APPLE AND PEAR SCAB ONTOLOGY
DOI:
https://doi.org/10.17770/etr2021vol2.6589Keywords:
ontology, pathogens, scabAbstract
An important issue in horticulture is ensuring plant disease, such as scab, prevention and treatment. Apple and pear are among the most widely grown (approximately 43% of all fruit tree area [1]) and economically important fruit crops specified worldwide and in Latvia. Scab diseases caused by ascomycetous fungi Venturia inaequalis and V.pyrina are economically the most important diseases worldwide. Research projects have produced research data covering various aspects of plant-pathogen interactions, but there is no internal linkage analysis, as well as implementation of other types of data (such as environmental and meteorological data, etc.). Establishing such a data integration system would allow the identification of new regularities in plant-pathogen interactions, and provide mechanisms for disease control decisions. Semantic analysis is one of information technology approaches to finding relationships in data. The product of analysis is ontology. There are plant disease ontologies which provide classification of diseases and describe their reasons. However, there is no ontology which describes a specific plant and relations among its farming parameters and disease probability. Such an ontology for apple and pear scab is presented in this paper. The constructed ontology can be applied to develop guidelines or digital expert systems.
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References
Fruit trees and berry bushes (including strawberries) (2016). Central Statistical Bureau. [Online]. Available: http://data.csb.gov.lv/pxweb/en/lauks/lauks__03Augk__ikgad/LAG070.px/?rxid=ce8aac91-f2b0-4f13-a25d-29f57b1468fb, [Accessed: 15.03.2021.]
I. Tenzer, C. Gessler, Subdivision and genetic structure of four populations of Venturia inaequalis in Switzerland. Eur J Plant Pathol. 1997; 103: pp. 565–571.
W. E. MacHardy, Apple scab: biology, epidemiology, and management. APS Press: St. Paul, Minnesota. 1996.
L. Gao, A. Berrie, J. Yang, X. Xu, Within- and between-orchard variability in the sensitivity of Venturia inaequalis to myclobutanil, a DMI fungicide, in the UK. Pest Manag Sci. 2009; 65: pp. 1241–1249.
C. Stehmann, S. Pennycook, K.M. Plummer, (2001). Molecular identification of a sexual interloper: the pear pathogen, Venturia pirina, has sex on apple. Phytopathology, 91, pp. 633-641.
G. Schnabel, E. L. Schnabel and A. L. Jones, Characterization of ribosomal DNA from Venturia inaequalis and ITS phylogenetic relationship to rDNA from other tree-fruit Venturia species, 1998.
A. Beck, A. Ritchel, K. Schubert, U. Braun, and D. Triebel 2005. Phylogenetic relationship of the anamorphic genus Fusicladium s. lat. as inferred by ITS nrDNA data. Mycol. Prog. 4: pp. 111-116.
J. K. Bowen, C. H. Mesarich, V. G. M. Bus, R. M. Beresford, K. M. Plummer, and M. D. Templeton, Venturia inaequalis: The causal agent of apple scab. Mol. Plant Pathol., 2011, 12: pp. 105-122.
C. L. Schoch, K. A. Seifert, S. Huhndorf et al, Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proccedings of the National Academy of Sciences of the USA, Vol. 109 (16), 2012, pp. 6241 – 6246.
I. Tenzer, and C. Gessler, Genetic diversity of Venturia inaequalis across Europe. Eur. J. Plant Pathol., 1999, 105: pp. 545-552.
X. Xu, J. Yang, V. Thakur, A. Roberts, D. J. Barbara, Population variation of apple scab (Venturia inaequalis) isolates from Asia and Europe. Plant Disease, Vol. 92(2), 2008, pp. 247- 252.
P. Gladieux, X. Zang, D. Afoufa-Bastien, R. V. Sanhueza, M. Sbaghi, and B. Le Cam, On the Origin and spread of the scab disease of apple: Out of central Asia. PLoS One 3:e1455, 2008. https://doi.org/10.1371/journal.pone.0001455 Crossref, Medline, ISI, Google Scholar.
