As a plant pathology graduate student at UC Davis, I am interested in understanding and mitigating biotic threats to our domestic and international food supply.
I am thankful to be jointly mentored by Dr. Gitta Coaker and Dr. Jorge Dubcovsky.
In the Dubcovsky lab, I have been challenged with elucidating the mode of action of a wheat NLR protein.
My research will hopefully contribute to the breeding of durable rust resistance in wheat.
Nov 2013-Present Postdoctoral training
Dubcovsky’s lab, Department of Plant Sciences
University of California, Davis, California, USA
Aug 2008-Dec 2013 PhD in Plant Science
Department of Plant, Soil & Entomological Sciences
University of Idaho, Moscow, Idaho, USA
Sep 2004-Jul 2008 Bachelor of Agronomy
College of Agronomy
Northwest A&F University, Shaanxi, China
Bio:
Fine mapping and cloning of genes related to yield components and drought in wheat.
Genome-wide association study (GWAS) of water use efficiency (WUE) and yield components using a spring wheat association mapping panel and nested association mapping panel.
Publications:
Dong, Z., J.M. Hegarty, J. Zhang, W. Zhang, S. Chao, X. Chen, Y. Zhou, and J. Dubcovsky. 2017. Validation and characterization of a QTL for adult plant resistance to stripe rust on wheat chromosome arm 6BS (Yr78). Theor Appl Genet: Available at https://link.springer.com/article/10.1007/s00122-017-2946-9. (First 3 authors contributed equally)
Liu, Y., J. Zhang, Y.-G. Hu, and J. Chen. 2017. Dwarfing genes Rht4 and Rht-B1b affect plant height and key agronomic traits in common wheat under two water regimes. Field Crops Research 204: 242–248.
Wang, R., J. Chen, J.A. Anderson, J. Zhang, W. Zhao, J. Wheeler, N. Klassen, D.R. See, and Y. Dong. 2017. Genome-wide association mapping of Fusarium head blight resistance in spring wheat lines developed in the Pacific Northwest and CIMMYT. Phytopathology: Available at http://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-02-17-0073-R.
Bulli, P., J. Zhang, S. Chao, X. Chen, and M. Pumphrey. 2016. Genetic architecture of resistance to stripe rust in a
global winter wheat germplasm collection. G3 6(8): 2237–2253.
Chen, J., M.J. Guttieri, J. Zhang, D. Hole, E. Souza, and B. Goates. 2016a. A novel QTL associated with dwarf bunt resistance in Idaho 444 winter wheat. Theor Appl Genet: 1–10.
Chen, J., J. Wheeler, K. O’Brien, W. Zhao, N. Klassen, J. Zhang, B. Bowman, Y. Wang, C. Jackson, J.M. Marshall, and
X.M. Chen. 2016b. Registration of “UI Platinum” hard white spring wheat. Journal of Plant Registrations 10(1):
36–40.
Bowman B.C., J. Chen, J. Zhang, J. Wheeler, Y. Wang, W. Zhao, S. Nayak, N. Heslot, H. Bockelman, and J.M. Bonman. 2015. Evaluating Grain Yield in Spring Wheat with Canopy Spectral Reflectance. Crop Sci. In Press.
Bonman, J.M., E.M. Babiker, A. Cuesta-Marcos, K. Esvelt-Klos, G. Brown-Guedira, S. Chao, D. See, J. Chen, E. Akhunov, J. Zhang, H.E. Bockelman, T.C. Gordon. 2015. Genetic Diversity among Wheat Accessions from the USDA National Small Grains Collection. Crop Sci. 55:1243-1253.
