Advanced methods of plant disease detection. A review

Agati G, Foschi L, Grossi N, Guglielminetti L, Cerovic ZG, Volterrani M (2013) Fluorescence-based versus reflectance proximal sensing of nitrogen content in Paspalum vaginatum and Zoysia matrella turfgrasses. Eur J Agron 45:39–51. doi:10.1016/j.eja.2012.10.011 Ahmed MU, Hossain MM, Tamiyaa E (2008) Electrochemical biosensors for medical and food applications. Electroanalysis 20:616–626. doi:10.1002/elan.200704121 Aksenov A, WHK C, Zhao W, Bardaweel H, Martinelli F, Fiehn O, Dandekar AM, Davis CE (2012) Reagentless detection of citrus pathogens using differential mobility spectrometry. Citrograph 3:54–56 Aksenov AA, Pasamontes A, Peirano DJ, Zhao W, Dandekar AM, Fiehn O, Eshani R, Davis CE (2014) Detection of Huanglongbing disease using differential mobility spectrometry. Anal Chem 86:2481–2488. doi:10.1021/ac403469y Alarcon B, López MM, Cambra M, Gorris MT, Guerri J (1990) Differentiation of Erwinia carotovora subsp. carotovora and Erwinia carotovora subsp. atroseptica isolated from potato by Western blot and subsequent indirect ELISA. J Appl Biol 69:17–24. doi:10.1111/j.1365-2672.1990.tb02906.x Anderson MC, Neale CMU, Li F, Norman JM, Kustas WP, Jayanthi H, Chavez J (2004) Upscaling ground observations of vegetation water content, canopy height, and leaf area index during SMEX02 using aircraft and Landsat imagery. Remote Sens Envir 92:447–464. doi:10.1016/j.rse.2004.03.019 Andris-Widhopf J, Rader C, Steinberger P, Fuller R, Barbas CF III (2000) Methods for the generation of chicken monoclonal antibody fragments by phage display. J Immunol Method 242:159–181. doi:10.1016/S0022-1759(00)00221-0 Arthur CL, Pawliszyn J (1990) Solid phase microextraction with thermal desorption using fused silica optical fibers. Anal Chem 62:2145–2148. doi:10.1021/ac00218a019 Baldwin IT, Halitschke R, Paschold A, von Dahl CC, Preston CA (2006) Volatile signaling in plant-plant interactions: ‘talking trees’ in the genomics era. Science 311:812–814. doi:10.1126/science.1118446 Baltussen E, Sandra P, David F, Cramers C (1999) Stir bar sorptive extraction (SBSE), a novel extraction technique for aqueous samples: theory and principles. J Microcolumn Sep 11:737–747. doi:10.1002/(SICI)1520-667X(1999)11:10<737::AID-MCS7>3.0.CO;2-4 Baltussen E, Cramers CA, Sandra PJF (2002) Sorptive sample preparation—a review. Anal Bioanal Chem 373:3–22. doi:10.1007/s00216-002-1266-2 Barbas CF III, Burton DR, Scott JK, Silverman GJ (2001) Phage display: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor Baret F, Houlès V, Guèrif M (2007) Quantification of plant stress using remote sensing observations and crop models: the case of nitrogen management. J Exp Bot 58:869–880. doi:10.1093/jxb/erl231 Bates SR, Baldwin DA, Channing A, Gifford LK, Hsu A, Lu P (2005) Cooperativity of paired oligonucleotide probes for microarray hybridization assays. Anal Biochem 342:59–68. doi:10.1016/j.ab.2005.03.030 Bauriegel E, Giebel A, Geyer M, Schmidt U, Herppich WB (2011) Early detection of Fusarium infection in wheat using hyper-spectral imaging. Comput Electron Agric 75:304–312. doi:10.1016/j.compag.2010.12.006 Berdugo CA, Zito R, Paulus S, Mahlein AK (2014) Fusion of sensor data for the detection and differentiation of plant diseases in cucumber. Plant Pathol doi:10.1111/ppa.12219 Blake RS, Monks PS, Ellis AM (2009) Proton-transfer reaction mass spectrometry. Chem Rev 109:861–896. doi:10.1021/cr800364q Blasco J, Aleixos N, Gómez J, Moltó E (2007) Citrus sorting by identification of the most common defects using multispectral computer vision. J Food Engin 83:384–393. doi:10.1016/j.jfoodeng.2007.03.027 Bleecker AB, Kende H (2000) Ethylene: a gaseous signal molecule in plants. Ann Rev Cell Develop Biol 16:1–18. doi:10.1146/annurev.cellbio.16.1.1 Bock CH, Parker PE, Cook AZ, Gottwald TR (2008) Visual rating and the use of image analysis for assessing different symptoms of citrus canker on grapefruit leaves. Plant Dis 92:530–541. doi:10.1094/PDIS-92-4-0530 Bock CH, Poole GH, Parker PE, Gottwald TR (2010) Plant disease severity estimated visually, by digital photography and image analysis, and by hyperspectral imaging. Crit Rev Plant Sci 29:59–107. doi:10.1080/07352681003617285 Bravo C, Moshou D, West J, McCartney A, Ramon H (2003) Early disease detection in wheat fields using spectral reflectance. Biosys Eng 84:137–145. doi:10.1016/S1537-5110(02)00269-6 Calderón R, Navas-Cortés JA, Lucena C, Zarco-Tejada PJ (2013) High-resolution airborne hyperspectral and thermal imagery for early detection of Verticillium wilt of olive using fluorescence, temperature and narrow-band spectral indices. Remote Sens Environ 139:231–245. doi:10.1016/j.rse.2013.07.031 Camargo A, Smith JS (2009) Image pattern classification for the identification of disease causing agents in plants. Comput Electron Agric 66:121–125. doi:10.1016/j.compag.2009.01.003 Cardoza YJ, Alborn HT, Tumlinson JH (2002) In vivo volatile emissions from peanuts plants induced by simultaneous fungal infection and insect damage. J Chem Ecol 28:161–173. doi:10.1023/A:1013523104853 Cardoza YJ, Teal PEA, Tumlinson