Evolutionary dynamic of rDNA during diploidization in allopolyploid Zea

This study explores the chromosomal localisation and evolutionary dynamics of ribosomal DNA (45S and 5S rDNA) in the allopolyploid genus Zea L. Using fluorescence in situ hybridization (FISH), along with silver staining and fluorescent banding techniques, we mapped rDNA loci across Zea species. Our results indicate that all 2n = 4x = 20 species consistently exhibit a single 45S rDNA locus located at the secondary constriction of chromosome pair 6 and a 5S rDNA locus on the long arm of chromosome pair 2. Zea perennis, with 2n = 8x = 40, displays distinctive rDNA patterns, comprising both 45S and 5S rDNA sites on two different chromosome pairs each. The observation that all species possess only half the expected number of 5S and 45S rDNA loci, given their polyploid nature, allows us to propose that these sequences were likely lost early during the cytological and genetic diploidisation of the genus, possibly as a consequence of genome downsizing that occurred during their diversification. rDNA loci mapped on meiocytes of Z. perennis and the hybrid Z. perennis × maize suggested that ribosomal genes have been retained within the pivotal subgenome A, while rDNA sequences from the B subgenome may have been lost due to biased fractionation. This study improves our understanding of how patterns of rDNA loss and retention following allopolyploidy have shaped the genomic architecture of Zea species.