FISH painting for chromosome identification of aneuploid cauliflower (Brassica oleracea L. var. botrytis)

Abstract A common problem in the cultivation and breeding of cauliflower ( Brassica oleracea L. var. botrytis ) is the occurrence of aneuploids in offspring families. To reveal the chromosomal cause of such numerical variants, it was necessary to develop karyotype tools with which chromosomes can be easily identified. Since mitotic chromosomes in this crop are morphologically similar and lack differentiating banding patterns, we tested two Fluorescent in situ Hybridization (FISH) procedures for chromosome identification: (1) FISH painting with diagnostic repetitive DNA patterns and (2) cross-species chromosome painting. The first method consists of a five-colour FISH with 5s rDNA, 45S rDNA, and two Brassica rapa centromere-specific repeats, and a B. rapa BAC (KBrH092N02) containing a dispersed repeat of an unknown class. The second method is an advanced FISH technology based on hybridising DNA probes of a related species under adapted stringency conditions to identify their homoeologous loci. To this end, we applied four pools of BACs from Arabidopsis thaliana in a multicolour FISH for a banding pattern on the chromosomes of cauliflower ( Brassica oleracea L. var. botrytis ). Due to the genome triplication and various chromosome rearrangements of Brassica oleracea compared to Arabidopsis, we used MUMmer whole-genome alignment plot information to select Arabidopsis BAC pools with which all cauliflower chromosomes could be identified. In a sample of 21 plants with aberrant phenotypes, we demonstrated primary trisomy for chromosomes 1–6 and 8, and telo-trisomy for chromosomes 7 and 9. Finally, we discuss the advantages and drawbacks of the two painting methods and eventual alternatives for demonstrating numerical aberrations in the cauliflower populations. Graphical Abstract