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Tropical Plant Pathology (2023) 48:97–103

https://doi.org/10.1007/s40858-022-00543-8

SHORT COMMUNICATION

Nucleic acid extraction and multiplex analysis for simultaneous


detection of the corn stunt complex pathogens in plant and insect
tissues
Eduardo Silva Gorayeb1 · Matheus Rodrigues Magalhães Albuquerque1 · Jacson Ferreira2 ·
Samara Campos do Nascimento1 · Thiago da Silva da Silva1 · Daian Marcos Savaris2 · Leandro Prado Ribeiro2 ·
Maria Cristina Canale2 · Fábio Nascimento da Silva1

Received: 2 June 2022 / Accepted: 10 November 2022 / Published online: 28 November 2022
© The Author(s), under exclusive license to Sociedade Brasileira de Fitopatologia 2022

Abstract
The corn stunting complex (CSC), composed of two Mollicutes (phytoplasma and spiroplasma) and one marafivirus (maize
rayado fino virus, MRFV), is the most important phytosanitary problem of maize crops in Brazil. Currently, MRFV detection
is performed separately from mollicutes, which contributes to the omission of virus detection in CSC monitoring activities
and basic studies. Here, a complete diagnostic method for simultaneous detection of CSC pathogens is presented, comprising
the optimization of an RNA/DNA extraction protocol and a triplex PCR, in which a newly designed MRFV-specific primer
pair was included along with the widely used R16F2n/R2 and CSSF2/CSSR6 primers for the mollicutes. As a result, a newly
designed MRFV-specific primer targeting the 5′ end of the polyprotein gene was developed and efficiently amplified MRFV
from different geographical locations and tissues (plant and insect) in the multiplex reaction. The designed MRFV primer
pair was species-specific, sensitive, and did not form secondary structures or dimerize with each other, nor with the other
primers used to detect the mollicutes. This method proved to be effective, cheaper, faster, and easier to perform than other
methods previously reported. Thus, it is a helpful tool for both basic and applied studies as well as monitoring programs
aiming to understand the MRFV presence in the CSC and maize crops.

Keywords Corn stunt spiroplasma · Maize bushy stunt phytoplasma · Molecular virus-detection · Plant disease
monitoring · Triplex PCR

The corn stunt is one of the most important diseases affect- et al. 1980; Hammond and Bedendo 2005; Orlovskis et al.
ing maize in the American Continent. It is associated with 2017).
a complex of three pathogens: the maize bushy stunt phyto- Maize bushy stunt phytoplasma is a wall-less pleo-
plasma (MBSP) (‘Candidatus Phytoplasma asteris’), corn morphic prokaryote, classified in the the16S rRNA gene
stunt spiroplasma (CSS) (Spiroplasma kunkelii), and maize group 16SrI, subgroup I-B (Lee et al. 2004). It has a cir-
rayado fino virus (MRFV) (Maize rayado fino virus) (Nault cular genome of 576,118 base pairs (bp), containing 531
genes, similar to that of endosymbiotic bacteria (Orlovskis
et al. 2017). The corn stunt spiroplasma is a characteristi-
* Maria Cristina Canale
cristinacanale@epagri.sc.gov.br cally helical motile bacterium. It is a wall-less prokaryote
with an internal cytoskeleton, which is composed of fibrils
* Fábio Nascimento da Silva
fabio.silva@udesc.br located under the cell membrane. Its genome has been fully
sequenced and consists of a 1,463,926 bp circular chromo-
1
Departament of Agronomy, Universidade do Estado de some and four plasmids (Davis et al. 2015).
Santa Catarina, Luís de Camões 2090, Conta Dinheiro, Maize rayado fino virus is the type species of the Marafi-
88.520‑000, Lages, SC, Brazil
2
virus genus (Family Tymoviridae), along with ten other spe-
Research Center for Family Agriculture, Agricultural cies (ICTV 2020). It is a phloem-restricted virus, possessing
Research and Rural Extension Company of Santa Catarina
(CEPAF/EPAGRI), Ferdinando Tusset – São Cristóvão, an icosahedral particle of approximately 30 nm in diam-
89.801‑970, Chapecó, SC, Brazil eter, containing a single 6336 bp long positive-sense RNA

