Gene-Specific Length Polymorphism - a Simple Tool for Routine Analysis of Homogeneity of Carrot (Daucus carota L.) Breeding Stocks

Control of homogeneity of breeding materials and seed purity of F-1 hybrid cultivars is an important task. It can be facilitated by the use of simple identification of a set of diagnostic DNA polymorphisms. We developed a three-locus assay for identification of carrot parental lines used to produce seed of an F-1 hybrid, based on intron length polymorphisms of isopentenyl pyrophosphate isomerase (ipi), carotenoid isomerase (crtiso) and chalcone synthase (chs2). We were able to identify length variants in each of these loci following PCR amplification with primers anchored in exons and flanking introns of variable length, and separation of the amplification products in agarose. We used the assay to select plants from parental stocks of an F-1 hybrid that would carry homozygous variants of ipi, crtiso and chs2, in such way that the CMS and the maintainer differed from the pollinator in terms of their allele composition. This, in turn, would allow for a routine low cost homogeneity evaluation of the parental stocks - only homozygous individuals were expected, as well as hybrid seed purity testing based on the presence of different alleles originating from the female and the male parent.