JH (2003) Effect of peanut plant fungal infection on oviposition preference by Spodoptera exigua and on host-searching behavior by Cotesia marginiventris. Environ Entomol 32:970–976. doi:10.1603/0046-225X-32.5.970 Carter DJ, Cary RB (2007) Lateral flow microarrays: a novel platform for rapid nucleic acid detection based on miniaturized lateral flow chromatography. Nucleic Acids Res 35:e74. doi:10.1093/nar/gkm269 Caruso P, Gorris MT, Cambra M, Palomo JL, Collar J, López MM (2002) Enrichment double-antibody sandwich indirect enzyme-linked immunosorbent assay that uses a specific monoclonal antibody for sensitive detection of Ralstonia solanacearum in asymptomatic potato tubers. Appl Environ Microbiol 68:3634–3638. doi:10.1128/AEM.68.7.3634-3638.2002 Caruso P, Bertolini E, Cambra M, López MM (2003) A new and co-operational polymerase chain reaction (Co-PCR) for rapid detection of Ralstonia solanacearum in water. J Microbiol Method 55:257–272. doi:10.1016/S0167-7012(03)00161-1 Chaerle L, Van Der Straeten D (2000) Imaging techniques and the early detection of plant stress. Trends Plant Sci 5:495–501. doi:10.1016/S1360-1385(00)01781-7 Chaerle L, Van Caeneghem W, Messens E, Lambers H, Van Montagu M, Van Der Straeten D (1999) Presymptomatic visualization of plant–virus interactions by thermography. Nat Biotechnol 17:813–816. doi:10.1038/11765 Chaerle L, Hulsen K, Hermans C, Strasser RJ, Valcke R, Höfte M, Van Der Straeten D (2003) Robotized time-lapse imaging to assess in-planta uptake of phenylurea herbicides and their microbial degradation. Physiol Plant 118:613–619. doi:10.1034/j.1399-3054.2003.00143.x Chen B, Wang K, Li S, Wang J, Bai J, Xiao C, Lai J (2008) Spectrum characteristics of cotton canopy infected with Verticillium wilt and inversion of severity level. In: Li D (ed) Computer and computing technologies in agriculture, volume II. Springer, 259:1169–1180. doi:10.1016/S1671-2927(08)60053-X Cheung W, Xu Y, Thomas CLP, Goodacre R (2009) Discrimination of bacteria using pyrolysis-gas chromatography-differential mobility spectrometry (Py-GC-DMS) and chemometrics. Analyst 134:557–563. doi:10.1039/b812666f Choi YH, Tapias EC, Kim HK, Lefeber AW, Erkelens C, Verhoeven JTJ, Verpoorte R (2004) Metabolic discrimination of Catharanthus roseus leaves infected by phytoplasma using 1H-NMR spectroscopy and multivariate data analysis. Plant Physiol 135:2398–2410. doi:10.1104/pp. 104.041012 Cirvilleri G, Scuderi G, Bonaccorsi A, Scortichini M (2007a) Occurrence of Pseudomonas syringae pv. coryli on hazelnut orchards in Sicily, Italy and characterization by fluorescent amplified fragment length polymorphism. J Phytopathol 155:397–402. doi:10.1111/j.1439-0434.2007.01249.x Cirvilleri G, Scuderi G, Catara V, Scortichini M (2007b) Typing of Pseudomonas syringae pv. pisi strains by fluorescent AFLP fingerprinting. J Plant Pathol 89:421–425. doi:10.4454/jpp.v89i3.776 Clerc A, Manceau C, Nesme X (1998) Comparison of randomly amplified polymorphic DNA with amplified fragment length polymorphism to assess genetic diversity and genetic relatedness within genospecies III of Pseudomonas syringae. Appl Environ Microbiol 64:1180–1187 Compton J (1991) Nucleic acid sequence-based amplification. Nature 350:91–92. doi:10.1038/350091a0 Costa G, Noferini M, Fiori G, Spinelli F (2007) Innovative application of non-destructive techniques for fruit quality and disease diagnosis. Acta Hortic 753:275 Costa JM, Grant OM, Chaves MM (2013) Thermography to explore plant–environment interactions. J Exp Bot 64:3937–3949. doi:10.1093/jxb/ert029 Daley PF (1995) Chlorophyll fluorescence analysis and imaging in plant stress and disease. Can J Plant Pathol 17:167–173. doi:10.1080/07060669509500708 Damm A, Erler A, Hillen W, Meroni M, Schaepman ME, Verhoef W, Rascher U (2011) Modeling the impact of spectral sensor configurations on the FLD retrieval accuracy of sun-induced chlorophyll fluorescence. Remote Sens Environ 115:1882–1892. doi:10.1016/j.rse.2011.03.011 Dandekar AM, Martinelli F, Davis CE, Bhushan A, Zhao W, Fiehn O, Skogerson K, Wohlgemuth G, D’Souza R, Roy S, Reagan RL, Lin D, Bruce Cary R, Pardington P, Gupta G (2010) Analysis of early host responses for asymptomatic disease detection and management of specialty crops. Crit Rev Immunol 30:277–289. doi:10.1615/CritRevImmunol.v30.i3.50 D’Asaro F, Grillone G (2012) Empirical investigation of Curve Number method parameters in the Mediterranean area. J Hydr Eng 17:1141–1152. doi:10.1061/(ASCE)HE.1943-5584.0000570 Davino S, Napoli C, Davino M, Accotto GP (2006) Spread of Tomato yellow leaf curl virus: partial displacement of another geminivirus originally present. Eur J Plant Pathol 114:293–299 Davino S, Miozzi L, Panno S, Rubio L, Davino M, Accotto GP (2012) Recombination profiles between Tomato yellow leaf curl virus and tomato yellow leaf curl Sardinia virus in laboratory and field condition: evolutionary and taxonomic implications. J Gen Virol 93:2712–2717. doi:10.1099/vir.0.045773-0 Dawkins R, Krebs JR (1979) Arms races between and within species. Proc Royal Soc Lond B 205:489–511. doi:10.1098/rspb.1979.0081 Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ et al (2005) The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434:980–986. doi:10.1038/nature03449 de Lacy Costello BPJ, Evans P, Ewen RJ, Gunson HE, Jones PRH, Ratcliffe NM, Spencer-Phillips PTN (2001) Gas chromatography-mass spectrometry analyse of volatile compounds from potato tubers inoculated with Phytohthora infestans or Fusarium coeruleum. Plant Pathol 50:489–496. doi:10.1046/j.1365-3059.2001.00594.x De Jong S, van der Meer FD (2006) Remote sensing image analysis: including the spatial domain. Springer editions, Dordrecht Delalieux S, Van Aardt JAN, Keulemans W, Schrevens E, Coppin P (2007) Detection of biotic stress (Venturia inaequalis) in apple trees using hyperspectral data: non-parametric statistical approaches and physiological implications. Eur J Agron 27:130–143. doi:10.1016/j.eja.2007.02.005 Delwiche SR, Kim MS (2000) Hyperspectral imaging for detection of scab in wheat. Biol Qual Prec Agric II, Proc SPIE 4203:13–20. doi:10.1117/12.411752 Doleman BJ, Severin EJ, Lewis NS (1997) Trends in odor intensity for human and electronic noses: relative roles of odorant vapor pressure vs. molecularly specific odorant binding. PNAS 95:5442–5447. doi:10.1073/pnas.95.10.5442 Ellington AD, Szostak J (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822. doi:10.1038/346818a0 Egerton FN (2012) History of Ecological Sciences. Part 44: Phytopathology during the 1800s. Bull Ecol Soc Am 93:303–339. doi:10.1890/0012-9623-93.4.303 Fehsenfild FC, Ferguson EE, Schmeltekopf AL (1966) Thermal energy ion—neutral reaction rates. III. The measured rate constant for the reaction O+(4S)+CO2 (1Σ)→O2+(2Π)+CO (1Σ). J Chem Phys 44:3022–3024. doi:10.1063/1.1727173 Fend R, Kolk A, Bessant C, Buijtels P, Klatser PR, Woodman AC (2006) Prospects for clinical application of electronic-nose technology to early detection of Mycobacterium tuberculosis in culture and sputum. J Clin Microb 44:2039–2045. doi:10.1128/JCM.01591-05 Ferguson EE, Fehsenfeld FC, Schmeltekopf AL (1969) Flowing afterglow measurements of ion-neutral reactions. Adv At Mol Phys 5:1–56. doi:10.1016/S0065-2199(08)60154-2 Franke J, Menz G (2007) Multi-temporal wheat disease detection by multi-spectral remote sensing. Precision Agric 8:161–172 Gardner JW, Bartlett PN (1994) A brief history of electronic noses. Sens Actuators B Chem 18:210–211. doi:10.1016/0925-4005(94)87085-3 Gascoyne PRC, Vykoukal JV, Schwartz JA, Anderson TJ, Vykoukal DM, Current KW, McConaghy C, Becker FF, Andrews C (2004) Dielectrophoresis-based programmable fluidic processors. Lab Chip 4:299–309. doi:10.1039/b404130e Grillone G, Agnese C, D’Asaro F (2012) Estimation of daily solar radiation from measured air temperature extremes in the mid-Mediterranean area. J Irr Drain Eng 138:939–947. doi:10.1061/(ASCE)IR.1943-4774.0000480 Grillone G, Baiamonte G, D’Asaro F (2014) Empirical determination of the average annual runoff coefficient in the Mediterranean area. Am J Appl Sci 11:89–95. doi:10.3844/ajassp.2014.89.95 Goulart LR, Vieira CU, Freschi AP, Capparelli FE, Fujimura PT, Almeida JF, Ferreira LF, Goulart IMB, Brito-Madurro AG, Madurro JM (2010) Biomarkers for serum diagnosis of infectious diseases and their potential application in novel sensor platforms. Crit Rev Immunol 30:201–222. doi:10.1615/CritRevImmunol.v30.i2.70 Gowen AA, O’Donnell C, Cullen PJ, Downey G, Frias JM (2007) Hyperspectral imaging–an emerging process analytical tool for food quality and safety control. Trends Food Sci Tech 18:590–598. doi:10.1016/j.tifs.2007.06.001 Graeff S, Link J, Claupein W (2006) Identification of powdery mildew (Erysiphe graminis sp. tritici) and take-all disease (Gaeumannomyces graminis sp. tritici) in wheat (Triticum aestivum L.) by means of leaf reflectance measurements. Central Eur J Biol 1:275–288. doi:10.2478/s11535-006-0020-8 Grisham MP, Johnson RM, Zimba PV (2010) Detecting sugarcane yellow leaf virus infection in asymptomatic leaves with hyperspectral remote sensing and associated leaf pigment changes. J Virol Method 167:140–145. doi:10.1016/j.jviromet.2010.03.024 Grothues D, Rudolph K (1991) Macrorestriction analysis of plant pathogenic Pseudomonas species and pathovars. FEMS Microbiol 79:83–88. doi:10.1016/0378-1097(91)90532-F Hadjiloucas S, Walker GC, Bowen JW, Zafiropoulos A (2009) Propagation of errors from a null balance terahertz reflectometer to a sample’s relative water content. J Phys Sensor Appl 178:1–5. doi:10.1088/1742-6596/178/1/012012 Hampton R, Ball E, De Boer S (1990) Serological methods for detection and identification of viral and bacterial plant pathogens. A laboratory manual. APS Press, St. Paul Harper K, Kerschbaumer RJ, Ziegler A, Macintosh SM, Cowan GH, Himmler G, Mayo MA, Torrance L (1997) A scFv-alkaline phosphatase fusion protein which detects potato leafroll luteovirus in plant extracts by ELISA. J Virol Method 63:237–242. doi:10.1016/S0166-0934(96)02133-7 Hendriks MMWB, van Eeuwijk FA, Jellema RH, Westerhuis JA, Reijmers TH, Hoefsloot HCJ, Smilde AK (2011) Data-processing strategies for metabolomics studies. Trends Anal Chem 30:1685–1698. doi:10.1016/j.trac.2011.04.019 