Open Access Research article

Molecular insights into how a deficiency of amylose affects carbon allocation – carbohydrate and oil analyses and gene expression profiling in the seeds of a rice waxy mutant

Ming-Zhou Zhang1, Jie-Hong Fang1, Xia Yan23, Jun Liu1, Jin-Song Bao4, Gunnel Fransson5, Roger Andersson5, Christer Jansson6, Per Åman5 and Chuanxin Sun2*

Author affiliations

1 College of Life Science, China JiLiang University, Hangzhou, 310018, China

2 Department of Plant Biology & Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, P.O. Box 7080, SE, 75007, Uppsala, Sweden

3 Heihe Key Laboratory of Ecohydrology and Integrated River Basin Science, Cold and Arid Regions Environmental and Engineering Institute, Chinese Academy of Sciences, 260 Donggang West Road, Lanzhou, 730000, China

4 Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang, 310029, China

5 Department of Food Science, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7051, SE, 75007, Uppsala, Sweden

6 Lawrence Berkeley National Laboratory, Earth Sciences Division, 1 Cyclotron Road, Berkeley, CA, 94720, U.S.A

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Citation and License

BMC Plant Biology 2012, 12:230  doi:10.1186/1471-2229-12-230

Published: 5 December 2012



Understanding carbon partitioning in cereal seeds is of critical importance to develop cereal crops with enhanced starch yields for food security and for producing specified end-products high in amylose, β-glucan, or fructan, such as functional foods or oils for biofuel applications. Waxy mutants of cereals have a high content of amylopectin and have been well characterized. However, the allocation of carbon to other components, such as β-glucan and oils, and the regulation of the altered carbon distribution to amylopectin in a waxy mutant are poorly understood. In this study, we used a rice mutant, GM077, with a low content of amylose to gain molecular insight into how a deficiency of amylose affects carbon allocation to other end products and to amylopectin. We used carbohydrate analysis, subtractive cDNA libraries, and qPCR to identify candidate genes potentially responsible for the changes in carbon allocation in GM077 seeds.


Carbohydrate analysis indicated that the content of amylose in GM077 seeds was significantly reduced, while that of amylopectin significantly rose as compared to the wild type BP034. The content of glucose, sucrose, total starch, cell-wall polysaccharides and oil were only slightly affected in the mutant as compared to the wild type. Suppression subtractive hybridization (SSH) experiments generated 116 unigenes in the mutant on the wild-type background. Among the 116 unigenes, three, AGP, ISA1 and SUSIBA2-like, were found to be directly involved in amylopectin synthesis, indicating their possible roles in redirecting carbon flux from amylose to amylopectin. A bioinformatics analysis of the putative SUSIBA2-like binding elements in the promoter regions of the upregulated genes indicated that the SUSIBA2-like transcription factor may be instrumental in promoting the carbon reallocation from amylose to amylopectin.


Analyses of carbohydrate and oil fractions and gene expression profiling on a global scale in the rice waxy mutant GM077 revealed several candidate genes implicated in the carbon reallocation response to an amylose deficiency, including genes encoding AGPase and SUSIBA2-like. We believe that AGP and SUSIBA2 are two promising targets for classical breeding and/or transgenic plant improvement to control the carbon flux between starch and other components in cereal seeds.

Carbon allocation; Rice (Oryza sativa); Waxy seeds; Suppression subtractive hybridization (SSH); Quantitative polymerase chain reaction (qPCR); Gene expression