Transcriptome analysis of pale-green leaf rice reveals photosynthetic regulatory pathways

Chlorophyll metabolic pathways and chloroplast development have been studied systematically by both biochemical and genetic approaches. However, the effect of them on photosynthesis has not been thoroughly elucidated to date. To gain expression profiles of genes involved in crucial pathways and regulators of photosynthetic metabolism in rice seedling, biochemical characteristics and transcriptome of two rice genotypes were compared. Zhefu802 and Chl-8 are the recurrent parent (dark-green leaf) and its near-isogenic lines (pale-green leaf), respectively. The net photosynthetic rate, Fv/Fm and ΦPSII of Chl-8 were markedly higher than those of Zhefu802, although the chlorophyll content of Chl-8 was approximately one-third of Zhefu802. In this research, photosynthesis is controlled by delicate but complex genetic networks. In addition to DEGs directly involved in photosynthesis, DEGs involved in response to oxidative stress, energy metabolism and nitrate metabolism co-regulated photosynthetic efficiency in rice. DEGs categorized to signal transduction supported the regulation. Chloroplasts possessing an abundant thylakoid membrane system were not favored to photosynthesis. Five DEGs assigned to chloroplast category (GO:0009507) was genetic basis of difference on thylakoid membrane. Meanwhile, suitable chlorophyll content, chlorophyll a:b and ratio of chlorophyll to carotenoid, which caused by leaf and chloroplast structure, also promoted high photosynthesis. In summary, high photosynthetic efficiency involves coordinated regulation of the synthesis of multiple pigments, chloroplast development, response to oxidative stress, energy metabolism and nitrate metabolism.