Dr. Philippe Charles Rott

Professor, Plant Pathology

Sugarcane is an important crop in Florida that is affected by several diseases. The long-term goal of my research and extension program is to understand the biology and genetics of plant pathogen interactions, and to impart this knowledge to the growers, in order to improve the control of sugarcane diseases in Florida and to limit their impact on sugarcane production. This work includes basic and applied research on diseases currently limiting sugarcane production or that are potential threats to the industry such as brown rust (caused by Puccinia melanocephala), orange rust (caused by P. kuehnii), and yellow leaf (caused by Sugarcane yellow leaf virus).

Program Areas

  • Understanding plant-pathogen interactions for improved control of sugarcane diseases in Florida:

    Florida’s climate conditions such as relatively high temperatures and humidity are very conducive to disease epidemics. Understanding how sugarcane diseases emerge and develop is essential to develop efficient and sustainable methods of control. This project therefore seeks to enhance our knowledge about sugarcane diseases in Florida, and to improve their control through the use of resistant cultivars or healthy planting material. The benefit of this research will be the improved management of sugarcane diseases and the prevention of future losses from more virulent strains of existing pathogens or early detection of emerging pathogens.

    Our research has several main objectives:

    1/ Analyze the population structure (diversity and evolution) of sugarcane pathogens such as Puccinia melanocephala (causal agent of brown rust), Puccinia kuehnii (causal agent of orange rust), and Sugarcane yellow leaf virus (causal agent of yellow leaf), including sustainability of sugarcane resistance to various isolates/strains of these pathogens.

    2/ Investigate the epidemiological factors and characteristics that favor progress and spread of diseases such as brown rust, orange rust, and yellow leaf.

    3/ Determine the impact of sugarcane diseases that limit production of the major sugarcane cultivars grown in Florida, and analyze the impact of management measures (growth of resistant cultivars, planting date, fungicide treatments) to control these diseases.  

    4/ Explore the possible occurrence of hidden pathogens that may pose a threat to the sugarcane industry in the future.


Reducing losses caused by sugarcane diseases:

Sugarcane is a major agricultural crop due to its high sucrose content and remarkable bioenergy potential. It is the highest-value row crop in Florida. The Florida Sugar Industry has an economic impact of about $3.1 billion on the state and provides over 25,000 direct jobs (http://www.sugarcaneleague.org/index.html). Because Florida’s climate (high temperatures and humidity) is very conducive to disease, disease is the limiting factor in sugarcane production. Currently, sugarcane rust diseases are controlled with fungicides and their application represents several millions of dollars to the sugarcane industry every year. Clean seed-cane programs have been tried for control of SCYLV, but have not proved to be very successful. Disease resistant cultivars have the potential to control fungal and virus pathogens.

The University of Florida participates in a tripartite cooperative breeding program agreement with USDA and the Florida Sugar Cane League to produce the Canal Point (“CP”) sugarcane clones. This program is aimed at developing high-yielding, disease and stress-tolerant sugarcane cultivars. It is a national program that makes crosses for the Florida sugarcane industry and for the USDA-ARS Sugarcane Cultivar Development Program in Houma, Louisiana. CP cultivars are grown on more than 90% of the sugarcane acreage in the Everglades Agricultural Area. Growers’ interest in improved sugarcane germplasm is tremendous, yet the use of a given cultivar is finite as disease pressures reduce its production.

Our extension activities have several main objectives:

  1. Improve county extension faculty and growers knowledge on identification, biology, and impact of pathogens causing sugarcane diseases.
  2. Educate county extension faculty, growers, crop consultants and chemical companies on timing of application of recommended fungicides for control of orange and brown rust.
  3. Educate county extension faculty, growers, crop and consultants on appropriate control measures to limit spread of Sugarcane yellow leaf virus to control yellow leaf disease.
  4. Assist in the selection of disease resistant sugarcane clones developed through the tripartite Canal Point breeding program.
Graduate Students


Wardatou Boukari, PhD Student

My PhD research focuses mainly on genetic diversity, epidemiology, and impact on yield of Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf of sugarcane, in Florida. This includes surveying the genotypes of the virus that are present in Florida, the characterization of virulence of these genotypes and how SCYLV is spread in the EAA. I am also investigating potential new hosts of SCYLV and working on characterization of a new virus species recently found in Florida.


Bhim Chaulagain, PhD Student

Bhim's research focuses on sustainable management of two fungal diseases currently impacting sugarcane production in Florida: brown rust caused by Puccinia melanocephala and orange rust caused by Puccinia kuehnii. This research includes laboratory and field experiments to investigate the efficacy, timing and frequency of fungicide applications to control brown and orange rust of sugarcane. He is also working on the development of a sugarcane rust forecasting system based on weather variables such as temperature.


