Classification of Colletotrichum coccodes isolates into vegetative compatibility groups using infrared attenuated total reflectance spectroscopy and multivariate analysis

A. Salman, E. Shufan, L. Tsror, R. Moreh, S. Mordechai, M. Huleihel

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

In this study the potential of infrared (IR) spectroscopy for the classification of Colletotrichum coccodes (C. coccodes) isolates into vegetative compatibility groups (VCGs) was evaluated. Isolates which belong to the same VCG may have similar pathological and physiological traits that differ from those that are not assigned to the same VCG. Early classification of isolates into VCGs is of a great importance for a better understanding of the epidemiology of the disease and improves its control. The main goal of the present study was to classify 14 isolates of C. coccodes into VCGs and differentiate between them, based on their IR absorption spectra as obtained by the FTIR-ATR sampling technique. Advanced statistical and mathematical methods, including Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA), were applied to the spectra after manipulation. The results show that it is possible to assign the isolates into VCGs with more than 90% success based on the wavenumber low region (1800-800cm-1) and using 15 PCs. However, on the isolate level, the best differentiation results were obtained using PCA (15 PCs) and LDA for the combined regions (2990-2800cm-1, 1800-800cm-1), with identification success rates of 87.2%.

Original languageEnglish
Pages (from-to)325-330
Number of pages6
JournalMethods
Volume68
Issue number2
DOIs
StatePublished - 1 Jul 2014

Keywords

  • Colletotrichum coccodes (C. coccodes)
  • FTIR-ATR
  • Fungal detection
  • LDA
  • PCA
  • VCG

ASJC Scopus subject areas

  • Molecular Biology
  • General Biochemistry, Genetics and Molecular Biology

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