the short arm of chromosome 1 and the long arm of chromosome 9 respectively. 60% of the duplications on chromosome 8 are shared with chromosomes 3 and 6. While the duplications shared by chromosome 6 and 8 map to the long arm of chromosome 8, the duplications shared by chromosomes 3 and 8 map to both arms of chromosome 8. It is worth noting that while chromosome 2 shares duplications with both chromosomes 7 and 10, chromosomes 7 and 10 do not share any duplicated markers between them. Similarly, chromosomes 3 and 6 share only one marker between them, while chromosomes 5 and 9 share three markers between them.

Figure 2. An example of the typical higher order pattern of duplicated markers within a chromosome "set" such as is seen in the chromosomes 10-2-7.

We believe this type of information will be useful to researchers who have isolated clones for specific gene interruptions originating within one of these duplicated regions. A careful perusal of the maize map in the corresponding region is probably warranted to determine if a homologous disruption is located there which might be due to a related sequence gene, as has been found for B and R, orp1 and orp2, D8 and D9, etc. We are also using some of the markers which are duplicated on the chromosome set 10-2-7 in maize to analyze evolutionary relationships within the Andropogoneae tribe by screening for duplications shared with some of the close relatives of maize such as teosinte, Tripsacum, and Coix, as well as with other genera in the Gramineae family.

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