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Hosseini, B.; Voegele, R.T.; Link, T.I. Fungal and Oomycete Soybean Pathogens and Molecular Detection. Encyclopedia. Available online: https://encyclopedia.pub/entry/46939 (accessed on 17 May 2024).
Hosseini B, Voegele RT, Link TI. Fungal and Oomycete Soybean Pathogens and Molecular Detection. Encyclopedia. Available at: https://encyclopedia.pub/entry/46939. Accessed May 17, 2024.
Hosseini, Behnoush, Ralf Thomas Voegele, Tobias Immanuel Link. "Fungal and Oomycete Soybean Pathogens and Molecular Detection" Encyclopedia, https://encyclopedia.pub/entry/46939 (accessed May 17, 2024).
Hosseini, B., Voegele, R.T., & Link, T.I. (2023, July 18). Fungal and Oomycete Soybean Pathogens and Molecular Detection. In Encyclopedia. https://encyclopedia.pub/entry/46939
Hosseini, Behnoush, et al. "Fungal and Oomycete Soybean Pathogens and Molecular Detection." Encyclopedia. Web. 18 July, 2023.
Fungal and Oomycete Soybean Pathogens and Molecular Detection
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Soybean (Glycine max) is among the most important crops. Soybean was domesticated in China over 3000 years ago and introduced to other Asian countries and, later, the Americas, Africa, and Europe. Soybean production amounted to 355,605 million tons in 2021–2022, which illustrates the enormous economic importance of this crop. Soybean is threatened by several abiotic and biotic stress factors, which result in reduction of soybean yield and quality. Pathogens, pests, and weeds cause significant losses to soybean. Important fungal and oomycete pathogens of soybean and molecular methods to detect them are presented.

seed-borne fungi soil borne pathogens molecular detection methods species

1. Genus Diaporthe

The genus Diaporthe Nitschke (1870) (asexual state Phomopsis (Sacc.) Bubák) includes hundreds of species. Diaporthe species are widespread and they are non-pathogenic endophytes (biotrophic fungi), saprotrophs, and fungal pathogens of many plants and even mammals [1][2].
Phytopathogenic Diaporthe species have been intensively studied, especially those affecting economically important crops, such as soybean, sunflower, grapes, citrus, and fruit, and ornamental trees [3]. Diseases caused by Diaporthe spp. on soybean are stem canker, pod and stem blight, and seed decay (Table 1) [4][5][6].
Morphological evaluation of fungal growth from surface sterilized soybean seeds plated on acidified potato dextrose agar (APDA) is still common in the identification of Diaporthe spp. [7]. However, because of strong similarities and overlaps in shapes and colors of cultures and in conidial size, delimitation of Diaporthe spp. is not valid just based on morphology [1][2][8]. Species diversity in the genus Diaporthe was explored by assays using PCR [8][9][10]. The nuclear ribosomal internal transcribed spacer (ITS) can be used for discrimination of Diaporthe spp. [11][12][13]. The primers Phom.I and Phom.II were designed on the ITS sequences of D. phaseolorum and D. longicolla for the detection of many Diaporthe spp. [9]. The primers DphLe and DphRi were developed for detection of D. aspalathi [14]. There are also real-time (q)PCR assays based on ITS to detect and quantify Diaporthe spp. on soybean. The first was developed by Zhang et al. [15]. The TaqMan primer-probe sets PL-3, PL-5, and DPC-3 were designed for D. longicolla, D. aspalathi, D. caulivora, and D. sojae. For additional information on the mentioned primers and assays, see Table 1.
Table 1. Primers and corresponding assays for the diagnosis of Diaporthe spp. on soybean.
However, ITS sequence data alone are not sufficient to resolve all Diaporthe species [17][18]. Therefore, translation elongation factor 1-α (TEF1), beta-tubulin (TUB), calmoduline (CAL), histone-3 (HIS), and large ribosomal subunit (LSU) are also used to differentiate Diaporthe species [19][20][21].
Recently, the TaqMan primer-probe sets DPCL, DPCC, DPCE, and DPCN were designed based on TEF1 to identify, discriminate, and quantify D. longicolla, D. caulivora, D. eres, and D. novem simultaneously in a quadruplex real-time PCR [16].
In a study on expression of soybean defense-related genes, the TUB-based primers DPM were used with SYBR® Green real-time PCR to detect and quantify D. aspalathi in soybean tissues [22]. The same assay was also used to quantify the fungal biomass in soybean stems infected with D. caulivora [23].
There are additional PCR assays for the identification of Diaporthe spp.: random amplified polymorphic DNA (RAPD), PCR-restriction fragment length polymorphism (RFLP), and amplified fragment length polymorphism (AFLP) have been used to distinguish Diaporthe species [9][10][24][25][26]. The species D. caulivora, D. aspalathi, and D. sojae could only be defined after finding differences between the D. phaseolorum varieties caulivora, meridionalis, and sojae using RAPD [24]. After that, PCR-RFLP was used to distinguish D. longicolla, D. caulivora, D. aspalathi, and D. sojae [9].

2. Genus Sclerotinia

Sclerotinia sclerotiorum (Lib.) de Bary is among the most destructive plant pathogens. It is the only relevant pathogen of the genus Sclerotinia on soybean. This fungus can infect over 400 species of plants, including sunflower, soybean, and oilseed rape [27]. On soybean S. sclerotiorum causes white mold, which reduces yield by more than 40% in wet and mild weather [28]. Since the pathogen disseminates via seeds, sowing seeds with certified health quality is the first step to avoid this disease.
Molecular detection has been established independently more than once. Primers SSFWD/SSREV were designed for the identification of S. sclerotiorum [29] and the specificity and sensitivity of these primers were confirmed experimentally by performing PCR and real-time (q)PCR (SYBR Green) using the touchdown method, to distinguish S. sclerotiorum isolates from Aspergillus, Cercospora, Colletotrichum, Corynespora, Fusarium, Macrophomina, Diaporthe, and Botrytis species [30]. Other primers were used to identify S. sclerotiorum ascospores and detect S. sclerotiorum in infected plant tissue [31][32][33]. When tested on soybean seeds inoculated with S. sclerotiorum, these primers were not useful [30]. Variability among isolates from this species from different regions or hosts can lead to these differences. In a separate study, the primer pair SSFWD/SSREV [29] was tested to detect S. sclerotiorum in inoculated and in naturally infected soybean seeds using the seed soaking procedure [28]. Since the ITS region did not allow for fully reliable diagnosis the mitochondrial small rRNA and SS1G_00263, coding for a hypothetical secreted protein was used [33][34]. For additional information on the mentioned primers and assays, see Table 2.

3. Genus Colletotrichum

The ascomycete genus Colletotrichum is quite large, with more than 200 species. Some of the species are clearly defined, but there also are several species complexes [35][36][37]. Colletotrichum spp. are causal agents of anthracnose in more than 3000 plant species and are among the top 10 fungal pathogens [38][39][40]. C. truncatum, C. destructivum, C. coccodes, C. chlorophyte, C. gloeosporioides, C. incanum, C. plurivorum, C. sojae, C. musicola, and C. brevisporum can all cause anthracnose on soybean [36][41][42][43][44][45][46][47][48]. Among those species C. truncatum is the most notorious [41] and there is relatively little information about the other species infecting soybean. Phylogenetic resolution is still in progress, with many studies addressing the issue [35][36][37][38][49][50][51][52][53][54].
Variation in the ITS region is not sufficient to discriminate all species, so Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH), TUB2, CHS-1, and ACT are used along with ITS, also when using with the soybean pathogens [36][49]. Among those GAPDH is most informative, at least for distinguishing the most important pathogen C. truncatum [55]. Based on ITS, three primers were designed and used to distinguish C. gloeosporioides and C. truncatum on soybean by performing classical multiplex-PCR [56]. The intergenic spacer (IGS) has been used as an alternative to ITS. An advantage is that it contains more polymorphic sites. It was efficiently used for detecting C. lupini in lupins by PCR and can be considered an alternative target for Colletotrichum species [57].
A multiplex TaqMan qPCR assay targeting the GAPDH gene was developed to detect and quantify C. truncatum along with Corynespora cassiicola and S. sclerotiorum in soybean seeds [58]. A multiplex qPCR assay targeting the cox1 gene has also been established to distinguish the four soybean-infecting Colletotrichum species C. chlorophyti, Glomerella glycines (Colletotrichum sp.), C. incanum, and C. truncatum, by using two duplex sets. Successful detection was achieved with 0.1 pg of C. truncatum DNA, but when published, the assay had not yet been tested on host tissue samples [59].
For some Colletotrichum species that can infect soybean, diagnostic assays were developed because of damages on other host plants. These are C. acutatum on strawberries and grapevines [60][61], C. coccodes in soil and on potato tubers [62], C. kahawae on coffee [63], and C. lagenarium on cucurbit crops [64]. These assays may be transferred and used for diagnostics on soybean, too.
In addition to PCR and real-time PCR also LAMP (loop-mediated isothermal amplification) assays were established to detect C. truncatum, targeting the large subunit of RNA polymerase II (Rpb1) coding gene [65], and C. gloeosporioides, for which the target gene was a glutamine synthetase (GS) [66]. While these assays offer the advantage of diagnosis directly on the field because no PCR cycler is necessary and the reaction can be observed directly without any equipment, they are an order of magnitude less sensitive than the corresponding real-time PCR assays. For additional information on the mentioned primers and assays, see Table 3.

