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

Scientific Publications

Peer-Reviewed Journal Articles (Recent)


Bertier, L., Ron, M., Huo, H., Bradford, K.J., Britt, A.B., Michelmore, R.W. 2018. High-resolution analysis of the efficiency, heritability, and editing outcomes of CRISPR/Cas9-induced modifications of NCED4 in lettuce
(Lactuca sativa). G3: Genes Genomes Genetics 8: 1513-1521 Doi: 10.1534/g3.117.300396

Bradford, K.J. 2018. Interpreting biological variation: Seeds, populations and sensitivity thresholds. Seed Scientific Research 28:158-167 Doi: 10.1017/S0960258518000156

Bradford, K.J., Chrispeels, M.J. 2018. Plant propagation by seeds and vegetative processes. In Plants, Genes and Agriculture: Sustainability through Biotechnology, M.J. Chrispeels, P. Gepts, Eds., Sinauer Associates, Oxford University Press, Sunderland, MA, pp. 268-292

Bradford, K.J., Dahal, P., Van Asbrouck, J., Kunusoth, K., Bello, P., Thompson, J., Wu, F. 2018. The dry chain: reducing postharvest losses and improving food safety in humid climates. Trends in Food Science & Technology 71: 84-93

Chang, Y., Liu, H., Liu, M., Liao, X., Van Deynze, A., et al. 2018. The draft genomes of five agriculturally important African orphan crops. GigaScience 8(3)

Chunthawodtiporn, J., Hill, T., Stoffel, K., Van Deynze, A. 2018. Quantitative trait loci controlling fruit size and other horticultural traits in bell pepper (Capsicum annuum). The Plant Genome 11(1)

Gonda, I., Ashrafi, H., Lyon, D.A., Strickler, S.R., Hulse-Kemp, A.M., Van Deynze, A., et al. 2018. Sequencing-based bin map construction of a tomato mapping population, facilitating high-resolution quantitative trait loci detection The Plant Genome 12:180010

Hulse-Kemp, A.M., Maheshwari, S., Stoffel, K., Hill, T.A., Jaffe, D., et al. 2018. Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library. Hortic Res 5:4,https://www.ncbi.nlm.nih. gov/pubmed/29423234

Li, M., An, H., Angelovici, R., Bagaza, C., Batushansky, A., Van Deynze, A., et al. 2018. Topological data analysis as a morphometric method: Using persistent homology to demarcate a leaf morphospace. Frontiers in Plant Science 9(553)

Spalink, D., Stoffel, K., Walden, G.K., Hulse-Kemp, A.M., Hill, T.A., Van Deynze, A., et al. 2018. Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae). Molecular Phylogenetics and Evolution 126:293-302

Timsina, K.P., Bradford, K.J., Dahal, P., Shivakoti, G.P., Kunusoth, K., Van Asbrouck, J., Bajracharya, J., Pandey, I.R. 2018. Potential impacts of desiccant-based drying and hermetic storage on the value chain for onion seeds in Nepal. J. Agribusiness in Developing and Emerging Economies 8(2):363-390

Van Deynze, A., Zamora, P., Delaux, P.-M., Heitmann, C., Jayaraman, D., Van Deynze, A., et al. 2018. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLoS Biology 16(8):e2006352

Zohoungbogbo, H.P.F., Houdegbe, C.A., Sogbohossou, D.E.O., Tossou, M.G., Maundu, P., Van Deynze, A., et
al. 2018. Andromonoecy in Gynandropsis gynandra (L.) Briq. (Cleomaceae) and effects on fruit and seed production. Genetic Resources and Crop Evolution 65(8):2231-2239


Vegh, A., Incze, N., Fábián, A., Huo, H., Bradford, K.J., Balázs, E. and Soós, V. 2017. Comprehensive analysis of DWARF14-LIKE2 (DLK2) reveals its functional divergence from strigolactone-related paralogs. Frontiers in Plant Science 8: 1641. doi: 10.3389/fpls.2017.01641.

Sogbohossou, E.O.D., Achigan-Dako, E.G., Maundu, P., Solberg, S., Deguenon, E.M.S., Mumm, R.H., Hale, I., Van Deynze, A. and Schranz, M.E. 2017. A roadmap for breeding orphan leafy vegetable species: A case study of Gynandropsis gynandra (Cleomaceae). Horticulture Research, 5. 2 doi: 10.1038/s41438-017-0001-2.

Chunthawodtiporn, J., Hill, T.A., Stoffel, K.M. and Van Deynze, A.E. 2017. Quantitative trait loci (QTL) controlling fruit size and other horticultural traits in bell pepper (Capsicum annuum). Plant Genome
11:160125. doi: 10.3835/plantgenome2016.12.0125.

