Distribution of various types of repetitive DNAs in Allium cepa L. based on dual color FISH

Abstract

Fluorescence in situ hybridization (FISH) is a powerful tool for the detection of DNA sequences in a specific region of a chromosome as well as for integrated physical mapping. The detailed karyotypes of two onion cultivars (‘Eumjinara’ and ‘Sinseonhwang’), which are resources for the onion genome sequencing project were constructed based on dual color FISH using 5S and 45S rDNAs, telomeric tandem repeats, and Cot-1 DNA. All materials showed 2n = 2x = 16. Four loci of 5S rDNAs were located on the interstitial regions of the short arms of one pair of chromosomes in both onion cultivars. One loci of 45S rDNA signal was distally detected on each short arm of the two pairs of chromosomes in ‘Eumjinara’ and ‘Sinseonhwang’, but the latter possessed another locus of 45S rDNA on the distal part of the long arm in one homolog of a chromosome pair. Co-localization of telomeric tandem repeats and 45S rDNA signals was observed in ‘Eumjinara’ and ‘Sinseonhwang’. A difference in the distribution of 45S rDNA sites and the co-localization of signals observed between the two cultivars are indicators of recent activities in the nuclear genome that may involve homologous recombination or transposition of certain repeats. Cot-1 DNA signals are distributed throughout the chromosomes and show stronger signals in the terminal regions. The elucidation of Cot-1 DNA through in-situ hybridization would only show a large amount of tandemly repeating, non-coding and dispersedly repetitive DNAs in onion genome.