Soybean seeds begin to form on the plant at the R4 stage when the parent plant has between 13 and 20 leaf nodes. At this stage, the seed is going through multiple cycles of cell division as well as tissue differentiation. Invertase in the seed coat cleaves sucrose giving rise to hexose which surrounds the embryo of the minuscule soybean seed. The seeds grow at a rapid rate between the R4 and R7 stages as they accumulate carbon, nitrogen, and seed storage proteins. Seeds increase in size from 25 mg to 500 mg fresh weight during the R5 and R6 stages. Towards the end of the R6 stage, nutrient accumulation in the seed begins to decrease. By R7 the seed has amassed almost all the dry weight it will acquire and contains approximately 60% moisture and has begun to yellow. After reaching the maximum fresh weight, near 400�C500 mg, the seed readies itself for desiccation and begins to lose total fresh weight. By the R8 stage, most of the pods and seeds have browned and are dry. Intact seed coats are preferred but a mutation known as the ����net pattern���� in soybean results in SMI-4a defective seed coats that have ruptured by maturity to expose the cotyledons Dydrogesterone underneath. The trait has been backcrossed to create isolines in two different genetic backgrounds; however, very little is known about the histology or molecular nature of the trait. Using RNA blots, we have previously reported a developmental delay in the decline of transcripts for a specific proline-rich protein of the cell wall leading to higher levels of this transcript in the defective seed coats at the middle weight range of 100�C200 mg seed weight. The effect on PRP1 transcript levels was assumed to be a downstream effect of the net pattern mutation. In this report, we present the global gene expression analysis of the net pattern cell wall mutant in soybean using transcriptome analyses of three different stages of seed development at 50�C100 mg, 100�C200 mg, and 400�C500 mg. By comparing RNA-Seq data from the two lines containing the defective seed coat trait compared to their standard counterpart isolines using Bowtie alignments to the soybean genes models from the sequenced soybean genome, 364 significantly differentially expressed genes in common between the two isolines were revealed, many of which were involved in cell wall processes.