Extension Publications (EDIS)
  • Wei C., Hincapie M., Larsen N., Nuessly G., Rott P., 2016. First report of Sugarcane yellow leaf virus infecting grain sorghum (Sorghum bicolor) in the United States. Plant Disease 100(8):1798-1799.

  • Mollov D., Tahir M.N., Wei C., Kaye C., Lockhart B., Comstock J.C., Rott P., 2016. First report of Sugarcane mosaic virus infecting Columbus Grass (Sorghum almum) in the United States. Plant Disease 100(7):1510.

  • Espinoza Delgado H.V., Kaye C., Hincapie M., Boukari W., Wei C., Fernandez J.V., Mollov D., Comstock J.C., Rott P., 2016. First report of Sugarcane yellow leaf virus infecting Columbus Grass (Sorghum almum) in Florida. Plant Disease 100(5):1027.

  • Amata R.L., Fernandez E., Filloux D., Martin D.P., Rott P., Roumagnac P., 2016. Prevalence of Sugarcane yellow leaf virus in sugarcane producing regions in Kenya revealed by reverse transcription loop-mediated isothermal amplification method. Plant Disease 100(2):260-268.

  • Mensi I., Daugrois J., Pieretti I., Gargani D., Fleites L.A., Noëll J., Bonnot F., Gabriel D.W., Rott P., 2016. Surface polysaccharides and quorum sensing are involved in the attachment and survival of Xanthomonas albilineans on sugarcane leaves. Molecular Plant Pathology 17(2):236-246.

  • Cociancich S., Pesic A., Uhlmann S., Petras D., Kretz J., Schubert V., Vieweg L., Duplan S., Marguerettaz M., Noëll J., Pieretti I., Hügelland M., Kemper S., Rott P., Royer M., Süssmuth R.D., 2015. The gyrase inhibitor albicidin consists of para-aminobenzoic acids and cyanoalanine. Nature Chemical Biology DOI:10.1038/NCHEMBIO.1734

  • Pieretti I., Bolot S., Carrère S., Barbe V., Cociancich S., Rott P., Royer M., 2015a. Draft genome sequence of Xanthomonas sacchari LMG 476. Genome Announcements 3(2):e00146-15. doi:10.1128/genomeA.00146-15.

  • Pieretti I., Cociancich S., Bolot S., Carrère S., Morisset A., Rott P., Royer M., 2015b. Full genome sequence analysis of two isolates reveals a novel Xanthomonas species close to the sugarcane pathogen Xanthomonas albilineans. Genes 6:714-733.

  • Ash G., Lang J.M., Triplett L.R., Stodart B.J., Verdier V., Vera Cruz C., Rott P., Leach J.E., 2014. Development of a genomics-based LAMP (Loop-mediated isothermal amplification) assay for detection of Pseudomonas fuscovaginae from rice. Plant Disease 98:909-915.

  • Daugrois J.-H., Boisne-Noc R., Rott P., 2014. Leaf surface colonization of sugarcane by Xanthomonas albilineans and subsequent disease progress vary according to the host cultivar. Plant Disease 98:191-196.
  • ElSayed A.I., Boulila M., Rott P., 2014. Molecular evolutionary history of Sugarcane yellow leaf virus based on sequence analysis of RNA-dependent RNA polymerase and putative aphid transmission factor coding genes. Journal of Molecular Evolution 78:349-365.

  • Girard J.-C., Noëll J., Larbre F., Roumagnac P., Rott P., 2014. First report of Acidovorax avenae subsp. avenae causing sugarcane red stripe in Gabon. Plant Disease 98(5):684.

  • Mensi I., Vernerey M.S., Gargani D., Nicole M., Rott P., 2014. Breaking dogmas: The plant vascular pathogen Xanthomonas albilineans is able to invade non-vascular tissues despite its reduced genome. Open Biology 4:130116.

  • Darrasse A., Carrère S., Barbe B., Boureau T., Arrieta-Ortiz M.L., Bonneau S., Briand M., Brin C., Cociancich S., Durand K., Fouteau S., Gagnevin L., Guérin F., Guy E., Indiana A.,  Koebnik R., Lauber E., Munoz A., Noël L.D., Pieretti I., Poussier S., Pruvost O., Robène-Soustrade I., Rott P., Royer M., Serres-Giardi L., Szurek B., Van Sluys M.-A., Verdier V., Vernière C., Arlat M., Manceau C., Jacques M.A., 2013. Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads. BMC Genomics 14:761.

