Coexpression Analysis Identifies Rice Starch Regulator1, a Rice AP2/EREBP Family Transcription Factor, as a Novel Rice Starch Biosynthesis Regulator

Fang-Fang Fu,Hong-Wei Xue

doi:10.1104/pp.110.159517

Abstract

Starch biosynthesis is important for plant development and is a critical factor in crop quality and nutrition. As a complex metabolic pathway, the regulation of starch biosynthesis is still poorly understood. We here present the identification of candidate regulators for starch biosynthesis by gene coexpression analysis in rice (Oryza sativa). Starch synthesis genes can be grouped into type I (in seeds; sink tissues) and type II (in vegetative tissues; source tissues), and 307 and 621 coexpressed genes are putatively involved in the regulation of starch biosynthesis in rice seeds and vegetative tissues, respectively. Among these genes, Rice Starch Regulator1 (RSR1), an APETALA2/ethylene-responsive element binding protein family transcription factor, was found to negatively regulate the expression of type I starch synthesis genes, and RSR1 deficiency results in the enhanced expression of starch synthesis genes in seeds. Seeds of the knockout mutant rsr1 consistently show the increased amylose content and altered fine structure of amylopectin and consequently form the round and loosely packed starch granules, resulting in decreased gelatinization temperature. In addition, rsr1 mutants have a larger seed size and increased seed mass and yield. In contrast, RSR1 overexpression suppresses the expression of starch synthesis genes, resulting in altered amylopectin structure and increased gelatinization temperature. Interestingly, a decreased proportion of A chains in rsr1 results in abnormal starch granules but reduced gelatinization temperature, whereas an increased proportion of A chains in RSR1-overexpressing plants leads to higher gelatinization temperatures, which is novel and different from previous reports, further indicating the complicated regulation of starch synthesis and determination of the physicochemical properties of starch. These results demonstrate the potential of coexpression analysis for studying rice starch biosynthesis and the regulation of a complex metabolic pathway and provide informative clues, including the characterization of RSR1, to facilitate the improvement of rice quality and nutrition.

Highlights

Starch biosynthesis is important for plant development and is a critical factor in crop quality and nutrition
Rice Starch Regulator1 (RSR1) Regulates Rice Starch Biosynthesis developing endosperm and embryo (Xue et al, 2009), showed that type I guide genes were preferentially expressed in developing endosperm, whereas type II guide genes were preferentially expressed in vegetative tissues and embryos (Fig. 1B)
Based on the number of correlated guide genes, genes that correlated with more than eight type I guide genes or more than six type II guide genes were classified as coexpressed genes that might be involved in regulating starch biosynthesis

Summary

Introduction

Starch biosynthesis is important for plant development and is a critical factor in crop quality and nutrition. Coexpression analysis, which is based on the assumption that genes with similar expression patterns are more likely to be functionally associated, has proven to be a powerful tool for identifying regulatory factors in transcriptional networks, especially those related to a specific biological process, in different organisms such as yeast (Saccharomyces cerevisiae), Arabidopsis (Arabidopsis thaliana), and human (Ihmels et al, 2004; Lee et al, 2004; Persson et al, 2005; Aoki et al, 2007; Hirai et al, 2007) In plants, this strategy has been used to identify factors regulating several metabolic pathways, including two genes involved in cellulose synthesis (Persson et al, 2005) and two MYB (for v-myb avian myeloblastosis viral oncogene homolog) TFs that regulate the aliphatic glucosinolate biosynthesis pathway (Hirai et al, 2007)

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Conclusion