Hill, T., Chunthawodtiporn, J., Ashrafi, H., Stoffel, K., Weir, A. and Van Deynze, A. 2017. Regions underlying population structure and the genomics of organ size determination in Capsicum annuum. Plant Genome. doi: 10.3835/plantgenome2017.03.0026.

Tchokponhoué, D.A., N'Danikou, S., Hale, I., Van Deynze, A.E. and Achigan-Dako, E.G. 2017. Early fruiting in Synsepalum dulcificum (Schumach. & Thonn.) Daniell juveniles induced by water and inorganic nutrient management. F1000Research:

Bradford KJ, Dahal P, Van Asbrouck J, Kunusoth K, Bello P, Thompson J, Wu F (2018) The dry chain: Reducing postharvest losses and improving food safety in humid climates. Trends in Food Science & Technology 71: 84-93 Link to the original in the journal is


Bello, P. and Bradford, K.J. 2016. Single-seed oxygen consumption measurements and population-based threshold models link respiration and germination rates under diverse conditions. Seed Science Research 26(3):199-221. doi:10.1017/S0960258516000179

Bradford, K.J., Dahal, P. and Bello, P. 2016. Using relative humidity indicator paper to measure seed and commodity moisture contents. Agricultural and Environmental Letters 1:160018. doi:10.2134/ael2016.04.0018

Ho, W.K., Muchugi, A., Muthemba, S., Kariba, R., Mavenkeni, B.O., Hendre, P., Song, B., Van Deynze, A., Massawe, F. and Mayes, S. 2016. Use of microsatellite markers for the asssessment of bambara groundnut breeding system and varietal purity before genome sequencing. Genome. 59(6):427-31. doi:10.1139/gen-2016-0029

Huang, Z., Liu, S., Bradford, K.J., Huxman, T.E. and Venable, D.L. 2016. The contribution of germination functional traits to population dynamics of a desert plant community. Ecology 97(1):250-61. doi:10.1890/15-0744.1

Hulse-Kemp, A.M., Ashrafi, H., Plieske. J., Lemm, J., Stoffel K., Hill, T., Luerssen, H., Pethiyagoda, C.L., Lawley, C.T., Ganal, M.W. and Van Deynze, A. 2016. A HapMap leads to a Capsicum annuum SNP infinium array: A new tool for pepper breeding. Horticulture Research 3. Article number 16036. doi:10.1038/hortres.2016.36

Huo, H., Henry, I.M., Coppoolse, E.R., Verhoef-Post, M., Schut, J.W., de Rooij, H., Vogelaar, A., Joosen, R.V.L., Woudenberg, L., Comai, L. and Bradford, K.J. 2016. Rapid identification of lettuce seed germination mutants by bulked segregant analysis and whole genome sequencing. Plant J. 88:345–360. doi:10.1111/tpj.13267

Huo, H., Wei, S. and Bradford, K.J. 2016. DELAY OF GERMINATION1 (DOG1) regulates both seed dormancy and flowering time through microRNA pathways. PNAS 10:1073. doi:10.1073/pnas.1600558113

Iorizzo, M., Ellison, S., Senalik, D., Zeng, P., Satapoomin, P., Huang, J., Bowman, M., Iovene, M., Sanseverino, W., Cavagnaro, P., Yildiz, M., Macko-Podgórni, A., Moranska, E., Grzebelus, E., Grzebelus, D., Ashrafi, H., Zheng, Z., Cheng, S., Spooner, D., Van Deynze, A. and Simon, P. 2016. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nature Genetics 48(6):657-666. doi:10.1038/ng.3565 

Page, J.T., Liechty, Z.S., Alexander, R.H., Clemons, K., Hulse-Kemp, A.M., Ashrafi, H., Van Deynze, A., Stelly, D.M. and Udall, J.A. 2016. DNA sequence evolution and rare homoeologous conversion in tetraploid cotton. PLoS Genet. 12(5). doi:10.1371/journal.pgen.1006012

Rinaldi, R., Van Deynze, A., Portis, E., Rotino, G.L., Toppino, l., Hill, T., Ashrafi, H., Barchi, L. and Lanteri, S. 2016. New insights on eggplant/tomato/pepper synteny and identification of eggplant and pepper orthologous QTL. Front. Plant Sci. 7:1031. doi:10.3389/fpls.2016.01031