Maccaferri, M., J. Zhang, P. Bulli, Z. Abate, S. Chao, D. Cantu, E. Bossolini, X. Chen, M. Pumphrey, J. Dubcovsky. 2015. A Genome-Wide Association Study of Resistance to Stripe Rust (Puccinia striiformis f. sp. tritici) in a Worldwide Collection of Hexaploid Spring Wheat (Triticumaestivum L.). G3: Genes, Genomes, Genetics 5: 449-465. (First three authors have equal contribution)
Zhang, J., J. Chen, C. Chu, W. Zhao, J. Wheeler, E.J. Souza, R.S. Zemetra. 2014. Genetic Dissection of QTL Associated with Grain Yield in Diverse Environments. Agronomy 4: 556-578.
Zhang, J., J. Chen, B.C. Bowman, K. O’Brien, J.M. Marshall, J.M. Bonman. 2014. Association Mapping of Hagberg Falling Number in Hard White Spring Wheat. Crop Sci. 54: 1243-1252.
Chen, J., G. Hu, J. Zhang, C. Chu, Y. Wu. 2014. Mapping of STS Markers Developed From Drought Tolerance Candidate Genes and Preliminary Analysis of Their Association With Yield-related Traits in Common Wheat (Triticum aestivum). Cereal Research Communications 42: 199-208.
Chen, J., J. Wheeler, J. Clayton, W. Zhao, K. O’Brien, J. Zhang, C. Jackson, J.M. Marshall, B.D. Brown, K. Campbell, X.M. Chen, R. Zemetra, and E.J. Souza. 2013. Registration of “UI Stone” Soft White Spring Wheat. J. Plant Reg. 7: 1–6.
Li, P., J. Chen, P. Wu, J. Zhang, C. Chu, D. See, G. Brown-Guedira, R. Zemetra, and E. Souza. 2011. Quantitative Trait Loci Analysis for the Effect of Rht-B1 Dwarfing Gene on Coleoptile Length and Seedling Root Length and Number of Bread Wheat. Crop Sci. 51: 2561–2568.
Elementary school teacher. Tertiary School Mariano Acosta, 1977.
BS in Biological Sciences. University of Buenos Aires. 1984.
PhD in Biological Sciences. University of Buenos Aires. 1989.
Postdoctoral training. Molecular Biology Institute. INTA. 1991.
Postdoctoral training. Dept. Agronomy and Range Sciences, Univ. Calif. Davis. 1992-1994.
Bio:
Awards:
2001. National Assoc. Wheat Growers. Excellence in Research.
2007. USDA-NRI “Discovery Award” best research program.
2009. American Society of Plant Biology “Hoagland Award”.
2011. Howard Hughes Medical Institute Investigator (2011-2024).
2011. USDA Secretary’s Honor Award.
2013. "Konex Award" Argentina, Genetics & Genomics 2003-2013.
2013. Fellow ASA and CSSA.
2013. Member National Academy of Science of the USA.
2014. Wolf World Award in Agriculture.
2015. USDA-NIFA Partnership Award.
2017. University of California, Davis Innovator of the Year Award.
2019 and 2020. Highly cited researcher (top 0.1% worldwide).
2022. CSSA Frank N. Meyer Medal for Plant Genetic Resources.
Publications:
Google Scholar Citation Metrics
Publications : 282
Times cited: >42,000
h-index: 109. i10 index= 256
Durum wheat (5): Desert King, Tipai, Desert King-High Protein, Miwok, Dessert Gold. Common wheat red (5): Kern, Lassik, Yurok, UC-Central Red, Yecora Rojo 515. Common wheat white (5) Clear White, Patwin, Patwin 515, Patwin-515HP, UC-Central White. Yellow flour wheat (1) UC-Amarillo. High resistant starch wheat (3): UC-Desert King-RS (durum), UC-Lassik-RS , UC-Patwin RS Malting barley (2): UC-Tahoe, UC-Capay, and UC-Alameda. Triticale (2): UC-Atrea, UC-Bopak.
Collaborations with industry (5): Blanca Grande 515, Summit 515, Expresso, New Dirkwin, Westmore.