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98 Tropical Plant Pathology (2023) 48:97–103

genome (Edwards and Weiland 2011; ICTV 2020; Mlotshwa inoculation, and yield losses ranging from 10 to 100%,
et al. 2020). depending on genotype susceptibility, insect vector inci-
All CSC pathogens are obligate parasites, being, in the dence, and climate conditions (Vásquez and Mora 2007).
plant, restricted to the phloem tissues, and transmitted by While the mollicutes are widespread in Brazil, MRFV
corn leafhopper [Dalbulus maidis (Delong and Wolcott was reported in the states of São Paulo, Minas Gerais, Par-
1923) (Hemiptera: Cicadellidae)] in a circulative-propaga- aná, and more recently in Santa Catarina (CABI and EPPO
tive manner (Özbek et al. 2003; Massola Junior 2004). 1997; Hammond and Bedendo 2005; Gonçalves et al. 2007;
Infected plants develop symptoms of shortening of the Albuquerque et al. 2022). As the three pathogens are trans-
internodes, over-production of ears, sterility of tassels, low mitted by the same vector, it is expected that MRFV is pre-
grain formation, short-grain cobs, root tipping, chlorotic sent in other CSC-affected maize production regions.
streaks between leaf veins, and leaf reddening (Henríquez In the present study, a faster and easier diagnostic method
et al. 1999). than those previously used was developed, requiring only
In Brazil, the adoption of a second crop season during the one nucleic acid extraction procedure and one triplex PCR to
1980s reduced the interval between cultivations favoring the detect the mollicutes, unlike what was being used, in which
permanence of the corn leafhopper and, consequently, the two nucleic acid extractions and two PCRs were necessary to
corn stunt complex (CSC) occurrence in the field (Oliveira detect the same three pathogens. For detecting the three CSC
et al. 2002). Since then, several outbreaks have been pathogens in a single end-point multiplex PCR, an DNA/
observed in different Brazilian states, such as Goiás, Minas RNA extraction protocol was adapted, and new primer pair
Gerais, Rio Grande do Sul, Santa Catarina, and Bahia, gen- targeting MRFV was designed and tested in combination
erating up to 100% losses in some areas (Sabato 2017). with the already widely used R16F2n/R2 (Gundersen and
Currently, CSC is mainly managed through insecticide Lee 1996) and CSSF2/CSSR6 (Barros et al. 2001) primer
usage, targeting the leafhopper vector through seed treat- pairs.
ment and post-emergence spraying (Sabato 2017). However, The simultaneous extraction of DNA and RNA of all
since the 2017/2018 season, the constant presence of the samples was performed using a CTAB protocol adapted
corn leafhopper in Brazilian maize cultivations has resulted from Marzachi et al. (1998) (detailed in supplementary File
in a significant increase in the usage of insecticides (around 1). The extracted nucleic acid's concentration and quality
75%), which has increased production costs and can contrib- were assessed through spectrophotometry (NanoDrop®
ute to reduce pesticide effectiveness, as well as, the contami- 2000, Thermo Fisher Scientific) and agarose gel electro-
nation of maize kernels (Jones and Medina 2020). phoresis (1%).
One possible solution for this problem is in the associa- In order to design a new pair of MRFV-specific prim-
tion between insecticide applications and CSC monitoring ers, the two MRFV complete sequences (AF2655566 and
programs, which involve the molecular detection of patho- KM523134) available in GenBank (https://​www.​ncbi.​nlm.​
gens in plants and/or insects, and consequently, help grow- nih.​gov/​genba​nk/) were downloaded and aligned using the
ers plan their actions in the field (Carloni et al. 2013). In muscle tool available in MEGA X software (Kumar et al.
addition, pest monitoring can reveal the distribution of D. 2018). A unique consensus sequence was generated and
maidis and CSC pathogens among regions, which helps to used as a template for designing primer pairs with Primer3
focus management strategies in the most affected regions, software (v. 0.4.0) (Koressaar and Remm 2007; Untergasser
combining different control methods, such as the elimination et al. 2012) following the recommendations proposed by
of voluntary plants, sanitary empty (a period without maize Hyndman and Mitsuhashi (2003). The occurrence of second-
cultivation), the usage of tolerant cultivars, and chemical or ary structures and primer dimerization (also including het-
biological insect control. erodimer analyses with R16F2n/R16R2 and CSSF2/CSSR6
However, monitoring activities are mainly focused on primer pairs), as well as primer specificity, were evaluated in
mollicute detection since different nucleic acid extraction silico with the IDT oligo analyzer (https://​www.​idtdna.​com/​
and PCR methods are used to detect MRFV, given its genetic pages/t​ ools/o​ ligoa​ nalyz​ er) and the blastn tools (https://b​ last.​
material’s RNA genome (Prince et al. 1993; Hammond et al. ncbi.​nlm.​nih.​gov), respectively.
1997; Marzachi et al. 1998; Barros et al. 2001; Gomes et al. The best pair of primers obtained from in silico analy-
2004; Gonçalves et al. 2007; Galvão et al. 2021). ses were denominated MRFVAF (Forward, 5′ TCG​CAC​
Although studies showed the presence of MRFV along TCT​TCT​TCG​TTG​ 3′) and MRFVAR (Reverse, 5′ GTC​
with the mollicutes causing the corn stunt (Hammond and TCG​ATG​GTC​TTG​TGG​A 3′). The primers aligned at the
Bedendo 2001), the full contribution of the virus to CSC is 5′ end of the ORF1 and the 5′ end of ORF2, resulting in
still not completely elucidated. However, this virus infec- a fragment of ~ 274 bp of a region that encodes methyl-
tion can generate symptoms of long chlorotic dotted stripes transferase. Both primers presented similar melting tem-
along the leaf veins generally between 7 and 14 days after peratures and acceptable GC content (50 and 52.6%, for

