Integrative Seed Biology is a NSF-funded seed biology program in the Department of Horticulture at Oregon State University. The program consists of research and learning activities on plant seeds. This website introduces you to our research projects and useful information on seeds.     Home   Comments or Questions   National Science Foundation

What is our goal?

Seed biology deals with wide range of events in the plant life cycle such as pollination, fertilization, embryogenesis, seed maturation, dormancy, and germination. Our research focuses mainly on the mechanisms of seed development, dormancy and germination. Understanding the mechanism of seed dormancy and germination is of great significance to our basic knowledge in plant biology and it has economically important agricultural applications.

The current research in the Integrative Seed Biology Program at Oregon State University focuses on the fundamental question: how do plant seeds germinate? We try to elucidate the mechanism of seed germination using biochemical and molecular biological approaches. 

Arabidopsis Seed Research

Arabidopsis is a powerful tool for plant biology research. We use this model system for our seed biology research. Arabidopsis seed has the embryo surrounded by a single cell layer of endosperm and multiple layers of testa, providing an excellent model system for research on the interplay between the embryo and the covering tissues. When germination occurs in Arabidopsis seed, the radicle penetrates the endosperm and testa and emerges from seed (Fig. 1).

Figure 1. Arabidopsis seed germination. The radicle penetrates testa and the endosperm at the micropyle.

Seed Enhancer Trap

Enhancer trap is a powerful approach to identify tissue- and stage-specific gene expression in plant and animal. For Arabidopsis research, b-glucuronidase (GUS) enhancer-trap lines have been created and successfully used for identifying tissue-specific gene expression in many plant organs. We have isolated more than 120 individual lines showing the GUS reporter gene expression in imbibed seeds.

Diverse tissue-specific GUS expression patterns including embryo- and endosperm-specific expression have been observed. In the embryo, radicle, axis-, hypocotyls-, and cotyledon-specific GUS expressions were detected. The predominant pattern in the endosperm was micropylar region-specific one (Fig. 2).  

Figure 2.  GUS Expression in BME (Blue Micropylar End) Arabidopsis enhancer-trap seeds. Representative images of GUS expression observed in the BME lines. Three different views of seeds of a BME line (ABRC CS24447) are shown. In most BME lines, GUS activity was detected in both the embryo and the endosperm before (Stages I-III, Germination) and after radicle emergence (stage IV, Post-germination).

 

Genes responsible for GUS expression are identified by genome-walking PCR. The biological function of the identified gene is analyzed using T-DNA knockout plants. BME3 (GATA type zinc finger protein) has been identified as a positive regulator of seed germination (Liu et al., 2005: The Plant Journal 44, 960-971).

Research tools available for the international seed biology community

We have donated the Seed-GUS-Expression library to the Arabidopsis Biological Resource Center for the international seed biology research community to access the seeds and identify and characterize more seed germination-associated genes. Seeds are available from ABRC. Please contact at hiro.nonogaki@oregonstate.edu for more information.

  

 

 

 

microRNA in Seeds

microRNAs (miRNA) are small (~21-24 nucleotides), single-stranded RNAs that downregulate target gene expression at transcriptional and posttranscriptional levels (Fig.3). miRNAs play crucial roles in plant development, maintenance of homeostasis and responses to environmental signals. miRNAs and their target genes, which can be computationally predicted in plants, are expressed in developing and germinating seeds as in other plant tissues (Fig. 4), suggesting the potential involvement of miRNAs in the regulation of gene expression in seeds.

 

To obtain insights into the biological function of seed-expressed miRNA target genes (and the ability of miRNAs to negatively regulate their targets), silent mutations can be introduced in the region of the target gene complementary to the miRNA without changing the amino acid sequences so that intact and functional target proteins will over-accumulate. This 'de-regulation' or 'de-repression' approach, which generates miRNA target genes resistant to the cleavage by miRNA-guided RISC (RNA-Induced Silencing Complex), is efficient and provides useful information for plant development. Currently, functional analysis of microRNAs and their targets is being conducted.