Germplasm (61): PI 638738 - PI 638742, PI 603918, PI 603919, PI 651012, GSTR 13606, GSTR 13634, GSTR 13600, GSTR 13664, GSTR 13504, GSTR 13618, GSTR 13501-13687 (186 RILs), PI 656793, PI 664549; SbeII mutants tetraploid: PI 670159-PI 670161, 9 FT-B1: PI 671995 - PI 672004. 1RS: PI 672837 - PI 672839; GPC-B1mutants: PI 673410 - PI 673415, 10NILsGlu-A3 & Glu-B3 alleles: PI 674000 - PI 674009. 6Gw2 mutants grain size: PI 675010-675015, 3 Glu-D12+12 isogenic lines in durum wheat: PI 672996 (UC 1113-GpcB1-Glu-D12+12), PI 672997 (UC1171-Glu-D12+12), PI 672998 (UC1308-Glu-D12+12). Synthetic vrn2-null PI 676269, SbeII mutants hexaploid: PI 675644-675647. RHT-B1E529K intermediate height: PI 687144, PI 689563 (Sr60). PI 692251 (Glu-B1x mutant), PI 692253 (Glu-B1y mutant), PI 692252 (Glu-B1x Glu-B1y double mutant). PI 698812 (vrn1 vrn2 combined mutant), PI 698814 (ful2 vrn2 combined mutant), PI 698815 (ful3 vrn2 combined mutant), PI 698811 (vrt2 mutant), PI 698813 (svp1 mutant), PI 698810 (Wapo-A1b into Kronos). PI 699107 (FT-A2 A10 allele into Kronos). PI 700734 (SrKN (Sr9e) in Fielder), PI 700735 (Sr22b in Fielder), PI 701905 (Ppd-A1b photoperiod sensitive Kronos), PI 701906 (elf3 phyB combined mutant: ), PI 701907 (elf3 ppd1 combined mutant). PI 702421 (platz-A1 platz-B1 combined mutant).
Graduate students
30 PhD students (2 in progress)
2000-2006 Major Professor, PhD, Gabriela Tranquilli (UCD-Argentina). Researcher INTA
2001-2005 Co-director, PhD, Sofia Olmos (UCD-Argentina). Professor Argentina
2002-2006 Major Professor, Ph D, Cristobal Uauy (UCD). Project Leader John. Innes UK
2004-2009 Major Professor, Ph D, Juan Brevis (UCD). Now Breeder private company
2005-2010 Major Professor, Ph D, Malena Faricelli (UCD). Now Breeder private company
2006-2011 Major Professor, Ph D, Iago Lowe (UCD). Now Professor U. of New England
2007-2011 Major Professor, Ph D, Marcos Bonafede (UCD-Argentina). Researcher INTA
2007-2011 Major Professor, Ph D, Baoju Yang (UCD-China). Postdoc UCD.
2009-2013 Major Professor, Ph D, Rebecca Nitcher (UCD). May 2014.
2010-2015 Co-director, Ph D, Facundo Tabbita (UBA). March 2015.
2011-2015 Major Professor, Ph D, Brittany Hazard (UCD, IGG). June 2015.
2012-2015 Co-Director, Ph D Shisheng Chen, Sichuan Agricultural University, May 2015
2011-2015 Major Professor, Ph D, Nestor Kippes, (Univ. of Bs. As., Argentina), Dec. 2015.
2012-2016 Co-Director, Ph D Kun Li, Shandong Agricultural University, Jan 2016.
2011-2016 Major Professor, Ph D, Tyson Howell (UCD, IGG). Completed 2016.
2011-2016 Major Professor, Ph D, Alejandra Alvarez (Univ. San Martin Arg.), May 2016
2012-2015 Co-Director, PhD Xiaodong Zhang, Professor Ag. Univ. Hebei
2014-2016 Co director, PhD, Zhenzhen Dong, (China Ag. Univ., China). Completed 2017.
