Distribution of 5S and 18S–28S rDNA loci in a tetraploid cotton (Gossypium hirsutum L.) and its putative diploid ancestors

Abstract

The most widely cultivated species of cotton, Gossypium hirsutum, is a disomic tetraploid (2n=4x=52). It has been proposed previously that extant A- and D-genome species are most closely related to the diploid progenitors of the tetraploid. We used fluorescent in situ hybridization (FISH) to determine the distribution of 5S and 18S-28S rDNA loci in the A-genome species G. herbaceum and G. arboreum, the D-genome species G. raimondii and G. thurberi, and the AD tetraploid G. hirsutum. High signal-to-noise, single-label FISH was used to enumerate rDNA loci, and simultaneous, dual-label FISH was used to determine the syntenic relationships of 5S rDNA loci relative to 18S-28S rDNA loci. These techniques provided greater sensitivity than our previous methods and permitted detection of six new G. hirsutum 18S-28S rDNA loci, bringing the total number of observed loci to 11. Differences in the intensity of the hybridization signal at these loci allowed us to designate them as major, intermediate, or minor 18S-28S loci. Using genomic painting with labeled A-genome DNA, five 18S-28S loci were localized to the G. hirsutum A-subgenome and six to the D-subgenome. Four of the 11 18S-28S rDNA loci in G. hirsutum could not be accounted for in its presumed diploid progenitors, as both A-genome species had three loci and both D-genome species had four. G. hirsutum has two 5S rDNA loci, both of which are syntenic to major 18S-28S rDNA loci. All four of the diploid genomes we examined contained a single 5S locus. In g. herbaceum (A1) and G. thurberi (D1), the 5S locus is syntenic to a major 18S-28S locus, but in G. arboreum (A2) and G. raimondii (D5), the proposed D-genome progenitor of G. hirsutum, the 5S loci are syntenic to minor and intermediate 18S-28S loci, respectively. The multiplicity, variation in size and site number, and lack of additivity between the tetraploid species and its putative diploid ancestors indicate that the behavior of rDNA loci in cotton is nondogmatic, and considerably more complex and dynamic than previously envisioned. The relative variability of 18S-28S rDNA loci versus 5S rDNA loci suggests that the behavior of tandem repeats can differ widely.

Assessment of Gene Flow BetweenGossypium hirsutumandG. herbaceum: Evidence of Unreduced Gametes in the Diploid Progenitor

“…Results of the FISH analysis at mitosis showed that G. hirsutum (A t A t D t D t ) carried six 45S loci with two loci on A t genome (Figure 5, A and B), in accordance with previous reports (Hanson et al 1996; Gan et al 2013). However, six 45S loci were also observed on the A genome of G. herbaceum (A 1 A 1 ) (Figure 5C).…”

Conservation and loss of ribosomal RNA gene sites in diploid and polyploid Fragaria (Rosaceae)

“…Thus, physical association of rDNA clusters between both homologous and nonhomologous sites is possible, supported by the fact that rDNA-bearing chromosomes appear to be non-randomly associated with each other at mitotic metaphase [36]. It is widely accepted that association of genes with highly repetitive sequences would increase the opportunity for unequal exchanges.…”

“…Size polymorphism of the hybridization signals, among and within homologous sites could be explained by such events. On the other hand, somatic exchanges taking place between different sites could make homogenization and changes in rDNA copy number occur especially quickly [36]. Therefore, it is reasonable to suggest that the rDNA repeats in strawberry are in a highly dynamic state because of their terminal positions and potentially high degree of association between sites.…”

Comparative chromosomal localization of 45S and 5S rDNAs and implications for genome evolution inCucumis

“…FISH mapping of ribosomal DNAs directly on the chromosomes provides a useful approach for identification of chromosome and studies of chromosome organization and evolution. FISH has been applied to conduct the physical mapping of chromosomes in important economic and medicinal plants, and the organization and differentiation of rDNAs in closely related species has provided important information for analysis of chromosome evolution and species formation (Abbo et al 1994;Hanson et al 1996;Adachi et al 1997;Chen et al 1999;Taketa et al 1999;Han et al 2008;Martina et al 2010;Zhao et al 2011). To extend our knowledge of chromosome organization and evolutionary changes of wild species of Cucumis, we conducted FISH experiments with 45S and 5S rDNA probes on metaphase spreads of 20 Cucumis accessions to investigate their site numbers and physical positions.…”