High-Throughput RNA-Seq Data for Amino Acid Pathways in Developing Soybean Seeds

One measure of protein quality in soybeans is determined by the composition of amino acids in the seed protein, with different groups such as industrial users or farmers having different needs. Understanding the metabolic pathways that lead to synthesis of amino acids such as lysine, methionine, and threonine is the first step to being able to modify them to add value to the soybean seed protein. Here we have examined the flux of gene expression of various enzymes in multiple amino acid biosynthetic pathways, using high-throughput RNA-Seq data on 79,000 gene models in soybean over seven stages of seed development. The stages range from very young whole seeds just four days after flowering, through cotyledons during seed-fill, to dry whole seeds. Previously, we examined the global view of changes in gene expression over these seven soybean seed stages (Jones and Vodkin 2013, PLOS One) and here we focus on specific enzymes in amino acid biosynthetic pathways such as aspartate kinase, threonine synthase, and homoserine dehydrogenase. Many of these enzymes show gene expression at very low levels, less than 20 RPKMs, with only a few being highly expressed with over 100 RPKMs. Therefore, it may be possible to increase the expression of these enzymes to ultimately change the amino acid composition of the soybean seed protein, perhaps through discovery of the transcription factors which regulate these genes.