Agriculture has an estimated value of $1500 billion US dollars (USD) per year (Agrios, 2005). However, an important amount of agricultural product is lost every year due to multiple diseases, and this problem is especially acute developing countries (Agrios, 2005; Strange, 2012) making crop disease management a priority in agriculturally based economies. In cases were resistant varieties are not available, the best option is to detect the presence of pathogens in the field as early as possible and thus avoid the onset of the disease. Hence, the effectiveness of many integrated pest management strategies are highly dependent on the availability of fast, sensitive and specific diagnostic methods. It is therefore important to develop more efficient technologies to detect crop diseases and effectively link them to decision bodies in order to efficiently deploy the necessary responses and safeguard agricultural systems.

Many methods have been developed to identify plant pathogens (Punja et al., 2007). The earliest conventional methods used symptom observation, involving field inspections to identify disease symptoms as well as laboratory tests such as pathogen culture on selective media followed by physiological, biochemical and pathogenicity tests (Horsfall and Cowling, 1977). Although conventional methods are reliable, they are time consuming and require experienced plant pathologists to identify the pathogen responsible for the disease. These reasons made it desirable to develop detection methods with higher sensitivity, specificity and speed for plant pathogen identification.

Antibody technology has been used in plant diagnostics since the 1980s and many reviews on this technology have been published (Alvarez, 2004; Narayanasamy, 2011). Antibody-based diagnostic methods for plant pathogen detection have become popular and powerful tools because of their speed, sensitivity and inexpensive nature. However, polyclonal antibodies (PAbs) against plant pathogens produced by animal immunization may show cross-reactivity with unrelated pathogenic species due to their limited specificity (Macario and Conway de Macario, 1985). With the development of monoclonal antibodies (MAbs), specificity was improved since they target a single epitope in a pathogen protein (Thornton, 2009). Hence, various antibody-based diagnostic methods such as enzyme-linked immunosorbent assays (ELISAs) (Comstock, 1992; Kokoskova and Janse, 2009), immunoblot (Novakova et al., 2006), immunofluorescent test (Malin et al., 1983) and lateral flow devices (LFD) (Tomlinson et al., 2010d) have been developed and widely used to identify plant pathogens. However, MAbs are expensive to produce and it has been reported that closely related species may share common epitopes and cause MAbs to react positively (Teitelbaum et al., 1991; Gorris et al., 1994).

The advent of the polymerase chain reaction (PCR) in the 1980s enabled scientists to explore and develop DNA-based approaches for plant pathogen detection. As a result many PCR-based diagnostic methods for the identification of plant pathogens have been reported (Ward et al., 2004; Vincelli and Tisserat, 2008). Furthermore, the amplification of pathogen-specific sequences and the coupling of PCR with other techniques have been described in order to improve specificity and sensitivity (Merighi et al., 2000; Brasileiro et al., 2004; Carrasco-Ballesteros et al., 2007). For example highly specific immunocapture-PCR (IC-PCR) has been used for viral detection combining conventional PCR amplification with antibody-captured viral particles. This approach increased sensitivity by 250-fold compared to direct PCR amplification (Wetzel et al., 1992) enabling successful detection of the bacterial blight disease in Anthurium propagation material (Xanthomonas axonopodis pv. dieffenbachiae) (Khoodoo et al., 2005).

A combination of conventional PCR and enzyme-linked immunosorbent assay (ELISA) termed PCR-ELISA was developed in the early 1990s (Nutman et al., 1994). The assay involves hybridization of the labeled PCR product to an immobilized probe on an ELISA plate followed by addition of an enzyme conjugate and a substrate to analyze the captured PCR product using a photometric measurement. This assay enabled the detection of a single amplicon population among several others that were generated in a multiplex reaction (Laitinen et al., 2002). This technique has been successfully used to detect viruses (Shindo et al., 1994), bacteria (Daly et al., 2002) and fungi (Bailey et al., 2002; Somai et al., 2002) with higher specificity than conventional PCR. However, despite its high specificity, the assay generated false positive results while detecting Neisseria meningitides (Borrow et al., 1998) and Mycobacterium tuberculosis (Kent et al., 1995; Gillespie et al., 1997) as the PCR amplified DNA was found to hybridize with the ELISA probe from other species.

An important improvement in DNA-based diagnostic methods came with the development of real-time quantitative PCR which allowed not only to detect the presence of pathogens but also to quantify pathogen levels in tissue samples thus allowing to determine the severity of the pathogen infection (Heid et al., 1996). A drawback of this technology is the requirements of expensive equipment and reagents which limits its use as a rapid cost-effective diagnostic method. In addition, the high sensitivity of the assay increases the risk of detecting even small amounts of contamination in the reagents or biological samples resulting in the diagnosis of false positives creating the need for normalization steps or pre-read runs to guarantee accuracy of results (Wong and Medrano, 2005; Nowrouzian et al., 2009).