Hillnhütter C, Mahlein AK, Sikora RA, Oerke EC (2011) Remote sensing to detect plant stress induced by Heterodera schachtii and Rhizoctonia solani in sugar beet fields. Field Crop Res 122:70–77. doi:10.1016/j.fcr.2011.02.007 Holzloehner P, Schliebs E, Maier N, Füner J, Micheel B, Heilmann K (2013) Production of monoclonal camelid antibodies by means of hybridoma technology. J Immunol 190:135.14 Huang W, Lamb DW, Niu Z, Zhang Y, Liu L, Wang J (2007) Identification of yellow rust in wheat using in-situ spectral reflectance measurements and airborne hyperspectral imaging. Precision Agric 8:187–197. doi:10.1007/s11119-007-9038-9 Huang J, Liao H, Zhu Y, Sun J, Sun Q, Liu X (2012) Hyperspectral detection of rice damaged by rice leaf folder (Cnaphalocrocis medinalis). Comput Electron Agric 82:100–107. doi:10.1016/j.compag.2012.01.002 Hufkens K, Bogaert J, Dong QH, Lu L, Huang CL, Ma MG, Che T, Li X, Veroustraete F, Ceulemans R (2008) Impacts and uncertainties of upscaling of remote-sensing data validation for a semi-arid woodland. J Arid Environ 72:1490–1505. doi:10.1016/j.jaridenv.2008.02.012 Ibanez AM, Martinelli F, Uratsu SL, Vo A, Tinoco MA, Phu ML, Chen Y, Rocke DM, Dandekar AM (2014) Transcriptome and metabolome analysis of Citrus fruit to elucidate puffing disorder. Plant Sci 217:87–98. doi:10.1016/j.plantsci.2013.12.003 Jacquemoud S, Baret F (1990) PROSPECT: a model of leaf optical properties spectra. Remote Sens Environ 34:75–91 Jacquemoud S, Ustin SL (2001) Leaf optical properties: a state of the art. In: Proc Int Symp Phys Meas Sign Rem Sens, pp 223–232 Jacquemoud S, Verhoef W, Baret F, Bacour C, Zarco-Tejada PJ, Asner GP, François C, Ustin SL (2009) PROSPECT + SAIL models: a review of use for vegetation characterization. Remote Sens Environ 113:S56–S66. doi:10.1016/j.rse.2008.01.026 Jansen RMC, Hofstee JW, Wildt J, Verstappen FWA, Bouwmeester HJ, van Henten EJ (2009) Induced plant volatiles allow sensitive monitoring of plant health status in greenhouses. Plant Signal Behav 4:824–829. doi:10.4161/psb.4.9.9431 Jansen RMC, Wildt J, Kappers IF, Bouwmeester HJ, Hofstee JW, van Henten EJ (2011) Detection of diseased plants by analysis of volatile organic compound emission. Ann Rev Phytopathol 49:157–174. doi:10.1146/annurev-phyto-072910-095227 Johnson DA, Alldredge JR, Hamm PB, Frazier BE (2003) Aerial photography used for spatial pattern analysis of late blight infection in irrigated potato circles. Phytopathology 93:805–812. doi:10.1094/PHYTO.2003.93.7.805 Klerks MM, Leone G, Lindner JL, Schoen CD, van den Heuvel JFJM (2001) Rapid and sensitive detection of Apple stem pitting virus in apple trees through RNA amplification and probing with fluorescent molecular beacons. Phytopathology 91:1085–1091. doi:10.1094/PHYTO.2001.91.11.1085 Krebs MD, Cohen SJ, Lowzo J, Kang J, Tingley RD, Davis CE (2006) Two-dimensional alignment of differential mobility spectrometer data. Sensors and Actuators B-Chemical 119:475–482 Laothawornkitkul J, Moore JP, Taylor JE, Malcom G, Tim D, Hewitt CN, Paul ND (2008) Discrimination of plant volatile signatures by an electronic nose: a potential technology for plant pest and disease monitoring. Environ Sci Tech 42:8433–8439. doi:10.1021/es801738s Lichtenthaler HK, Lang M, Sowinska M, Heisel F, Miehe JA (1996) Detection of vegetation stress via a new high resolution fluorescence imaging system. J Plant Physiol 148:599–612. doi:10.1016/S0176-1617(96)80081-2 Lin CH, Tsai CH, Pan CW, Fu LM (2007) Rapid circular microfluidic mixer utilizing unbalanced driving force. Biomed Microdevice 9:43–50. doi:10.1007/s10544-006-9009-3 Lins EC, Belasque J Jr, Marcassa LG (2009) Detection of Citrus canker in citrus plants using laser induced fluorescence spectroscopy. Precision Agric 10:319–330. doi:10.1007/s11119-009-9124-2 Little EL, Bostock RM, Kirkpatrick BC (1998) Genetic characterization of Pseudomonas syringae pv. syringae strains from stone fruit in California. Appl Environ Microbiol 64:3818–3823, aem.asm.org/content/64/10/3818. Accessed June 2014 Liu CX, Lagae L, Borghs G (2007) Manipulation of magnetic particles on chip by magnetophoretic actuation and dielectrophoretic levitation. Appl Phys Lett 90:184109. doi:10.1063/1.2736278 Lorenzen B, Jensen A (1991) Spectral properties of a barley canopy in relation to the psectral properties of single leaves and the soil. Remote Sens Environ 37:23–34. doi:10.1016/0034-4257(91)90047-A López MM, Llop P, Olmos A, Marco-Noales E, Cambra M, Bertolini E (2009) Are molecular tools solving the challenges posed by detection of plant pathogenic bacteria and viruses? Mol Biol 11:13–46, swfrec.ifas.ufl.edu/hlb/database/pdf/00002423.pdf. Accessed June 2014 Louws FJ, Rademaker JLW, Brujin FJ (1999) The three Ds of PCR-based genomic analysis of phytobacteria: diversity, detection, and disease diagnosis. Ann Rev Phytopathol 37:81–125. doi:10.1146/annurev.phyto.37.1.81 Luppa PB, Sokoll LJ, Chan DW (2001) Immunosensors-principles and applications to clinical chemistry. Clin Chim Acta 314:1–26. doi:10.1016/S0009-8981(01)00629-5 Lytovchenko A, Beleggia R, Schauer N, Isaacsin T, Leuendorf JE, Hellmann H, Rose