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Tropical Plant Pathology (2023) 48:97–103 99

MRFVAF and MRFVAR, respectively). Secondary struc- Polymerase (Promega), following the manufacturer’s
ture analysis revealed that primers are not likely to form recommendations.
hairpins at temperatures above 25.8 °C. The potential for For testing primer analytical sensitivity, the cDNA of the
homodimer formation was low, with changes of Gibbs free MRFV-positive sample was subjected to serial dilutions,
energy of bonding (ΔG) of − 3.61 and − 6.76 for MRFVAF decreasing by one order of magnitude from 10 to 1­ 0−6 ng/
and MRFVAR, respectively. The potential for heterodimer µL, and used as a template for PCR. Clear bands were
formation with ΔG below − 9 was not found among the six observed in all dilutions, detecting the presence of MRFV
primers used in the multiplex analysis, and blastn analysis cDNA down to a concentration of 13 pg/µL (Fig. 1A).
showed that except for the complete MRFV sequences cur- The best annealing temperature was assessed with a PCR
rently available, the primers designed did not hybridize to using the following thermocycler (Veriti™, Thermo Fisher)
any distinct type of pathogen or any sequence of the maize conditions: 94 °C for 30 s; 35 cycles of 94 °C for 15 s, 50,
genome, confirming in silico tests. 52, 54, 56, 58, or 60 °C for 15 s, and 72 °C for 20 s, followed
The MRFV-specific primer pair was tested in vitro by a final extension at 72 °C for 5 min. The PCR products
using an MRFV-positive sample [detected using MRFV- were analyzed on 2% agarose gels and stained with SYBR
09/MRFV-10 primers (Hammond et al. 1997)] from Pin- Safe™ (Invitrogen).
hão, Paraná, Brazil (25°41′54.2″S, 51°39′30.6″W). First, Clear bands were observed in all temperatures, but
complementary DNA (cDNA) was synthesized using slightly unspecific amplification was seen in reactions using
the MMLV reverse transcriptase enzyme (Promega), higher annealing temperatures (54–60 °C) (Fig. 1B). Given
with approximately 0.5–2 ug of nucleic acid from each this result, the temperature of 52 °C was chosen for primer
extracted sample as a template, following the manufac- validation and multiplex analyses, which is also closest to
turer’s instructions and the newly designed MRFV reverse the optimal annealing temperature calculated for each primer
primer (MRFVAR). The obtained cDNA was used as a (51 and 51.3 for MRFVAF and MRFVAR, respectively)
template for PCR with the enzyme GoTaq® Flexi DNA (Rychlik et al. 1990).

Fig. 1  In vitro sensitivity test of


MRFVAF/MRFVAR primers
(A) and temperature gradient
PCR testing (B). Lanes 1 and
9: 1 kb DNA ladder (Promega).
Lanes 8 and 16: no template
control. Lanes 2–7: sensitivity
test of MRFV-specific primers
using an MRFV-infected sample
(extracted from a single maize
plant), with a cDNA (produced
with MRFVAR primer) concen-
tration gradient of 1300 ng/µL,
130 ng/µL, 13 ng/µL, 1.3 ng/
µL, 130 pg/µL, and 13 pg/µL,
respectively. Lanes 10–15: PCR
testing using an MRFV-infected
sample (extracted from a single
maize plant) with a temperature
gradient ranging from 50, 52,
54, 56, 58, to 60 °C, respec-
tively