4. Genus Fusarium

Multiple Fusarium species are among the most important phytopathogenic and mycotoxigenic fungi [67][68]. Several Fusarium species are associated with soybean, causing Fusarium blight/wilt (F. oxysporum), sudden death syndrome (SDS, F. virgiliforme formerly F. solani f. sp. glycines), and root rot and seedling diseases (several Fusarium spp.) [69][70][71][72][73][74][75]. Diagnosis of the root pathogens may be difficult because they may either be the primary pathogen or infect together with other soilborne fungi (e.g., Macrophomina, Phytophthora, Pythium, and Rhizoctonia) [71][76]. Fusarium species have some differences in their housekeeping genes, and molecular identification has been widely used. Relevant genes for this genus are TEF1, TUB, mitochondrial small subunit rDNA (mtSSU), 28S rDNA, ITS, and IGS [77][78][79][80].
The causal agent of SDS, F. solani (Mart.) Sacc. f. sp. glycines [81], was first identified in 1989 [82][83]. At first, its identification has relied on morphological characteristics, which did not fully resolve the species complex. Using nuclear ribosomal DNA sequences of species within the F. solani complex, SDS-causing isolates were identified and F. solani f. sp. phaseoli was defined [77]. However, non-SDS-causing isolates are still included within F. solani f. sp. phaseoli. Another study using RAPD, could show that SDS-causing isolates form a cluster representing a biological subgroup within F. solani f. sp. phaseoli, and the authors suggested that it represents a separate forma specialis [84]. The differences between F. solani f. sp. glycines causing SDS and other F. solani are important for specific identification and detection. Differences in the mtSSU rRNA gene can be used to distinguish isolates of F. solani [78]. Detection of F. solani f. sp. glycines from plant and soil samples was enabled by a PCR assay using primers based on mtSSU and TEF1 [78][85].
Two TaqMan probe qPCR assays for quantification of F. virguliforme from soybean plant samples based on mtSSU sequences are available [86][87]. Due to similarities in the F. solani species complex, the mitochondrial DNA (mtDNA) region is too conserved to differentiate F. virguliforme from the dry bean root rot pathogens F. cuneirostrum and F. phaseoli and other SDS causal agents, such as F. tucumaniae, F. crassistipitatum, and F. brasiliense, which dominate in South America [88][89]. However, the IGS region of the rDNA can resolve F. virguliforme from the other closely related Fusarium species, as demonstrated in multilocus genotyping studies of clade 2 F. solani species [88][89]. Following this, a TaqMan primer/probe set based on IGS to detect and quantify F. virguliforme in field-grown soybean roots and soil was established [90]. The FvTox1 gene was also used to distinguish F. virguliforme from the other species within the SDS-BRR (bean root rot) clade in soil and soybean root samples with a species-specific TaqMan real-time qPCR assay [91].
Since the assay based on the FvTox1 gene has a much higher limit of detection than assays based on the rDNA, yet another assay specific for F. virguliforme was developed, based on the IGS region [92]. This primer/probe set was later also used in a duplex qPCR assay for simultaneous detection of F. virguliforme and F. brasiliense [93]. Most recent (to our knowledge, 2022) is a series of primer/probe sets to detect F. acuminatum, F. graminearum, F. proliferatum, and F. solani, based on TEF1 and F. oxysporum, and F. equiseti, based on IGS [94]. In this case, there are limits in specificity, especially of the F. solani primers/probe set (Fsol), which also amplifies F. graminearum, F. equiseti, and F. virguliforme, though much later than F. solani. For additional information on the mentioned primers and assays, see Table 4.

5. Genus Cercospora

Two species of genus Cercospora can infect soybeans. C. kikuchii (T. Matsumoto and Tomoy; M. W. Gardner) causes Cercospora leaf blight (CLB) and purple seed stain (PSS), while Frogeye leaf spot is caused by C. sojina Hara [69][95][96]. Production of a red toxin called cercosporin by C. kikuchii is recognized as a pathogenicity factor during colonization of soybean seeds and other aerial parts of the plant, including leaves, petioles, stems, and pods [97][98][99]. Cercosporin is also responsible for the symptoms of PSS: presence of purple spots against the natural color of the soybean seed coat [97] and causes membrane damage and cell death [100]. Cercosporin production is regulated by CFP (Cercosporin Facilitator Protein), which is specific for the genus and encoded by the gene cfp [101].
Seven nuclear gene regions and the mitochondrial (cyb) gene region were evaluated to study Cercospora species phylogenetically [102]. The seven regions included ACT, CAL, HIS, ITS, and TEF1, which were used in previous studies [103][104][105][106]. In addition, two primer pairs were designed based on cfp of C. kikuchii and one new primer Ck_Betatub-F1 to amplify tub-1 after the complete TUB from C. beticola was analyzed [102]. TUB and cfp are excellent sources for polymorphic markers to investigate the relationships between the CLB and PSS pathogens.
The CNCTB6F/CNCTB6F primer pair, which targets the NADPH-dependent oxidoreductase gene (CTB6) from C. nicotianae [107], can be used to detect C. kikuchii and to differentiate between C. kikuchii and C. sojina [108]. The ITS1 and ITS2 sequences of genus Cercospora are too similar to develop primers for species-specific detection [108]. Therefore, a TaqMan real-time PCR assay was developed based on the CTB6 gene to detect C. kikuchii [108] (Table 5).

6. Genus Septoria

Septoria glycines Hemmi causes Septoria brown spot, a foliar disease on soybean [69]. The pathogen infects pods and seeds but is rarely transmitted by seeds [109]. Early in the season, the symptoms are similar to those of bacterial blight (Pseudomonas syringae pv. glycinea) [110][111]. Later in the season, Septoria brown spot occurs together with frogeye leaf spot (Cercospora sojina) and Cercospora leaf blight (C. kikuchii) [112], making molecular diagnosis especially useful.
Three primers/probe sets were developed for qPCR based on ACT, TUB, and CAL [113]. The CAL set was not as specific as anticipated. The ACT set (Table 6) was specific to S. glycines for both conventional PCR and qPCR and the TUB set was specific only in qPCR.

7. Genus Macrophomina

The species in genus Macrophomina that is relevant to soybean is Macrophomina phaseolina (Tassi) Goid. This is one of the most severe soil and seed borne pathogens, attacking a wide range of hosts [114]. The fungus causes damping off, seedling blight, collar rot, stem rot, charcoal rot, and root rot diseases in various crops [115]. In soybean, M. phaseolina causes charcoal rot.
There is sequence variation between isolates of M. phaseolina. There have been several attempts to correlate this variation in several genetic markers with sampling region and host plant association, but while some groups found correlations [116], other publications could not [117][118][119], so that no forma speciales for soybean or another host plant have been defined, yet.
Consequently, the molecular detection assays that were established so far aim to detect all strains of M. phaseolina. In one approach that targets the ITS, the authors made sure to find primers on regions in the ITS that are conserved among M. phaseolina isolates, but different from other species [120]. The other approach to find a sequence conserved among M. phaseolina isolates was the sequence characterized amplified regions (SCAR) method. Using the universal rice primer URP-9F, a PCR product could be obtained that was the same for all M. phaseolina isolates and the resulting sequence (gene of unknown function) was used to design primers and probe for qPCR, enabling either SYBR green based or probe based qPCR [121]. A LAMP assay for detection of the species also uses the ITS sequence [122]. For additional information on the mentioned primers and assays, see Table 7.

8. Genus Phialophora

Brown stem rot (BSR) is a vascular disease caused by the soil-borne fungus Phialophora gregata f. sp. sojae (Allington and Chamberlain) Gams. This pathogen has two genotypes, “A” and “B” [123]. Genotypic differences among isolates correspond to phenotypic differences in the type and severity of symptoms. Isolates of genotype “A” are more aggressive than isolates of genotype “B” [124][125]. Genotypes “A” and “B” differ by a 188-bp insertion/deletion (INDEL) in the IGS of the ribosomal DNA and they also display cultivar preference [126][127][128].
Primers based on ITS were developed to identify P. gregata in infected soybean stems [129]. This primer pair was also used in combination with primer pair Plect1/Plect2 specific for Plectosporium tabacinum, to differentiate these two pathogens, which are associated with BSR [130]. Once the IGS region was found useful to distinguish “A” and “B”, primers BSRIGS1 and BSRIGS2 were designed [126]. In 2007, a qPCR assay was developed to quantify P. gregata f. sp. Sojae in plant tissue and in soil [131]. This qPCR assay does not yet distinguish between genotypes “A” and “B”. In 2009, a qPCR to specifically detect genotype “A” was developed. In combination with a specific primer/probe set [131], genotype “B” can also be quantified by determining the difference between the total P. gregata f. sp. sojae DNA amount and that of genotype “A” [132]. For additional information on the mentioned primers and assays, see Table 8.

