Comparative genetic mapping of allotetraploid cotton and its diploid progenitors

Allotetraploid cotton species (Gossypium) belong to a 1–2 million year old lineage that reunited diploid genomes that diverged from each other 5–10 million years ago. To characterize genome evolution in the diploids and allotetraploids, comparative RFLP mapping was used to construct genetic maps for the allotetraploids (AD genome; n = 26) and diploids (A and D genomes; n = 13). Comparisons among the 13 suites of homoeologous linkage groups permitted comparisons of synteny and gene order. Two reciprocal translocations were confirmed involving four allotetraploid At genome chromosomes, as was a translocation between the two extant A genome diploids. Nineteen locus order differences were detected among the two diploid and two allotetraploid genomes. Conservation of colinear linkage groups among the four genomes indicates that allopolyploidy in Gossypium was not accompanied by extensive chromosomal rearrangement. Many inversions include duplicated loci, suggesting that the processes that gave rise to inversions are not fully conservative. Allotetraploid At and Dt genomes and the A and D diploid genomes are recombinationally equivalent despite a nearly two-fold difference in physical size. Polyploidization in Gossypium is associated with enhanced recombination, as genetic lengths for allotetraploid genomes are over 50% greater than those of their diploid counterparts.