In contrast, many of the genes that are overexpressed in the standard line appear to be increasing during late seed development in both standard and defective lines as does PRP2. There were 21 hormone regulated genes that were differentially expressed in the seed coat of wild type and defective isolines of both Clark and Harosoy background including representative auxin and gibberellin regulated genes that are shown in Tables 3 & 4. One gene model Glyma10g35870.1 showed the best match to the authentic ADR12 gene from NCBI. It showed approximately 16 fold lower Cinoxacin expression in the Clark defective seed coats and 4-fold lower expression expression in Harosoy defective seed coats. Auxin is an important phytohormone that plays several important roles in plant growth and development. The expression level of this gene at different stages of seed development in both standard and defective seed coat isolines is presented in Figure 5A for RNA-Seq data. In the Clark standard isoline, this gene showed higher expression in earlier stages, and there was BAY 80-6946 continuous decrease in the expression level at later stages of seed development. There was significant differential expression at all the seed developmental stages. In the Harosoy standard isoline, expression of ADR12 increased continuously with developmental stages and also increased in the defective seed coats at the two older stages, although the levels were significantly lower in the defective seed coats. The expression pattern of ADR12 using RNA blots coincides well with the RNA-Seq data in that the defective seed coats have reduced expression especially in the Clark isolines. In addition, the blots confirm that the ADR12 is more highly expressed in standard seed coats of Clark than in Harosoy. As presented in the blots in Figure 5B, bottom panel, there was no differential expression observed from 4�C5 days old soybean hypocotyls in standard and defective isolines of Clark and Harosoy. Thus, the differential expression of this gene is likely confined to the seed coats that manifest the defective cell wall structure. The expression pattern of two other hormone regulated genes in Tables 3 and 4 that showed significant differential expression in the seed coat of wild type and defective isolines of both Clark and Harosoy backgrounds is presented in Figures S6-L and S7-N.