Polyploid formation in cotton is not accompanied by rapid genomic changes

Recent work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes in the early generations fol lowing polyploid synthesis. To address the question of whether rapid genomi c changes also occur in allopolyploid cotton (Gossypium) species, amplified fragment length polymorphism (AFLP) analysis was performed to evaluate nin e sets of newly synthesized allotetraploid and allohexaploid plants, their parents, and the selfed progeny from colchicine-doubled synthetics. Using b oth methylation-sensitive and methylation-insensitive enzymes, the extent o f fragment additivity in newly combined genomes was ascertained for a total of approximately 22 000 genomic loci. Fragment additivity was observed in nearly all cases, with the few exceptions most likely reflecting parental h eterozygosity or experimental error. In addition, genomic Southern analysis on six sets of synthetic allopolyploids probed with five retrotransposons also revealed complete additivity. Because no alterations were observed usi ng methylation-sensitive isoschizomers, epigenetic changes following polypl oid synthesis were also minimal. These indications of genomic additivity an d epigenetic stasis during allopolyploid formation provide a contrast to re cent evidence from several model plant allopolyploids, most notably wheat a nd Brassica, where rapid and unexplained genomic changes have been reported . In addition, the data contrast with evidence from repetitive DNAs in Goss ypium, some of which are subject to non-Mendelian molecular evolutionary ph enomena in extant polyploids. These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phen omena, which will vary among both genomic constituents and taxa.