David Francis

David Francis
210 Williams Hall
(330) 263-3893
Areas Of Interest: 
Plant Breeding and Genetics
Disease Resistance
Nutritional Quality
Domestication & Evolution of Tomato




2013-present Professor, Department of Horticulture & Crop Science, OSU/OARDC
2003-2013 Associate Professor, Department of Horticulture & Crop Science, OSU/OARDC
1999-2003 Assistant Professor, Department of Horticulture & Crop Science, OSU/OARDC
1995-1999 Research Scientist, Department of Horticulture & Crop Science, OSU/OARDC
1991-1995 Postdoctoral Research Associate, Vegetable Crops, U. C. Davis
1985-1991 Gradaduate Research Assistant, Vegetable Crops, U. C. Davis
1984-1985 Research Technician, Pathology, USC, School of Medicine


2012 Ohio Agricultural Research and Development Innovator of the Year Award
2011 United States Department of Agriculture, Honor Award for Excellence
2010 Mid-America Food Processors Association H. D. Brown Food Processing Person of the Year Award. 
2006 Ohio Agricultural Research and Development Center Distinguished Research Award.
2002 Mid-America Food Processors Association Tomato Achievement Award.
2002.Indiana Horticulture Society Red Tie Award for outstanding contributions


Current Courses Taught: HCS 8825 "Advanced Plant Breeding", HCS 8806. "Methods in Plant Sciences”


My research aims to define the genetic basis of field resistance, humid environment adaptation, and fruit quality, while contributing innovative strategies for crop improvement. The tomato breeding and genetics program has strengths in both the basic and applied sciences. Emphasis is placed on translating the results of plant genomics through the development of techniques for genetic mapping and selection in breeding populations. Individual projects stress multi-disciplinary approaches to breeding for disease resistance and end-product quality, understanding the genetic determinants of nutritional quality in tomato fruit, mechanisms of plant resistance to disease, population genetics of cultivated tomato, and the evolution of tomato and its wild relatives. We provide fundamental knowledge related to the genetic and molecular mechanisms that control disease resistance, tomato fruit quality, and the domestication of plants. Knowledge gained from these studies has directly resulted in the release of tomato varieties with improved disease resistance, enhanced processing quality, and enhanced nutritional value. Processing tomato hybrids and parents released by the program are used commercially and rank among the best in the Great Lakes industry for factory quality grade.


Mid-America Food Processors Association
USDA/NIFA Plant Breeding, Genetics and Genomics
Ohio Plant Biotechnology Consortium


Peer Reviewed Publications (last five years):

