Polyploid formation in cotton is not accompanied by rapid genomic changes

Abstract

Recent work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes in the early generations following polyploid synthesis. To address the question of whether rapid genomic changes also occur in allopolyploid cotton (Gossypium) species, amplified fragment length polymorphism (AFLP) analysis was performed to evaluate nine sets of newly synthesized allotetraploid and allohexaploid plants, their parents, and the selfed progeny from colchicine-doubled synthetics. Using both methylation-sensitive and methylationinsensitive enzymes, the extent of 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 heterozygosity 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 using methylation-sensitive isoschizomers, epigenetic changes following polyploid synthesis were also minimal. These indications of genomic additivity and epigenetic stasis during allopolyploid formation provide a contrast to recent evidence from several model plant allopolyploids, most notably wheat and Brassica, where rapid and unexplained genomic changes have been reported. In addition, the data contrast with evidence from repetitive DNAs in Gossypium, some of which are subject to non-Mendelian molecular evolutionary phenomena in extant polyploids. These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phenomena, which will vary among both genomic constituents and taxa.Key words: polyploidy, genome evolution, cotton, Gossypium, amplified fragment length polymorphism (AFLP).Résumé : De récents travaux ont démontré que la spéciation via l'allopolyploïdisation chez les plantes s'accompagne parfois de changements génomiques non-mendéliens au cours des premières générations. Afin de déterminer si des changements génomiques rapides surviennent chez des espèces allopolyploïdes du cotonnier (Gossypium), une analyse AFLP (polymorphisme de longueur des fragments amplifiés) a été faite pour évaluer neuf jeux d'hybrides synthétiques allotétraploïdes ou allohexaploïdes, leurs parents et la progéniture obtenue par autofécondation suite au doublement chromosomique induit par la colchicine. À l'aide d'enzymes sensibles ou insensibles à la méthylation, le degré d'additivité des fragments a été évalué chez les génomes nouvellement combinés pour environ 22 000 locus génomi-ques. L'additivité des fragments a été observée dans presque tous les cas et les quelques rares exceptions reflétaient vraisemblablement une hétérozygotie parentale ou une erreur expérimentale. De plus, des analyses Southern sur six jeux d'allopolyploïdes examinés à l'aide de sondes constituées de rétrotransposons ont également révélé une complète additivité. Comm...

Gene copy number evolution during tetraploid cotton radiation

“…Liu et al (2001) did not find any loss in nine sets of newly synthesized allotetraploid and allohexaploid cotton plants, their parents, and the self-crossed progeny from colchicine-doubled synthetics among 22 000 genomic loci analyzed using AFLP or five retrotransposons using southern hybridization. The few clear cases of gene loss we report are striking exceptions to the otherwise high level of DNA sequence preservation in polyploid cotton.…”

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

“…This process has been observed in paleopolyploid maize 20 and in newly synthesized allopolyploid wheat 21 , Brassica 22 and Tragopogon 23 . Some other allopolyploids, such as cotton 24 and Arabidopsis 25 , do not show many changes in their genomic sequences. Recent genome sequencing studies revealed a relatively stable genome organization in cultivated hexaploid wheat 6 and Brassica napus 9 .…”

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

“…(14) Contrary to the rapid genomic changes observed in Brassica and wheat allotetraploids, synthetic cotton allotetraploids display a negligible amount of changes in genomic sequences. Using AFLP analysis of over 22,000 fragments, Liu et al (2001) found additive patterns for nearly all AFLP fragments examined. (58) Molecular phylogenetic analysis indicated that the orthologous genes in the progenitors evolve independently at relatively similar rates to the homoeologous loci that are combined in the allotetraploids.…”

“…Using AFLP analysis of over 22,000 fragments, Liu et al (2001) found additive patterns for nearly all AFLP fragments examined. (58) Molecular phylogenetic analysis indicated that the orthologous genes in the progenitors evolve independently at relatively similar rates to the homoeologous loci that are combined in the allotetraploids. (59) Similarly, genomic changes in Spartina polyploids occur at a very low frequency.…”

“…Hence, they may represent just one of the diverse array of molecular evolutionary phenomena observed in polyploids in general. (16,58) Genomic and chromosomal changes observed in Arabidopsis allopolyploids fall between those detected in cotton and wheat synthetic allopolyploids. A relatively low frequency ($1%) of genomic changes was detected in Arabidopsis allotetraploids.…”