Seed Biotechnology Center
Seed Biotechnology Center
Seed Biotechnology Center
University of California
Seed Biotechnology Center

Archived SBC Peer-Reviewed Journal Article Publications


Berman, J., Zhu, C., Pérez-Massot, E., Arjó, G., Zorrilla-López, U., Masip, G., Banakar, R., Sanahuja, G., Farré, G., Miralpeix, B., Bai, C., Vamvaka, E., Sabalza, M., Twyman, R., Bassié, L., Capell, T. and Christou, P. 2013. Can the world afford to ignore biotechnology solutions that address food insecurity? Plant Molecular Biology 83:5-19. doi:10.1007/s11103-013-0027-2

Bewley, J.D., Bradford, K.J., Hilhorst, H.W.M. and Nonogaki, H. 2013. Seeds: Physiology of Development, Germination and Dormancy. Third Edition. (New York: Springer).

Boddy, L.G., Bradford, K.J. and Fischer, A.J. 2013. Stratification requirements for seed dormancy alleviation in a wetland weed. PLOS One 8(9) e71457. doi:10.1371/journal.pone.0071457

Bradford, K.J., Bello, P., Fu, J.C. and Barros, M. 2013. Single-seed respiration: A new method to assess seed quality. Seed Sci. & Technol. 41:420-438. doi:10.15258/sst.2013.41.3.09

Hill, T.A., Ashrafi, H., Reyes-Chin-Wo, S., Yao, J., Stoffel, K., Trucio, M-J., Kozik., A., Michelmore, R.W. and Van Deynze, A. 2013. Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene pepper genechip. PLoS ONE 8:1-16. doi:10.1371/journal.pone.0056200 

Hirsch, C.N., Hirsch, C.D., Felcher, K., Coombs J., Zarka, D., Van Deynze, A., De Jong, W., Veilleux, R.E., Jansky, S., Bethke, P., Douches, D.S and Buell, C.R. 2013. Retrospective view of North American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries. G3 (Genes Genomes Genetics) 3:1003-13. doi:10.1534/g3.113.005595

Huo, H., Dahal, P., Kunusoth, K., McCallum, C.M. and Bradford, K.J. 2013. Expression of 9-cis-EPOXYCAROTENOID DIOXYGENASE4 is essential for thermoinhibition of lettuce seed germination but not for seed development or stress tolerance. Plant Cell 28:884-900. doi:10.1105/tpc.112.108902. 

Iorizzo, M., Senalik, D.A., Ellison, S.L., Grzebelus, D., Cavagnaro, P.F., Allender, C., Brunet, J., Spooner, D.M., Van Deynze, A. and Simon, P.W. 2013. Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae). American Journal of Botany 100:930-8. doi:10.3732/ajb.1300055

Page, J.T., Huynh, M.D., Liechty, Z.S., Grupp, K., Stelly, D., Hulse, A.M., Ashrafi, H. Van Deynze, A., Wendel, J.F., and Udall J.A. 2013. Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.G3 (Genes Genomes Genetics) 3:1809-1818. doi:10.1534/g3.113.007229

Truco, M.J., Ashrafi, H., Kozik, A., van Leeuwen, H., Bowers, J., Reyes Chin-Wo, S., Stoffel, K., Xu, H., Hill, T., Van Deynze, A.E. and Michelmore, R.W. 2013. An ultra-high-density, transcript-based, genetic map of lettuce. G3 (Genes Genomes Genetics). doi:10.1534/g3.112.004929.

Yarnes, S., Ashrafi, H., Hill, T.A., Reyes Chin-Wo, S., Stoffel, K. and Van Deynze, A.E. 2013. Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population. Genome 56(1):61-74. doi:10.1139/gen-2012-0083


Ashrafi, H., Hill, T., Stoffel, K., Kozik, A., Yao, J., Chin-Wo, S.R. and Van Deynze, A. 2012. De novo assembly of the pepper transcriptome (Capsicum annuum): A benchmark for in silico discovery of SNPs, SSRs and candidate genes. BMC Genomics. 30(13):571. doi:10.1186/1471-2164-13-571

Boddy, L.G., Bradford, K.J. and Fischer, A.J. 2012. Population-based threshold models describe weed germination and emergence patterns across varying temperature, moisture and oxygen conditions. Journal of Applied Ecology 49:1225-1236. doi:10.1111/j.1365-2664.2012.02206.x

Hamilton J.P., Sim S.C., Stoffel K., Van Deynze A., Buell C.R. et al. 2012. Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. The Plant Genome 5(1):17-29. doi:10.3835/plantgenome2011.12.0033

Merk, H.L., Yarnes, S.C., Van Deynze, A., Tong, N., Menda, N., Mueller, L.A., Mutschler, M.A., Lowen, S.A., Myers, J.R. and Francis, D.M. 2012. Trait diversity and potential for selection indices based on variation among regionally adapted processing tomato germplasm. Journal of the American Society for Horticultural Sciences 137(6):427-437.

