Molecular characterisation and chromosomal localisation of a telomere-like repetitive DNA sequence highly enriched in the C genome of <i>Brassica</i>

Abstract

The aim of this work was to find C genome specific repetitive DNA sequences able to differentiate the homeologous A (B. rapa) and C (B. oleracea) genomes of Brassica, in order to assist in the physical identification of B. napus chromosomes. A repetitive sequence (pBo1.6) highly enriched in the C genome of Brassica was cloned from B. oleracea and its chromosomal organisation was investigated through fluorescent in situ hybridisation (FISH) in B. oleracea (2n = 18, CC), B. rapa (2n = 20, AA) and B. napus (2n = 38, AACC) genomes. The sequence was 203 bp long with a GC content of 48.3%. It showed up to 89% sequence identity with telomere-like DNA from many plant species. This repeat was clearly underrepresented in the A genome and the in situ hybridisation showed its B. oleracea specificity at the chromosomal level. Sequence pBo1.6 was localised at interstitial and/or telomeric/subtelomeric regions of all chromosomes from B. oleracea, whereas in B. rapa no signal was detected in most of the cells. In B. napus 18 to 24 chromosomes hybridised with pBo1.6. The discovery of a sequence highly enriched in the C genome of Brassica opens the opportunity for detailed studies regarding the subsequent evolution of DNA sequences in polyploid genomes. Moreover, pBo1.6 may be useful for the determination of the chromosomal location of transgenic DNA in genetically modified oilseed rape.

Subgenome Discrimination in Brassica and Raphanus Allopolyploids Using Microsatellites

“…Our data corroborated the abundance of a telomeric repeat-like C-genome-specific microsatellite (ACBR_msat20) previously identified in B. napus using conventional molecular techniques [25]. However, although we only identified the consensus TTTCGGG sequence of ACBR_msat20, a previous study presented an intermittent organization of TTTCGGG, TTTGGGG, and a few imperfect derivative sequences [25], demonstrating that molecular analyses are relevant in defining actual sequences. However, for the FISH and genome discrimination, our results were comparable to previously reported data for discriminating the C-genome chromosomes from the A and B Brassica genomes.…”

“…Microsatellites can have genome-specific distribution. Therefore, they can be useful in discriminating subgenomes in allopolyploids, as demonstrated in previous studies [25,26,29,54] and this study. Here, we identified 22 high-abundance microsatellites from the A, C, and B genomes of Brassica and the R genome of R. sativus using short next-generation sequencing reads.…”

“…However, GISH-like results have been achieved using conventional fluorescence in situ hybridization (FISH) with microsatellite repeats as probes instead of genomic DNA. This approach discriminated C from the A genome in B. napus [24,25] and the B genome in Triticum aestivum [26].…”