Transcriptomics

Dataset Information

181

Expression data from the seed coats of black (iRT) and brown (irT) soybean variant for alleles of the R locus


ABSTRACT: The seed coat of black (iRT) soybean with the dominant R allele begins to accumulate cyanic pigments at the transition stage of seed development (300 – 400 mg fresh seed weight), whereas the brown (irT) nearly-isogenic seed coat with the recessive r allele lacks cyanic pigments at all stages of seed development. We used microarrays to determine global gene expression differences between black (iRT) and brown (irT) soybean seed coats at the transition stage of seed development (300 – 400 mg fresh seed weight). To identify the complete set of gene transcripts that are differentially expressed between the seed coats of black (iRT) and brown (irT) Clark isolines, seed coats were dissected at the transition stage of seed development (300 – 400 mg fresh seed weight) for microarray analysis using the Affymetrix Soybean GeneChip. To ensure seed coats were of the same stage of development, the days post anthesis, pod length, pod color, embryo morphology, and transcript levels of the developmental marker gene Gm-r1083-1191, a putative cutin biosynthesis gene, and DFR1 were ensured to be equivalent between black (iRT) and brown (irT) isolines.

ORGANISM(S): Glycine max  

SUBMITTER: Nik Kovinich   Brian Miki  Nikola Kovinich 

PROVIDER: E-GEOD-26208 | ArrayExpress | 2011-08-22

SECONDARY ACCESSION(S): GSE26208PRJNA134963

REPOSITORIES: GEO, ArrayExpress

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Publications

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.

Kovinich Nik N   Saleem Ammar A   Arnason John T JT   Miki Brian B  

BMC genomics 20110729


BACKGROUND: The R locus controls the color of pigmented soybean (Glycine max) seeds. However information about its control over seed coat biochemistry and gene expressions remains limited. The seed coats of nearly-isogenic black (iRT) and brown (irT) soybean (Glycine max) were known to differ by the presence or absence of anthocyanins, respectively, with genes for only a single enzyme (anthocyanidin synthase) found to be differentially expressed between isolines. We recently identified and chara  ...[more]

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