Abstract
A dominant loss of function mutation in myo-inositol phosphate synthase (MIPS) 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 a set of putative candidate transcription factors and their regulatory interactions with genes that have functions in myo-inositol biosynthesis, auxin-ABA signaling, and seed dormancy. We evaluated the performance of our unsupervised network inference method by comparing the predicted regulatory network with published regulatory interactions in Arabidopsis. Some contrasting regulatory interactions were observed in low phytic acid mutants compared to non-mutant lines. 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 https://lilabatvt.github.io/LPANetwork/.
Highlights
Seed development is a complex metabolic process, which involves both synthesis and breakdown of macromolecules for growth and maintenance of the embryo (Weber et al, 2005; Le et al, 2007)
For example (Table 2), we found that a bZIP transcription factor (Glyma.19G244800, whose most similar Arabidopsis gene is AT5G28770) is regulating module 57 in our predicted network
We identified co-expression gene modules with distinct and genotype specific expression patterns. These gene modules are enriched with genes with various functional categories that are related to different stages of seed development
Summary
Seed development is a complex metabolic process, which involves both synthesis and breakdown of macromolecules for growth and maintenance of the embryo (Weber et al, 2005; Le et al, 2007). Glucose-6-phosphaste is converted to myo-inositol, an intracellular signaling molecule, which is phosphorylated several times to form phytic acid (Raboy, 1997). A mutation in myo-inositol phosphate synthase (MIPS) gene results in reduced phytic acid, stachyose, raffinose, and elevated sucrose, and low seed emergence in soybean (Hitz et al, 2002; Saghai Maroof and Buss, 2008). Other non-biosynthetic pathway genes such as multi-drug resistance protein (MRP) genes encoding ATPbinding cassette transporters that are believed to be involved in the transport of phytic acid to storage vacuoles, are known to regulate phytic acid levels and affect seed emergence (Shi et al, 2007; Nagy et al, 2009; Saghai Maroof et al, 2009; Xu et al, 2009; Jervis et al, 2015)
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