Although PCR based assays have improved the sensitivity and have been used for multiplex pathogen detection (Price et al., 2010; Araujo et al., 2012; Dai et al., 2013), the assays are still prone to non-specific DNA amplification resulting in false positive results while performing multiplex detection on unknown pathogens in diseased plants tissues (Markoulatos et al., 2002; Sint et al., 2012).

Point-of-care (POC) diagnostic assays which do not require sophisticated equipment and can be rapidly and cheaply performed in the field are in high demand (Yager et al., 2006). PCR based methods have multiple advantages over other technologies but require an electricity supply to perform the temperature changes required for DNA amplification; seriously limiting its adequacy for POC applications (Barany, 1991). As an alternative, isothermal DNA amplification methods are ideally suited to overcome this limitation (Gill and Ghaemi, 2008; Craw and Balachandran, 2012). For instance, isothermal amplification combined with lateral flow strips and portable fluorometers has been successfully used for POC detection of pathogen DNA (Notomi et al., 2000; Vincent et al., 2004; Piepenburg et al., 2006; Chow et al., 2008; Lutz et al., 2010; Mahalanabis et al., 2010; Rohrman and Richards-Kortum, 2012). Nevertheless, portable fluorometers are expensive and not necessarily suited for use in the field exposed to adverse weather conditions, thus limiting their widespread adoption. A POC diagnostic assay technology integrating the entire process from sample preparation to visualization of results is still elusive. Agricultural industries could greatly benefit from the availability of convenient and cheap POC assays as crop field locations can be far away from analytical laboratory setups and sample transport can pose logistical problems.

An effective POC DNA extraction method is essential to develop rapid and user friendly molecular diagnostic assays but in-field sampling is rarely discussed when describing DNA-based diagnostic methods. This non-trivial task to consistently generate a fixed DNA input of good quality (i.e., absent of potential inhibitors) has repercussions on any assays’ performance. When dealing with plant tissues, the DNA extraction method requires the ability to efficiently remove a number of chemicals that can inhibit the DNA amplification reaction (Ikeda et al., 2008).

A LFD DNA extraction method has been reported as rapid and efficient for POC testing and has been successfully used in plant pathogen detection (Tomlinson et al., 2010a,b). This method involves sample disruption in extraction buffer using metal ball bearings before transferring the lysate onto the release pad of a LFD nitrocellulose membrane. A small piece of membrane is then excised and added into the DNA amplification reaction such as PCR or other isothermal amplification methods. The isolated DNA is very stable on the membrane at room temperature which allows the extraction to be performed in the field (Tomlinson et al., 2010a).

Solid Phase Reversible Immobilization (SPRI) is another DNA extraction method with potential POC application (Wee et al., 2015). A low cost DNA/RNA purification process using common filter pipette tips in conjunction with SPRI technology (Deangelis et al., 1995) to consistently extract DNA/RNA to a precise concentration that can be used immediately for downstream isothermal amplification has been recently reported (Wee et al., 2015). Magnetic SPRI bead-based extraction is ideal for POC applications because the only equipment required are a magnet and a micropipette. After macerating a single leaf disk with a plastic pestle in lysis buffer, the plant lysate was cleared of cellular debris by passing the lysate through a filtered pipette tip. DNA was then purified from the lysate using SPRI and the extracted DNA was directly used in the amplification reaction. This DNA extraction method has been used on various diagnostic applications including human and plant diseases (Ng et al., 2015; Wee et al., 2015).

A recent report has described the development of an extremely simple cellulose-based dipstick that allows plant sample processing in as little as 30 s (Zou et al., 2017). Plant tissues are macerated by shaking in a tube containing extraction buffer and 1–2 ball bearings for 8–10 s. A cellulose dipstick is inserted in the tube containing the sample before washing it three times in a second tube containing wash buffer and finally into the tube containing the amplification mix. The technology works efficiently in multiple cultivated species including rice, wheat tomato and sorghum as well as notoriously difficult tissues such as leaves from mature trees (mandarin, lime, and lemon). It can be used to detect pathogen DNA as well as RNA from infected tissues and works with multiple amplification methods such as PCR, LAMP, and RPA. Direct comparison studies have shown that this technology is as sensitive as SPRI but is cheaper, faster and does not require any pipetting steps.