9. Genus Rhizoctonia

Rhizoctonia solani Kühn (Teleomorph: Thanatephorus cucumeris (Frank) Donk) is a soil-borne fungal pathogen. R. solani is a species complex that was subdivided into anastomosis groups (AGs) based on an assessment of hyphal fusions [133][134]. AGs are subdivided into subgroups based on cultural morphology and physiological characteristics [135]. There are “13 AGs with 14 subgroups” [135][136][137]. The AGs vary in morphology, pathogenicity, and susceptibility to fungicides [138]. AG 1 to 4 cause disease in several economically important crops [133]. The other groups have more restricted host ranges or are less important. AG 12 is a special case: it forms mycorrhiza [136]. Molecular phylogenies have confirmed the AGs and the nomenclature was kept, even though the AGs may represent different species. The AGs important for soybean are AG 1-IA and AG 1-IB [69].
PCR detection assays were established for most of the AGs. Here, researchers present the assays for AG 1-IA and AG 1-IB. An assay based on ITS to detect AG 1-IA, AG 1-IB, and other AGs was designed in 2002 [139]. Later, two other groups [140][141] reported additional assays for the two AGs, respectively. As part of a real-time PCR study to detect and discriminate 11 AGs of R. solani using ITS regions, AG 1-IA was also detected [142]. In 2015, a LAMP assay was developed to detect R. solani in infected soybean tissues in the field [122]. For additional information on the mentioned primers and assays, see Table 9.

10. Genus Phakopsora

Soybean rust (SBR) is considered the economically most important disease on soybean. SBR is caused by two closely related fungi, Phakopsora pachyrhizi and P. meibomiae [143][144]. P. pachyrhizi, also called Asian soybean rust (ASR) since it originates from East Asia, is more aggressive and causes considerably greater yield loss [144]. The two species may be confused and early symptoms can be confused with bacterial pustule [69]. Therefore, molecular diagnosis of the soybean rust has been established. The ITS region has more than 99% nucleotide sequence similarity among different isolates of either P. pachyrhizi or P. meibomiae, but only 80% between the two species. Using the differences within the ITS region, four sets of primers were designed for P. pachyrhizi (Ppa1/Ppa2, Ppa3/Ppa4, Ppm1/Ppa2, and Ppm1/Ppa4) and two sets for P. meibomiae (Pme1/Pme2 and Ppm1/Pme2). The primers were tested and Ppm1/Ppa2 used as specific for P. pachyrhizi and Ppm1/Pme2 for P. meibomiae [145]. A VIC-labeled probe and the primers Ppm1/Ppm2 were designed as specific for genus Phakopsora.
P. pachyrhizi urediospores are wind-dispersed and, apart from diagnosis on plants, detection of spores in the air can be useful to predict epidemics or for scouting efforts. For this, the assay described above and another assay [146] were tested for sensitivity and from these assays another nested assay was created with a newly designed TaqMan probe (ITS1PhpFAM1). The nested assay combines the reverse primer Ppa2 specific to P. pachyrhizi [145] and a more general rust fungal forward primer ITS1rustF4a in the first round. In the second round ITS1rustF10d and ITS1rustR3d are combined with the probe. The assay can detect single and so is sensitive enough to find spores deposited in rain [147]. For additional information on the mentioned primers and assays, see Table 10.

11. Genus Phytophthora

Phytophthora sojae (Kaufm. and Gerd.) causes seed decay, root rot, damping off that may occur before or after emergence, stem rot, and sometimes foliar blight [148]. Soybean is the only major host of P. sojae [149]. Another Phytophthora species, P. sansomeana, has been isolated since 1981 from soybean in the USA and China [150][151][152][153][154].
The first target for molecular diagnosis was the ITS region. One PCR assay developed for P. sojae utilized primers PS1/PS2 [155]. The primers were also used in a SYBR-green based qPCR assay with a 10 pg limit of detection. Another group using the primers found problems with discrimination against other Phytophthora species from soybean [156]. Consequently, they developed their own PSOJF1/PSOJR1 primers, also targeting the ITS region [157]. Other researchers [158] using these primers reported a limit of detection of 10 fg in absolute quantifications. Other targets described for P. sojae detection are a Ras-related protein (Ypt1) coding gene [159] and an A3aPro transposon-like element [160].
A hierarchical approach to Phytophthora genus- and species-specific qPCR assays based on mitochondrial genes [161] provides new targets. Here, two loci were used, one for detecting all Phytophthora spp., the tRNA locus (trnM-trnP-trnM), and another, atp9, and the spacer between atp9 and nad9 (atp9-nad9) for genus- and species-specific detection. This approach was utilized to design specific probes for many Phytophthora spp. [162]. The system was also adapted for the isothermal technique recombinase polymerase amplification (RPA) [163]. Building on these approaches, a diagnostic assay for P. sojae and P. sansomeana was developed [164]. Using a genus specific probe and probes specific to P. sojae and P. sansomeana this multiplex qPCR assay can simultaneously determine if a sample is infected by any Phytophthora spp. and if it contains either P. sojae, P. sansomeana, or both [164]. The assay is highly specific and sensitive. A plant mitochondrial internal control for quantification relative to soybean and to determine the presence of PCR inhibitors can also be included in the assay. Another artificial internal control can be added when testing soil samples. Primer sets for RPA also exist [164].
Other groups [165][166] used the Ty3/Gypsy retroelement as target. This transposable element is widely distributed in the Phytophthora genus and forms lineages that predate the separation of the species [167]. This sequence is a good target because it is present in all isolates and has multiple copies per genome. Primers PS12 and PS6R were developed for this sequence and produced a 282 bp amplicon in all P. sojae isolates, but not on other Phytophthora spp. and other fungal soybean pathogens, as well as soybean itself [165]. This was developed into a probe-based qPCR assay for P. sojae [166]. For additional information on the mentioned primers and assays, see Table 11.
Table 11. Primers and corresponding assays for diagnosis of Phytophthora spp. on soybean.
Target Gene Target Species (Specificity) Primer/Probe (Combination) Sequence (5′-3′) Tm (°C) Fragment Length (bp) Assay Ref.
ITS P. sojae a PS1 CTGGATCATGAGCCCACT 66 330 PCR/qPCR b [155]
PS2 GCAGCCCGAAGGCCAC
ITS P. sojae PSOJF1 GCCTGCTCTGTGTGGCTGT 50 127 qPCR b [157]
PSOJR1 GGTTTAAAAAGTGGGCTCATGATC
Ypt1 P. sojae F3 CCTTGTCTGCCCTCTCGA 65 b   LAMP [159]
B3 AGAAGCGTACACCCACCA
FIP GAATTTTCTGGGCGGGACAACGCCAGGATGGCTAAGGTTTCC
BIP GAGCTGGACGGCAAGACCATCCATAAGTGCGCTTAACCGG
LF GCACAATATTGTCAGCAACTGGATC
LB CAAGCTCCAGATTGTACGTTCA
A3aPro P. sojae F3 GCGTATTGAGGGTTGCTG 64 c   LAMP [160]
B3 GCGTCCTATCACCTAGTGC
FIP ACGTGGGTTCGGATTGGACC-CTTGGGTACTGTGTACCAG
BIP CGCCACCGATGATTCGACGA-AATCAACCATCACTCACCG
LB GTAGGATGATTGGATGAACAC
atp9 Phytophthora PhyG_ATP9_2FTail AATAAATCATAACCTTCTTTACAACAAGAATTAATG 57   multiplex qPCR [161][164]
nad9 PhyG-R6_Tail AATAAATCATAAATACATAATTCATTTTTATA
atp9-nad9 Phytophthora genus-specific TaqMan probe FAM-AAAGCCATC [ZEN] ATTAAACARAATAAAGC-IABkFQ
atp9-nad9 P. sojae P. sojae species-specific TaqMan probe HEX-TTGATATAT [ZEN] GAATACAAAGATAGATTTAAGTAAAT-IABkFQ
atp9-nad9 P. sansomeana P. sansomeana species-specific TaqMan probe Quasar670-TATTAGTACTAAYTACTAATATGCATTATTTTTAG-BHQ-2
tRNA-M Phytophthora TrnM-F ATGTAGTTTAATGGTAGAGCGTGGGAATC 39 d   RPA [163][164]
TrnM-R GAACCTACATCTTCAGATTATGAGCCTGATAAG
TrnM-P TAGAGCGTGGGAATCATAATCCTAATGTTG [FAM-dT] A [THF] G [BHQ1-dT] TCAAATCCTACCATCAT [3′-C3SPACER]
atp9   Atp9-F CCTTCTTTACAACAAGAATTAATGAGAACCGCTAT
atp9-nad9 P. sojae Psojae-nad9-R TTAAATCTATCTTTGTATTCATATATCAA
P. sansomeana Psan-nad9-R TTAGTAGTTAGTACTAATATAACAAAAATATAATA
atp9   Atp9-P TTGCTTTATTYTGTTTAATGATGGCWTTY (T-FAM) T [THF] A (T-BHQ1) YTTATTTGCTTTTT [3′-C3SPACER]
Ty3/Gypsy retroelement C. truncatum Pso12-F CAGGTTTTCAGCGATCTCATCCAAGTG 60 282 qPCR [166]
Pso6-R CACATTGCGGAAAAGGAGGTGATTGCT
Pso-P5 FAM-TGCCGACTGCGAGGTCAGCAACCACTTCAA-IBFQ
a Specificity contradicted by [156][157]. b Incubation for the LAMP assay. Incubation for 60 min. c Incubation for the LAMP assay. Incubation for 80 min. d Incubation for the RPA assay. Incubation for 29 min; details see [164].

