During the next 50 years, we need to produce more food than in the entire history of humankind on a decreasing amount of land for crop production. A major challenge for the 21st century is to increase the yields of major crop plants, such as soybean, using state-of-the-art genetic technologies. One way to accomplish this task is to use genomics to understand all of the genes and genetic processes required to ?make a seed? in order to engineer plants for yield traits such as more seeds, bigger seeds, and seeds with improved nutritional composition. Increasing seed yield should contribute significantly to enhancing our food supply, because over half of the major crops used for human consumption are seed crops.
My laboratory has been investigating gene activity during seed development in order to identify the genes and gene regulatory networks required to program seed development. We have been carrying out experiments to 1) profile the mRNAs present in every soybean and Arabidopsis seed compartment (e.g., embryo, endosperm, seed coat), region (embryo proper, suspensor), and tissue (e.g., inner integument, endothelium, seed coat epidermis) throughout development, 2) characterize the epigenetic events at the DNA and chromatin level to understand their role in seed development, and 3) determine the targets of critical transcription factor genes programming seed development. The main focus of our experiments is to identify transcription factor genes that program differentiation events and determine how they form regulatory networks that program seed differentiation and function. The long-term goal of research being carried out in my laboratory is to understand ?how to make a seed? in order to use this information for the improvement of crop plants.
Chen, M., Lin, J.Y., Hur, J., Pelletier, J.M., Baden, R., Pellegrini, M., Harada, J.J., and Goldberg, R.B., "Seed genome hypomethylated regions are enriched in transcription factor genes", Proc. Natl. Acad. Sci. USA 115: 8315-8322 (2018).
Henry, Kelli F., Bui, Anhthu Q., Kawashima, T., and Goldberg, R.B., "A shared cis-regulatory module activates transcription in the suspensor of plant embryos", Proc. Natl. Acad, Sci. USA 115: 5824-5833 (2018).
Pelletier, J.M., Kwong, R.W., Park, S., Lee, B.H., Baden, R., Cagliari, A., Hashimoto, M., Munoz, M.D., Fischer, R.L., Goldberg, R.B., and Harada, J.J., "LEC1 sequentially regulates the transcription of genes involved in diverse developmental processes during seed development", Proc. Natl. Acad. Sci USA 114: 6710-6719 (2017).
Danzer, J., Mellot, E., Bui, A.Q., Le, B.H., Martin, P., Hashimoto, M., Perez-Lesher, J., Chen, M., Pelletier, J.M., Somers, D.A., Goldberg, R.B., Harada, J.J., "Downregulating the expression of 53 soybean transcription factor genes uncovers a role for SPEECHLESS in initiating stomatal cell lineages during embryo development", Plant Physiology 168: 1025-1035 (2015).
Khan, D., Miller, J.L., Girard, I.J., Chan, A., Kirkbride, R.C., Pelletier, J.M., Becker, M.G., Yeung, E.C., Stasolla, C., Goldberg, R.B., Harada, J.J., and Belmonte, M. F., "Transcriptome atlas of the Arabidopsis funiculus - a study of maternal seed subregions", Plant Journal 82: 41-53 (2015).
Belmonte, M. F., Kirkbride, R. C., Stone, S., Pelletier, J. M., Bui, A. Q., Yeung, E. C., Hashimoto, M, Fei, J., Harada, C. M., Munoz, M. D., Le, B. H., Drews, G. N., Brady, S. M., Goldberg, R. B., and Harada, J .J., "Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed", Proc. Natl. Acad. Sci USA 110 (5): 434-444 (2013).
Le, B.H., Cheng, C., Bui, A.Q., Wagmaister, J., Henry, K.F., Pelletier, J., Kwong, L., Belmonte, M., Kirkbride, R., Horvath, S., Drews, G.N., Fisher, R.L., Okamuro, J.K., Harada, J.J., and Goldberg, R.B., "Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors", Proc. Natl. Acad. Sci. USA 170: 8063-8070 (2010). [link]
Ohto, M., Floyd, S.K., Fischer, R.L., Goldberg, R.B. and Harada, J.J., "Effects of APETALA2 on embryo, endosperm and seed coat development determine seed size in Arabidopsis", Sex Plant Reprod 22: 277-289 (2009).
Kawashima, T. and Goldberg, R.B., "The suspensor: not just suspending the embryo", Trends In Plant Science 15 (1): 23-30 (2009). [link]
Kawashima, T., Wang, X., Henry, K.F., Bi, Y., Weterings, K., Goldberg, R.B., "Identification of cis-regulatory sequences that activate transcription in the suspensor of plant embryos", Proc Natl Acad Sci U S A 106 (9): 3627-3632 (2009). [link]
Goldberg, R.B., "The Plant Cell: 20 Years Young", The Plant Cell 21: 3-12 (2009). [link]
Stone S.L., Braybrook S.A., Paula S.L., Kwong L.W., Meuser J., Pelletier J., Hsieh T.F., Fischer R.L., Goldberg R.B., Harada J.J., "Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: Implications for somatic embryogenesis", Proc Natl Acad Sci U S A 105: 3151-3156 (2008). [link]
Le, B.H., Wagmaister, J.A., Kawashma, T., Bui, A.Q., Harada, J.J., and Goldberg, R.B., "Using Genomics to Study Legume Seed Development", Plant Physiology 144: 562-574 (2007). [link]
Xiao, W., Custard, K.D., Brown, R.C., Lemmon, B.E., Harada,J.J., Goldberg, R.B., and Fischer, R.L., "DNA Methylation is crtical for Arabidopsis embryogenesis and seed viability", Plant Cell (2006).
Braybrook., S. A., Stone, S. L., Park, S., Bui, A. Q., Le, B.L., Fischer, R.L., Goldberg, R.B., and Harada, J.J., "Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis", Proc. Natl. Acad. Sci. USA 103: 3468-3473 (2006).