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

Published: 5 December 2012

Additional files

Additional file 1:

Phenotypic traits of BP034 and GM077.

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Additional file 2:

Absorbance spectra of the iodine-stained starch samples from BP034 and GM077. Starch standard samples with known amylose contents are included in the spectra. ST (standard), AC (amylose content). The iodine-staining was performed as described previously [35].

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Additional file 3:

Content of carbohydrates, Klason lignin and oil in BP034 and GM077.

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Additional file 4:

Functional categories in Clusters of Orthologous Groups (COGs) for proteins deduced from the obtained cDNAs after subtraction of GM077 (tester) with BP034 (driver).

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Additional file 5:


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Additional file 6:

Putative SURE-elements in promoter regions of the upregulated genes indentified in GM077. GenBank accession number for each gene is listed in Table 3. The putative SURE-element sequence (in green) was based on Sun et al. [34] & Grierson et al. [63]. The nucleotide position is relative to translation initiate site (the ATG codon). GBSS (gene for granule-bound starch synthase), AGP (gene for ADP-glucose pyrophosphorylase), SS (gene for starch synthase), BE (gene for branching enzyme), ISA (gene for isoamylase), SUSIBA2-like (gene for sugar signaling in barley 2-like), UGP (gene for UDP-glucose pyrophosphorylase), SUS (gene for sucrose synthase).

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Additional file 7:

Gene expression profiling of three selected genes (SUSIBA2-like, ISA1 and AGPS) from the SSH experiment during plant development of rice and Arabidopsis. The microarray data from two publicly available websites was used for rice ( webcite) and Arabidopsis ( webcite), respectively. (A) Rice SUSIBA2-like (GenBank Ac No. AK121838). (B) Arabidopsis WRKY20 (a homologue of SUSIBA2, GenBank Ac No. NM_11898). (C) Rice ISA1 (GenBank Ac No. AB015615). (D) Arabidopsis ISA1 (GenBank Ac No. NM_128551). (E) Rice AGPS (GenBank Ac No. AK103906). (F) Arabidopsis AGPS (GenBank Ac No. NM_124205).

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Additional file 8:

A flow chart of DSN-mediated (duplex-specific nuclease) suppression subtractive hybridization (SSH). A small amount of RNA samples from tester (GM077) and driver (BP034) was used for template-switching cDNA synthesis and step-out PCR amplification [78]. SP6 and T7 RNA polymerases were then employed to generate sufficient tester and driver transcripts, respectively. After a secondary reverse transcription and RNA digestion, the tester cDNAs were subjected to an excess amount of driver RNA for hybridization. Hybridization was performed by denaturation and ressociation. cDNAs in hybrids with RNA were digested by duplex-specific nuclease. The left-over single-stranded cDNAs from hybridization were only the temples for exponential PCR amplification to generate cDNA fragments for construction of a cDNA library. Tsp (template-switching primer), 3’ap (adaptor primer), PI (primer I).

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