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We reported earlier that  7B-1  mutant in tomato ( Solanum lycopersicum  L., cv. Rutgers), an ABA overproducer, is defective in blue light (B) signaling leading to B-specific resistance to abiotic and biotic stresses. Using a methylation-sensitive amplified polymorphism (MSAP) assay, a number of genes were identified, which were differentially methylated between  7B-1  and its wild type (WT) seedlings in white (W), blue (B), red (R) lights and dark (D) or in response to exogenous ABA and mannitol-induced stresses. The genomic methylation level was almost similar in different lights between  7B-1  and WT seedlings, while significant differences were observed in response to stresses in D, but not B. Using a cDNA-AFLP assay, several transcripts were identified, which were differentially regulated between  7B-1  and WT by B or D or in response to stresses. Blue light receptors  cryptochrome 1  and  2  ( CRY1  and  CRY2 ) and  phototropin 1  and  2  ( PHOT1  and  PHOT2 ) were not affected by the  7B-1  mutation at the transcriptional level, instead the mutation had likely affected downstream components of the light signaling pathway. 5-azacytidine (5-azaC) induced DNA hypomethylation, inhibited stem elongation and differentially regulated the expression of a number of genes in  7B-1 . In addition, it was shown that mir167 and mir390 were tightly linked to auxin signaling pathway in 5-azaC-treated  7B-1  seedlings via the regulation of auxin-response factor ( ARF ) transcripts. Our data showed that DNA methylation remodeling is an active epigenetic response to different lights and stresses in  7B-1  and WT, and highlighted the differences in epigenetic and transcriptional regulation of light and stress responses between  7B-1  and WT. Furthermore, it shed lights on the crosstalk between DNA hypomethylation and miRNA regulation of  ARF s expression. This information could also be used as a benchmark for future studies of male-sterility in other crops.

DNA Methylation and Transcriptomic Changes in Response to Different Lights and Stresses in 7B-1 Male-Sterile Tomato