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All multiplex PCR testing were performed with 25 µL PCR conditions for the reaction. Clear bands were observed
reactions, using 7.5 units of the enzyme the GoTaq® Flexi in all temperatures, but unspecific amplification was seen in
DNA Polymerase (Promega), 7.5 mM ­MgCl2 (Promega), reactions using higher annealing temperatures (56–60 °C)
1.2 mM dNTP mix (Promega), R16F2n/R16R2, CSSF2/ (Fig. 2B), which confirmed 52 °C as the annealing tempera-
CSSR6, and MRFVAF/MRFVAR primers (0.1 µM each), 1 ture for the multiplex reaction.
µL of cDNA, and 2 µL of DNA of each sample. The standardized multiplex-PCR was validated with nine
An initial test was performed with three separate posi- plant and nine insect samples collected from commercial and
tive controls (previously tested using R16F2n/R2, CSSF6/ experimental areas. All plant samples were symptomatic,
CSSR2, and MRFV09/MRFV10 primers). Two insect sam- exhibiting at least one typical symptom of CSC, whereas
ples (pool of three insects), infected with CSS and MBSP/ insects were collected using yellow sticky traps installed
MRFV, respectively, obtained in experimental colonies at the border of commercial maize plantations. In addition,
from the Superior School of Agriculture Luiz de Quei- CSC-free samples (two originated from maize plants and two
roz, Piracicaba, SP, Brazil, and one MRFV-infected sam- from insects) were analyzed using the triplex PCR, in order
ple, from corn plants, obtained from Pinhão, PR, Brazil to test the possible formation of nonspecific amplifications.
(25°41′54.2″S, 51°39′30.6″W). Bands of approximately 274, Plants were obtained in the Brazilian municipalities
500, and 1250 bp were clearly observed for MRFV, CSS, and of Piracicaba, SP, (22°42′47.1″S, 47°37′37.6″W); Fran-
MBSP, respectively (Fig. 2A). In order to confirm primer cisco Beltrão, PR, (26°05′57.7″S, 52°57′35.7″W); Pinhão,
functionality, positive samples were purified (Wizard® PR, (25°44′28″S, 51°50′14″W); Caiapônia, GO, Brazil
SV Gel and PCR Clean-Up System, Promega) and sent for (16°55′25.9″S 51°47′46.7″W); Mineiros, GO (17°33′24.5″S
Sanger sequencing (ACTGene, Alvorada, RS, Brazil). The 52°35′59.8″W); Rio Verde, GO (two samples, 17°50′41.5″S
sequences obtained for MRFV (215 bp), MSBP (935 bp), 50°55′04.4″W); and Chapadão do Sul, MS (two samples,
and CSS (466 bp) were compared with those in GenBank 18°49′08.8″S, 52°39′32.8″W).
using the blastn tool (https://​blast.​ncbi.​nlm.​nih.​gov), show- Insect samples were obtained in the municipali-
ing 88.8%, 99.3%, and 100% of identity with MRFV (Gen- ties of Piracicaba, SP, (three samples, 22°42′47.1″S,
Bank Accession N° AF2655566 and KM523134), Aster 47°37′37.6″W); Chapecó, SC (two samples, 27°04′24.3″S,
yellows phytoplasma (GenBank Accession N° EU416200), 52°44′52.1″W); Morro da Fumaça, SC (two samples,
and CSS (GenBank Accession N° KX925443) isolates, 28°38′25.7″S, 49°14′50.6″W); Videira, SC (27°00′58.9″S,
respectively. In addition, a triple-infected plant (previously 51°05′00.3″W); and São Miguel do Oeste, SC (26°46′34.3″S,
indexed using R16F2n/R2, CSSF6/CSSR2, and MRFV09/ 53°30′33.8″W). The previously used triple-infected sam-
MRFV10 primers), collected in a commercial area from ple from Campos Novos, SC, Brazil (27°22′00.1″S,
Campos Novos, SC, Brazil (27°22′00.1″S, 51°15′28.5″ W), 51°15′28.5″W) was used as a positive control. Nucleic acid
was subjected to a PCR using a temperature gradient ranging extraction, cDNA synthesis, and PCR conditions were per-
from 50 to 60 °C in the annealing step, to verify the optimal formed as described earlier (using 52 °C for annealing).