References

  1. Udayanga, D.; Liu, X.; Mckenzie, E.H.C.; Chukeatirote, E.; Bahkali, A.H.A.; Hyde, K.D. The genus Phomopsis: Biology, applications, species concepts and names of common phytopathogens. Fungal Divers. 2011, 50, 189–225.
  2. Gomes, R.R.; Glienke, C.; Videira, S.I.R.; Lombard, L.; Groenewald, J.Z.; Crous, P.W. Diaporthe: A genus of endophytic, saprobic and plant pathogenic fungi. Persoonia 2013, 31, 1–41.
  3. Udayanga, D.; Liu, X.; Crous, P.W.; Mckenzie, E.H.C.; Chukeatirote, E.; Hyde, K.D. A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis). Fungal Divers. 2012, 56, 157–171.
  4. Petrović, K.; Skaltsas, D.; Castlebury, L.A.; Kontz, B.; Allen, T.W.; Chilvers, M.I.; Gregory, N.; Kelly, H.M.; Koehler, A.M.; Kleczewski, N.M.; et al. Diaporthe seed decay of soybean is endemic in the United States, but new fungi are involved. Plant Dis. 2021, 105, 1621–1629.
  5. Sinclair, J.B. Phomopsis seed decay of soybeans-a prototype for studying seed disease. Plant Dis. 1993, 77, 329–334.
  6. Hosseini, B.; El-Hasan, A.; Link, T.; Voegele, R.T. Analysis of the species spectrum of the Diaporthe/Phomopsis complex in European soybean seeds. Mycol. Prog. 2020, 19, 455–469.
  7. Walcott, R.R. Detection of seedborne pathogens. HortTechnology 2003, 13, 40–47.
  8. Santos, J.M.; Vrandečić, K.; Ćosić, J.; Duvnjak, T.; Phillips, A.J.L. Resolving the Diaporthe species occurring on soybean in Croatia. Persoonia 2011, 27, 9–19.
  9. Zhang, A.W.; Hartman, G.L.; Riccioni, L.; Chen, W.D.; Ma, R.Z.; Pedersen, W.L. Using PCR to distinguish Diaporthe phaseolorum and Phomopsis longicolla from other soybean fungal pathogens and to detect them in soybean tissues. Plant Dis. 1997, 81, 1143–1149.
  10. Zhang, A.W.; Riccioni, L.; Pedersen, W.L.; Kollipara, K.P.; Hartman, G.L. Molecular identification and phylogenetic grouping of Diaporthe phaseolorum and Phomopsis longicolla isolates from soybean. Phytopathology 1998, 88, 1306–1314.
  11. van Rensburg, J.C.; Lamprecht, S.C.; Groenewald, J.Z.; Castlebury, L.A.; Crous, P.W. Characterisation of Phomopsis spp. associated with die-back of rooibos (Aspalathus linearis) in South Africa. Stud. Mycol. 2006, 55, 65–74.
  12. Santos, J.; Phillips, A. Resolving the complex of Diaporthe (Phomopsis) species occurring on Foeniculum vulgare in Portugal. Fungal Divers. 2009, 34, 111–125.
  13. Schoch, C.L.; Seifert, K.A.; Huhndorf, S.; Robert, V.; Spouge, J.L.; Levesque, C.A.; Chen, W. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc. Natl. Acad. Sci. USA 2012, 109, 6241–6246.
  14. Vechiato, M.H.; Maringoni, A.C.; Martins, E.M.F. Development of primers and method for identification and detection of Diaporthe phaseolorum var. meridionalis in soybean seeds. Summa Phytopathologica 2006, 32, 161–169.
  15. Zhang, A.W.; Hartman, G.L.; Curio-Penny, B.; Pedersen, W.L.; Becker, K.B. Molecular detection of Diaporthe phaseolorum and Phomopsis longicolla from soybean seeds. Phytopathology 1999, 89, 796–804.
  16. Hosseini, B.; Voegele, R.T.; Link, T.I. Establishment of a quadruplex real-time PCR assay to distinguish the fungal pathogens Diaporthe longicolla, D. caulivora, D. eres, and D. novem on soybean. PLoS ONE 2021, 16, e0257225.
  17. Farr, D.F.; Castlebury, L.A.; Rossman, A.Y. Morphological and molecular characterization of Phomopsis vaccinii and additional isolates of Phomopsis from blueberry and cranberry in the eastern United States. Mycologia 2002, 94, 494–504.
  18. Santos, L.; Alves, A.; Alves, R. Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe. PeerJ 2017, 5, e3120.
  19. Udayanga, D.; Castlebury, L.A.; Rossman, A.Y.; Chukeatirote, E.; Hyde, K.D. The Diaporthe sojae species complex: Phylogenetic re-assessment of pathogens associated with soybean, cucurbits and other field crops. Fungal Biol. 2015, 119, 383–407.
  20. Petrović, K.; Riccioni, L.; Vidić, M.; Đorđević, V.; Balešević-Tubić, S.; Đukić, V.; Miladinov, Z. First report of Diaporthe novem, D. foeniculina, and D. rudis associated with soybean seed decay in Serbia. Plant Dis. 2016, 100, 2324.
  21. Chaisiri, C.; Liu, X.Y.; Lin, Y.; Li, J.B.; Xiong, B.; Luo, C.X. Phylogenetic analysis and development of molecular tool for detection of Diaporthe citri causing melanose disease of citrus. Plants 2020, 9, 329.
  22. Upchurch, R.G.; Ramirez, M.E. Defense-related gene expression in soybean leaves and seeds inoculated with Cercospora kikuchii and Diaporthe phaseolorum var. meridionalis. Physiol. Mol. Plant Pathol. 2010, 75, 64–70.
  23. Mena, E.; Stewart, S.; Montesano, M.; Ponce de Leon, I. Soybean Stem Canker caused by Diaporthe caulivora; pathogen diversity, colonization process, and plant defense activation. Front. Plant Sci. 2020, 10, 1733.
  24. Fernández, F.A.; Hanlin, R.T. Morphological and RAPD analyses of Diaporthe phaseolorum from soybean. Mycologia 1996, 88, 425–440.
  25. Moleleki, N.; Preisig, O.; Wingfield, M.J.; Crous, P.W.; Wingfield, B.D. PCR-RFLP and sequence data delineate three Diaporthe species associated with stone and pome fruit trees in South Africa. Eur. J. Plant Pathol. 2002, 108, 909–912.
  26. Brumer, B.B.; Lopes-Caitar, V.S.; Chicowski, A.S.; Beloti, J.D.; Castanho, F.M.; Gregório da Silva, D.C.; de Carvalho, S.; Lopes, I.O.N.; Soares, R.M.; Seixas, C.D.S.; et al. Morphological and molecular characterization of Diaporthe (anamorph Phomopsis) complex and pathogenicity of Diaporthe aspalathi isolates causing stem canker in soybean. Eur. J. Plant Pathol. 2018, 151, 1009–1025.
  27. Boland, G.J.; Hall, R. Index of plant hosts to Sclerotinia sclerotiorum. Can. J. Plant Pathol. 1994, 16, 93–108.
  28. Grabicoski, E.M.G.; Jaccoud Filho, D.S.; Pileggi, M.; Henneberg, L.; Pierre, M.L.C.; Vrisman, C.M.; Dabul, A.N.G. Rapid PCR-based assay for Sclerotinia sclerotiorum detection on soybean seeds. Sci. Agric. 2015, 72, 69–74.
  29. Freeman, J.; Ward, E.; Calderon, C.; McCartney, A. A polymerase chain reaction (PCR) assay for the detection of inoculum of Sclerotinia sclerotiorum. Eur. J. Plant Pathol. 2002, 108, 877–886.
  30. Botelho, L.S.; Barrocas, E.N.; Machado, J.C.; Martins, R.S. Detection of Sclerotinia sclerotiorum in soybean seeds by conventional and quantitative PCR techniques. J. Seed Sci. 2015, 37, 055–062.
  31. Yin, Y.; Ding, L.; Liu, X.; Yang, J.; Ma, Z. Detection of Sclerotinia sclerotiorum in planta by a real-time PCR assay. J. Phytopathol. 2009, 157, 465–469.
  32. Kim, T.G.; Knudsen, G.R. Quantitative real-time PCR effectively detects and quantifies colonization of sclerotia of Sclerotinia sclerotiorum by Trichoderma spp. Appl. Soil Ecol. 2008, 40, 100–108.
  33. Rogers, S.L.; Atkins, S.D.; West, J.S. Detection and quantification of airborne inoculum of Sclerotinia sclerotiorum using quantitative PCR. Plant Pathol. 2009, 58, 324–331.
  34. Ziesman, B.R.; Turkington, T.K.; Basu, U.; Strelkov, S.E. A quantitative PCR system for measuring Sclerotinia sclerotiorum in canola (Brassica napus). Plant Dis. 2016, 100, 984–990.
