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ARS Home » Midwest Area » St. Paul, Minnesota » Plant Science Research » Research » Publications at this Location » Publication #92971
Title: A NEW KNOB-ASSOCIATED TANDEM REPEAT IN MAIZE CAPABLE OF FORMING FOLD-BACK DNA SEGMENTS: ARE CHROMOSOME KNOBS MEGATRANSPOSONS?

Author
item ANANIEV, EVGUENI - UNIVERSITY OF MINNESOTA
item PHILLIPS, RONALD - UNIVERSITY OF MINNESOTA
item Rines, Howard

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/15/1998
Publication Date: N/A
Citation: N/A

Interpretive Summary: Decoding how the genetic material, the DNA, of our major cereal crop corn is organized is a challenging task because of its great complexity. The amount of DNA in a cell of a corn plant is similar to that in a human cell--about 2.5 billion basic chemical units called nucleotides strung together. Much research effort and dollars, both public and private, are now being focused on deciphering the sequence organization of the nucleotides that make up the genetic information in corn. Such information would then allow researchers to modify or manipulate the DNA to improve the crop. We have used some novel genetic materials that we recently developed, oat plants with some corn genetic material added to them, together with modern molecular analysis techniques to study the micro organization of special blocks of segments of corn DNA called knobs. The origin and function of these knob structures is still a mystery, but we hope to gain ideas on this question by understanding better their DNA sequence organization. What we found is the presence of a novel 350 nucleotide sequence that is repeated numerous times in succession within these knob structures. The amount of this repeated sequence varies among different knobs as does the amount of a 180 nucleotide repeated sequence identified earlier. The discovery of this aspect of knob DNA organization puts us one step closer to understanding corn DNA organization and how it affects inheritance and gene function.

Technical Abstract: A new class of tandemly repeated DNA sequence (TR-1) about 350 bp long were isolated from the knob DNA of chromosome 9 of Zea mays (L.). Comparative fluorescence in situ hybridization revealed that the TR-1 elements are present in other cytologtically detectable knobs in different proportions relative to the 180-bp repeats. At least one of these knobs is composed predominantly of this newly discovered TR-1 repeat. In addition, several small clusters of the TR-1 and 180-bp repeats have been found in different chromosomes. Variation in restriction fragment fingerprints and copy number of the TR-1 elements was found among different maize lines and among different maize chromosomes. The TR-1 elements may form tandem arrays of different lengths up to 70 kb, which can be interspersed with stretches of 180-bp tandem repeat arrays. DNA sequence analysis and restriction mapping of one particular stretch of tandemly arranged copies of TR-1 indicate that tthese elements may be organized in the form of fold-back DNA segments. Th TR-1 repeat shares two short segments of homology with the 180-bp repeat. The longest of these segments (31-bp; 64% identify) corresponds to the conserved region within the 180-bp repeat. The polymorphism and complex structure of knob DNA suggests that, like the fold-back DNA containing giant transposons that have been described in Drosophila, maize chromosome knobs may possess some properties of transposable elements.