A systems biology approach toward understanding seed composition in soybean.

Ling Li,Jackie Shanks,Vidya Iyer,Manhoi Hur,Wenxu Zhou,Cumhur Yusuf Demirkale,Zebulun Arendsee,Joon-Yong Lee,Zhihong Song,Nick Ransom,Basil Nikolau,Eve Syrkin Wurtele,Dan Nettleton,Mark Westgate

doi:10.1186/1471-2164-16-s3-s9

Abstract

BackgroundThe molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed. Many of the genes and metabolites that participate in seed metabolism are unknown or poorly defined; even more remains to be understood about the regulation of their metabolic networks. A global omics analysis can provide insights into the regulation of seed metabolism, even without a priori assumptions about the structure of these networks.ResultsWith the future goal of predictive biology in mind, we have combined metabolomics, transcriptomics, and metabolic flux technologies to reveal the global developmental and metabolic networks that determine the structure and composition of the mature soybean seed. We have coupled this global approach with interactive bioinformatics and statistical analyses to gain insights into the biochemical programs that determine soybean seed composition. For this purpose, we used Plant/Eukaryotic and Microbial Metabolomics Systems Resource (PMR, http://www.metnetdb.org/pmr, a platform that incorporates metabolomics data to develop hypotheses concerning the organization and regulation of metabolic networks, and MetNet systems biology tools http://www.metnetdb.org for plant omics data, a framework to enable interactive visualization of metabolic and regulatory networks.ConclusionsThis combination of high-throughput experimental data and bioinformatics analyses has revealed sets of specific genes, genetic perturbations and mechanisms, and metabolic changes that are associated with the developmental variation in soybean seed composition. Researchers can explore these metabolomics and transcriptomics data interactively at PMR.

Highlights

The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed
Systems biology approach Many current models of biological networks are based solely on transcript accumulation data [51], which cannot give a complete picture of cellular metabolism [52]
Additional functional annotations of the 37,593 Glycine max probes were deduced via sequence homology with Arabidopsis genome annotations (TAIR10)

Summary

Introduction

The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed. As the propagule that ensures the dissemination of plants, seeds support human activity as one of the major products of agriculture. Both of these functions are contingent on biochemical storage reserves that are deposited within the seed during its development. Oil, carbohydrate and protein reserves are biosynthesized by the programmed expression of a metabolic network during seed development. This metabolic network converts imported photosyntheticallyderived carbon (usually in the form of sucrose) and imported nitrogen (usually as amino acids) into the final proportion of protein, oil and carbohydrate [3,4,5]

Methods

Results

Conclusion