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Originally published as Genetics Published Articles Ahead of Print on May 6, 2005.
Genetics, Vol. 170, 1221-1230, July 2005, Copyright © 2005
doi:10.1534/genetics.105.041616
Pericentromeric Regions of Soybean (Glycine max L. Merr.) Chromosomes Consist of Retroelements and Tandemly Repeated DNA and Are Structurally and Evolutionarily Labile
Jer-Young Lin*,
Barbara Hass Jacobus*,
Phillip SanMiguel
,
Jason G. Walling*,
Yinan Yuan*,
Randy C. Shoemaker
,
Nevin D. Young
and
Scott A. Jackson*,1
* Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
Purdue University Genomics Core, Department of Horticulture, Purdue University, West Lafayette, Indiana 47907
USDA-ARS-CICGR and Department of Agronomy, Iowa State University, Ames, Iowa 50011
Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108
1 Corresponding author: Department of Agronomy, Purdue University, 915 W. State St., West Lafayette, IN 47907.
E-mail: sjackson{at}purdue.edu
Little is known about the physical makeup of heterochromatin in the soybean (Glycine max L. Merr.) genome. Using DNA sequencing and molecular cytogenetics, an initial analysis of the repetitive fraction of the soybean genome is presented. BAC 076J21, derived from linkage group L, has sequences conserved in the pericentromeric heterochromatin of all 20 chromosomes. FISH analysis of this BAC and three subclones on pachytene chromosomes revealed relatively strict partitioning of the heterochromatic and euchromatic regions. Sequence analysis showed that this BAC consists primarily of repetitive sequences such as a 102-bp tandem repeat with sequence identity to a previously characterized 
120-bp repeat (STR120). Fragments of Calypso-like retroelements, a recently inserted SIRE1 element, and a SIRE1 solo LTR were present within this BAC. Some of these sequences are methylated and are not conserved outside of G. max and G. soja, a close relative of soybean, except for STR102, which hybridized to a restriction fragment from G. latifolia. These data present a picture of the repetitive fraction of the soybean genome that is highly concentrated in the pericentromeric regions, consisting of rapidly evolving tandem repeats with interspersed retroelements.
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