Ashrafi, H.A.,Hulse-Kemp, A.M., Wang, F., Yang, S.S., Guan, X., Jones, D.C., Matvienko, M., Mocaitis, K., Chen, Z.J., Stelly, D.M. and Van Deynze, A. 2015. A long-read transcriptome assembly of cotton (Gossypium hirsutum L.) and intraspecific SNP discovery. The Plant Genome 8(2). doi:10.3835/plantgenome2014.10.0068

Donohue, K., Burghardt, L.T., Runcie, D., Bradford, K.J. and Schmitt, J. 2015. Applying developmental threshold models to evolutionary ecology. Trends in Ecology & Evolution 30(2):66-77. doi:10.1016/j.tree.2014.11.008

Hill, T., Ashrafi, H., Chin-Wo, S.R., Stoffel, K., Truco, M.J., Kozik, A., Michelmore, R. and Van Deynze, A. 2015. Ultra-high density, transcript-based genetic maps of pepper define recombination in the genome and synteny among related species. G3 (Genes/Genomes/Genetics) 5(11):2341-55. doi:10.1534/g3.115.020040 

Hulse-Kemp, A.M., Ashrafi, H., Stoffel, K., Zheng, X., Saski, C.A., Scheffler, B.E., Fang, D.D., Chen, Z.J., Van Deynze, A. and Stelly, D.M. 2015. BAC-end sequence-based SNP mining in allotetraploid cotton (Gossypium) utilizing resequencing data, phylogenetic inferences, and perspectives for genetic mapping. G3 (Genes/Genomes/Genetics) 5(6):1095-105. doi:10.1534/g3.115.017749

Yoong, F.-Y., O’Brien, L.K., Truco, M.J., Huo, H., Sideman, R., Hayes, R., Michelmore, R.W. and Bradford, K.J. 2015. Genetic variation for thermotolerance in lettuce seed germination is associated with temperature-sensitive regulation of ETHYLENE RESPONSE FACTOR1 (ERF1). Plant Physiology 170: 472-488. doi:10.1104/pp.15.01251


Brand, A., Borovsky, Y., Hill, T., Rahman, K.A., Bellalou, A., Van Deynze, A. and Paran, I. 2014. CaGLK2 regulates natural variation of chlorophyll content and fruit color in pepper fruit. Theoretical and AppliedGenetics 127:2139-2148. doi:10.1007/s00122-014-2367-y

Camacho, A., Van Deynze, A., Chi-Ham, C. and Bennett, A.B. 2014. Genetically engineered crops that fly under the US regulatory radar. Nat Biotechnol. 32(11):1087-91. doi:10.1038/nbt.3057.

Gimeno, J., Eaatock, N., Van Deynze, A. and Blumwald, E. 2014. Selection and validation of reference genes for gene expression analysis in Switchgrass (Panicum virgatum) using quantitative real-time RT-PCR. PLoS ONE 10:1371. doi:10.1371/journal.pone.0091474

Hulse-Kemp, A.M., Ashrafi, H., Zheng, X., Wang, F., Hoegenauer, K.A., Maeda, A.B., Yang, S.S., Stoffel, K., Matvienko, M., Clemons, K., Udall, J.A., Van Deynze, A., Jones, D.C. and Stelly, D.M. 2014. Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. BMC Genomics. 30(15):945. doi:10.1186/1471-2164-15-945

Naegele, R., Ashrafi, H.A., Hill, T., Chin-Wo, S.R., Van Deynze, A. and Hausbeck, M. 2014. QTL mapping of fruit rot resistance to the plant pathogen Phytophthora capsici in a recombinant inbred line Capsicum annuum population. Phytopathology 104:479-483. doi:10.1094/PHYTO-05-13-0143-R

Rehrig, W.Z., Ashrafi, H., Hill, T., Prince, J. and Van Deynze, A. 2014. CaDMR1 co-segregates with QTL Pc5.1 for resistance to Phytophthora capsici in pepper (Capsicum annuum). The Plant Genome 7:1-12. doi:10.3835/plantgenome2014.03.0011

Seungill, K., ….. Van Deynze, A., Ashrafi, H., Hill, T., Kim, R.W., …. and Choi, D. 2014. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nature Genetics 46:270-8. doi:10.1038/ng.2877

View earlier Peer-Reviewed Journal Articles (2002 — 2013)

Extension & Outreach Publications

Agricultural Biotechnology in California (ABC) Series. This is a series of outreach publications on a variety of topics of including co-existance and agricultural biotechnologies.

Bradford, K. J. 2006. Methods to Maintain Genetic Purity of Seed Stocks .  Agricultural Biotechnology in California Series. Publication 8189.

Van Deynze, A., Bradford, K., and Eenennaam, A. 2004. Crop Biotechnology- Feeds for Livestock .  Agricultural Biotechnology in California Series. Publication 8145. Supplemental information .

