Soybean(Glycine max) is derived from Glycine soja Sieb. and Zucc., the undomesticated ancestor of G. max. Because of its importance as a crop, G. max was fully sequenced, and densely populated genetic map (SoyBase.org) and Bacterial Artificial Chromosome(BAC) libraries of both species are available (SoyMap.org). Several reciprocal translocations, leading to reduced fertility or segregation distortion, have been detected in the soybean genome, including one chromosomal rearrangement between chromosomes 11 and 13. Chromosomal rearrangements have been widely regarded to associate with transposable elements and repeats in plants. The aim of this research is to identify chromosomal rearrangements in G. max’s genome in relation to repeats and transposable elements. I hypothesize that chromosomal rearrangements are associated with repeats and transposable elements, and speciation from G. soja to G. max. The first aim is to find the position of chromosomal rearrangements and keep track of them. A physical map of G. soja has been constructed by fingerprinting and anchored to the G. max genome sequence. Several contigs, whose BAC End Sequences are aligned to two chromosomes, will be confirmed using paired BES blast results. The second aim is to identify the sequences which are correlated with chromosomal rearrangements. The BAC clones containing breakpoints will be sequenced to identify breakpoints at the base pair resolution, as well as tandem repeats, satellite repeats, and traces of transposons near the breakpoints. The third aim is to characterize the effect of chromosomal rearrangements on speciation from G. soja to G. max. Translocations and segregation distortion blocks will be compared with several varieties which were used for genetic mapping. The chromosomal rearrangements which affect segregation distortion and fertility between two species will be determined. At the end of this project, I am expecting to identify the sequences which are associated with chromosomal rearrangements in soybean and to find the effect of these chromosomal rearrangements which have accumulated in G. max’s genome during domestication from G. soja to G. max.