Phytopathogenic fungal species can cause enormous losses in quantity and quality of crop yields and this is a major economic issue in the global agricultural sector. Precise and rapid detection and identification of plant infecting fungi are essential to facilitate effective management of disease. DNA-based methods have become popular methods for accurate plant disease diagnostics. Recent developments in standard and variant polymerase chain reaction (PCR) assays including nested, multiplex, quantitative, bio and magnetic-capture hybridization PCR techniques, post and isothermal amplification methods, DNA and RNA based probe development, and next-generation sequencing provide novel tools in molecular diagnostics in fungal detection and differentiation fields. These molecular based detection techniques are effective in detecting symptomatic and asymptomatic diseases of both culturable and unculturable fungal pathogens in sole and co-infections. Even though the molecular diagnostic approaches have expanded substantially in the recent past, there is a long way to go in the development and application of molecular diagnostics in plant diseases. Molecular techniques used in plant disease diagnostics need to be more reliable, faster, and easier than conventional methods. Now the challenges are with scientists to develop practical techniques to be used for molecular diagnostics of plant diseases. Recent advancement in the improvement and application of molecular methods for diagnosing the widespread and emerging plant pathogenic fungi are discussed in this review.

Macadamia (Macadamia integrifolia) is native to eastern Australia and produces an edible nut that is extensively cultivated in commercial orchards in several countries. Little is known about the diversity of fungi associated with diseases of macadamia inflorescences. A survey of fungi associated with the dry flower disease of macadamia detected several isolates of Neopestalotiopsis (Pestalotiopsidaceae, Sordariomycetes). Five new species of Neopestalotiopsis were identified based on molecular phylogenetic analyses of concatenated gene sequences of the internal transcribed spacer (ITS), β-tubulin (TUB), and the translation elongation factor 1-alpha (TEF1α). The new species are named Neopestalotiopsis drenthii, N. maddoxii, N. olumideae, N. vheenae, and N. zakeelii, and are described by molecular, morphological, and cultural characteristics. The ecology of the isolates and their pathogenic, saprophytic, or commensal ability were not determined.

Plant disease control is mainly based on the use of fungicides, bactericides, and insecticides-chemical compounds toxic to plant invaders, causative agents, or vectors of plant diseases. However, the detrimental effect of these chemicals or their degradation products on the environment and human health strongly imposes the search for novel, harmless means of disease control. Therefore, it is essential to introduce environmentally-friendly alternative measures for management of plant diseases. Induced plant resistance is one of the promising non-chemical strategies for the effective management of diseases. The host plant mediated resistance is governed by defense response genes encoding for production of various pathogenesis-related (PR) proteins. This review chiefly explains the biochemical response of plant defense mechanism pertaining to defense-related enzymes which have been identified as PR proteins.

Macadamia (Macadamia integrifolia) is endemic to eastern Australia and produces an edible nut that is widely cultivated in commercial orchards globally. A survey of fungi associated with the grey and green mold symptoms of macadamia flowers found mostly species of Botrytis (Sclerotiniaceae, Leotiomycetes) and Cladosporium (Cladosporiaceae, Dothideomycetes). These isolates included B. cinerea, C. cladosporioides, and unidentified isolates. Amongst the unidentified isolates, one novel species of Botrytis and three novel species of Cladosporium were delimited and characterized by molecular phylogenetic analyses. The new species are Botrytis macadamiae, Cladosporium devikae, C. macadamiae, and C. proteacearum.

Flower diseases threaten macadamia production, but there is a limited understanding of their aetiology. This study was undertaken to establish the ecology of the causal agents in commercial orchards in Australia. Raceme samples at different developmental stages were collected from 42 commercial macadamia orchards during the 2018–2020 flowering seasons. Morphological and molecular phylogenetic analyses of the isolates obtained from the samples with symptoms revealed that 16 fungal species, including two Botrytis spp., six Cladosporium spp., six Neopestalotiopsis spp. and two Pestalotiopsis spp., were associated with the flower blights. Twelve of the fungal species were identified as new records in macadamia. A comparison of the fungal genera showed that Neopestalotiopsis spp. (48%) and Cladosporium spp. (47%) were the most prevalent in the majority of macadamia production regions and were obtained from all four raceme developmental stages. The genus Botrytis was more commonly distributed (16%) in the production areas where humidity was high and was mostly isolated from the mature developmental raceme stages. Based on in planta infection assays under field conditions, the fungal pathogens varied in aggressiveness on macadamia racemes, with B . cinerea , B . macadamiae , C . cladosporioides , C . devikae , N . drenthii , N . macadamiae , N . maddoxii , N . vheenae , P . macadamiae and P . telopeae as the most aggressive and C . angulosum and C . proteacearum as the least aggressive. This study improves our understanding of the aetiology and distribution of the causal agents of flower blight complex in macadamia.