Van Deynze, A., Putnam, D., Orloff, S., Lanini, T., Canevari, M., Vargas, R., Hembree, K., Mueller, S., and  Tueber, L. 2004. Roundup Ready Alfalfa: An Emerging Technology . Agricultural Biotechnology in California Series. Publication 8153.  

Sundstrom, F.J., Williams, J., Van Deynze, A., and Bradford, K. 2002. Identity Preservation of Agricultural Commodities . Agricultural Biotechnology in California Series. Publication 8077.

Suslow, T., Thomas, B., and Bradford, K. 2002. Biotechnology Provides New Tools for Plant Breeding . Agricultural Biotechnology in California Series. Publication 8043.

Thomas, B., Van Deynze, A., and Bradford, K. 2002. Production of Therapeutic Proteins in Plants . Agricultural Biotechnology in California Series. Publication 8078.

Voss, R., Murray, M., Bradford, K., Maryberry, K., and Miller, I. 1999. Onion Seed Production in California . Agricultural Biotechnology in California Series. Publication 8008.

Murray, M., Hartz, T., and Bradford, K. 1997. Cucurbit Seed Production in California .


The Science of Gene Flow (PDF) in Agriculture and its Role in Co-existence Proceedings, 2011.

SBC - 10 years of service, education and research 1999-2009 (PDF). 2009.

100 Years of Breeding (PDF). 2008.

Van Deynze, A.E., Martins, J., Bradford, K.J., 2007. An Analysis of Transgenic Field Trials in the United States . Seed Biotechnology Center. See Trial Slides for additional information.

Essays & Editorials

Fraser, R.L. 2010. Changes in Academic Seed Research. Growing Magazine.

Tennison, R.I. September 2010. A Dying Breed. Seed World.

Tennison, R.I. September 2010. A Career with a Growing Future. Seed World.

Van Deyze, A. December 2009. Plant Breeding Education is a Group Effort. Seed World

Drotleff, L. 2007. Cultivating New Breeders. Greenhouse Grower Magazine.

Fehr, S. An Endangered Species Germination Magazine - A special edition for the International Seed Federation. Also published in the May 2006 edition and in the Seed World June 2007 issue.

Van Deynze, A.E. 2006. Seed Biotechnology Center provides input on international biotechnology regulations. SeedQuest.

Van Deynze, A.E, and Bradford, K.J. 2006. Academic training of plant breeders no longer meets demand. Seed World 144: 20-21.

Bradford, K.J. June 2005. Biotech Seed Traceability & Labeling: Hindrance or Asset to Marketing & Trade? Seed World 16-22.

Books & Book Chapters

Bradford, K.J., and Chrispeels, M.J. 2017. Plant propagation by seeds and vegetative processes. In, M.J. Chrispeels, P. Gepts, ed., Plants, Genes and Agriculture. Sustainability through Biotechnology, Sinauer Associates, Oxford University Press, Sunderland, MA.

Van Deynze, A., Bradford, K.J., Daniell, H., DiTomaso, J.M., Kalaitzandonakes, N., Mallory-Smith, C., Stewart, C.N. Jr., Strauss, S.H., Van Acker, R. 2016. The science of gene flow in agriculture and its role in co-existence. In, Kalaitzandonakes, N., P. Philips, S. Smyth and J. Wesseler (eds.) The Coexistence of Genetically Modified, Organic and Conventional Foods: Government Policies and Market Practices, Springer, New York, pp. 13-37.

Huo, H. and Bradford, K.J. 2015. Molecular and hormonal regulation of thermoinhibition of seed germination. In J.V. Anderson (ed.), Advances in Plant Dormancy, Springer, pp. 3-33.

Pluskota, W.E., Bradford, K.J. and Nonogaki H. 2011. Tissue printing methods for localization of RNA and proteins that control seed dormancy and germination. In A.R. Kermode ed, Seed Dormancy: Methods and Protocols, Methods in Molecular Biology. 773:329-339. doi:10.1007/978-1-61779-231-1_19.

Bradford, K.J. 2010. Review of Genetically Modified Plants: Assessing Safety and Managing Risk by G.T. Tzotzos, G.P. Head, R. Hull, Field Crops Research 118: 36-307.

Van Deynze, A.E., Douches, D., De Jong, W. and Francis, D. 2007. Summary of Solanaceae Coordinating Meetings. In ISHS Acta Horticulturae 745. VI International Solanaceae Conference: Genomics Meets Biodiversity.

Bradford, K.J. and Nonogaki, H. Ed. 2007. Seed Development, Dormancy and Germination. Blackwell Scientific Publishers, Oxford, UK.



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