  • 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; Mutschelr, M.; Myers, J.R.; 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): e45520. doi:10.1371/journal.pone.0045520
  • Sim, S.C.; Surstewitz, G.; Plieske, J.; Ganal, M.W.; Van Deynze, A.; Stoffel, K.; Hamilton, J.; Buell, C.R.; Zarka, D.; Douches, D.S.; Francis, D.M.. 2012.  Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.  PLoS ONE 7(7): e40563.
  • Hamilton, J. P.; Sim, S. C.; Stoffel, K.; Van Deynze, A.; Buell, C. R.; Francis, D. M. 2012. Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis. The Plant Genome. 5: 17-29.
  • Bohn T, Blackwood M, Francis D, Tian Q, Schwartz SJ, Clinton SK., 2012. Bioavailability of Phytochemical Constituents From a Novel Soy Fortified Lycopene Rich Tomato Juice Developed for Targeted Cancer Prevention Trials. Nutr Cancer. [Epub ahead of print]
  • Pei C, Wang H, Zhang J, Wang Y, Francis DM, Yang W., 2012. Fine mapping and analysis of a candidate gene in tomato accession PI128216 conferring hypersensitive resistance to bacterial spot race T3.  Theor Appl Genet. [Epub ahead of print]  http://www.springerlink.com/content/t6401p88174334x3/
  • Rubio-Diaz D, Francis D, Rodriguez-Saona L. 2011. External calibration models for the measurement of tomato carotenoids by infrared spectroscopy. J. Food Compos. Anal. 24(1):121-126.
  • Baldo, A.M., Francis, D., Caramante, M., Robertson, L.D., Labate, J.A. 2011. AlleleCoder: a PERL script for coding codominant polymorphism data for PCA analysis. Plant Genetic Resources: Characterization and Utilization. 10: 1-3.
  • Zale, P. J., D. K. Struve, P. Jourdan, and D. M. Francis.  2011.  Rapid Assessment of Genetic Variation for Morphological Traits in Sweetbay Magnolia Using a Container Production System  J. Amer. Soc. Hrot. Sci. 136 (2) 135-144
  • Wang H, Hutton SF, Robbins MD, Sim SC, Scott JW, Yang W, Jones JB, Francis DM., 2011. Molecular mapping of hypersensitive resistance from tomato 'Hawaii 7981' to Xanthomonas perforans race T3. Phytopathology. 101(10):1217-1223.
  • Galmés J, Conesa MÀ, Ochogavía JM, Perdomo JA, Francis DM, Ribas-Carbó M, Savé R, Flexas J, Medrano H, Cifre J. 2011. Physiological and morphological adaptations in relation to water use efficiency in Mediterranean accessions of Solanum lycopersicum.  Plant Cell Environ. 34(2):245-260.
  • Rodríguez, GR, Muños, S., Anderson, C.,  Sim, S-C., Michel, A., Causse, M., McSpadden, G., Francis, D. and van der Knaap, E.  2011.  Distribution of SUN, OVATE, LC, and FAS in the tomato germplasm and the relationship to fruit shape diversity.  Plant Physiology 156: 275-285.
  • Robbins, M.D., Sim, S-C., Yang, W., Van Deynze, A., van der Knaap, E., Joobeur, T., and Francis, D.M. 2011. Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato.  Journal of Experimental Botany.  62(6):1831-1845.
  • 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 (Edinb). 106 (6):927-935
  • Tan H.L., Thomas-Ahner J.M., Grainger E.M., Wan L., Francis D.M., Schwartz S.J., Erdman J. W. Jr, Clinton S.K. 2010. Tomato-based food products for prostate cancer prevention: what have we learned?  Cancer Metastasis Rev. 29(3):553-568.
  • Robbins, M.D., Masud, M.A.T., Panthee, D.P., Gardner, R.G., Francis, D.M., Stevens, M.R.  2010.  Marker-assisted Selection for Coupling Phase Resistance to Tomato spotted wilt virus and Phytophthora infestans (Late Blight) in Tomato. Hortscience 45(10):1424–1428.
  • Hutton S.F., Scott J.W., Yang W., Sim S.C., Francis D.M., Jones JB.  2010.  Identification of QTL associated with resistance to bacterial spot race T4 in tomato. Theor Appl Genet. 121(7):1275-1287.
  • Wang Y., Chen J., Francis D.M., Shen H., Wu T., Yang W. 2010.  Discovery of intron polymorphisms in cultivated tomato using both tomato and Arabidopsis genomic information.  Theor Appl Genet. 121(7):1199-1207
  • Rodríguez GR, Moyseenko JB, Robbins MD, Huarachi Morejón N, Francis DM, van der Knaap E.  2010. Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects. J. Vis. Exp. (JoVE). 37.
  • Rubio-Diaz, D.E., De Nardo, T., Santos, A., de Jesus, S., Francis, D. and Rodriguez-Saonaa, L.E. 2010. Profiling of nutritionally important carotenoids from genetically-diverse tomatoes by infrared spectroscopy.  Food Chemistry 120 (1), Pages 282-289.
  • Rubio-Diaz D.E., A. Santos, D. M. Francis, L. E. Rodriguez-Saona. 2010. Carotenoid stability during production and storage of tomato juice made from tomatoes with diverse pigment profiles measured by infrared spectroscopy. J Agric Food Chem. 58(15):8692-868.
  • Gupta R., V. M. Balasubramaniam , S. J. Schwartz ., and D. M. Francis. 2010. Storage stability of lycopene in tomato juice subjected to combined pressure-heat treatments.  J Agric Food Chem. 58(14):8305-8313.
  • Bai S, Willard B, Chapin LJ, Kinter MT, Francis DM, Stead AD, Jones ML. 2010. Proteomic analysis of pollination-induced corolla senescence in petunia. J Exp Bot. 61(4):1089-109.
  • De Nardo T, Shiroma-Kian C, Halim Y, Francis D, Rodriguez-Saona LE.  2009.  Rapid and simultaneous determination of lycopene and beta-carotene contents in tomato juice by infrared spectroscopy.  J Agric Food Chem. 2009 Feb 25;57(4):1105-12.
  • Sim S. C., Robbins M. D., Chilcott C., Zhu ., Francis D. M. 2009. Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding. BMC Genomics. 10:466.
  • Robbins M.D., Darrigues A., Sim S.C., Masud M.A., Francis D.M.  2009.  Characterization of hypersensitive resistance to bacterial spot race T3 (Xanthomonas perforans) from tomato accession PI 128216. Phytopathology. 99(9):1037-1044.
  • Darrigues, A., J. Hall, N. Dujmovic, S. Gray, E. van der Knaap, and D. M. Francis. 2008a.  Tomato Analyzer – Color Test: a new tool for efficient digital phenotyping.  J. Amer. Soc. Hort. Sci. 133(4):579–586.
  • Darrigues, A., S. Schwartz, D. M. Francis.  2008b. Optimizing sampling of tomato fruit for carotenoid content with application to assessing the impact of ripening disorders.  Journal of Agricultural and Food Chemistry 56: 483–487.
  • Bentley, S.D., C. Corton, A. Barron, L. Clark, J. Doggett, B. Harris, D. Ormond, M.A. Quail, S.E. Brown, D. Knudson, D. Francis, J. Parkhill, C. Ishimaru.  2008. Genome of the actinomycete plant pathogen Clavibacter michiganensis subspecies sepedonicus suggests recent niche adaptation.  J. Bact. 190:2150-2160.
  • Van Deynze, A., K. Stoffel, C. R. Buell, A. Kozik, J. Liu, E. van der Knaap, D. M. Francis.  2007.  Diversity in conserved genes in tomato.  BMC Genomics 8:465.
  • Clivati McIntyre, A., T. K. Hartz, C. Gunter, D. M. Francis. 2007.  Fertility influence of the U.S. Midwestern soils on Yellow Shoulder Disorder in processing tomatoes.  HortScience 42: 1468-1472.
  • Unlu, N. Z., T. Bohn, D. Francis, S. J. Clinton, S. J. Schwartz. 2007.  Carotenoid Absorption in Humans Consuming Pasta Sauces Obtained from Tangerine or High-B-Carotene Varieties of Tomatoes.  Journal of Agricultural and Food Chemistry. 55(4):1597-1603.
  • Unlu, N. Z., Bohn, T., Francis, D. M., Nagaraja, H. N., Clinton, S. K., and Schwartz, S. J. 2007. Lycopene from heat-induced cis-isomer-rich tomato sauce is more bioavailable than from all-trans-rich tomato sauce in human subjects. Br. J. Nutr. 98: 140-146 .