  35. Marin-Felix, Y.; Groenewald, J.Z.; Cai, L.; Chen, Q.; Marincowitz, S.; Barnes, I.; Bensch, K.; Braun, U.; Camporesi, E.; Damm, U.; et al. Genera of phytopathogenic fungi: GOPHY 1. Stud. Mycol. 2017, 86, 99–216.
  36. Damm, U.; Sato, T.; Alizadeh, A.; Groenewald, J.Z.; Crous, P.W. The Colletotrichum dracaenophilum, C. magnum and C. orchidearum species complexes. Stud. Mycol. 2019, 92, 1–46.
  37. Jayawardena, R.S.; Hyde, K.D.; Damm, U.; Cai, L.; Liu, M.; Li, X.H.; Zhang, W.; Zhao, W.S.; Yan, J.Y. Notes on currently accepted species of Colletotrichum. Mycosphere 2016, 7, 1192–1260.
  38. Cannon, P.F.; Damm, U.; Johnston, P.R.; Weir, B.S. Colletotrichum-current status and future directions. Stud. Mycol. 2012, 73, 181–213.
  39. Dean, R.; Van Kan, J.A.; Pretorius, Z.A.; Hammond-Kosack, K.E.; Di Pietro, A.; Spanu, P.D.; Rudd, J.J.; Dickman, M.; Kahmann, R.; Ellis, J.; et al. The Top 10 fungal pathogens in molecular plant pathology. Mol. Plant Pathol. 2012, 13, 414–430.
  40. da Silva, L.L.; Moreno, H.L.A.; Correia, H.L.N.; Santana, M.F.; de Queiroz, M.V. Colletotrichum: Species complexes, lifestyle, and peculiarities of some sources of genetic variability. Appl. Microbiol. Biotechnol. 2020, 104, 1891–1904.
  41. Sharma, S.K.; Gupta, G.K.; Ramteke, R. Colletotrichum truncatum , the causal agent of anthracnose of soybean —A review. Soybean Res. 2011, 9, 31–52.
  42. Riccioni, L.; Conca, G.; Hartman, G.L. First report of Colletotrichum coccodes on soybean in the United States. Plant Dis. 1998, 82, 959.
  43. Yang, H.C.; Haudenshield, J.S.; Hartman, G.L. First report of Colletotrichum chlorophyti causing soybean anthracnose. Plant Dis. 2012, 96, 1699.
  44. Mahmodi, F.; Kadir, J.B.; Wong, M.Y.; Nasehi, A.; Puteh, A.; Soleimani, N. First report of anthracnose caused by Colletotrichum gloeosporioides on soybean (Glycine max) in Malaysia. Plant Dis. 2013, 97, 841.
  45. Yang, H.C.; Haudenshield, J.S.; Hartman, G.L. Colletotrichum incanum sp. nov., a curved-conidial species causing soybean anthracnose in USA. Mycologia 2014, 106, 32–42.
  46. Barbieri, M.C.G.; Ciampi-Guillardi, M.; Moraes, S.R.G.; Bonaldo, S.M.; Rogério, F.; Linhares, R.R.; Massola Júnior, N.S. First report of Colletotrichum cliviae causing anthracnose on soybean in Brazil. Plant Dis. 2017, 101, 1677.
  47. Boufleur, T.R.; Castro, R.R.L.; Rogério, F.; Ciampi-Guillardi, M.; Baroncelli, R.; Massola Júnior, N.S. First report of Colletotrichum musicola causing soybean anthracnose in Brazil. Plant Dis. 2020, 104, 1858.
  48. Shi, X.; Wang, S.; Duan, X.; Gao, X.; Zhu, X.; Laborda, P. First report of Colletotrichum brevisporum causing soybean anthracnose in China. Plant Dis. 2020, 105, 707.
  49. Damm, U.; Woudenberg, J.H.C.; Cannon, P.F.; Crous, P.W. Colletotrichum species with curved conidia from herbaceous hosts. Fungal Divers. 2009, 39, 45–87.
  50. Damm, U.; Cannon, P.F.; Woudenberg, J.H.C.; Crous, P.W. The Colletotrichum acutatum species complex. Stud. Mycol. 2012, 73, 37–113.
  51. Damm, U.; Cannon, P.F.; Woudenberg, J.H.C.; Johnston, P.R.; Weir, B.S.; Tan, Y.P.; Shivas, R.G.; Crous, P.W. The Colletotrichum boninense species complex. Stud. Mycol. 2012, 73, 1–36.
  52. Damm, U.; O’Connell, R.J.; Groenewald, J.Z.; Crous, P.W. The Colletotrichum destructivum species complex-hemibiotrophic pathogens of forage and field crops. Stud. Mycol. 2014, 79, 49–84.
  53. Liu, F.; Cai, L.; Crous, P.W.; Damm, U. The Colletotrichum gigasporum species complex. Persoonia 2014, 33, 83–97.
  54. Weir, B.S.; Johnston, P.R.; Damm, U. The Colletotrichum gloeosporioides species complex. Stud. Mycol. 2012, 73, 115–180.
  55. Vieira, W.A.D.S.; Bezerra, P.A.; Silva, A.C.D.; Veloso, J.S.; Câmara, M.P.S.; Doyle, V.P. Optimal markers for the identification of Colletotrichum species. Mol. Phylogen. Evol. 2020, 143, 106694.
  56. Chen, L.S.; Chu, C.; Liu, C.D.; Chen, R.S.; Tsay, J.G. PCR-based detection and differentiation of anthracnose pathogens, Colletotrichum gloeosporioides and C. truncatum, from vegetable soybean in Taiwan. J. Phytopathol. 2006, 154, 654–662.
  57. Pecchia, S.; Caggiano, B.; Da Lio, D.; Cafa, G.; Le Floch, G.; Baroncelli, R. Molecular detection of the seed-borne pathogen Colletotrichum lupini targeting the hyper-variable IGS region of the ribosomal cluster. Plants 2019, 8, 222.
  58. Ciampi-Guillardi, M.; Ramiro, J.; Moraes, M.H.D.; Barbieri, M.C.G.; Massola, N.S., Jr. Multiplex qPCR assay for direct detection and quantification of Colletotrichum truncatum, Corynespora cassiicola, and Sclerotinia sclerotiorum in soybean seeds. Plant Dis. 2020, 104, 3002–3009.
  59. Yang, H.C.; Haudenshield, J.S.; Hartman, G.L. Multiplex real-time PCR detection and differentiation of Colletotrichum species infecting soybean. Plant Dis. 2015, 99, 1559–1568.
  60. Debode, J.; Van Hemelrijck, W.; Baeyen, S.; Creemers, P.; Heungens, K.; Maes, M. Quantitative detection and monitoring of Colletotrichum acutatum in strawberry leaves using real-time PCR. Plant Pathol. 2009, 58, 504–514.
  61. Garrido, C.; Carbu, M.; Fernandez-Acero, F.J.; Boonham, N.; Colyer, A.; Cantoral, J.M.; Budge, G. Development of protocols for detection of Colletotrichum acutatum and monitoring of strawberry anthracnose using real-time PCR. Plant Pathol. 2009, 58, 43–51.
  62. Cullen, D.W.; Lees, A.K.; Toth, I.K.; Duncan, J.M. Detection of Colletotrichum coccodes from soil and potato tubers by conventional and quantitative real-time PCR. Plant Pathol. 2002, 51, 281–292.
  63. Tao, G.; Hyde, K.D.; Cai, L. Species-specific real-time PCR detection of Colletotrichum kahawae. J. Appl. Microbiol. 2013, 114, 828–835.
  64. Kuan, C.-P.; Wu, M.-T.; Huang, H.C.; Chang, H. Rapid detection of Colletotrichum lagenarium, causal agent of anthracnose of Cucurbitaceous crops, by PCR and real-time PCR. J. Phytopathol. 2011, 159, 276–282.
  65. Tian, Q.; Lu, C.; Wang, S.; Xiong, Q.; Zhang, H.; Wang, Y.; Zheng, X. Rapid diagnosis of soybean anthracnose caused by Colletotrichum truncatum using a loop-mediated isothermal amplification (LAMP) assay. Eur. J. Plant Pathol. 2017, 148, 785–793.
  66. Wang, S.; Ye, W.; Tian, Q.; Dong, S.; Zheng, X. Rapid detection of Colletotrichum gloeosporioides using a loop-mediated isothermal amplification assay. Australas. Plant Pathol. 2017, 46, 493–498.
  67. Wang, H.; Xiao, M.; Kong, F.; Chen, S.; Dou, H.-T.; Sorrell, T.; Li, R.-Y.; Xu, Y.-C. Accurate and practical identification of 20 Fusarium species by seven-locus sequence analysis and reverse line blot hybridization, and an in vitro antifungal susceptibility study. J. Clin. Microbiol. 2011, 49, 1890–1898.
  68. Munkvold, G.P. Fusarium species and their associated mycotoxins. In Mycotoxigenic Fungi, Methods and Protocols; Moretti, A., Susca, A., Eds.; Methods in Molecular Biology; Humana: New York, NY, USA, 2017; Volume 1542, pp. 51–106.
  69. Hartman, G.L.; Rupe, J.C.; Sikora, E.J.; Domier, L.L.; Davis, J.A.; Steffey, K.L. (Eds.) Compendium of Soybean Diseases and Pests, 5th ed.; APS Press: St. Paul, MN, USA, 2015.
  70. Armstrong, G.M.; Armstrong, J.K. Biological races of Fusarium causing wilt of cowpeas and soybeans. Phytopathology 1950, 40, 181–193.
