Genetics, Vol. 161, 1293-1305, July 2002, Copyright © 2002

Dasheng: A Recently Amplified Nonautonomous Long Terminal Repeat Element That Is a Major Component of Pericentromeric Regions in Rice

Ning Jianga, Zhirong Baob, Svetlana Temnykhc, Zhukuan Chengd, Jiming Jiangd, Rod A. Winge, Susan R. McCouchc, and Susan R. Wesslera
a Departments of Plant Biology and Genetics, University of Georgia, Athens, Georgia 30602,
b Department of Genetics, Washington University, Saint Louis, Missouri 63110,
c Department of Plant Breeding, Cornell University, Ithaca, New York 14853,
d Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
e Clemson University Genomics Institute, Clemson, South Carolina 29634

Corresponding author: Susan R. Wessler, University of Georgia, Athens, GA 30602., sue{at}dogwood.botany.uga.edu (E-mail)

Communicating editor: C. S. GASSER

A new and unusual family of LTR elements, Dasheng, has been discovered in the genome of Oryza sativa following database searches of ~100 Mb of rice genomic sequence and 78 Mb of BAC-end sequence information. With all of the cis-elements but none of the coding domains normally associated with retrotransposons (e.g., gag, pol), Dasheng is a novel nonautonomous LTR element with high copy number. Over half of the ~1000 Dasheng elements in the rice genome are full length (5.6–8.6 kb), and 60% are estimated to have amplified in the past 500,000 years. Using a modified AFLP technique called transposon display, 215 elements were mapped to all 12 rice chromosomes. Interestingly, more than half of the mapped elements are clustered in the heterochromatic regions around centromeres. The distribution pattern was further confirmed by FISH analysis. Despite clustering in heterochromatin, Dasheng elements are not nested, suggesting their potential value as molecular markers for these marker-poor regions. Taken together, Dasheng is one of the highest-copy-number LTR elements and one of the most recent elements to amplify in the rice genome.




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