Acta Physiologiae Plantarum

, 39:274 | Cite as

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

  • Xia Zhao
  • Baohua Feng
  • Tingting Chen
  • Caixia Zhang
  • Longxing TaoEmail author
  • Guanfu FuEmail author
Original Article


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, F v/F m 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.


Transcriptome analysis Chlorophyll Chloroplast development Photosynthesis Rice (Oryza sativa L.) Oxidative stress 



We thank Chen Zheng and Wang Yi for valuable advice on RNA-Seq analysis and quantitative RT-PCR. We thanks for assistance from Meiqin Shao, Xueqin Yang and Yongjie Yang from China National Rice Research Institution during research process.

Compliance with ethical standards


This work was funded by the National Natural Science Foundation of China (Grant nos. 31501264, 31561143003 and 31671619), National Food Science and Technology Project (2016YFD0300208), Zhejiang Provincial Natural Science Foundation, China (LQ15C130003), the China National Rice Research Institute (Grant no. 2014RG004-4), and the MOA Special Fund for Agro-scientific Research in the Public Interest of China (Grant no. 201203029).

Conflict of interest

All authors of this paper declare that the research was not involved with any commercial or financial relationships that could form a potential conflict of interest.

Supplementary material

11738_2017_2571_MOESM1_ESM.docx (14 kb)
Supplementary material 1 (DOCX 13 kb)


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Copyright information

© Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków 2017

Authors and Affiliations

  1. 1.State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
  2. 2.Yibin UniversityYibinChina

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