  71. Nelson, B.D.; Hansen, J.M.; Windels, C.E.; Helms, T.C. Reaction of soybean cultivars to isolates of Fusarium solani from the Red River Valley. Plant Dis. 1997, 81, 664–668.
  72. Aoki, T.; O’Donnell, K.; Scandiani, M.M. Sudden death syndrome of soybean in South America is caused by four species of Fusarium: Fusarium brasiliense sp. nov., F. cuneirostrum sp. nov., F. tecumaniae, and F. virguliforme. Mycoscience 2005, 46, 162–183.
  73. Broders, K.D.; Lipps, P.E.; Paul, P.A.; Dorrance, A.E. Evaluation of Fusarium graminearum associated with corn and soybean seed and seedling disease in Ohio. Plant Dis. 2007, 91, 1155–1160.
  74. Ellis, M.L.; Diaz Arias, M.M.; Cruz Jimenez, D.R.; Munkvold, G.P.; Leandro, L.F. First report of Fusarium commune causing damping-off, seed rot, and seedling root rot on soybean (Glycine max) in the United States. Plant Dis. 2013, 97, 284.
  75. Okello, P.N.; Mathew, F.M. Cross pathogenicity studies show South Dakota isolates of Fusarium acuminatum, F. equiseti, F. graminearum, F. oxysporum, F. proliferatum, F. solani, and F. subglutinans from either soybean or corn are pathogenic to both crops. Plant Health Progress 2019, 20, 44–49.
  76. Ross, J.P. Predispositions of soybeans to Fusarium wilt by Heterodera glycines and Meloidogyne incognita. Phytopathology 1965, 55, 361–364.
  77. O’Donnell, K.; Gray, L.E. Phylogenetic relationships of the soybean sudden death syndrome pathogen Fusarium solani f. sp. phaseoli inferred from rDNA sequence data and PCR primers for its identification. Mol. Plant-Microbe Interact. 1995, 8, 709–716.
  78. Li, S.; Tam, Y.K.; Hartman, G.L. Molecular differentiation of Fusarium solani f. sp. glycines from other F. solani based on mitochondrial small subunit rDNA sequences. Phytopathology 2000, 90, 491–497.
  79. Filion, M.; St-Arnaud, M.; Jabaji-Hare, S.H. Quantification of Fusarium solani f. sp. phaseoli in mycorrhizal bean plants and surrounding mycorrhizosphere soil using real-time polymerase chain reaction and direct isolations on selective media. Phytopathology 2003, 93, 229–235.
  80. Abd-Elsalam, K.A.; Aly, I.N.; Abdel-Satar, M.A.; Khalil, M.S.; Verreet, J.A. PCR identification of Fusarium genus based on nuclear ribosomal-DNA sequence data. Afr. J. Biotechnol. 2003, 2, 82–85.
  81. Roy, K.W.; Rupe, J.C.; Hershman, D.E.; Abney, T.S. Sudden death syndrome of soybean. Plant Dis. 1997, 81, 1100–1111.
  82. Roy, K.W.; Lawrence, G.W.; Hodges, H.H.; Mclean, K.S.; Killebrew, J.F. Sudden death syndrome of soybean: Fusarium solani as incitant and relation of Heterodera glycines to disease severity. Phytopathology 1989, 79, 191–197.
  83. Rupe, J.C. Frequency and pathogenicity of Fusarium solani recovered from soybeans with sudden death syndrome. Plant Dis. 1989, 73, 581–584.
  84. Achenbach, L.A.; Patrick, J.; Gray, L. Use of RAPD markers as a diagnostic tool for the identification of Fusarium solani isolates that cause soybean sudden death syndrome. Plant Dis. 1996, 80, 1228–1232.
  85. Li, S.; Hartman, G.L. Molecular detection of Fusarium solani f. sp. glycines in soybean roots and soil. Plant Pathol. 2003, 52, 74–83.
  86. Gao, X.; Jackson, T.A.; Lambert, K.N.; Li, S.; Hartman, G.L.; Niblack, T.L. Detection and quantification of Fusarium solani f. sp. glycines in soybean roots with real-time quantitative polymerase chain reaction. Plant Dis. 2004, 88, 1372–1380.
  87. Li, S.; Hartman, G.L.; Domier, L.L. Quantification of Fusarium solani f. sp. glycines isolates in soybean roots by colony-forming unit assays and real-time quantitative PCR. Theor. Appl. Genet. 2008, 117, 343–352.
  88. Aoki, T.; O’Donnell, K.; Homma, Y.; Lattanzi, A. Sudden-death syndrome of soybean is caused by two morphologically and phylogenetically distinct species within the Fusarium solani species complex F. virguliforme in North America and F. tucumaniae in South America. Mycologia 2003, 95, 660.
  89. O’Donnell, K.; Sink, S.; Scandiani, M.M.; Luque, A.; Colletto, A.; Biasoli, M.; Lenzi, L.; Salas, G.; Gonzalez, V.; Ploper, L.D.; et al. Soybean sudden death syndrome species diversity within North and South America revealed by multilocus genotyping. Phytopathology 2010, 100, 58–71.
  90. Westphal, A.; Li, C.; Xing, L.; McKay, A.; Malvick, D. Contributions of Fusarium virguliforme and Heterodera glycines to the disease complex of sudden death syndrome of soybean. PLoS ONE 2014, 9, e99529.
  91. Mbofung, G.C.Y.; Fessehaie, A.; Bhattacharyya, M.K.; Leandro, L.F.S. A new TaqMan real-time polymerase chain reaction assay for quantification of Fusarium virguliforme in soil. Plant Dis. 2011, 95, 1420–1426.
  92. Wang, J.; Jacobs, J.L.; Byrne, J.M.; Chilvers, M.I. Improved diagnoses and quantification of Fusarium virguliforme, causal agent of soybean sudden death syndrome. Phytopathology 2015, 105, 378–387.
  93. Roth, M.G.; Oudman, K.A.; Griffin, A.; Jacobs, J.L.; Sang, H.; Chilvers, M.I. Diagnostic qPCR assay to detect Fusarium brasiliense, a causal agent of soybean sudden death syndrome and root rot of dry bean. Plant Dis. 2020, 104, 246–254.
  94. Rocha, L.F.; Srour, A.Y.; Pimentel, M.; Subedi, A.; Bond, J.P.; Fakhoury, A.; Ammar, H.A. A panel of qPCR assays to detect and quantify soybean soil-borne pathogens. Lett. Appl. Microbiol. 2022, 76, ovac023.
  95. Orth, C.E.; Schuh, W. Resistance of 17 soybean cultivars to foliar, latent, and seed infection by Cercospora kikuchii. Plant Dis. 1994, 78, 661–664.
  96. Hartman, G.L.; Sinclair, J.B.; Rupe, J.C. Compendium of Soybean Diseases, 4th ed.; APS Press: St. Paul, MN, USA, 1999.
  97. Matsumoto, T.; Tomoyasu, R. Studies on the purple speck of soybean seed. Ann. Phytopathol. Soc. Jpn. 1925, 1, 1–14.
  98. Walters, H.J. Soybean leaf blight caused by Cercospora kikuchii. Plant Dis. 1980, 64, 961–962.
  99. Ehrenshaft, M.; Upchurch, R.G. Host protein(s) induces accumulation of the toxin cercosporin and mRNA in a phytopahtogenic strain of Cercospora kikuchii. Physiol. Mol. Plant Pathol. 1993, 43, 95–107.
  100. Daub, M.E.; Ehrenshaft, M. The photoactivated Cercospora toxin cercosporin: Contributions to plant disease and fundamental biology. Annu. Rev. Phytopathol. 2000, 38, 461–490.
  101. Callahan, T.M.; Rose, M.S.; Meade, M.J.; Ehrenshaft, M.; Upchurch, R.G. CFP, the putative cercosporin transporter of Cercospora kikuchii, is required for wild type cercosporin production, resistance, and virulence on soybean. Mol. Plant-Microbe Interact. 1999, 12, 901–910.
  102. Soares, A.P.G.; Guillin, E.A.; Borges, L.L.; da Silva, A.C.T.; de Almeida, Á.M.R.; Grijalba, P.E.; Gottlieb, A.M.; Bluhm, B.H.; de Oliveira, L.O. More Cercospora species infect soybeans across the Americas than meets the eye. PLoS ONE 2015, 10, e0133495.
  103. Davidson, R.M.; Hanson, L.E.; Franc, G.D.; Panella, L. Analysis of β-tubulin gene fragments from benzimidazole-sensitive and -tolerant Cercospora beticola. J. Phytopathol. 2006, 154, 321–328.
  104. Imazaki, I.; Ishikawa, K.; Yasuda, N.; Miyasaka, A.; Kawasaki, S.; Koizumi, S. Incidence of thiophanate-methyl resistance in Cercospora kikuchii within a single lineage based on amplified fragment length polymorphisms in Japan. J. Gen. Plant Pathol. 2006, 72, 77–84.