Publications

Journals

Hewitt JR, Coppersmith JL, Hong K, Liu P-P, Homrichhausen TM, Sun J, Martin RC, Nonogaki H. 2008. An Arabidopsis thaliana embryo arrest mutant exhibiting germination potential. Seed Science Research (accepted). 

Nonogaki, H. 2008. Repression of transcription factors by microRNA during seed germination and postgerminaiton: Another level of molecular repression in seeds? Plant Signaling and Behavior 3: 65-67.

Nonogaki H, Liu P-P, Hewitt JR, Martin RC. 2008. Regulation of seed germination and stand establishment - Importance of repression of developmental programs. Acta Horticulture, in press.

Liu P-P, Montgomery TA, Fahlgren N, Kasschau KD, Nonogaki H, Carrington  JC. 2007. Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. The Plant Journal, 52, 133-146.

Yuan JS, Yang X, Lai J, Lin H, Cheng ZM, Nonogaki H, Chen F. 2007. The endo-β-mannanase gene families in Arabidopsis, rice and poplar. Functional and Integrative Genomics 7, 1-16.

Nonogaki H. 2006. Seed germination - The biochemical and molecular mechanisms. Breeding Science 56, 93-105.

Martin RC, Liu P-P, Nonogaki H. 2006. MicroRNAs in seeds - Modified techniques and potential applications. Canadian Journal of Botany 84, 189-198.

Martin RC, Liu P-P, Nonogaki H. 2005. Simple purification of small RNAs from seeds and efficient detection of multiple microRNAs expressed in Arabidopsis thaliana and tomato (Lycopersicon esculentum) seeds. Seed Science Research 15, 319-328.

Liu P-P, Koizuka N, Martin RC, Nonogaki H. 2005. The BME3 (Blue Micropylar End 3) GATA zinc finger transcription factor is a positive regulator of Arabidopsis seed germination. The Plant Journal 44, 960-971.

Liu P-P, Koizuka N, Homrichhausen TM, Hewitt JR, Martin RC, Nonogaki H. 2005. Large scale screening of Arabidopsis enhancer-trap lines for seed germination-associated genes. The Plant Journal 41, 936-944.

Filichkin SA, Leonard JM, Monteros A, Liu P-P, Nonogaki H. 2004. A novel endo-β-mannanase gene in tomato LeMAN5 is associated with anther and pollen development. Plant Physiology 134, 1080-1087.

Homrichhausen TM, Hewitt JR, Nonogaki H. 2003. Endo-β-mannanase activity is associated with embryo development in germinating carrot (Daucus carota L.) seeds. Seed Science Research 13, 219-227.

Witmer X-H, Nonogaki H, Beers EP, Bradford KJ, Welbaum GE. 2003. Characterization of chitinase activity and gene expression in muskmelon seeds. Seed Science Research 13, 167-178.

Downie B, Gurusinghe S, Dahal P, Thacker RR, Snyder JC, Nonogaki, H, Yim K, Fukanaga K, Alvarado V, Bradford KJ. 2003. Expression of a GALACTINOL SYNTHASE gene in tomato seeds is up-regulated before maturation desiccation and again after imbibition whenever radicle protrusion is prevented. Plant Physiology 131, 1347-1359.

Zou X-H, Nonogaki H, Welbaum GE. 2002. A gel diffusion assay for visualization and quantification of chitinase activity. Molecular Biotechnology 22, 19-24.

Chen F, Nonogaki H, Bradford, KJ. 2002. A gibberellin-regulated xyloglucan endotransglycosylase gene is expressed in the endosperm cap during tomato seed germination. Journal of Experimental Botany 53, 215-223.

Nonogaki H, Gee OH, Bradford KJ.  2000. A germination-specific endo-β-mannanase gene is expressed in the micropylar endosperm cap of tomato seeds. Plant Physiology 123, 1235-1245.