Fig. 2  In vitro separate testing of primers (A) and temperature gradi- infected sample (extracted from a sample composed of three Dalbu-
ent multiplex PCR testing (B). Lanes 1 and 6: 1 kb DNA ladder (Pro- lus maidis adults). Lane 5: MRFV-infected sample (extracted from a
mega). Lanes 2 and 13: no template control. Lane 3: corn stunt spiro- single maize plant). Lanes 7–12: PCR testing with the triple-infected
plasma-infected sample (extracted from a single maize plant). Lane 4: sample (extracted from a single maize plant), with temperature gradi-
maize bushy stunt phytoplasma and maize rayado fino virus (MRFV)- ent ranging from 50 to 60 °C, changing 2 °C respectively

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Tropical Plant Pathology (2023) 48:97–103 101

All tested samples resulted in clear positive bands with which became evident with the results of the analyses pre-
the expected size for at least one CSC pathogen, giving sented in Figs. 1, 2, and 3. In addition, this protocol aims
conclusive results for both insect and plant-borne samples. to reduce extraction costs by avoiding virus-RNA extrac-
MRFV was the most prevalent CSC pathogen, present in 16 tion separately.
out of 18 samples, followed by CSS in 12 out of the 18 sam- The insertion of a primer pair for MRFV detection in
ples tested, and MBSP, found in three samples (Fig. 3). The the multiplex technique broadens the diagnostic process of
differences in the size of the amplified bands correspond- the CSC pathogens since the MBSP and CSS are already
ing to the spiroplasma observed in samples 5 and 6 (Fig. 3) detected simultaneously (Gomes et al. 2004; Albuquerque
may be related to a shift in the mobility of the amplified et al. 2022). Therefore, it would make more sense to design
DNA, already observed for SYBr safe, other SYBr products, a third pair of primers corresponding to MRFV to be used
GelRed, and other gel staining dyes (Huang and Fu 2005; in combination with those already utilized than to design
Truman et al. 2022). In addition, no unspecific bands were new pairs for all pathogens. In addition, in silico analyses
observed when the triplex PCR was performed with CSC- of other MRFV-specific primers available in the literature
free samples, regardless of whether they originated from (Hammond et al. 1997; Mlotshwa et al. 2020) revealed high
insects or plants (Supplementary file 2). probabilities of self-dimerization and heterodimer forma-
This study presents for the first time an innovative tion with the mollicutes-specific primers (data not shown).
protocol of a fast and sensitive technique for molecular Avoiding primer dimerization is crucial for performing good
diagnosis of the three pathogens involved in the CSC PCR because when two primers interact, the efficiency of
simultaneously. Herein, a complete method (from nucleic hybridizing the target is significantly reduced (Hyndman and
acid extraction to pathogen detection) was developed Mitsuhashi 2003).
and adjusted, allowing researchers to extract RNA/DNA In this study, we successfully obtained a single primer
from plant and insect samples rapidly, as well as to detect pair in which those undesirable features were not happen-
MRFV, MBSP, and CSS in a single end-point multiplex ing, and, in addition to the standardization of the method,
PCR (Fig. 3). The extraction protocol was efficient for another factor of great importance was the absence of
gathering enough nucleic acids from both D. maidis and primer-dimers and unspecific amplification in the multiplex
maize tissue samples, containing the parameters required reaction (Figs. 2 and 3), thus evidencing the high precision
for performing cDNA synthesis and conventional PCR, and efficiency of the presented multiplex technique.

Fig. 3  Results of the primer validation test (geographic location were originated from insects. Samples in lanes 16 [Pinhão, PR,
of each sample is in parenthesis). Lanes 1 and 13: 1 kb DNA lad- Brazil (25°44′28″S, 51°50′14″W)], 17 [Piracicaba, SP, Brazil
der (Promega). Lanes 2 and 14: positive control (extracted from (22°42′47.1″S, 47°37′37.6″W)], 18 [Francisco Beltrão, PR, Bra-
maize plants). Lanes 3 and 15: no template control. Samples in zil (26°05′57.7″S, 52°57′35.7″W)], 19 [Caiapônia, GO, Bra-
lanes 4, 5, 6 [Piracicaba, SP, Brazil (22°42′47.1″S, 47°37′37.6″W)], zil (16°55′25.9″S 51°47′46.7″W)], 20, 21 [Rio Verde, GO, Bra-
7, 8 [Chapecó, SC, Brazil (27°04′24.3″S, 52°44′52.1″W)], 9, 10 zil (17°50′41.5″S 50°55′04.4″W)], 22 [Mineiros, GO, Brazil
[Morro da Fumaça, SC, Brazil (28°38′25.7″S, 49°14′50.6″W)], (17°33′24.5″S 52°35′59.8″W)], 23, and 24 [Chapadão do Sul, MS,
11 [Videira, SC, Brazil (27°00′58.9″S, 51°05′00.3″W)], and 12 Brazil (18°49′08.8″S, 52°39′32.8″W)] were originated from maize
[São Miguel do Oeste, SC, Brazil (26°46′34.3"S, 53°30′33.8"W)] plants

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The target region amplified by the primer corre- References


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