  • Fleites L., Mensi I., Gargani D., Zhang S., Rott P., Gabriel D.W., 2013. Xanthomonas albilineans OmpA1 appears to be functionally modular and both the OMC and C-like domains are necessary for leaf scald disease of sugarcane. Molecular Plant-Microbe Interactions 26(10):1200-1210.

  • Mensi I., Girard J.-C., Pieretti I., Larbre F., Roumagnac P., Royer M., Rott P., 2013. First report of a highly virulent strain of Xanthomonas albilineans causing sugarcane leaf scald in Gabon. Plant Disease 97(7):988.

  • Rott P., Fleites L., Mensi I., Sheppard L., Daugrois J.-H., Dow J. M., Gabriel D.W., 2013. The RpfCG two-component system negatively regulates the colonization of sugarcane stalks by Xanthomonas albilineans. Microbiology SGM 159:1149-1159.

  • Royer M., Koebnik R., Marguerettaz M., Barbe V., Robin G.P., Brin C., Carrere S., Gomez C., Hügelland M., Völler G.H., Noëll J., Pieretti I., Rausch S., Verdier V., Poussier S., Rott P., Süssmuth R., Cociancich S., 2013. Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides. BMC Genomics 14:658.

  • Daugrois J.-H., Boisne-Noc R., Champoiseau P., Rott P., 2012. The revisited infection cycle of Xanthomonas albilineans, the causal agent of leaf scald of sugarcane. Functional Plant Science and Biotechnology 6 (Special issue 2):91-97.

  • Pieretti I., Royer M., Barbe V., Carrere S., Koebnik R., Couloux A., Darrasse A., Gouzy J., Jacques M.-A., Lauber E., Manceau C., Mangenot S., Poussier S., Segurens B., Szurek B., Verdier V., Arlat M., Gabriel D.W., Rott P., Cociancich S., 2012. Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels. BMC Genomics 13:658.

  • Daugrois J.-H., Edon-Jock C., Bonoto S., Vaillant J., Rott P., 2011. Spread of Sugarcane yellow leaf virus in disease-free sugarcane plots is linked to rainfall and host resistance in the humid tropical environment of Guadeloupe. European Journal of Plant Pathology 129:71-80.

  • Marguerettaz M., Pieretti I., Gayral P., Puig J., Brin C., Cociancich S., Poussier S., Rott P., Royer M., 2011. Genomic and evolutionary features of the SPI-1 type III secretion system that is present in Xanthomonas albilineans but not essential for xylem colonization and symptom development of sugarcane leaf scald. Molecular Plant-Microbe Interactions 24:246-259.

  • Rott P., Fleites L., Marlow G., Royer M., Gabriel D.W., 2011. Identification of new candidate pathogenicity factors in the xylem-invading pathogen Xanthomonas albilineans by transposon mutagenesis. Molecular Plant-Microbe Interactions 24:594-605.

  • Champoiseau P., Rott P., Daugrois J.-H., 2009. Epiphytic populations of Xanthomonas albilineans and subsequent sugarcane stalk infection are linked to rainfall in Guadeloupe. Plant Disease 93:339-346.

  • Pieretti I., Royer M., Barbe V., Carrere S., Koebnik R., Cociancich S., Couloux A., Darrasse A., Gouzy J., Jacques M.-A., Lauber E., Manceau C., Mangenot S., Poussier S., Segurens B., Szurek B., Verdier V., Arlat M., Rott P., 2009. The complete genome of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae. BMC Genomics 10:616.

  • Abu Ahmad Y., Costet L., Daugrois J.-H., Nibouche S., Letourmy P., Girard J.-C., Rott P., 2007. Variation in infection capacity and in virulence exists between genotypes of Sugarcane yellow leaf virus. Plant Disease 91:253-259.

  • Abu Ahmad Y., Girard J.-C., Fernandez E., Pauquet J., Lockhart B.E.L., Letourmy P., Rott P., 2007. Variation in virus populations and growth characteristics of two sugarcane cultivars naturally infected by Sugarcane yellow leaf virus in different geographical locations. Plant Pathology 56(5):743-754.

  • Renier A., Vivien E., Cociancich S., Letourmy P., Perrier X., Rott P.C., Royer M., 2007. Substrate specificity-conferring regions of the non ribosomal peptide synthase adenylation domains involved in albicidin pathotoxin biosynthesis are highly conserved within the species Xanthomonas albilineans. Applied and Environmental Microbiology 73(17):5523-5530.

  • Vivien E., Pitorre D., Cociancich S., Pieretti I., Gabriel D., Rott P.C., Royer M., 2007. Heterologous production of albicidin: a promising approach to overproducing and characterizing this potent inhibitor of DNA gyrase. Antimicrobial Agents and Chemotherapy 51:1549-1552.