Nonogaki H, Morohashi Y. 1999 Temporal and spatial pattern of the development of endo-β-mannanase activity in germinating and germinated lettuce seeds. Journal of Experimental Botany 50, 1307-1313.

Nonogaki H, Nomaguchi M, Morohashi Y, Matsushima H. 1998. Development and localization of endo-β-mannanase in the embryo of germinating and germinated tomato seeds. Journal of Experimental Botany 49,1501-1507.

Nonogaki H, Nomaguchi M, Okumoto N, Kaneko Y, Matsushima H, Morohashi Y. 1998. Temporal and spatial pattern of the biochemical activation of the endosperm during and following imbibition of tomato seeds. Physiologia Plantarum 102, 236-242.

Nonogaki H, Morohashi Y. 1996. An endo-β-mannanase develops exclusively in the micropylar endosperm of tomato seeds prior to radicle emergence. Plant Physiology 110, 555-559.

Nonogaki H, Nomaguchi M, Morohashi Y. 1995. Endo-β-mannanases in the endosperm of germinated tomato seeds. Physiologia Plantarum 94, 328-334.

Nomaguchi M, Nonogaki H, Morohashi Y. 1995. Development of galactomannan-hydrolyzing activity in the micropylar endosperm tip of tomato seed prior to germination. Physiologia Plantarum 94, 105-109.

Nonogaki H, Matsushima H, Morohashi Y.1992. Galactomannan hydrolyzing activity develops during priming in the micropylar endosperm tip of tomato seeds. Physiologia Plantarum 85, 167-172.

Book Chapters

Nonogaki H, Chen F, Bradford KJ. 2007. Mechanisms and genes involved in germination sensu stricto. In K.J. Bradford, H. Nonogaki, eds, Seed Development, Dormancy and Germination, Blackwell Publishing Plant Science, Oxford, UK, pp 264-304.

Martin RC, Liu P-P, Nonogaki H. 2007. Seed microRNA research. In S. Adkins, S. Ashmore, S. Navie, eds, Seed Biology, Development and Ecology, CAB International, Wallingford, UK, pp 354-364.

Liu P-P, Martin RC, Hewitt JR, Koizuka N, Homrichhausen T, Nonogaki H. 2007. A Seed-GUS-Expression enhancer-trap library for germination research. In S. Adkins, S. Ashmore, S. Navie, eds, Seed Biology, Development and Ecology, CAB International, Wallingford, UK, pp 159-168.

Nonogaki H, Bradford KJ. 2003. Tissue printing for localization of mRNA expression in seeds. In K. J. Bradford, D. Come, G. Nicolas and H. Pritchard, eds, The Biology of Seeds: Recent Research Advances, CAB International, Wallingford, UK, pp 171-179.

Alvarado V, Nonogaki H, Bradford KJ. 2000. Expression of endo-β-mannanase and SNF related protein kinase genes in true potato seeds in relation to dormancy, gibberellin and abscisic acid. In Viemont J-D, Crabbe J, eds, Dormancy in Plants: From Whole Plant Behaviour to Cellular Control. CAB International, Wallingford, UK, pp 347-364.

Bradford KJ, Chen F, Cooley MB, Dahal P, Downie B, Fukunaga KK, Gee OH, Gurusinghe S, Mella RA, Nonogaki H, Wu C-T, Yim K-O. 2000. Gene expression prior to radicle emergence in imbibed tomato seeds. In Black M, Bradford KJ, Vazquez-Ramos J, eds, Seed Biology: Advances and Applications. CAB International, Wallingford, UK, pp 231-251.