JKC, Fernie A (2009) Application of GC-MS for the detection of lipophilic compounds in diverse plant tissues. BMC Plant Meth 5:1–11. doi:10.1186/1746-4811-5-4 Manceau C, Brin C (2003). Pathovars of Pseudomonas syringae are structured in genetic populations allowing the selection of specific markers for their detection in plant samples. In: Iacobellis NS et al. (eds) Pseudomonas syringae and related pathogens. Kluwer, pp. 503–512 Mahlein AK, Oerke EC, Steiner U, Dehne HW (2012a) Recent advances in sensing plant diseases for precision crop protection. Eur J Plant Pathol 133:197–209. doi:10.1007/s10658-011-9878-z Mahlein AK, Steiner U, Hillnhütter C, Dehne HW, Oerke EC (2012b) Hyperspectral imaging for small-scale analysis of symptoms caused by different sugar beet diseases. Plant Meth 8:3. doi:10.1186/1746-4811-8-3 Mahlein AK, Rumpf T, Welke P, Dehne HW, Plümer L, Steiner U, Oerke EC (2013) Development of spectral indices for detecting and identifying plant diseases. Remote Sens Environ 128:21–30. doi:10.1016/j.rse.2012.09.019 Malthus TJ, Madeira AC (1993) High resolution spectroradiometry: spectral reflectance of field bean leaves infected by Botrytis fabae. Remote Sens Environ 45:107–116 Marco S, Gutiérrez-Gálvez A (2012) Signal and data processing for machine olfaction and chemical sensing: a review. IEEE Sens J 12:469–479. doi:10.1109/JSEN.2012.2192920 Martinelli F, Basile B, Morelli G, D’Andria R, Tonutti P (2012a) Effects of irrigation on fruit ripening behavior and metabolic changes in olive. Sci Hortic 144:201–207. doi:10.1016/j.scienta.2012.07.012 Martinelli F, Uratsu SL, Albrecht U, Reagan RL, Phu ML et al. (2012b) Transcriptome profiling of citrus fruit response to Huanglongbing disease. PLoS One 7:e38039. doi:10.1371/journal.pone.0038039 Martinelli F, Reagan RL, Uratsu SL, Phu ML, Albrecht U et al. (2013a) Gene regulatory networks elucidating Huanglongbing disease mechanisms. PLoS One 8:e74256. doi:10.1371/journal.pone.0074256 Martinelli F, Remorini D, Saia S, Massai R, Tonutti P (2013b) Metabolic profiling of ripe olive fruit in response to moderate water stress. Sci Hortic 52–58. doi:10.1016/j.scienta.2013.04.039 Martinelli F, Scalenghe R, Giovino A, Pasquale M, Aksenov AA, Pasamontes A, Peirano DJ, Davis CE, Dandekar AM (2014) Proposal of a Citrus translational genomic approach for early and infield detection of Flavescence dorée in Vitis. Plant Biosyst. doi:10.1080/11263504.2014.908976 Mauck KE, De Moraes CM, Mescher MC (2010) Deceptive chemical signals induced by a plant virus attract insect vectors to inferior hosts. PNAS 23:3600–3605. doi:10.1073/pnas.0907191107 Meroni M, Rossini M, Colombo R (2010) Characterization of leaf physiology using reflectance and fluorescence hyperspectral measurements. In: Maselli F, Menenti M, Brivio PA (eds) Optical observation of vegetation properties and characteristics. Research Signpost, Trivandrum, pp 165–187 Mewes T, Franke J, Menz G (2011) Spectral requirements on airborne hyperspectral remote sensing data for wheat disease detection. Precision Agric 12:795–812. doi:10.1007/s11119-011-9222-9 Minsavage GV, Thompson CM, Hopkins DL, Leite RMVBC, Stall RE (1994) Development of a polymerase chain reaction protocol for detection of Xylella fastidiosa in plant tissue. Phytopathology 84:456–461, www.apsnet.org/publications/phytopathology/backissues/Documents/1994Articles/Phyto84n05_456.PDF. Accessed June 2014 Mirik M, Michels GJ Jr, Kassymzhanova-Mirik S, Elliott NC, Catana V, Jones DB, Bowling R (2006) Using digital image analysis and spectral reflectance data to quantify damage by greenbug (Hemitera: Aphididae) in winter wheat. Comput Electron Agric 51:86–98. doi:10.1016/j.compag.2005.11.004 Mirik M, Jones DC, Price JA, Workneh F, Ansley RJ, Rush CM (2011) Satellite remote sensing of wheat infected by wheat streak mosaic virus. Plant Dis 95:4–12. doi:10.1094/PDIS-04-10-0256 Mirik M, Ansley RJ, Price JA, Workneh F, Rush CM (2013) Remote monitoring of wheat streak mosaic progression using sub-pixel classification of Landsat 5 TM imagery for site specific disease management in winter wheat. Adv Remote Sens 2:16–28. doi:10.3390/rs5020612 Mori Y, Nagamine K, Tomita N, Notomi T (2001) Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem Biophys Res Commun 289:150–154. doi:10.1006/bbrc.2001.5921 Morris T, Robertson B, Gallagher M (1996) Rapid reverse transcription-PCR detection of hepatitis C virus RNA in serum by using the TaqMan fluorogenic detection system. J Clin Microbiol 34:2933–2936, jcm.asm.org/content/34/12/2933. Accessed on June 2014 Moshou D, Bravo C, West J, Wahlen S, McCartney A, Ramon H (2004) Automatic detection of ‘yellow rust’ in wheat using reflectance measurements and neural networks. Comput Electron Agric 44:173–188. doi:10.1016/j.compag.2004.04.003 Moshou D, Bravo C, Oberti R, West J, Bodria L, McCartney A, Ramon H (2005) Plant disease detection based on data fusion of hyper-spectral and multi-spectral fluorescence imaging using Kohonen maps. Real Time Imag J 11:75–83. doi:10.1016/j.rti.2005.03.003 Moshou D, Gravalos I, Bravo DKC, Oberti R, West JS, Ramon H (2012) Multisensor fusion of