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Accession IconSRP113229

Inference of transcription regulatory network in low phytic acid soybean seeds

Organism Icon Glycine max
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Technology Badge IconIllumina HiSeq 2000

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A dominant loss of function mutation in myo-inositol phosphate synthase gene and recessive loss of function mutations in two multidrug resistant protein type-ABC transporter genes not only reduce the seed phytic acid levels in soybean, but also affect the pathways associated with seed development, ultimately resulting in low emergence. To understand the regulatory mechanisms and identify key genes that intervene in the seed development process in low phytic acid crops, we performed computational inference of gene regulatory networks in low and normal phytic acid soybeans using a time course transcriptomic data and multiple network inference algorithms. We identified several transcription factors and their regulatory interactions with genes that have functions in myo-inositol biosynthesis, auxin-ABA signaling and seed dormancy. We validated the predicted regulatory network by comparing it with published regulatory interactions in Arabidopsis. Some regulatory interactions were found in the low phytic acid mutants but not in non-mutant plants. These findings provide important hypotheses on expression regulation of myo-inositol metabolism, and phytohormone signaling in developing low phytic acid soybeans. The computational pipeline used for unsupervised network learning in this study is provided as open source software and is freely available at Overall design: Four soybean experimental lines designated as: (i) 3mlpa, (ii) 3MWT, (iii) 1mlpa, and (iv) 1MWT were used in this study. The lpa mutant line, '3mlpa', carrying three mutations mips1/mrp-l/mrp-n, and its non-mutant sibling line with normal phytic acid, '3MWT', were derived from crossing of 'CX-1834' (lpa line with two mpr-l/mrp-n mutations on soybean chromosomes 19 and 3, respectively) with 'V99-5089' (lpa line with single mips1 mutation) (Saghai Maroof et al., 2009). Another lpa line, '1mlpa', carrying a single mips1 mutation on soybean chromosome 11, and its isogenic sibling line with normal phytic acid, '1MWT', were derived from crossing of 'Essex' (a normal phytic acid line with no mutations) with V99-5089 (Saghai Maroof and Buss, 2008; Glover, 2011). Developing seeds were sampled in triplicates for each experimental soybean line based on seed lengths corresponding to 2-4 mm (stage1), 4-6 mm (stage2), 6-8 mm (stage3), 8-10 mm (stage4), and 10-12 mm (stage5), respectively. Samples were flash frozen using liquid nitrogen and stored at -70°C. High-quality total RNA (RIN 9-10) was extracted from frozen samples using RNeasy Plant Mini Kit, with on-column DNase digestion (QIAGEN). Total of 60 mRNA libraries were prepared from total RNA samples and sequenced as 100SE using HiSeq2000. This study includes the re-analysis of all samples in GSE75575
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