Allele-specific transcription of nrITS. Frequency of allele-specific bases for three SNPs in PCR products from genomic DNA and from cDNA pools of small and large flower buds were obtained by pyrosequencing for the plants (H13, H19, H20) and are presented as boxplots consisting of sample minimum, lower quartile, median, upper quartile and sample maximum. Black boxes refer to genomic DNA, white boxes to cDNAs. Dotted lines represent the proposed frequency of an allele-specific base in genomic DNA and the null hypothesis of equal transcription for all alleles referring to their copy number: Alleles with one copy have an expected frequency of 0.2; alleles with two copies have an expected frequency of 0.4 and alleles with three copies have an expected frequency of 0.6 in pentaploids. SNP2 and SNP4 did not differentiate between the Canina-1 and Canina-2 allele, thus boxplots of genomic DNA summarize the frequency of both alleles. Because allelic composition in the genomic DNA varied between individuals H13, H20 and H19, results are presented separately. P-values of GLM statistics (additional file 2) comparing base frequencies of genomic and cDNA pools at a SNP are given above boxplots. Significant results are presented in bold.