Rapid identification and determination of purity of flow-sorted plant chromosomes using C-PRINS

Background: Flow-sorted plant chromosomes are being increasingly used in pl ant genome analysis and mapping. Consequently, there is a need for a rapid method for identification of sorted chromosomes and for determination of th eir purity. We report on optimization of procedures for primed in situ DNA labeling (PRINS) and cycling-PRINS (C-PRINS) for fluorescent labeling of re petitive DNA sequences on sorted plant chromosomes suitable for their ident ification. Methods: Chromosomes of barley, wheat, and field bean were sorted onto micr oscope slides, dried, and subjected to PRINS or C-PRINS with primers for GA A microsatellites (barley and wheat) or FokI repeat (field bean). The follo wing parameters were optimized to achieve the highest specificity and inten sity of fluorescent labeling: ratio of labeled versus unlabeled nucleotides , nucleotide concentration, and the number and concentration of primers. Results: Under optimal conditions, C-PRINS resulted in strong and specific labeling of GAA microsatellites on sorted barley and wheat chromosomes and FokI repeats on sorted held bean chromosomes. The labeling patterns were ch aracteristic for each chromosome and permitted their unequivocal identifica tion as well as determination of purity after sorting, which ranged from 96 % to 99%. A standard polymerase chain reaction (PCR) with chromosome-specif ic primers was not sensitive enough to detect low-frequency contamination. Conclusions: The results indicate that a single C-PRINS assay with primers that give chromosome-specific labeling pattern is sufficient not only to de termine chromosome content of peaks on flow karyotype but also to determine the purity of sorted chromosome fractions. The whole procedure can be perf ormed in less than 3 h on the next day after sorting. Numerous applications are expected in the area of plant flow cytogenetics. Cytometry 41: 102-108 , 2000. (C) 2000 Wiley-Liss, Inc.