Location: Plant Genetics Research
2013 Annual Report
We have predicted a large number of transcription factor genes and microRNA genes potentially controlling oil quality traits in soybean seeds, and modeled their underlying gene regulatory networks. In this plan, we will select a minimum of two transcription factor genes and microRNA genes, and validate their functions in Sub-Objective 1A and 1B respectively through altering their activities in soybean transgenic seeds. It is time consuming to evaluate gene functions using a transgenic approach in soybean so we have decided to use a bioinformatics approach to improve the prediction of gene function in the proposed research. This approach will entail a genomic and evolutionary based comparison of expression profiles of protein coding sequences and miRNAs in soybean and Arabidopsis seeds over the course of seed maturation in Sub-Objective 1C. This will also enable us to translate knowledge and resources from model plant research into soybean oil quality improvement.
MicroRNA species that regulate oil production pathways in soybean seeds will be validated bioinformatically and by direct testing using standard molecular technologies. Transgenic approaches will be used to determine the functions of the miRNAs in regulating oil content and composition in seeds and their underlying gene regulatory networks by overexpressing or suppressing activity of the selected miRNAs in soybean.
The functions of selected soybean genes in the control of oil composition and content will be explored by comparative bioinformatics approaches using Arabidopsis as a model seed. The soybean/Arabidopsis orthologous genes encoding candidate seed specific transcription factors will be preferentially selected for functional validation. The functional significance and equivalence of the paired Arabidopsis and soybean genes will be validated by selecting a minimum of two pairs of Arabidopsis/soybean genes, examine the oil and transcriptomic phenotypes of mutants that can be identified in Arabidopsis, use complementation transgenic strategies to determine if the soybean genes can functionally complement the phenotypes of the Arabidopsis mutants. The soybean genes that exhibit functions in oil composition and content will then be directly tested in soybean transgenic plants.
To further select key regulatory gene candidates with the highest confidence in regulation of oil content and composition to validate their regulatory functions and underlying regulatory networks, we inferred miRNA gene regulatory networks, and characterized their topology. In addition, we determined the RNA degradome and constructed cDNA libraries in soybean cotyledon for RNA-seq. We are integrating the miRNA regulatory networks with transcription factor regulatory networks and the oil quality related genes identified in 9 soybean germplasm to select the genes regulating oil content and composition through a variety of data mining strategies.