Integrated analyses of rice dark response and leaf color regulation reveal links with porphyrin and chlorophyll metabolism

Background Light is a key regulatory signal for rice growth and development. Under dark stress, rice shows leaf yellowing. Whole genome transcriptomic analysis will identify differentially expressed genes (DEG) in dark-treated rice seedlings and DEG-enriched metabolic pathways. Rice leaf color is an essential agronomic trait. Traditional genetic experiments have reported over a hundred of leaf color-related (LCR) genes and some of them were also regulated by light signal. Thus, an integrated analysis for the two set of data will be helpful for illustration of the mechanism for both dark-response and leaf color regulation. Results Transcriptome changes in response to dark treatment were surveyed by RNA-Seq analysis. About 13,115 DEGs were identified. One hundred and fifty rice LCR genes were collected. It was found that 102 LCR genes (68.0%) were also dark-response DEGs, which suggests an overlap between dark response and LCR networks. Fifty DEG overlapped LCR genes was associated with chloroplast development. KEGG analysis revealed enrichment of LCR genes in porphyrin and chlorophyll metabolism (PCM) (18/44, 40.9%). Of the 18 LCR genes in the PCM pathway, 15 were dark-response DEGs (83.3%). More interestingly, most of them are involved in a central PCM sub-pathway, chlorophyll biosynthesis. Conclusions Integrated analysis for dark stress-response and leaf color regulation identified the correlation between the two processes and mutually supported evidences were obtained. It was found that PCM pathway, particularly chlorophyll biosynthesis process, is a core component of the overlap and plays important roles in rice LCR and dark stress-response. This study provides important clues for identifying additional LCR genes, understanding the mechanisms of dark response and leaf color regulation.