2015-2019 Co director, PhD, Guo Yan, (China Ag. Univ., China). Completed 2017.
2011-2016 Major Professor, Ph D, Josh Hegarty (UCD, GGHA). Completed 2018.
2011-2016 Major Professor, Ph D, Nicolas Cobo (UCD, GGHA). Completed 2018.
2014-2018 Major Professor, Ph D, Youngjun Mo (UCD, GGHA). Completed 2018.
2014-2018 Major Professor, Ph D, André Schönhofen (UCD, GGHA). Completed 2018.
2014-2018 Major Professor, Ph D, Stephen Bolus (UCD, PBGG). Completed 2019.
2014-2018 Major Professor, Ph D, Hans Vasquez-Gross (UCD, IGG). Completed 2021.
2016-2020 Major Professor, PhD, Saarah Kuzay (UCD, GGHA).Completed 2021.
2017-2021 Major Professor, PhD, Priscilla Glenn (UCD, GGHA).Completed 2022.
2017-2023 Major Professor, Ph D, Chen Dang (UCD, GGHA). In progress.
2023-continue Major Professor, Ph D, Maria G. Rottersman (UCD, PBGG). In progress.
9 MS students (1 in progress)
1990-1991 Co-director, MS, Silvina Marta Lewis (Argentina). Now Scientist INTA
1997-1999 Major Professor, MS, Martha Jimenez (UCD). Now Teacher
1999- 2002 Major Professor, MS, Chialing Chan (UCD).
1999-2001 Major Professor, MS, Boryana Stamova (UCD). Now Researcher USDA
1999-2004 Co-director, MS, Laura Appendino (Argentina). Now Professor Univ. of Bs.As.
2002-2005 Major Professor, MS, Andrea Miller (UCD). Now researcher Monsanto
2008-2010 Major Professor, MS. Kati Wu (UCD). Now associate scientist at Amyris Biotech.
2014-2015 Major Professor, MS. Felix Dubach (ETH Zurich-UCD). Tech. Andermatt Biocontrol.
2017-2023 Major Professor, MS. Francine Paraiso (UCD).
Ph.D. Genetics, University of California, Davis (June, 2015)
B.S. Genetics, University of California, Davis (December, 2009)
Bio:
Brittany Hazard is interested in crop improvement and trait development. The general objectives of her research project include determining how induced mutations in SBEII genes affect the amylose and resistant starch (RS) content in wheat grain, as well as integrating the high-amylose and high-RS traits into commercial varieties of durum and common wheat.
Publications:
Hazard B., X. Zhang, M. Naemeh,M. K. Hamilton , B. Rust, H. E. Raybould, J. W. Newman, R. Martin and J. Dubcovsky. 2015. Mutations in Durum Wheat SBEII Genes Conferring Increased Amylose and Resistant Starch affect Grain Yield Components, Semolina and Pasta Quality and Fermentation Responses in Rats. Crop Science, In Press.
PhD. Microbiology, Designated Emphasis in Computational Biology. University of California, Berkeley. 2011.
BS. Microbiology, Genetics and Plant Biology. Honors. University of California, Berkeley. 2005.
Bio:
My research involves comparative genomics, plant cell biology and plant-microbe interactions.
I received my PhD from Brian Staskawicz group at University of California, Berkeley where I studied the molecular mechanisms of plant-pathogen interactions.
My interest in bioinformatics started from wonderful classes taught at Berkeley by inspirational faculty members and students. Under the guidance of Kimmen Sjolander I completed a designated emphasis in Genomics and Computational Biology as a part of my PhD. This motivated me to fully apply my computational skill during my postdoc.