Presentations

Nonogaki H. 2008. Hormonal regulation of seed germination - Repression and de-repression of developmental programs. Donald Danforth Plant Science Center (St. Louis, MO)  

Nonogaki H, Liu, P-P, Hewitt JR, Homrichhausen TM, Martin RC, Montgomery TA, Fahlgren N, Kasschau KD, Carrington JC, Gonzalez-Garcia M-P,  Lorenzo O. 2007. Potential crosstalk between auxin and ABA during seed germination and postgermination. 19th International Plant Growth Substances Association Meeting (Puerto Vallarta, Mexico)

Nonogaki H. 2007. The molecular mechanisms of seed germination - Repression and de-repression. De Ruiter Seeds (Rotterdam, The Netherlands)

Nonogaki H. 2007. Molecular repression in seed germination. CEBAS-CSIC, Departamento de Nutricion Vegetal, Campus Universitario de Espinardo (Murcia, Spain)

Nonogaki H, Liu P-P, Pupel P, Asahina M, Montgomery TA, Fahlgren N, Kasschau KD, Carrington JC, Martin RC. 2007. De-repression during seed germination. 2nd International Society for Seed Science (ISSS) Workshop on Molecular Aspects of Seed Dormancy and Germination (Salamanca, Spain)

Nonogaki H. 2007. Seed germination research update: It's all about repression? Plant Science Center, RIKEN, (Yokohama, Japan)

Nonogaki H, Liu PP, Montgomery TA, Fahlgren N, Kasschau KD, Carrington JC. 2007.Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for plant development. 18th International Conference on Arabidopsis Research (Beijing, China)

Nonogaki H. 2007. Plant genome project in relationship to seed germination and plant hormones, 19th Annual Western Plant Growth Regulator Conference (San Diego, CA)

Nonogaki, H, Liu P-P, Hewitt JR, Martin RC. 2006. Regulation of seed germination and stand establishment - Importance of repression of developmental programs. 4th ISHS International Symposium on Seed, Transplant and Stand Establishment of Horticultural Crops (San Antonio, TX) 

Hewitt JR, Liu P-P, Nonogaki H. 2006. An Arabidopsis mutant exhibiting early arrested embryos with partial desiccation tolerance. The American Society of Plant Biologists Annual Meeting. (Boston, MA)

Liu P-P, Nonogaki H. 2006. Functional characterization of the BME3 GATA zinc finger protein in Arabidopsis seed germination. The American Society of Plant Biologists Annual Meeting. (Boston, MA)

Nonogaki H. 2006. De-regulation of transcription factors from miRNAs in seeds. INRA (Versailles, France)

Nonogaki H. 2006. MicroRNA in seeds and Darwin's book. University of Freiburg, Germany (Freiburg, Germany)

Nonogaki H. 2006. Transcriptional and post-transcriptional gene regulation in Arabidopsis seed germination. University of Angers, France (Angers, France)

Nonogaki H. 2006. De-repression of transcription factor from microRNA in seed germination. University of Salamanca, Spain (Salamanca, Spain)

Nonogaki H. 2006. Transcription factors and microRNAs in seed germination. Molecular Plant Sciences Seminar, Washington State University. (Pullman, WA)

Nonogaki H. 2006. Seed transcription factors, microRNAs and Darwin's book. Plant Science Center, RIKEN, Japan. (Yokohama, Japan)

Nonogaki H. 2005. Seed, microRNA and Darwin's last book. Plant and Soil Science Seminar Series, University of Kentucky. (Lexington, KY)

Koizuka N, Homrichhausen TM, Hewitt JR, Liu P-P, Martin RC, Nonogaki H. 2005. Tissue- and stage-specific expression of a PWWP protein gene in Arabidopsis seeds during germination sensu stricto. The American Society of Plant Biologists Annual Meeting. (Seattle, WA)

Hewitt JR, Liu P-P, Koizuka N, Homrichhausen TM, Martin RC, Nonogaki H. 2005. Tissue-specific transcription factors expressed in germinating Arabidopsis seeds. 8th International Workshop on Seeds. (Brisbane, Australia)