Enzyme mediated in vitro amplification of nucleic acids has become an essential tool in molecular biology since 1980’s (White et al., 1989). PCR is one of the most widely used methods for the detection and identification of pathogens by targeting specific sequences in their genomic DNA. Although PCR is highly sensitive and robust, it is constrained by a number of technical limitations. For instance, specificity is highly dependent on the primers used and its inherent sensitivity makes it prone to false positives due to sample cross-contamination. Besides, PCR also requires electrically powered equipment to perform the thermal cycling which limits its use for point-of-care diagnostics. A number of alternative isothermal techniques are now available that can obviate the need for a thermal cycler although each has strengths and weaknesses.

Development of technologies with multiplex detection capability is another challenge in plant disease diagnostics as they are more cost effective, reduce assay time and require minimal amount of sample. High throughput multiplex detection has been successfully achieved using real-time PCR on an OpenArray^TM platform (van Doorn et al., 2007), microsphere immunoassay technology (Charlermroj et al., 2013) and microarrays (Szemes et al., 2005). However, simpler but efficient multiplex detection methods capable to identify multiple pathogens simultaneously are still needed.

Molecular inversion probes (MIPs) enable cost effective multiplex diagnostics and has been often used in clinical applications. MIP is a long single stranded probe in excess of >100 nt long with two binding domains at the 5′ and 3′ ends (B1 and B2 in Figure 6). The binding domains are designed to be complementary to the target region of interest (Figure 6; Lau et al., 2014). This enables the MIP to form a circular loop with a single stranded gap in between the two binding regions. After annealing of the MIP, a DNA polymerase lacking 5′–3′ exonuclease and strand displacement activities initiates DNA synthesis from the 3′ end of the gap in a gap-fill reaction. DNA ligase is then used to ligate the newly synthesized strand and generate a circular DNA molecule. To ensure the sensitivity of the assay, an exonuclease digestion step is performed to remove the linear probes. The ligated MIPs are then amplified in a PCR reaction using a universal primer set targeted P1 and P2.

The highly multiplexable nature of MIP probes, which are able to distinguish thousands of targets in a single reaction is a major advantage of this assay. The binding domains at the 3′ and 5′ ends are connected by a DNA backbone; this design feature physically restricts the binding domains to a small region of the genome that needs to contain both recognition sequences, dramatically increasing the specificity of the MIP assays. In addition, the noise signal of the assay is decreased by enzymatically degrading the non-ligated linear MIPs by the exonuclease digestion with up to 99% efficiency. MIPs have been designed to detect up to 330 000 targets in a single reaction (Diep et al., 2012). The MIP multiplexing capability has been demonstrated in various clinical studies such as high-throughput analysis of single nucleotide polymorphisms, DNA methylation, detection of genomic copy number changes and other genotyping applications (Hardenbol et al., 2003; Wang et al., 2005; Diep et al., 2012). However, applications for plant diagnostics are still limited with the first report describing the successful detection of Fusarium oxysporum f.sp. conglutinans in infected Arabidopsis thaliana with a detection limit of 2.5 ng (Lau et al., 2014). In order to improve the efficiency of MIP assays, the MIPgen software has been developed for the design and performance prediction of individual MIPs (Boyle E.A. et al., 2014).

Serious limitations of these assays are the requirement for several temperature settings throughout the assay and a tedious yet complicated experimental process that makes it unsuitable for POC testing. Besides, the assay is time consuming taking in excess of 10 h to complete a reaction, making MIP assays only suitable for applications in the laboratory. MIPs with lengths of >100 bp require HPLC purification which increases the cost of oligonucleotide synthesis. Achieving a high level of multiplex detection involving thousands of MIPs in a single reaction requires a large initial investment. In addition, multiplex detection using MIP assays needs a complex read-out platform such as next generation sequencing, microarrays or biosensors (Lin et al., 2010; Wang et al., 2012; Carrascosa et al., 2014) further increasing the cost of the assay.

A recently published method using a combination of RPA and surface enhanced Raman scattering (SERS) has described the possibility of multiplex detection of plant pathogens in the field (Lau et al., 2016). Surface-enhanced Raman scattering (SERS) is a technique that provides enhanced Raman scattering patterns of the adsorbed molecules from metal nanoparticles surfaces upon a single laser excitation (Schlucker, 2014). SERS has been reported as a potentially powerful molecular spectroscopy detection tool (Moskovits, 2010), and a highly promising readout technology for rapid diagnostic assays (Anker et al., 2008; Bantz et al., 2011; Sharma et al., 2012). SERS produces narrow and distinct spectral peaks which provides higher precision after analysis compared to the standard fluorescent-based methods for highly multiplexed applications (Schlucker, 2009; Wang and Schlucker, 2013; Laing et al., 2016). Furthermore, SERS using different Raman reporters have enabled multiplex detection (Lai et al., 2015) especially in clinical applications (Maiti et al., 2011; Wang et al., 2015). The first report incorporating SERS with multiplex RPA for agricultural applications has appeared in 2016, detecting several plant pathogens (Lau et al., 2016). The technique has been successfully used to detect Botrytis cinerea in infected tomato plants in a field situation. Although this technique is ready for field application, it involves an expensive portable SERS reader which might limits its application.

