Deletions of loci detected by RFLPs

We originally observed that very few loci exhibited "null alleles" during our efforts to prepare a linkage map based upon loci detected by RFLPs. A null allele at a RFLP locus is characterized by the complete absence of a detectable fragment after Southern hybridization with a cloned maize sequence. As our studies were principally geared towards mapping loci detected by random cloned sequences in a small set of segregating populations, this observation could not be taken as an accurate measure of the occurrence of deleted sequences within commonly used germplasm. More recently, by expansion of the number of inbreds examined (sometimes greater than 150 inbreds specifically from Corn Belt germplasm), we have now identified 5 loci, out of the approximately 400 loci we use, which occasionally detect deletions of the target sequences.

Four of the 5 clones identified loci which are duplicated on more than one chromosome, with only one of the pair of duplicate loci in each case exhibiting a null allele. A possible terminal rearrangement was observed in a Mangelsdorf tester line on the long arm of chromosome 2 at our most distal marker locus, #32. This same clone detects a duplicate locus on the long arm of 1, marker #82, for which we have never observed a null allele. The locus on chromosome 2 does not fit the pattern we have more commonly observed before, where almost all of the duplicated loci on the long arm of 2 have corresponding sequences found on the long arm of chromosome 7. Perhaps the presence of the locus #32 sequence on the terminus of chromosome 2 represents a recent translocation from locus #82 on 1, which is then only found in some maize inbreds. Another possible terminal rearrangement, this time on the short arm of 2, marker #417, was observed in B73 and some of its derivatives. This sequence is also found to be duplicated on chromosome 10 as marker #484. A third terminal rearrangement is found on the long arm of chromosome 5 at marker locus #363. Its corresponding duplicate locus, #292, is located on the long arm of chromosome 4 where we have never observed a null allele.

Possible internal rearrangements of chromosomal segments have also been identified in 2 other cases. Locus #483 exhibits a null allele and has been tentatively located near the centromere on chromosome 2. The sequence which detects this locus is also duplicated as marker locus #391 on chromosome 7, which we previously thought to represent a unique sequence due to the prevalence of the null allele at locus #483 in most of our "mapping" populations. The fifth clone recognizes a single, unique chromosomal location, which is undetectable in some maize inbreds. Marker #432 on the long arm of 3 appears to be the only unduplicated sequence of this group which exhibits a null allele. This deletion is evident in a majority of the Lancaster-derived germplasm examined by us but present in most other maize pedigrees.

Three of the 4 rearrangements reported herein occur on chromosome 2, which has been shown previously to display two different cytological forms (Neuffer, Jones, and Zuber, Mutants of Maize, p. 4, 1968). It is interesting to speculate that the possible terminal differences observed cytologically might also be reflected in the rearrangements of RFLP loci we report here. We do not yet know how well our results, obtained with various inbreds, correlate with these cytological observations; however, extension of this type of analysis should prove revealing as to how these duplications/deletions were generated during the evolution of the structure of the maize genome.

V. Turner, Scott Wright, J. Suzuki and T Helentjaris

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

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