Thus, there are many processes related to the cell wall that are not affected at the transcript level by the net-pattern mutation. Auxin is a plant growth regulator that is Broxyquinoline required for cell expansion, division and differentiation. Auxin pathway related genes have been reported to regulate several cell wall related genes in Arabidopsis. Likewise gibberellins had been reported to alter the expression of cell wall loosening genes and to work in coordination with auxin and abscisic acid hormone pathways. Genes related to the jasmonic acid pathway and ethylene response may also be related to cell wall formation. As presented in the results, there were differentially expressed genes in the standard and defective isolines that showed ethylene response related, auxin and gibberline hormone related/regulated annotations suggesting an Dicyclomine hydrochloride effect of the seed coat mutation on these genes. The role of the auxin downregulated ADR12 transcript that showed high differential expression in the standard and defective seed coats but not in the hypocotyls is not known. The predicted peptide form the ADR12 transcript is small at only 71 amino acids. Likely, many of the transcript differences for the affected pathways are confined to the seed coats as is the case for the ADR12 transcript. Such an extensive disruption of cell wall metabolism by the suite of genes affected in the net pattern mutation that leads to producing tears in the walls would likely be detrimental to the growth of the seedlings but is tolerated in the latter stages of seed coat development. The proline-rich proteins are composed of small tandem repeats such as PPVYK or PPVEK, where the second proline is often hydroxyproline. In our study PRP1 and PRP2 were among the highly differentially expressed genes. PRP1 was previously identified and characterized based on cDNA and amino acid sequence. Likewise, PRP2 had also been characterized as a slightly smaller protein than PRP1, and both consist essentially of the repeating decamer PPVYKPPVEK. Gene model numbers corresponding to these genes were obtained from the Phytozome database that has genomic sequence from the Williams cultivar of Glycine max. The Williams PRP2 protein is smaller when compared with the PRP2 in the cultivar Wayne from which it was originally sequenced as presented by amino acid sequence alignment in Figure S4.