  105. Imazaki, I.; Iizumi, H.; Ishikawa, K.; Sasahara, M.; Yasuda, N.; Koizumi, S. Effects of thiophanate-methyl and azoxystrobin on the composition of Cercospora kikuchii populations with thiophanate-methyl-resistant strains. J. Gen. Plant Pathol. 2006, 72, 292–300.
  106. Groenewald, J.Z.; Nakashima, C.; Nishikawa, J.; Shin, H.D.; Park, J.H.; Jama, A.N.; Groenewald, M.; Braun, U.; Crous, P.W. Species concepts in Cercospora: Spotting the weeds among the roses. Stud. Mycol. 2012, 75, 115–170.
  107. Chen, H.; Lee, M.H.; Daub, M.E.; Chung, K.R. Molecular analysis of the cercosporin biosynthetic gene cluster in Cercospora nicotianae. Mol. Microbiol. 2007, 64, 755–770.
  108. Chanda, A.K.; Ward, N.A.; Robertson, C.L.; Chen, Z.-Y.; Schneider, R.W. Development of a quantitative polymerase chain reaction detection protocol for Cercospora kikuchii in soybean leaves and its use for documenting latent infection as affected by fungicide applications. Phytopathology 2014, 104, 1118–1124.
  109. MacNeill, B.H.; Zalasky, H. Histological study of host–parasite relationships between Septoria glycines Hemmi and soybean leaves and pods. Can. J. Bot. 1957, 35, 501–505.
  110. Williams, R.F.; Nyvall, D.J. Leaf infection and yield losses caused by brown spot and bacterial blight diseases of soybean. Phytopathology 1980, 70, 900–902.
  111. Basu, P.K.; Butler, G. Assessment of brown spot (Septoria glycines) alone and in combination with bacterial blight (Pseudomonas syringae pv. glycines) on soybeans in a short-season area. Can. J. Plant Pathol. 1988, 10, 78–82.
  112. Carmona, M.; Sautua, F.; Perelman, S.; Reis, E.M.; Gally, M. Relationship between late soybean diseases complex and rain in determining grain yield responses to fungicide applications. J. Phytopathol. 2011, 159, 687–693.
  113. Lin, H.-A.; Mideros, S.X. Accurate quantification and detection of Septoria glycines in soybean using quantitative PCR. Curr. Plant Biol. 2021, 25, 100192.
  114. Kunwar, I.K.; Singh, T.; Machado, C.C.; Sinclair, J.B. Histopathology of soybean seed and seedling infection by Macrophomina phaseolina. Phytopathology 1986, 76, 532–535.
  115. Raut, J.G. Transmission of seed borne Macrophomina phaseolina in seed. Sci. Technol. 1983, 11, 807–817.
  116. Jana, T.K.; Singh, N.K.; Koundal, K.R.; Sharma, T.R. Genetic differentiation of charcoal rot pathogen, Macrophomina phaseolina, in to specific groups using URP-PCR. Can. J. Microbiol./Rev. Can. Microbiol. 2005, 51, 159–164.
  117. Sarr, M.P.; Ndiaye, M.; Groenewald, J.Z.; Crous, P.W. Genetic diversity in Macrophomina phaseolina, the causal agent of charcoal rot. Phytopathol. Mediterr. 2014, 53, 250–268.
  118. Khan, A.N.; Shair, F.; Malik, K.; Hayat, Z.; Khan, M.A.; Hafeez, F.Y.; Hassan, M. Molecular identification and genetic characterization of Macrophomina phaseolina strains causing pathogenicity on sunflower and chickpea. Front. Microbiol. 2017, 8, 1309.
  119. Tančić Živanov, S.; Dedić, B.; Dimitrijević, A.; Dušanić, N.; Jocić, S.; Miklič, V.; Kovačević, B.; Miladinović, D. Analysis of genetic diversity among Macrophomina phaseolina (Tassi) Goid. isolates from Euro-Asian countries. J. Plant Dis. Prot. 2019, 126, 565–573.
  120. Babu, B.K.; Saxena, A.K.; Srivastava, A.K.; Arora, D.K. Identification and detection of Macrophomina phaseolina by using species-specific oligonucleotide primers and probe. Mycol. Helv. 2007, 99, 797–803.
  121. Babu, B.K.; Mesapogu, S.; Sharma, A.; Somasani, S.R.; Arora, D.K. Quantitative real-time PCR assay for rapid detection of plant and human pathogenic Macrophomina phaseolina from field and environmental samples. Mycologia 2011, 103, 466–473.
  122. Lu, C.; Song, B.; Zhang, H.; Wang, Y.; Zheng, X. Rapid diagnosis of soybean seedling blight caused by Rhizoctonia solani and soybean charcoal rot caused by Macrophomina phaseolina using LAMP assays. Phytopathology 2015, 105, 1612–1617.
  123. Gray, L.E. Variation in pathogenicity of Cephalosporium gregatum isolates. Phytopathology 1971, 61, 1410–1411.
  124. Hughes, T.J.; Chen, W.; Grau, C.R. Pathogenic characterization of genotype A and B of Phialophora gregata f. sp. sojae. Plant Dis. 2002, 86, 729–735.
  125. Harrington, T.C.; Steimel, J.; Workneh, F.; Yang, X.B. Characterization and distribution of two races of Phialophora gregata in the North-Central United States. Phytopathology 2003, 93, 901–912.
  126. Chen, W.; Grau, C.R.; Adee, E.A.; Meng, X.-Q. A molecular marker identifying subspecific population of the soybean brown stem rot pathogen, Phialophora gregata. Phytopathology 2000, 90, 875–883.
  127. Malvick, D.K.; Chen, W.; Kurle, J.E.; Grau, C.R. Cultivar preference and genotype distribution of the brown stem rot pathogen Phialophora gregata in the Midwestern United States. Plant Dis. 2003, 87, 1250–1254.
  128. Meng, X.-Q.; Grau, C.R.; Chen, W. Cultivar preference exhibited by two sympatric and genetically distinct populations of the soybean fungal pathogen Phialophora gregata f. sp. sojae. Plant Pathol. 2005, 54, 180–188.
  129. Chen, W.; Gray, L.E.; Grau, C.R. Molecular differentiation of fungi associated with brown stem rot and detection of Phialophora gregata in resistant and susceptible soybean cultivars. Phytopathology 1996, 86, 1140–1148.
  130. Chen, W.; Gray, L.E.; Kurle, J.E.; Grau, C.R. Specific detection of Phialophora gregata and Plectosporium tabacinum in infected soybean plants using polymerase chain reaction. Mol. Ecol. Notes 1999, 8, 871–877.
  131. Malvick, D.K.; Impullitti, A.E. Detection and quantification of Phialophora gregata in soybean and soil samples with a quantitative, real-time PCR assay. Plant Dis. 2007, 91, 736–742.
  132. Hughes, T.J.; Atallah, Z.K.; Grau, C.R. Real-time PCR assays for the quantification of Phialophora gregata f. sp. sojae IGS genotypes A and B. Phytopathology 2009, 99, 1008–1014.
  133. Parmeter, J.R.; Sherwood, R.T.; Pratt, W.D. Anastomosis grouping among isolates of Thanatephorus cucumeris. Phytopathology 1969, 59, 1270–1278.
  134. Adams, G.C., Jr.; Butler, E.E. Serological relationships among anastomosis groups of Rhizoctonia solani. Phytopathology 1979, 69, 629–633.
  135. Sneh, B. Anastomosis groups of multinucleate Rhizoctonia spp. In Rhizoctonia Species: Taxonomy, Molecular Biology, Ecology, Pathology and Disease Control; Sneh, B., Jabaji-Hare, S., Neate, S., Dijst, G., Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 1996; pp. 67–75.
  136. Carling, D.E.; Pope, E.J.; Brainard, K.A.; Carter, D.A. Characterization of mycorrhizal isolates of Rhizoctonia solani from an orchid, including AG-12, a new anastomosis group. Phytopathology 1999, 89, 942–946.
  137. Carling, D.E.; Baird, R.E.; Gitaitis, R.D.; Brainard, K.A.; Kuninaga, S. Characterization of AG-13, a newly reported anastomosis group of Rhizoctonia solani. Phytopathology 2002, 92, 893–899.