F. Guérin, P. Franck, A. Loiseau, M. Devaux, and B. Le Cam. Isolation of 21 new polymorphic microsatellite loci in the phytopathogenic fungus Venturia inaequalis. Mol. Ecol. Notes 4: pp. 268-270, 2004.
X. Xu, N. Harvey, A. Roberts, and D. Barbara, Population variation of apple scab (Venturia inaequalis) within mixed orchards in the UK. Eur. J. Plant Pathol. 135: pp. 97-104, 2013.
А. И. Насонов, Г.В. Якуба, Е. В. Лободина, Особенности морфотипного состава популяции Venturia inaequalis (Cooke) G. Winter на восприимчивых к парше сортах яблони // Плодоводство и ягодоводство России. Т. 58.С. pp. 151-157, 2019.
А. И. Насонов, Особенности морфолого -культуральных особенностей аскоспоровых изолятов возбудителя парши яблони. Научные труды СКЗНИИСиВ, Том 9, с. 187- 192, 2016.
M. Chevalier, Y. Lespinasse, S. Renaudin, A microscopic study of different classes of symptoms coded by the Vf gene in apple for resistance to scab (Venturia ineaqualis) Plant Pathology, 1991;40: pp. 249–256.
C. Gessler, A. Patocchi, S. Sansavini, S. Tartarini, L. Gianfranceschi, Venturia inaequalis resistance in apple. Critical Reviews in Plant Sciences. 2006;25(6): pp. 473–503.
L. Bouvier, M. Bourcy, M. Boulay, M. Tellier, P. Guérif, C. Denancé, C. Durel, Y. Lespinasse, A new pear scab resistance gene Rvp1 from the European pear cultivar ‘Navara’ maps in a genomic region syntenic to an apple scab resistance gene cluster on linkage group 2. Tree Genetics & Genomes, Vol. 8, Issue 1, pp. 53- 60, 2011.
V. G. M. Bus, E. H. A. Rikkerink, V. Caffier, C. E. Durel, K. M. Plummer, Revision of the nomenclature of the differential host – pathogen interactions of Venturia inaequalis and Malus. Annual Review of Phytopathology, No. 49, pp. 391-413, 2011.
D. M. Dooley, E. J. Griffiths, G. S. Gosal et al., FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration. npj Sci Food 2, 23, 2018. https://doi.org/10.1038/s41538-018-0032-6
W. Jearanaiwongkul et al., An Ontology-based Approach to Plant Disease Identification System, IAIT, pp. 1-8, 2018.
Crop Ontology Curation Tool. [Online]. Available: http://www.cropontology.org/ [Accessed: 12.03.2021.]
GitHub - Planteome/plant-stress-ontology: An ontology containing biotic and abiotic plant stresses. [Online]. Available: https://github.com/Planteome/plant-stress-ontology [Accessed: 16.03.2021.]
S. Abdelghany et al., An Agile Methodology for Ontology Development. International Journal of Intelligent Engineering and Systems, Vol.12, No.2, 2019. DOI: 10.22266/ijies2019.0430.17
G. Schnabel, E. L. Schnabel and A. L. Jones, Characterization of ribosomal DNA from Venturia inaequalis and ITS phylogenetic relationship to rDNA from other tree-fruit Venturia species, 1998.
T. A. Koopman, J. C. Meitz-Hopkins, A. E. Bester-van der Merwe, K. R. Tobutt, C. Bester, C. L. Lennox, Genetic diversity and gene flow of four South African Venturia inaequalis (apple scab) populations. Phytopathology, Vol. 107, pp. 455- 462, 2017.
H. A. Raja, A. N. Miller, C. J. Pearce and N. H. Oberlies, Fungal identification using molecular tools: a primer for the natural products research community. Journal of natural products, Vol. 8, No. 3, pp. 756-770, 2017.