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Open Access Research article

Combined analysis of transcriptome and metabolite data reveals extensive differences between black and brown nearly-isogenic soybean (Glycine max) seed coats enabling the identification of pigment isogenes

Nik Kovinich12*, Ammar Saleem3, John T Arnason3 and Brian Miki1

Author Affiliations

1 Bioproducts and Bioprocesses, Research Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6

2 Ottawa-Carleton Institute of Biology, Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6

3 Department of Biology and Center for Research in Biopharmaceuticals and Biotechnology, University of Ottawa, Ottawa, ON, Canada K1N 6N5

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BMC Genomics 2011, 12:381  doi:10.1186/1471-2164-12-381

Published: 29 July 2011

Additional files

Additional file 1:

Supplementary Table S1. Developmental properties of black (iRT) and brown (irT) soybean seed coats at the 400 mg fresh seed weight stage.

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Additional file 2:

Supplementary Figure S1. Proanthocyanidin (PA) subunit compositions, degree of polymerizations, and amounts from the seed coats of black (iRT) and brown (irT) soybean Clark isolines. (A, B, C) iRT top panels, irT bottom panels. (A) Phloroglucinol cleavage products of soluble PA polymers. HPLC retention times: ascorbic acid (1) (Rt: 2.0 min); phloroglucinol (2) (Rt: 3.1 min); epicatechin-phloroglucinol adduct (Rt: 5.5 min); epicatechin (4) (Rt: 9.4 min). (B) Phloroglucinol cleavage products of solvent insoluble PA polymers. HPLC retention times: ascorbic acid (1) (Rt: 2.0 min); phloroglucinol (2) (Rt: 3.1 min); epicatechin-phloroglucinol (Rt: 6.2 min); epicatechin (4) (Rt: 11.0 min). (C) Free monomers. HPLC retention times: epicatechin (1) (Rt: 12.5 min). (D) Mean degree of polymerization (mDP) of soluble PAs. (E) Total insoluble PAs. (E) Total soluble PAs. (D, E, F) iRT black bars, irT white bars. (E, D) Amounts are represented as milligrams procyanidin B2 equivalents per gram lyophilized seed coat (LSC).

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Additional file 3:

Supplementary Table S2. Gene probe sets up-regulated more than 2-fold in the seed coat of black (iRT) soybean compared to the brown (irT) isolinea.

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Additional file 4:

Supplementary Figure S2. Distribution of gene function categories of probe sets that were up-regulated more than 2-fold in the seed coat of black (iRT) soybean relative to the seed coat of brown (irT) soybean.

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Additional file 5:

Supplementary Table S3. Glycine max UGTsa,b.

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Additional file 6:

Supplementary Table S4. Glycine max OMTsa,b.

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Additional file 7:

Supplementary Table S5. Gene probe sets downregulated more than 2-fold in the seed coats of black (iRT) soybean compared to the seed coats of brown (irT) soybean at the 300 - 400 mg fresh seed weight stage of developmenta.

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Additional file 8:

Supplementary Figure S3. Distribution of gene function categories of probe sets that were down-regulated more than 2-fold in the seed coat of black (iRT) soybean relative to the seed coat of brown (irT) soybean.

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Additional file 9:

Supplementary Table S6. Genes located on chromosome 9 of the soybean genome sequence Glyma1 that are associated with probe sets differentially-regulated more than 2-fold in the seed coat of black (iRT) soybean variety Clarka.

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Additional file 10:

Supplementary Figure S4. Semi-qRT-PCR validation of the expressions of select genes found to be differentially expressed in black (iRT) and brown (irT) seed coats by microarray analysis. An asterix (*) represents genes located on Chromosome Gm09 of the soybean Glyma1 genome sequence. Genes and corresponding differentially regulated probe sets: 4CL-L, Gma.7423.2.S1_a_at; 4CL-2, Gma.8472.1.S1_at; CHS4 and CHS5, GmaAffx.42116.1.S1_at; LAR1, GmaAffx.34868.1.A1_at; DFR2, GmaAffx.80720.1.S1_at; ANS2/ANS3, Gma.1163.1.S1_at; UGT78K1, Gma.1002.2.S1_at; UGT78K2, GmaAffx.71999.1.S1_at; OMT-like, Gma.9647.1.S1_at; OMT5, GmaAffx.57777.1.S1_at; GST26, GmaAffx.71212.1.A1_at; GST21, Gma.5139.1.S1_at; MYB50, GmaAffx.81605.1.S1_at; MYB159, GmaAffx.39483.1.A1_at; C2H2 ZF, Gma.17736.1.S1_at; WD40, GmaAffx.45454.1.S1_at; SCOF-1, Gma.235.1.S1_at; AP2, GmaAffx.2469.1.S1_at; EF-hand, Gma.15972.1.A1_at; ProtK, GmaAffx.90491.1.A1_s_at; LRR, GmaAffx.12723.1.A1_at; G4DT, Gma.5621.1.S1_at; PAO1-L, Gma.3745.1.S1_at; Am Oxy, Gma.3745.1.S1_at; PCT, GmaAffx.78720.2.S1_at; PUB22, Gma.4530.1.A1_s_at; 9O12a, Gma.2605.1.S1_at; 9012b, Gma.2605.2.S1_at; Lipase, GmaAffx.90450.1.S1_at.

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Additional file 11:

Supplementary Figure S5. Alignment of G. max UF3GT proteins UGT78K2 and UGT78K1 from variety Clark using the ClustalW program with default parameters. Amino acid differences are shown with grey background.

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Additional file 12:

Supplementary Table S7. Primers.

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