remote sensing data for crop disease detection. In: Thakur JK, Singh SK, Ramanathan A, Prasad MBK, Gossel W (eds) Geospatial techniques for managing environmental resources. Springer, pp 201–219 Mottram R, DeJager JM, Duckworth JR (1983) Evaluation of a water stress index for maize using an infra-red thermometer. Crop Prod 12:26–28 Mumford R, Boonham N, Tomlinson J, Barker I (2006) Advances in molecular phytodiagnostics—new solutions for old problems. Eur J Plant Pathol 116:1–19. doi:10.1007/s10658-006-9037-0 Mundt CC, Sackett KE, Wallace LRD, Cowger C, Dudley JP (2009) Long-distance dispersal and accelerating waves of disease: empirical relationships. Am Nat 173:456–466. doi:10.1086/597220 Munkacsi AB, Stoxen S, May G (2007) Domestication of maize, sorghum and sugarcane did not drive the divergence of their smut pathogens. Evolution 61:388–403. doi:10.1111/j.1558-5646.2007.00036.x Naidu RA, Perry EM, Pierce FJ, Mekuria T (2009) The potential of spectral reflectance technique for the detection of grapevine leafroll-associated virus-3 in two red-berried wine grape cultivars. Comput Electron Agric 66:38–45. doi:10.1016/j.compag.2008.11.007 Natali L, Giordani T, Lercari B, Maestrini P, Cozza R, Pangaro T, Vernieri P, Martinelli F, Cavallini A (2007) Light induces expression of a dehydrin-encoding gene during seedling de-etiolation in sunflower (Helianthus annuus L.). J Plant Physiol 164:263–273. doi:10.1016/j.jplph.2006.01.015 Nilsson HE (1995) Remote sensing and image analysis in plant pathology. Ann Rev Phytopthol 33:489–527. doi:10.1146/annurev.py.33.090195.002421 Nolasco G, Sequeira Z, Soares C, Mansinho A, Bailey AM, Niblett CL (2002) Asymmetric PCR ELISA: increased sensitivity and reduced costs for the detection of plant viral nucleic acids. Eur J Plant Pathol 108:293–298. doi:10.1016/j.jviromet.2008.09.030 Nutter FW Jr (1989) Detection and measurement of plant disease gradients in peanut with a multispectral radiometer. Phytopathology 79:958–963, www.apsnet.org/publications/phytopathology/backissues/Documents/1989Articles/Phyto79n09_958.PDF. Accessed on April 2014 Nutter FW Jr, Schultz PM (1995) Improving the accuracy and precision of disease assessments: selection of methods and use of computer-aided training programs. Can J Plant Pathol 17:174–184. doi:10.1080/07060669509500709 Oerke EC, Steiner U, Dehne HW, Lindenthal M (2006) Thermal imaging of cucumber leaves affected by downy mildew and environmental conditions. J Exp Bot 57:2121–2132. doi:10.1093/jxb/erj170 Okamoto H, Murata T, Kataoka T, Hata SI (2007) Plant classification for weed detection using hyperspectral imaging with wavelet analysis. Weed Biol Manage 7:31–37. doi:10.1111/j.1445-6664.2006.00234.x Olmos A, Cambra M, Dasi MA, Candresse T, Esteban O, Gorris MT, Asensio M (1997) Simultaneous detection and typing of Plum pox potyvirus (PPV) isolates by heminested-PCR and PCR-ELISA. J Virol Meth 68:127–137. doi:10.1016/S0166-0934(97)00120-1 Olmos A, Bertolini E, Gil M, Cambra M (2005) Real-time assay for quantitative detection of non persistently transmitted Plum pox virus RNA targets in a single aphids. J Virol Meth 128:151–155. doi:10.1016/j.jviromet.2005.05.011 Omasa K (1990) Image instrumentation methods of plant analysis. In: Liskens HF, Jackson JF (eds) Modern methods of plant analysis. Springer-Verlag, Berlin, pp 203–243 Padlan EA (1994) Anatomy of the antibody molecule. Mol Immunol 31:169–217. doi:10.1016/0161-5890(94)90001-9 Panigada C, Rossini M, Meroni M, Cilia C, Busetto L, Amaducci S, Boschetti M, Cogliati S, Picchi V, Pinto F, Marchesi A, Colombo R (2014) Fluorescence, PRI and canopy temperature for water stress detection in cereal crops. Int J Appl Earth Obs 30:167–178. doi:10.1016/j.jag.2014.02.002 Panno S, Ferriol I, Rangel E, Olmos A, Han C-G, Martinelli F, Rubio L, Davino S (2014) Detection and identification of Fabavirus species by one-step RT-PCR and multiplex RT-PCR. J Virol Meth 197:77–82. doi:10.1016/j.jviromet.2013.12.002 Panno S, Davino S, Rubio L, Rangel EA, Davino M, Garcia-Hernandez J, Olmos A (2012) Simultaneous detection of the seven main tomato-infecting RNA viruses by two multiplex reverse transcription polymerase chain reactions. J Virol Meth 186:152–156. doi:10.1016/j.jviromet.2012.08.003 Pawliszyn J (1997) Solid phase microextraction—theory and practice. Wiley-VCH, Weinheim Peterson RB, Aylor DE (1995) Chlorophyll fluorescence induction in leaves of Phaseolus vulgaris infected with bean rust (Uromyces appendiculatus). Plant Physiol 108:163–171. doi:10.1104/pp. 108.1.163 Pinter PJ, Stanghellini ME, Reginato RJ, Idso SB, Jenkins AD, Jackson RD (1979) Remote detection of biological stresses in plants with infrared thermometry. Science 205:585–587. doi:10.1126/science.205.4406.585 Polischuk VP, Shadchina TM, Kompanetz TI, BI G, Sozinov AL (1997) Changes in reflectance spectrum characteristic of Nicotiana debneyi plant under the influence of viral infection. Arch Phytopathol Plant Prot 31:115–119 Prabhakar M, Prasad YG, Thirupathi M, Sreedevi G, Dharajothi B, Venkateswarlu B (2011) Use of ground based hyperspectral remote sensing for detection of stress