Paterson, A.H., …. Van Deynze, A., et al. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492:423-427. doi:10.1038/nature11798.

Powell, A.L., Nguyen, C.V., Hill, T., Cheng, K.L., Figueroa-Balderas, R., Aktas, H., Ashrafi, H., Pons, C., Fernández-Muñoz, R., Vicente, A., Lopez-Baltazar, J., Barry, C.S., Liu, Y., Chetelat, R., Granell, A., Van Deynze, A., Giovannoni, J.J. and Bennett, A.B. 2012. Uniform ripening encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development. Science 336(6089):1711-5. doi:10.1126/science.1222218

Sim, S.-C., Durstewitz, G., Plieske, J., Wieseke, R., Ganal, M.W., Van Deynze, A., Hamilton, J.P., Buell, C.R., Causse, M., Wijeratne, S. and D.M. Francis. 2012. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS ONE 7:e40563. doi:10.1371/journal.pone.0040563

Sim, S.C., Van Deynze, A., Stoffel, K., Douches, D.S., Zarka, D., Ganal, M.W., Chetelat, R.T., Hutton, S.F., Scott, J.W., Gardner, R.G., Panthee, D.R., Mutschler, M., Myers, J.R. and Francis D.M. 2012. High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding. PLoS One 7(9). doi:10.1371/journal.pone.0045520

Stoffel, K., van Leeuwen, H., Kozik, A., Caldwell, D., Ashrafi, H. et al. 2012. Development and application of a 6.5 million feature affymetrix genechip(R) for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.). BMC Genomics13(1):185. doi:10.1186/1471-2164-13-185

Yu, J.Z., Kohel, R.J., Fang, D.D., Cho, J., Van Deynze, A., Ulloa, M., Hoffman, S.M., Pepper, A.E., Stelly, D.E., Jenkins, J.N., Saha, S., Kumpatla, S.P., Shah, W.V. Hugie, M.R. and Percy, R.G. 2012. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. G3 (Genes|Genomes|Genetics) 2:43-58. doi:10.1534/g3.111.001552 


Argyris, J., Truco, M.J., Ochoa, O., McHale, L., Dahal, P., Van Deynze, A., Michelmore, R.W. and Bradford, K.J. 2011. A gene encoding an abscisic acid biosynthetic enzyme (LsNCED4) collocates with the high temperature germination locus Htg6.1 in lettuce (Lactuca sp.). Theoretical and Applied Genetics. 122:95-108. doi:10.1007/s00122-010-1425-3.

Hagler, J.R., Mueller, S., Teuber, L.R., Van Deynze, A. and Martin, J. 2011. A mark-capture method for tracking foraging honey bees originating from multiple apiary locations. Journal of Insect Science 143:1-14. doi:10.1673/031.011.14301

Hagler, J.R., Mueller, S., Teuber, L.R., Matchley, S.A. and Van Deynze, A. 2011. Honey bee foraging range in alfalfa seed production fields. Journal of Insect Science 144:1-13. doi:10.1673/031.011.14401

Hamilton, J., Hansey C., Whitty, B.R., Stoffel, K.M., Massa, A.N., Van Deynze, A., De Jong, W., Douches, D.S. and Buell, C.R. 2011. Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genomics 12:302. doi:10.1186/1471-2164-12-302

Hansey, C.N., Whitty, B.R., Stoffel, K., Massa, A.N., Van Deynze, A., De Jong, W.S., Douches, D.S. and Buell, C.R. 2011. Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genomics 12:302. doi:10.1186/1471-2164-12-302

Iorizzo, M., Senalik, D., Grzebelus, D., Bowman, M., Cavagnaro, P.F., Matvienko, M., Ashrafi, H., Van Deynze, A. and Simon, P.S. 2011. De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genomics12:389. doi:10.1186/1471-2164-12-389

Miller, J.K., Repinski, S.L., Hayes, K.N., Bliss, F.A. and Trexler, C.J. 2011. Designing graduate-level plant breeding curriculum: A delphi study of private sector stakeholder opinion. Journal of Natural Resources & Life Science Education 40:82-90. doi:10.4195/jnrlse.2010.0031g

Repinski, S.L., Hayes, K.N., Miller, J.K., Trexler, C.J. and Bliss, F.A. 2011. Plant breeding graduate education: Opinions about critical knowledge, experience and skill requirements from public and private stakeholders worldwide. Crop Science 51:2325-36. doi:10.2135/cropsci2011.03.0137

Robbins, M.D., Sim, S.C., Yang, W., Van Deynze, A., van der Knaap, E., Joobeur, T. and Francis, D.E. 2011. Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato. Journal of Experimental Botony 62:1831-45. doi:10.1093/jxb/erq367