In the Dubcovsky lab, I lead development of functional genomics tools for wheat. Specifically, I am focused on the tetraploid wheat species Triticum turgidum that provides us with pasta and couscous and serves as an important model for basic wheat research. With the help of gene capture technology and modern robotics, I am sequencing 1000 mutant wheat lines from a large TILLING collection that was developed by former graduate student Cristobal Uauy (currently a group leader at John Innes Center) and is maintained in the Dubcovsky lab by Francine Paraiso. On the bioinformatic side, I am leading group efforts to assemble a pipeline for processing exome capture data and identification of mutations in each line. This information is used for developing a reverse genomic database (indispensible contribution from Hans Vasquez-Gross) that will be publicly available to scientists and wheat breeders to identify and request lines with induced alleles of interest.
I am applying these genomic tools to continue my research on plant innate immunity. Specifically, I screened our mutagenized population for induced resistance/susceptibility to wheat pathogens. I am excited to understand the basis of increased resistance in plants and to develop robust and rapid methods of generating new phenotypic diversity in crop species.
Graduate school:
2010-2016
University of California, Davis, CA
Integrative Genetics and Genomics graduate group
Jorge Dubcovsky lab
Undergraduate:
2005-2009
University of California, Davis, CA
Bachelor of Science in Biotechnology
(Specializations in plants and microbiology)
Bio:
I am working on improving drought resistance in wheat. My project is focused on identifying a gene from the rye 1RS.1BL translocation that confers drought resistance in the field.
Using a variety of methods including high throughput phenopying, high throughput genotyping and custom marker development, I used near isogenic lines to identify a small distal region of the 1RS arm which is responsible for the drought resistance conferred by the 1RS translocation, summarized in my 2014 TAG publication.
I am now focused on fine mapping the region to identify candidate genes. This is complicated by the fact that recombination is suppressed between wheat and rye chromosomes, so I am using a deletion mapping approach. Using Illumina sequencing data on two flow sorted chromosome arms, I am using a kmer based bioinformatic approach for developing polymorphic markers in the region previously mapped.
PhD in Agronomic Sciences, School of Agriculture, University of Buenos Aires, Argentina [2010-2015]
BS/MS. Biotechnology, National University of San Martín, Buenos Aires, Argentina [2010]
Bio:
I completed my undergraduate studies in the University of San Martin (Argentina) with emphasis in Biotechnology in 2010. The same year I joined the Dubcovsky lab at UC Davis to apply different genetic approaches to understand the regulation of the vernalization requirement in wheat. I received my PhD from the University of Buenos Aires in 2015 under the supervision of Jorge Dubcovsky.
I am especially interested in the discovery and deployment of genes controlling relevant aspects of development and their utilization to produce improved crop varieties.
VERNALIZATION 4 gene identification
This project was focused on flowering regulation in wheat, principally understanding the gene networks controlling the vernalization requirement. VRN-D4is one of the major vernalization genes in wheat and the first aim of this project was to develop a fine map in the VRN-D4 gene region to facilitate the positional cloning and study its interactions with other flowering and photoperiod genes. Ultimately, a better understanding of this regulatory pathway will improve the knowledge of wheat adaptation to different environments. More..
Effect of PHYB and PHYC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods. Kippes N et al. BMC Plant Biol 2020
Single Nucleotide Polymorphisms in a regulatory site of VRN-A1 first intron are associated with differences in vernalization requirement lenght of winter wheat. Kippes N et al. Mol Genet Genomics 2018
RNA-seq studies using wheat PHYB and PHYC mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways. Pearce S et al. BMC Plant Biol 2016
Development and characterization of a spring hexaploid wheat line with no functional VRN2 genes. Kippes N et al. Theor Appl Genet 2016
Genetic and physical mapping of the earliness per se locus Eps-Am1 in Triticum monococcum identifies EARLY FLOWERING 3 (ELF3) as a candidate gene. Alvarez MA et al. Funct Integr Genomics 2016
Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia. Kippes N at al. Proc Natl Acad Sci USA 2015
Fine mapping and epistatic interactions of the vernalization gene VRN-D4 in hexaploid wheat. Kippes N et al. Mol Genet Genomics 2014
