Transcriptome Profiling of a Defective Seed Coat Mutation in Soybean

The net pattern mutation creates breaks in the seed coat of soybean (Glycine max). RNA-Seq data was used to analyze the transcriptome to understand expression of genes affected by this mutation. Seed coats from 100-200 mg seeds were used for RNA extraction and library formation from wild type and mutant isolines. Illumina GAII and Hiseq 2000 platforms were used to generate 75bp reads. For Clark standard and defective isolines, 62.3 and 41.1 million raw reads were obtained, while for Harosoy wild type and defective isolines raw reads were 38.7 and 38.2 million respectively. These reads were aligned to 78,773 target Glyma models from phytozome v8.0 using Bowtie. The genome-wide comparative study of the transcript profiles of these isolines revealed 378 differentially expressed genes that were further divided into 16 broad functional categories. The largest category at 26% of the genes had no functional annotations followed by 19% which were classified as cell wall related. Proline rich protein (PRP) and glycine rich protein genes were highly differentially expressed. PRP1 and PRP2 are major cell wall structural proteins in soybean. These genes showed significant differential expression in both of the isolines in this analysis.  Other genes showing higher differential expression in both of the isolines were auxin responsive genes, xylem serine proteinase, transparent testa1, stress response related and seed storage protein genes. Thus in this study we found genes affected by the mutation and some of these genes may be candidates for the cause of the mutation that specifies defective seed coats.