Schwember, A.R. and Bradford, K.J. 2011. Oxygen interacts with priming, moisture content and temperature to affect the longevity of lettuce and onion seeds. Seed Science Research 21:175-185. doi:10.1017/S0960258511000080

Sim, S.C., Robbins, M.D., Van Deynze, A., Michel, A.P. and Francis, D.M. 2011. Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.). Heredity 106:927-35. doi:10.1038/hdy.2010.139

Van Deynze, A.E., Hutmacher, R.E. and Bradford, K.J. 2011. Gene flow between Gossypium hirsutum and G. barbadense is asymmetric. Crop Science 51:298-305. doi:10.2135/cropsci2010.04.0213


Bradford, K.J. and Harada, J.J. 2010. Special Issue: Translational seed biology: From model systems to crop improvement. Plant Science 179:6. doi:10.1016/j.plantsci.2010.08.019

Cui, X., You, N., Girke, T., Michelmore, R. and Van Deynze, A. 2010. Single feature polymorphism detection using recombinant inbred line microarray expression data. Bioinformatics 26(16):1983-9. doi:10.1093/bioinformatics/btq316 

Miller, J.K., Herman, E.M., Jahn, M. and Bradford, K.J. 2010. Strategic research, education and policy goals for seed science and crop improvement. Plant Science 179:645-652.doi:10.1016/j.plantsci.2010.08.006 

Miller, J.K. and Bradford, K.J. 2010. The regulatory bottleneck for biotech specialty crops. Nature Biotechnology 28:1012-1014. doi:10.1038/nbt1010-1012

Rivero, R.M., Gimeno, J., Van Deynze, A.E., Walia, H. and Blumwald, E. 2010. Enhanced cytokinin synthesis in tobacco plants expressing PSARK::IPT prevents the degradation of photosynthetic protein complexes during drought. Plant Cell Physiology 51:1929-41. doi:10.1093/pcp/pcq143

Schwember, A.R. and Bradford, K.J. 2010. A genetic locus and gene expression patterns associated with the priming effect on lettuce seed germination at elevated temperatures. Plant Molecular Biology 73:105-118. doi:10.1007/s11103-009-9591-x

Schwember, A.R. and Bradford, K.J. 2010. Quantitative trait loci associated with longevity of lettuce seeds under conventional and controlled deterioration storage conditions. J. Exp. Bot. 61:4423-4436. doi:10.1093/jxb/erq248


Van Deynze, A.E., Stoffel, K., Lee, M., Wilkins, T. A., Kozik, A., Cantrell, R., Yu, J. Z., Kohel, R. J. and Stelly, D. M. 2009. Sampling nucleotide diversity in cotton. BMC Plant Biology 9:125. doi:10.1186/1471-2229-9-125 


Argyris, J., Dahal, P., Hayashi, E., Still, D.W. and Bradford, K.J. 2008. Genetic variation for lettuce seed thermoinhibition is associated with temperature-sensitive expression of abscisic acid, gibberellin, and ethylene biosynthesis, metabolism, and response genes. Plant Physiol. 148(2):926-47. doi:10.1104/pp.108.125807

Bradford, K.J., Benech-Arnold, R.L., Côme, D. and Corbineau, F. 2008. Quantifying the sensitivity of barley seed germination to oxygen, abscisic acid, and gibberellin using a population-based threshold model. J Exp Bot. 59(2):335-47. doi:10.1093/jxb/erm315

Van Deynze, A.E., Fitzpatrick, S., Hammon, R., McCaslin, M.H., Putnam, D.H., Teuber, L.R. and Undersander, D.J. 2008. Gene flow in alfalfa: Biology, mitigation, and potential impact on production. Council for Agricultural Science and Technology.

Yao, J., Lin, H., Van Deynze, A., Doddapaneni, H., Francis, M., Lemos, E.G. and Civerolo, E.L. 2008. PrimerSNP: A web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences. BMC Microbiol. 8:185. doi:10.1186/1471-2180-8-185


Chen, Z.J., .... Van Deynze, A.E. et al. 2007. Toward sequencing cotton (Gossypium) genomes. Plant Physiology 145:1303-1310. doi:10.1104/pp.107.107672

Gealy, D., ….. Bradford, K. et al. 2007. Implications of gene flow in the scale-up and commercial use of biotechnology-derived crops: Economic and policy considerations. Council for Agricultural Science and Technology.

Kalaitzandonakes, N., Alston, J.M. and Bradford, K.J. Compliance costs for regulatory approval of new biotech crops. 2007. Nat Biotechnol. 25(5):509-11. doi:10.1038/nbt0507-509.