Variety Release (selected)

Francis, D. M.  2008.  Ohio 2641 Processing tomato inbred parent.
Francis, D. M. and Miller, S.A. 2005. Ohio 9834 and Ohio 9816 Processing tomato inbred parents.
Francis, D. M. 2002.   Ohio ‘OX 325’ processing tomato.




Ochogavia, J.M.; Lopez, M.; Rigo, M.; Garau, M.dM.; March, J.; Moscardo, J.; Jaume, J.; Conesa, M.A.; Galames, J.; Bota, J.; Francis, D.; Medrano, H.; Martorell, A.; Cifre, J., Caracteritzacio de les poblacions de tomatiga de ramellet de les Illes Balears. Palma de Mallorca: Govern de les Illes Balears, Conselleria de Presidencia. 2011.

Journal Articles

Kopec RE, Cooperstone JL, Schweiggert RM, Young GS, Harrison EH, Francis DM, Clinton SK, Schwartz SJ, "Avocado consumption enhances human postprandial provitamin A absorption and conversion from a novel high-β-carotene tomato sauce and from carrots." J Nutr. 144 8 (2014) 1158-1166
Merk,Heather,L; Yarnes,Shawn,C; Van Deynze,Allen; Tong,Nankui; Menda,Naama; Mueller,Lukas,A; Mutschler,Martha,A; Loewen,Steven,A; Myers,James,R; Francis,David,M, "Trait Diversity and Potential for Selection Indices Based on Variation Among Regionally Adapted Processing Tomato Germplasm" JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE 137 6 (2012) 427-437
Sim,Sung-Chur; Van Deynze,Allen; Stoffel,Kevin; Douches,David,S; Zarka,Daniel; Ganal,Martin,W; Chetelat,Roger,T; Hutton,Samuel,F; Scott,John,W; Gardner,Randolph,G; Panthee,Dilip,R; Mutschler,Martha; Myers,James,R; Francis,David,M, "High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding" PLOS ONE 7 9 (2012)
Sim,Sung-Chur; Durstewitz,Gregor; Plieske,Joerg; Wieseke,Ralf; Ganal,Martin,W; Van Deynze,Allen; Hamilton,John,P; Buell,C,Robin; Causse,Mathilde; Wijeratne,Saranga; Francis,David,M, "Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato" PLOS ONE 7 7 (2012)


David M Francis; Matthew D Robbins; Dilip R Panthee; Randolph G Gardner; Mikel R Stevens. Marker Assisted Selection for Coupling Phase Resistance to Tomato Spotted Wilt Virus and Late Blight in Tomato.. Filed Jul 2010
Steven St. Martin; Anne Dorrance; Kara Burnham; Ron Fioritto; David Francis; Stuart G Gordon. IDENTIFICATION OF SOYBEANS HAVING RESISTANCE TO PHYTOPHTHORA SOJAE. Filed Dec 2007
St. Martin,Steven; Dorrance,Anne; Burnham,Kara; Fioritto,Ron; Francis,David; Gordon,Stuart,G. Identification of soybeans having resistance to Phytophthora sojae. 7435873 Filed Jan 2004 and Issued Sep 2008.
St. Martin,Steven; Dorrance,Anne; Burnham,Kara; Fioritto,Ron; Francis,David. Identification of soybeans having resistance to Phytophthora sojae. 7381862 Filed Apr 2003 and Issued May 2008.


"Tomato Breeding (Traditional and Molecular assisted) for disease resistance." InIV International Symposium on Tomato Diseases: Economically, Environmentally, and Socially Sustainable Tomato Disease Management. Orlado: 2013.
"Population Level Analysis to Move from Massive Sequence Data Sets to Application.." InTomato Breeers Rountable. Chiang-Mai: 2013.