in cotton caused by leafhopper (Hemiptera: Cicadellidae). Comput Electron Agric 79:189–198. doi:10.1016/j.compag.2011.09.012 Prabhakar M, Prasad YG, Rao MN (2012) Remote sensing of biotic stress in crop plants and its applications for pest management. In: Venkateswarlu B, Shanker AK, Shanker C, Maheswari M (eds) Crop stress and its management: perspectives and strategies. Springer, pp 517–545 Pradhanang PM, Elphinstone JG, Fox RTV (2000) Sensitive detection of Ralstonia solanacearum in soil: a comparison of different detection techniques. Plant Pathol 49:414–422. doi:10.1046/j.1365-3059.2000.00481.x Purcell DE, O’Shea MG, Johnson RA, Kokot S (2009) Near-infrared spectroscopy for the prediction of disease ratings for Fiji leaf gall in sugarcane clones. Appl Spectr 63:450–457. doi:10.1366/000370209787944370 Rader C, Barbas CF III (1997) Phage display of combinatorial antibody libraries. Curr Opin Biotechnol 8:503–508. doi:10.1016/S0958-1669(97)80075-4 Reynolds GJ, Windels CE, MacRae IV, Laguette S (2012) Remote sensing for assessing Rhizoctonia crown and root rot severity in sugar beet. Plant Dis 96:497–505. doi:10.1094/PDIS-11-10-0831 Rizzini FM, Bonghi C, Chkaiban L, Martinelli F, Tonutti P (2010) Effects of postharvest partial dehydration and prolonged treatments with ethylene on transcript profiling in skins of wine grape berries. Acta Hortic 877:1099–1104 Robison BJ (1995) Use of commercially available ELISA kits for detection of foodborne pathogens. In: Howard J, Whitcombe DM (eds) Diagnostic bacteriology protocols. Humana Press, pp 123–132. doi:10.1385/0-89603-297-3:123 Rodriguez-Làzaro D, Hernàndez M, D’Agostino M, Cook N (2006) Application of nucleic acid sequence-based amplification for the detection of viable foodborne pathogens: progress and challenges. J Rapid Meth Aut Mic 14:218–236. doi:10.1111/j.1745-4581.2006.00048.x Rumpf T, Mahlein AK, Steiner U, Oerke EC, Dehne HW, Plümer L (2010) Early detection and classification of plant diseases with support vector machines based on hyperspectral reflectance. Comput Electron Agric 74:91–99. doi:10.1016/j.compag.2010.06.009 Sankaran S, Mishra A, Ehsani R, Davis C (2010) A review of advanced techniques for detecting plant diseases. Comput Electron Agric 72:1–13. doi:10.1016/j.compag.2010.02.007 Schaad NW, Song W, Hutcheson S, Dane F (2001) Gene tagging systems for polymerase chain reaction based monitoring of bacteria released for biological control of weeds. Can J Plant Pathol 23:36–41. doi:10.1080/07060660109506906 Schaad NW, Frederick RD (2002) Real-time PCR and its application for rapid plant disease diagnostics. Can J Plant Pathol 24:250–258. doi:10.1080/07060660209507006 Schaad NW, Frederick RD, Shaw J, Schneider WL, Hickson R, Petrillo MD, Luster DG (2003) Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues. Ann Rev Phytopathol 41:305–324. doi:10.1146/annurev.phyto.41.052002.095435 Scholz BK, Jakobek JL, Lindgren PB (1994) Restriction fragment length polymorphism evidence for genetic homology within a pathovar of Pseudomonas syringae. Appl Environ Microbiol 60:1093–1100, aem.asm.org/content/60/4/1093. Accessed Apr 2014 Scortichini M, Marchesi U, Rossi MP, Di Prospero P (2001) Bacteria associated with hazelnut (Corylus avellana L.) decline are of two groups: Pseudomonas avellanae and strains resembling P. syringae pv. syringae. Applied Appl Environ Microbiol 68:476–484. doi:10.1128/AEM.68.2.476-484.2002 Scuderi G, Golmohammadi M, Cubero J, López MM, Cirvilleri G, Llop P (2010) Development of a simplified NASBA protocol for detecting viable cells of the citrus pathogen Xanthomonas citri subsp. citri under different treatments. Plant Pathol 59:764–772. doi:10.1111/j.1365-3059.2010.02305.x Seiffert U, Schweizer P (2005) A pattern recognition tool for quantitative analysis of in planta hyphal growth of powdery mildew fungi. Mol Plant Microbe Interact 18:906–912. doi:10.1094/MPMI-18-0906 Shnaydeman M, Mansfield B, Yip P, Clark HA, Krebs MD, Cohen SJ et al. (2005) Species-species bacteria identification using differential mobility spectrometry and bioinformatics pattern recognition. Anal Chem 77:5930–5937. doi:10.1021/ac050348i Sighicelli M, Colao F, Lai A, Patsaeva S (2009) Monitoring post-harvest orange fruit disease by fluorescence and reflectance hyperspectral imaging. Acta Hort 817:277–284 Simmonds P, Zhang LQ, Watson HG, Rebus S, Ferguson ED, Balfe P et al. (1990) Hepatitis C quantification and sequencing in blood products, haemophiliacs, and drug users. Lancet 336:1469–1472. doi:10.1016/0140-6736(90)93179-S Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F (2000) Maskless fabrication of lightdirected oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol 17:974–978. doi:10.1038/13664 Smith GP (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228:1315–1317. doi:10.1126/science.4001944 Smith D, Spanel P (2005) Selected ion flow tube mass spectrometry (SIFT-MS) for on line trace gas analysis. Mass Spectrom Rev 24:661–700. doi:10.1002/mas.20033 Smith SE, Dickson S (1991) Quantification of active vesicular-arbuscular mycorrhizal infection using image analysis and other