Macromolecular organization and genetic mapping of a rapidly evolving chromosome-specific tandem repeat family (B77) in cotton (Gossypium)

Isolation and characterization of the most prominent repetitive element fam ilies in the genome of tetraploid cotton (Gossypium barbadense L; [39]) rev ealed a small subset of families that showed very different properties in t etraploids than in their diploid progenitors, separated by 1-2 million year s. One element, B77, was characterized in detail, and compared to the well- conserved 5S and 45S rRNA genes. The 572 bp B77 repeat was found to be conc entrated in several discontinuous tandem arrays confined to a single 550 kb Sail fragment in tetraploid cotton. Genetic mapping based on the absence o f the pentameric 'rung' in the G. barbadense 'ladder' showed that B77 maps to a D-subgenome chromosome. In situ hybridization supports the contention that the array is confined largely to a single chromosomal site in the D-su bgenome. The B77 repeat has undergone a substantial increase in copy number since formation of tetraploid cotton from its diploid relatives. RFLPs obs erved among tetraploid cotton species suggest that amplification and/or rea rrangement of the repeat may have continued after divergence of the five te traploid cotton species. B77 contains many short direct repeats and shares significant DNA sequence homology with a Nicotiana alata retrotransposon Tn a1-2 integrase motif. The recent amplification of B77 on linkage group D04 suggests that the D-subgenome of tetraploid cotton may be subject to differ ent evolutionary constraints than the D-genome diploid chromosomes, which e xhibit few genome-specific elements. Further, the abundance of B77 in G. go ssypioides supports independent evidence that it may be the closest extant relative of the D-genome ancestor of cotton.