Martin RC, Liu P-P, Koizuka N, Nonogaki H. 2005. Development of a screening system for microRNAs in germinating Arabidopsis seeds. 8th International Workshop on Seeds. (Brisbane, Australia)

Hewitt JR, Liu P-P, Nonogaki H. 2004. Testa and endosperm rupture in germinating Arabidopsis seeds. The American Society of Plant Biologists Annual Meeting (Orlando, FL)

Homrichhausen TM, Liu P-P, Nonogaki H. 2004. Tissue-specific expression of a protein phosphatase 2C in germinated Arabidopsis seeds. The American Society of Plant Biologists Annual Meeting (Orlando, FL)

Liu P-P, Nonogaki H. 2004. Screening of Arabidopsis enhancer-trap lines for seed germination-associated genes. The American Society of Plant Biologists Annual Meeting. (Orlando, FL)

Nonogaki H, Liu P-P, Homrichhausen TM, Hewitt JR, Park EJ. 2004. Enhancer trap of germination-associated genes in Arabidopsis seeds. 9th International Symposium on Plant Seeds (Meisdorf, Germany)

Homrichhausen TM, Liu P-P, Nonogaki H. 2004. Screening of Arabidopsis enhancer-trap lines for genes expressed in seeds. 29th West Coast Biological Sciences Undergraduate Research Conference (San Diego, CA)

Hewitt JR, Liu, P-P, Nonogaki H. 2004. Physiological roles of the endosperm in Arabidopsis seed germination. 29th West Coast Biological Sciences Undergraduate Research Conference (San Diego, CA)

Homrichhausen TM, Hewitt JR, Nonogaki H. 2003. Endo-β-mannanase activity and completion of embryogenesis in imbibed carrot (Daucus carota L.) seeds. The American Society of Plant Biologists Annual Meeting (Honolulu, HI)

Hewitt JR, Nonogaki H. 2003. Development of a procedure to distinguish annual and perennial ryegrass seeds. Howard Hughes Medical Institute Undergraduate Summer Research Conference 2003 (Corvallis, OR)

Homrichhausen TM, Nonogaki H. 2003. Tissue-specific gene expression in plant seeds. Howard Hughes Medical Institute Undergraduate Summer Research Conference 2003 (Corvallis, OR)

Nonogaki H, Bradford KJ. 2002. Tissue printing for localization of mRNA expression in seeds. 7th International Workshop on Seed Biology. (Salamanca, Spain)

Zou X-H, Nonogaki H, Beers EP, Bradford KJ, Welbaum GE. 2002. Characterization of chitinase activity and gene expression in muskmelon seeds. VII International Workshop on Seed Biology. (Salamanca, Spain)

Nonogaki H. 2002. The mechanism of seed germination. National Institute of Vegetable and Tea Science [NIVTS], National Agricultural Research Organization [NARO] (Tsu, Japan)

Chen F, Nonogaki H, Bradford KJ. 2000 A xyloglucan endotransglycosylase (XET) gene is expressed during tomato seed germination. American Society of Plant Physiologist Annual Meeting 2000, (San Diego)

Nonogaki H, Gee OH, Bradford KJ. 2000. Molecular cloning of a germination-specific mannanase cDNA from tomato seeds. American Society of Plant Physiologist Annual Meeting 2000 (San Diego)

Zou X, Beers EP, Welbaum GE, Nonogaki H, Bradford KJ. 1999 Chitinase activities in germinating muskmelon (Cucumis melo) seeds. Plant Biology 99, American Society of Plant Physiologists (Baltimore)

Nonogaki H, Morohashi Y. 1999. Temporal and spatial patterns of endo-β-mannanase expression in lettuce seeds. VI International Workshop on Seed Biology (Merida, Mexico)

Bewley JD, Burton RA, Morohashi Y, Nonogaki H, Fincher GB. 1997. A cDNA encoding an endo-β-mannanase from germinated tomato seed. Plant Physiol 114 (Suppl): Abstract #1525.