Recent Diagnostics and Detection Tools: Implications for Plant Pathogenic Alternaria and Their Disease Management

Abstract

Alternaria spp. of ascomycete fungi are known as major plant pathogens causing 20–80 % agricultural losses in field crops, horticultural crops, plantation crops, forest plants and also post harvest storage. Conventional methods of phyto-pathogenic Alternaria spp. identification is only based on their symptomatology of diseases, morphological, physiological and biochemical studies. However, identification based on formae specials, strains, or ecotypes within a species of Alternaria has limitations for accurate diagnostics, identification and detection. The species identification of these pathogenic groups of fungi is somewhat difficult because of their special growth conditions and morphological differences. The advancement of immunological assays and serological methods has shown more sensitivity and accuracy compared with earlier isolation techniques. Enzyme analysis, metabolic profiling and gel electrophoretic mobility of these pathogen proteins found to be useful for the detection of some strains and species. There are different rapid molecular diagnostics available for the detection of pathogenic Alternaria sp. including a range of pathogenic fungi like Fusarium and Macrophomina sp. Various methods based on detection and analysis of the internal transcribed spacer (ITS)-5.8S ribosomal DNA (rDNA) region are designated to be a powerful tool for precise and rapid laboratory diagnosis. However, the developments of polymerase chain reaction (PCR) variants which employ nucleic acid-based diagnostic techniques including reverse transcription (RT)-PCR, nested-PCR, multiplex-PCR, RT-PCR, RAPD and nucleic acid hybridizations are more rapid, sensitive, specific and reliable. Various commercial kits for in situ detections are available with reproducible results in a short time. Recently, with development of DNA micro-array technology and Fourier transform infrared spectroscopy (FTIR) has revolutionized the fungal phytopathogens identification and has become possible to detect different isolates of Alternaria. Nevertheless, the genomics and proteomics studies through bioinformatics tools are also supplementing with promising results. Though, the wide ranges of diagnostics techniques are available for detection, identification and quantification of Alternaria spp., the polyphasic approaches is best and more reliable than only molecular and serological methods. The sensitivity, specificity, rapidity, cost-effectiveness and their on-site suitability determines choice of the diagnostic methods. In management practices, integrated disease management (IDM) including physical, cultural, chemical and biological methods is the best strategy for Alternaria diseases. Judicious use of resistant germplasm and multi target fungicides provides sustainable advantage for management of diseases. However, development of bioinoculents and disease forecasting module will enable better strategies for eco-friendly disease management. Diversified group of fungi that have been reported as opportunistic pathogens, it is imperative that their specific identification be made correctly by an experienced microbiologist or mycologist. The species detection specific to Alternaria and development of diagnostics using molecular tools and technique is an upcoming challenge for the researchers and sustainable plant disease management.