Alteration in the relative steady-state transcript abundance for a set of genes involved in DNA repairing and DNA methylation in calli and regenerants relative to their corresponding seed-plants as controls for each of the six rice genotypes (detailed in Figure1) based on q-RT-PCR analysis. A total of 41 genes were analyzed, which included those encoding for somatic homologous recombination proteins (SHR, 10 genes), mismatch repair proteins (MMR, 11 genes), checkpoint proteins (eight genes), DNA methyltransferases (six genes), 5-methylcytosine DNA glycosylases (two genes), and siRNA biogenesis-related proteins (four genes). Three rice house-keeping genes, a β-actin genes (Genbank accession no. X79378), a gene encoding for a protein synthesis elongation factor 1A, eEF-1a (Genbank accession no. AK061464) and a ubiquitin gene UBQ5 (Genbank accession no. AK061988), were used as internal controls for normalization. The steady-state transcript abundance for these genes are presented by fold-change (in log2) of original data (Additional file 8).