Van Deynze, A.E., Stoffel, K., Buell, R.C., Kozik, A., Liu, J., van der Knaap, E. and Francis, D. 2007. Diversity in conserved genes in tomato. BMC Genomics 8:465. doi:10.1186/1471-2164-8-465


Van Deynze, A.E. and Stoffel, K. 2006. High throughput DNA extraction from seeds. Seed Science and Technology 34:741-745. doi:10.15258/sst.2006.34.3.21

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Argyris, J., Truco, M.J., Ochoa, O., Knapp, S.J., Still, D.W., Lenssen, G.M., Schut, J.W., Michelmore, R.W. and Bradford, K.J. 2005. Quantitative trait loci associated with seed and seedling traits in Lactuca. Theor Appl Genet. 111(7):1365-76. doi:10.1007/s00122-005-0066-4

Bradford, K.J. 2005. Threshold models applied to seed germination ecology. New Phytol. 165(2):338-41. doi:10.1111/j.1469-8137.2004.01302.x.

Bradford, K.J., Van Deynze, A.E., Gutterson, N., Parrott, W. and Strauss, S. 2005. Regulating transgenic crops sensibly: Lessons from plant breeding, biotechnology and genomics. Nature Biotechnology 23: 439-444. doi:10.1038/nbt1084

       Letters: Wilson, A., Shubert, D. et al. 2005. Nature Biotechnology.

       Response: Bradford, K.J., 2005. Nature Biotechnology.

Gandhi, S.D., Heesacker, A.F., Freeman, C.A., Argyris, J., Bradford, K. and Knapp, S.J. 2005. The self-incompatibility locus (S) and quantitative trait loci for self-pollination and seed dormancy in sunflower. Theor Appl Genet. 111(4):619-29. doi:10.1007/s00122-005-1934-7

Kaput, J., Ordovas, J.M., Ferguson, L., van Ommen, B., Rodriguez, R.L., Allen, L., Ames, B.N., Dawson, K., German, B., Krauss, R., Malyj, W., Archer, M.C., Barnes, S., Bartholomew, A., Birk, R., van Bladeren, P., Bradford, K.J. …. and Zucker J.D. 2005. The case for strategic international alliances to harness nutritional genomics for public and personal health. Br J Nutr. 94(5):623-32. doi:10.1079/BJN20051585

Sánchez Mde, L., Gurusinghe, S.H., Bradford, K.J. and Vázquez-Ramos, J.M. 2005. Differential response of PCNA and Cdk-A proteins and associated kinase activities to benzyladenine and abscisic acid during maize seed germination. J Exp Bot. 56(412):515-23. doi:10.1093/jxb/eri029

Van Deynze, A.E., Sundstrom, F.J. and Bradford K.J. 2005. Pollen-mediated gene flow in California cotton depends on pollinator activity. Crop Science 45:1567-1570 


Bradford, K.J. 2004. Workshop on Biotechnology for Horticultural Crops. California Agriculture 58(2).

Bradford, K.J. and Alston, J.M. 2004. Horticultural Biotechnology: Challenges for Commercial Development. Chronica Horticulturea: A Publication of the International Society for Horticulture Science. 44:4-8.

Kende, H., Bradford, K., Brummell, D., Cho, H.T., Cosgrove, D., Fleming, A., Gehring, C., Lee, Y., McQueen-Mason, S., Rose, J. and Voesenek, L.A. 2004. Nomenclature for members of the expansin superfamily of genes and proteins. Plant Mol Biol. 55(3):311-4. doi:10.1007/s11103-004-0158-6


Bradford, K.J., Downie, A.B., Gee, O.H., Alvarado, V., Yang, H. and Dahal P. 2003. Abscisic acid and gibberellin differentially regulate expression of genes of the SNF1-related kinase complex in tomato seeds. Plant Physiol. 132(3):1560-76. 

Downie, B., Gurusinghe, S., Dahal, P., Thacker, R.R., Snyder, J.C., Nonogaki, H., Yim, K., Fukanaga, K., Alvarado, V. and 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 Physiol. 131(3):1347-59. doi:10.1104/pp.016386

Graff, G.D., Cullen, S.E., Bradford, K.J., Zilberman, D. and Bennett, A.B. 2003. The public-private structure of intellectual property ownership in agricultural biotechnology. Nat Biotechnol. 21(9):989-95. doi:10.1038/nbt0903-989

Wu, C.T. and Bradford, K.J. 2003. Class I chitinase and beta-1,3-glucanase are differentially regulated by wounding, methyl jasmonate, ethylene, and gibberellin in tomato seeds and leaves. Plant Physiol. 133(1):263-73.


Chen, F., Nonogaki, H. and Bradford, K.J. 2002. A gibberellin-regulated xyloglucan endotransglycosylase gene is expressed in the endosperm cap during tomato seed germination. J Exp Bot. 53(367):215-23.


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