Table 1.

Current list of isothermal based assays used in closed environment agriculture for fungal detection.

Molecular Assay	Summary	Fungal Pathogen/s Detected	Genes Targets	References
Loop-mediated isothermal amplification (LAMP)	Uses 4–6 primers for quick amplification. Performed at 60–68 °C	Sclerotinia sclerotiorum Fusarium oxysporum Botrytis cinerea	Suppressor Of Cytokine Signaling 5 (Ssos5) Intergenic spacer spacer (IGS)	[4,73,95,96]
Nucleic acid sequence-based amplification (NASBA):	Amplifies mRNA by using RNA polymerase, performed at 41 °C	Candida sp. Cryptococcosis	T7 promoter Capsular-associated protein (CAP10)	[4,23,97,98]
Rolling circle ampification (RCA)	Enzymatic assay that generates ssDNA. Performed between 25 °C and 37 °C	Candida sp. Fusarium sp.	Translation elongation factor 1-alpha (TEF-1α) Internal transcribed spacer (ITS)	[74,99,100,101]
Whole genome amplification (WGA)	Amplifies entire genome. Has no temperature modulated denaturation	Penicillum paxilli Epichloe festucae Pythium insidiosum	No gene target Requires DNA of 1–10 copies for initial input	[97,102,103,104]
Strand displacement amplification (SDA)	Performs enzymatic site specific nicks at 37–50 °C	Erysiphales spp.	β-tubulin1 (Tub1) Internal transcribed spacer (ITS)	[101,105,106,107]
Helicase dependent amplification (HDA)	Uses a thermostable helicase enzyme. Performed at 65 °C	Pythium insidiosum	Cytochrome c oxidase subunit 2 (COX2) BNI1 product (Bni1p)	[104,108,109]
Recombinase Polymerase Amplification (RPA)	Invades the double stranded DNA using enzymes and is performed at 30–42 °C	Bipolaris sorokiniana Candida albicans	Internal transcribed spacer (ITS) Calmodulin (cal)	[107,110,111]