Exploring and Exploiting Soybean Seed Transcriptome Diversity

Soybean genome diversity studies have received great attention since availability of next generation sequencing technologies. However, transcriptome diversity among different soybean germplasm has been less explored and exploited. We have sequenced seed transcriptomes of wild soybean (Glycine soja), and soybean (Glycine max) landraces and milestone cultivars representing 90 years of North American soybean breeding in addition a variety of seed mutant lines. The transcriptome sequencing approach enables us to specifically examine the genes related to soybean seed traits and to simultaneously determine two functional attributes of those genes, transcript sequence and accumulation.  Having developed and applied a variety of bioinformatic pipelines and data-mining strategies, we generated a large collection of transcript sequence and accumulation polymorphisms that potentially lead to functional variations of seed genes among those germplasm, and independently identified a number of transcript sequence and accumulation variations, DNA deletions and DNA amplifications that cause changes in oil composition and disease resistance.  Further analysis of the transcript sequence and accumulation variations among the germplasm also reveals new insights into genetic improvement and transcriptional program change associated with the 90 years of North American soybean breeding.