techniques. Aust J Plant Physiol 18:637–648. doi:10.1071/PP9910637 Spanel P, Rolfe P, Rajan B, Smith D (1996) The selected ion flow tube (SIFT) a novel technique for biological monitoring. Ann Occup Hyg 40:615–626. doi:10.1016/S0003-4878(96)00028-2 Stilwell AR, Hein GL, Zygielbaum AI, Rundquist DC (2013) Proximal sensing to detect symptoms associated with wheat curl mite-vectored viruses. Intern J Remote Sens 34:4951–4966. doi:10.1080/01431161.2013.783945 Szymańska E, Saccenti E, Smilde AK, Westerhuis JA (2012) Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies. Metabolomics 8:3–16. doi:10.1007/s11306-011-0330-3 Taylor MT, Belgrader PB, Furman J, Pourahmadi F, Kovacs GTA, Northrup MA (2001) Lysing bacterial spores by sonication through a flexible interface in a microfluidics system. Anal Chem 73:492–496. doi:10.1021/ac000779v Thelwell N, Millington S, Solinas A, Booth J, Brown T (2000) Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res 28:3752–3761. doi:10.1093/nar/28.19.3752 Tomlinson JA, Barker I, Boonham N (2007) Faster, simpler, more-specific methods for improved molecular detection of Phytophthora ramorum in the field. Appl Environ Microbiol 73:4040–4047. doi:10.1128/AEM.00161-07 Torres-Sánchez J, López-Granados F, de Castro-Megías AI, Peña-Barragán JM (2013) Configuration and specifications of an unmanned aerial vehicle (UAV) for early site specific weed management. PLoS One 8(3):e58210. doi:10.1371/journal.pone.0058210 Tosetti R, Martinelli F, Tonutti P (2012) Metabolomics approach to studying minimally processed peach (Prunus persica) fruit. Acta Hortic 934:1017–1022 Trygg J, Holmes E, Lundstedt T (2007) Chemometrics in metabolomics. J Prot Res 6:469–479. doi:10.1021/pr060594q van Doorn R, Szemes M, Bonants P, Kowalchuk GA, Salles JF, Ortenberg E, Schoen CD (2007) Quantitative multiplex detection of plant pathogens using a novel ligation probe-based system coupled with universal, high-throughput real-time PCR on open arrays. BMC Genom 14:276. doi:10.1186/1471-2164-8-276 Van Vuurde JW, Ruissen MA, Vruggink H (1987) Principles and prospects of new serological techniques including immunosorbent immunofluorescence, immunoaffinity isolation and immunosorbent enrichment for sensitive detection of phytopathogenic bacteria. In: Civerolo EL, Collmer A, Davis RE, Gillaspie AG (eds) Plant Pathogenic Bacteria. Curr Plant Sci Biotech Agric 4:835–842 Varga A, James D (2006) Use of reverse transcription loop-mediated isothermal amplification for the detection of Plum pox virus. J Virol Method 138:184–190. doi:10.1016/j.jviromet.2006.08.014 Verhoef W (1984) Light scattering by leaf layers with application to canopy reflectance modeling: the SAIL model. Remote Sens Environ 16:125–141. doi:10.1016/0034-4257(84)90057-9 Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414. doi:10.1093/nar/23.21.4407 Wang H, Guo J, Ma Z (2012) Monitoring wheat stripe rust using remote sensing technologies in China. In: Li D, Chen Y (eds) Computer and computing technologies in agriculture V. Springer, pp 163–175 West JS, Bravo C, Oberti R, Lemaire D, Moshou D, McCartney HA (2003) The potential of optical canopy measurement for targeted control of field crop diseases. Ann Rev Phytopathol 41:593–614 Woodcock CE, Strahler AH (1987) The factor of scale in remote sensing. Remote Sens Environ 21:311–332. doi:10.1016/0034-4257(87)90015-0 Zhao W, Bhushan A, Simon M, Santamaria A, Davis CE (2008) Machine learning: a crucial tool for developing sensors. Algorithms 1:130–152 Zhao W, Davis CE (2009) Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data. (2009). Anal Chim Acta 651:15–23 Yang CM, Cheng CH, Chen RK (2007) Changes in spectral characteristics of rice canopy infested with brown planthopper and leaffolder. Crop Sci 47:329–335. doi:10.2135/cropsci2006.05.0335 Yang W, Chen J, Chen G, Wang S, Fu F (2013) The early diagnosis and fast detection of blast fungus, Magnaporthe grisea, in rice plant by using its chitinase as biochemical marker and a rice cDNA encoding mannose-binding lectin as recognition probe. Biosens Bioelectron 41:820–826. doi:10.1016/j.bios.2012.10.032 Yuan L, Huang Y, Loraamm RW, Nie C, Wang J, Zhang J (2014) Spectral analysis of winter wheat leaves for detection and differentiation of diseases and insects. Field Crop Res 156:199–207. doi:10.1016/j.fcr.2013.11.012 Zarco-Tejada PJ, Miller JR, Morales A, Berjón A, Agüera J (2004) Hyperspectral indices and model simulation for chlorophyll estimation in open-canopy tree crops. Remote Sens Environ 90:463–476. doi:10.1016/j.rse.2004.01.017 Zhang Z, Yang MJ, Pawliszyn J (1994) Solid-phase micro-extraction. Anal Chem 66:844–853. doi:10.1021/ac00089a716 Zhang M, Qin Z, Liu X, Ustin SL (2003) Detection of stress in tomatoes induced by late blight disease in California, USA, using hyperspectral remote sensing. Intern J Appl Earth Observ Geoinf 4:295–310. doi:10.1016/S0303-2434(03)00008-4 Zhang J, Pu R, Loraamm RW, Yang G, Wang J (2014) Comparison between wavelet spectral features and conventional spectral features in detecting yellow rust for winter wheat. Comput Electron Agr 100:79–87. doi:10.1016/j.compag.2013.11.001