The main benefit of POC diagnostic testing is to provide rapid results in situ, enabling farmers to make immediate management decisions and minimize crop loses. An additional advantage is the reduction in logistic problems associated with sample transportation to centralized laboratories for disease analysis and the concomitant labor costs. POC diagnostic kits should be portable and user friendly allowing a single operator with no specialized scientific skills to carry out the test. In this paper, some of the commonly used nucleic acid-based methods for plant pathogen detection were discussed. Although the vast majority of current applications are PCR-based, numerous research reports have established that the existing isothermal techniques can perform as well as or even better than PCR-based assays. The ability to perform reactions at a constant temperature makes isothermal techniques promising candidates for point-of-care diagnostic assays in low resource settings. Each of the isothermal and non-isothermal technologies discussed here has inherent advantages and limitations therefore the choice on the best technology to adopt will depend on the specific problem; i.e., the nature of the pathogen, the crop being monitored and the technological capability of the country.

Among the available isothermal techniques, LAMP and RCA are the best candidates for hybridization based applications because the repeated sequences present in the amplification products are able to increase detection sensitivity (Gusev et al., 2001; Nallur et al., 2001; Hsieh et al., 2012). However, both techniques produce isothermal amplification products in various sizes and are therefore not suitable for applications where a specific DNA fragment size is needed for identification. HDA and RPA isothermal technologies do not require a heat denaturation step and as a result can be performed directly at a constant temperature, a big advantage for field applications. Nevertheless, HDA and RPA are limited to targets shorter than 100 and 500 bp, respectively. Furthermore, despite the sensitivity and specificity of these isothermal techniques, they are not highly multiplexable, limiting their application to the detection of a single, or at best a limited number of pathogens in a single assay. To achieve the multiplex detection of plant pathogens, MIP is a promising method which can provide high specificity but its application in the field is quite limited due to its technical complexity. The development of RPA-SERS technology allows multiplex field detection to be performed within 90 min at a single constant low temperature (37°C) with high sensitivity and specificity, however, portable SERS readers are expensive.

Next generation sequencing (NGS) technologies have a huge potential in the diagnostic space as they can identify multiple pathogens in a single analysis without any previous knowledge of their nature (Massart et al., 2014; Withers et al., 2016; Rott et al., 2017). Nevertheless, they still need to overcome a number of limitations before they can be used for POC applications. NGS equipment is quite sophisticated, requiring a clean laboratory environment as well as a reliable power supply. Sample preparation for analysis is quite complex, requiring multiple steps, pipetting of small volumes, occasional use of centrifuges and final quality checks using bio-analyzing equipment. Finally, the current cost of NGS sequencing technologies, in the range of hundreds or thousands of dollars, is too high for POC routine diagnostic analyses although future developments might make them affordable for this type of applications.

In summary, traditional laboratory methods are accurate but labor intensive and slow and, most importantly, need highly specialized technical personnel. Unfortunately the availability of skilled plant pathologists is becoming a problem worldwide (Horsfall and Cowling, 1977). Antibody-based diagnostic methods are clearly faster than traditional techniques but specificity of detection can be sometimes strongly compromised due to cross reactivity resulting in erroneous pathogen identification (Franken et al., 1992). The limitations of antibody-based methods are further compounded by their short shelf life and batch to batch variability (Murphy et al., 2012). Nucleic acid-based methods provide higher specificity and have the potential to solve many of the problems experienced in antibody-based diagnostics (Ward et al., 2004; Vincelli and Tisserat, 2008; Hindson et al., 2011; Miotke et al., 2014). PCR is the most popular DNA-based identification technique for plant pathogens but it needs a power supply to achieve the continuous changes in temperature that are crucial for this technology to work, limiting its suitability for POC field applications (Markoulatos et al., 2002; Sint et al., 2012). Isothermal amplification systems can address this limitation and provide better sensitivity, specificity as well as capability in POC applications either by themselves or coupled with other technologies such as rapid readout methods to analyse the DNA amplification products.

All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.