  • Abu Ahmad Y., Rassaby L., Royer M., Borg Z., Braithwaite K.S., Mirkov E., Irey M., Perrier X., Smith G., Rott P., 2006a. Yellow leaf of sugarcane is caused by at least three different genotypes of sugarcane yellow leaf virus, one of which predominates on the Island of Réunion. Archives of Virology 151:1355-1371.

  • Abu Ahmad Y., Royer M., Daugrois J.-H., Costet L., Lett J.-M., Victoria J.I., Girard J.-C., Rott P., 2006b. Geographical distribution of four Sugarcane yellow leaf virus genotypes. Plant Disease 90:1156-1160.

  • Champoiseau P., Daugrois J.-H., Girard J.-C., Royer M., Rott P.C., 2006. Variation in albicidin biosynthesis genes and in pathogenicity of Xanthomonas albilineans, the sugarcane leaf scald pathogen. Phytopathology 96:33-45.

  • Champoiseau P., Daugrois J.-H., Pieretti I., Cociancich S., Royer M., Rott P., 2006. High variation in pathogenicity of genetically closely related strains of Xanthomonas albilineans, the sugarcane leaf scald pathogen, in Guadeloupe. Phytopathology 96:1081-1091.

  • Falloon T., Henry E., Davis M.J., Fernandez E., Girard J.-C., Rott P., Daugrois J.-H., 2006. First report of Leifsonia xyli subsp. xyli, causal agent of ratoon stunting of sugarcane, in Jamaica. Plant Disease 90:245.

  • Rao G.P., Chatenet M., Girard J.-C., Rott P., 2006. Distribution of sugarcane mosaic and sugarcane streak mosaic in India. Sugar Tech 8(1):79-81.

    Refereed Proceeding publications

  • Rott P.C., Kaye C., Naranjo M., Shine Jr. J.M., Sood S., Comstock J.C., Raid R., 2016. Controlling sugarcane diseases in Florida: a challenge in constant evolution. Proceedings International Society of Sugarcane Technologists Congress (Chiang Mai, Thailand, 5-8 December 2016) 29:PA3.

  • Sood S., Glynn N., Yang X., Wang J., McCorkle K., Rott P., Comstock J.C., 2016. Orange rust resistance in sugarcane progenies. Proceedings International Society of Sugarcane Technologists Congress (Chiang Mai, Thailand, 5-8 December 2016) 29:PA21.

  • Rott P.C., Girard J.-C., Comstock J.C., 2013. Impact of pathogen genetics on breeding for resistance to sugarcane diseases. Proceedings International Society of Sugarcane Technologists Congress 28:PL07 (Plenary session invited paper); also published in 2015 in International Sugar Journal 117(1399):494-499.

  • Guinet-Brial I., Girard J.C., Roumagnac P., Daugrois J.H., Fernandez E., Rott P., 2013. Visacane, an innovative quarantine tool for the exchange of pest and disease-free sugarcane germplasm. Proceedings International Society of Sugarcane Technologists Congress 28:BP13; also published in 2015 in International Sugar Journal 117(1404):890-896.

  • Girard J.C., Fernandez E., Daugrois J.H., Roques D., Roumagnac P., Rott P., 2010. Genetic diversity of Sugarcane yellow leaf virus in a sugarcane selection plot in Guadeloupe (FWI). Proceedings International Society of Sugarcane Technologists Congress 27:1123-1129; also published in 2012 in International Sugar Journal 114(1358):96-100.

  • Rott P., Marguerettaz M., Fleites L., Cociancich S., Girard J.C., Pieretti I., Gabriel D.W., Royer M., 2010. Unravelling pathogenicity of Xanthomonas albilineans, the causal agent of sugarcane leaf scald. Proceedings International Society of Sugarcane Technologists Congress 27:1112-1121; also published in 2011 in International Sugar Journal 113(1351):490-496. (This paper obtained the “Robert Antoine” award for the best biology paper at the 27th congress of the International Society of Sugarcane Technologists).

  • Edon-Jock C., Rott P., Vaillant J., Fernandez E., Girard J-C., Daugrois J-H., 2007. Status of Sugarcane yellow leaf virus in commercial fields and risk assessment in Guadeloupe. Proceedings International Society of Sugarcane Technologists Congress 26:995-1004.

  • Rott P., Mirkov T.E., Schenck S., Girard J-C., 2007. Recent advances in research on Sugarcane yellow leaf virus, the causal agent of sugarcane yellow leaf. Proceedings International Society of Sugarcane Technologists Congress; also published in 2008 in Sugar Cane International 26(3):18-22.