  138. Campion, C.; Chatot, C.; Perraton, B.; Andrivon, D. Anastomosis groups, pathogenicity and sensitivity to fungicides of Rhizoctonia solani isolates collected on potato crops in France. Eur. J. Plant Pathol. 2003, 109, 983–992.
  139. Matsumoto, M. Trials of direct detection and identification of Rhizoctonia solani AG 1 and AG 2 subgroups using specifically primed PCR analysis. Mycoscience 2002, 43, 185–189.
  140. Grosch, R.; Schneider, J.H.M.; Peth, A.; Waschke, A.; Franken, P.; Kofoet, A.; Jabaji-Hare, S.H. Development of a specific PCR assay for the detection of Rhizoctonia solani AG 1-IB using SCAR primers. J. Appl. Microbiol. 2007, 102, 806–819.
  141. Sayler, R.J.; Yang, Y. Detection and quantification of Rhizoctonia solani AG-1 IA, the rice sheath blight pathogen, in rice using real-time PCR. Plant Dis. 2007, 91, 1663–1668.
  142. Budge, G.E.; Shaw, M.W.; Colyer, A.; Pietravalle, S.; Boonham, N. Molecular tools to investigate Rhizoctonia solani distribution in soil. Plant Pathol. 2009, 58, 1071–1080.
  143. Ono, Y.; Buritica, P.; Hennen, J.F. Delimitation of Phakopsora, Physopella, and Cerotelium and their species on Leguminosae. Mycol. Res. 1992, 96, 825–850.
  144. Goellner, K.; Loehrer, M.; Langenbach, C.; Conrath, U.; Koch, E.; Schaffrath, U. Phakopsora pachyrhizi, the causal agent of Asian soybean rust. Mol. Plant Pathol. 2010, 11, 169–177.
  145. Frederick, R.D.; Snyder, C.L.; Peterson, G.L.; Bonde, M.R. Polymerase chain reaction assays for the detection and discrimination of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae. Phytopathology 2002, 92, 217–222.
  146. Barnes, C.W.; Szabo, L.J. Detection and identification of four common rust pathogens of cereals and grasses using real-time polymerase chain reaction. Phytopathology 2007, 97, 717–727.
  147. Barnes, C.W.; Szabo, L.J.; Bowersox, V.C. Identifying and quantifying Phakopsora pachyrhizi spores in rain. Phytopathology 2009, 99, 328–338.
  148. Dorrance, A.E. Phytophthora root and stem rot. In Compendium of Soybean Diseases and Pests; Hartman, G.L., Rupe, J.C., Sikora, E.J., Domier, L.L., David, J.A., Steffey, K.L., Eds.; APS Press: St. Paul, MN, USA, 2015; pp. 73–76.
  149. Jones, J.P.; Johnson, H.W. Lupine, a new host for Phytophthora megasperma var. sojae. Phytopathology 1969, 59, 504–507.
  150. Hamm, P.B.; Hansen, E.M. Host specificity of Phytophthora megasperma from Douglas fir, soybean, and alfalfa. Phytopathology 1981, 71, 65–68.
  151. Reeser, P.W.; Scott, D.H.; Ruhl, G.E. Recovery of race non-classifiable Phytophthora megasperma f. sp. glycinea from soybean roots in Indiana in 1990. Phytopathology 1991, 81, 1201.
  152. Malvick, D.K.; Grunden, E. Traits of soybean-infecting Phytophthora populations from Illinois agricultural fields. Plant Dis. 2004, 88, 1139–1145.
  153. Tang, Q.H.; Gao, F.; Li, G.Y.; Wang, H.; Zheng, X.B.; Wang, Y.C. First report of root rot caused by Phytophthora sansomeana on soybean in China. Plant Dis. 2010, 94, 378.
  154. Zelaya-Molina, L.X.; Ellis, M.L.; Berry, S.A.; Dorrance, A.E. First report of Phytophthora sansomeana causing wilting and stunting on corn in Ohio. Plant Dis. 2010, 94, 125.
  155. Wang, Y.; Zhang, W.; Wang, Y.; Zheng, X. Rapid and sensitive detection of Phytophthora sojae in soil and infected soybeans by species-specific polymerase chain reaction assays. Phytopathology 2006, 96, 1315–1321.
  156. Bienapfl, J.C.; Percich, J.A.; Malvick, D.K. Evaluation of PCR-based methods for species specific detection of Phytophthora sojae. Phytopathology 2007, 98, S201.
  157. Bienapfl, J.C.; Malvick, D.K.; Percich, J.A. Specific molecular detection of Phytophthora sojae using conventional and real-time PCR. Fungal Biol. 2011, 115, 733–740.
  158. Catal, M.; Erler, F.; Fulbright, D.W.; Adams, G.C. Real-time quantitative PCR assays for evaluation of soybean varieties for resistance to the stem and root rot pathogen Phytophthora sojae. Eur. J. Plant Pathol. 2013, 137, 859–869.
  159. Zhao, W.; Wang, T.; Qi, R. Ypt1 gene-based detection of Phytophthora sojae in a loop-mediated isothermal amplification assay. J. Plant Dis. Prot. 2015, 122, 66–73.
  160. Dai, T.-T.; Lu, C.-C.; Lu, J.; Dong, S.; Ye, W.; Wang, Y.; Zheng, X. Development of a loop-mediated isothermal amplification assay for detection of Phytophthora sojae. FEMS Microbiol. Lett. 2012, 334, 27–34.
  161. Bilodeau, G.J.; Martin, F.N.; Coffey, M.D.; Blomquist, C.L. Development of a multiplex assay for genus- and species-specific detection of Phytophthora based on differences in mitochondrial gene order. Phytopathology 2014, 104, 733–748.
  162. Miles, T.D.; Martin, F.N.; Robideau, G.P.; Bilodeau, G.J.; Coffey, M.D. Systematic development of Phytophthora species-specific mitochondrial diagnostic markers for economically important members of the genus. Plant Dis. 2017, 101, 1162–1170.
  163. Miles, T.D.; Martin, F.N.; Coffey, M.D. Development of rapid isothermal amplification assays for detection of Phytophthora spp. in plant tissue. Phytopathology 2015, 105, 265–278.
  164. Rojas, J.A.; Miles, T.D.; Coffey, M.D.; Martin, F.N.; Chilvers, M.I. Development and application of qPCR and RPA genus- and species-specific detection of Phytophthora sojae and P. sansomeana root rot pathogens of soybean. Plant Dis. 2017, 101, 1171–1181.
  165. Song, J.; Jeon, N.; Li, S.; Kim, H.; Hartman, G.L. Development of PCR assay using species-specific primers for Phytophthora sojae based on the DNA sequence of its transposable element. Phytopathology 2007, 97, S110.
  166. Haudenshield, J.S.; Song, J.Y.; Hartman, G.L. A novel, multiplexed, probe-based quantitative PCR assay for the soybean root- and stem-rot pathogen, Phytophthora sojae, utilizes its transposable element. PLoS ONE 2017, 12, e0176567.
  167. Judelson, H.S. Sequence variation and genomic amplification of a family of Gypsy-like elements in the Oomycete genus Phytophthora. Mol. Biol. Evol. 2002, 19, 1313–1322.
  168. Jiang, Y.N.; Haudenshield, J.S.; Hartman, G.L. Characterization of Pythium spp. from soil samples in Illinois. Can. J. Plant Pathol. 2012, 34, 448–454.
  169. Pimentel, M.F.; Arnao, E.; Warner, A.J.; Rocha, L.F.; Subedi, A.; Elsharif, N.; Chilvers, M.I.; Matthiesen, R.; Robertson, A.E.; Bradley, C.A.; et al. Reduction of Pythium damping-off in soybean by biocontrol seed treatment. Plant Dis. 2022, 106, 2403–2414.
  170. Kageyama, K.; Ohyama, A.; Hyakumachi, M. Detection of Pythium ultimum using polymerase chain reaction with species-specific primers. Plant Dis. 1997, 81, 1155–1160.
  171. Wang, P.H.; Wang, Y.T.; White, J.G. Species-specific PCR primers for Pythium developed from ribosomal ITS1 region. Lett. Appl. Microbiol. 2003, 37, 127–132.
  172. Asano, T.; Senda, M.; Suga, H.; Kageyama, K. Development of multiplex PCR to detect five Pythium species related to turfgrass diseases. J. Phytopathol. 2010, 158, 609–615.
  173. Shen, D.; Li, Q.; Yu, J.; Zhao, Y.; Zhu, Y.; Xu, H.; Dou, D. Development of a loop-mediated isothermal amplification method for the rapid detection of Pythium ultimum. Australas. Plant Pathol. 2017, 46, 571–576.
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