Copy number variation of repeated DNA in inbred lines of maize

We have been looking at the extent of copy number variation of repeated DNA sequences in inbred lines of maize. The sequences are highly repetitive, representing 0.2 to a few percent of the genome. We have examined two transcribed sequences (5S and rDNA), a sequence we believe to be a chromosome knob constituent, and various random sequences whose expression and chromosome position we do not yet know. The copy number of the sequences was measured by affixing equal quantities of DNA isolated from 10 inbred lines to nitrocellulose filters through a slotted template, and then hybridizing the filters with nick translated probes of cloned repeated DNA sequences. The intensity of hybridization, measured by scanning the autoradiogram with a densitometer, is a measure of the relative copy number.

Each repetitive probe we have tested shows some copy number variation within the set of inbred lines. The putative knob sequence is the most variable, varying at least sixfold. Other repeated sequences vary in copy number between two and fourfold. DNAs extracted from individual plants of a single inbred line do not show any variation in hybridization intensity.

We find no evidence for a generalized control over sequence copy number. Inbreds with very high numbers of some cloned sequences are on the low end of the scale for others, and vice versa. Pairwise comparisons of the clones did not reveal any more limited copy number coordination between them. Each inbred line was also unique, both for the pattern of hybridization intensity for the various probes and for the actual quantities of each repeat in the genome.

Carol Rivin and Christopher Cullis

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

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