Genetic diversity of root-knot nematodes from Brazil and development of SCAR markers specific for the coffee-damaging species

Optimization and utilization of emerging waste (fly ash) for growth performance of chickpea (Cicer arietinum L.) plant and mitigation of root-knot nematode (Meloidogyne incognita) stress

The sustainable management of large amounts of fly ash (FA) is a concern for researchers, and we aim to determine the FA application in plant development and nematicidal activity in the current study. A pot study is therefore performed to assess the effects of adding different, FA-concentrations to soil (w/w) on the infection of chickpea plants with the root-knot nematode Meloidogyne incognita. Sequence characteristic amplified region (SCAR) and internal transcribed spacer (ITS) region-based-markers were used to molecularly confirm M. incognita. With better plant growth and chickpea yield performance, FA enhanced the nutritious components of the soil. When compared with untreated, uninoculated control (UUC) plants, the inoculation of M. incognita dramatically reduced chickpea plant growth, yield biomass, and metabolism. The findings showed that the potential of FA to lessen the root-knot nematode illness in respect of galls, egg-masses, and reproductive attributes may be used to explain the mitigating effect of FA. Fascinatingly, compared with the untreated, inoculated control (UIC) plants, the FA treatment, primarily at 20%, considerably (p ≤ 0.05) boosted plant growth, yield biomass, and pigment content. Additionally, when the amounts of FA rose, the activity of antioxidants like superoxide dismutase-SOD, catalase-CAT, and peroxidase-POX as well as osmo-protectants like proline gradually increased. Therefore, our findings imply that 20% FA can be successfully applied as a potential strategy to increase biomass yield and plant growth while simultaneously reducing M. incognita infection in chickpea plants.

Parasitism of Hirsutella rhossiliensis on Different Nematodes and Its Endophytism Promoting Plant Growth and Resistance against Root-Knot Nematodes

The endoparasitic fungus Hirsutella rhossiliensis is an important biocontrol agent of cyst nematodes in nature. To determine the potential parasitism of the fungus on a non-natural host, the pinewood nematode (Bursaphelenchus xylophilus) living in pine trees and the endophytic ability of the fungus on plants, in this paper, we first constructed and utilized a green fluorescent protein (GFP)-tagged H. rhossiliensis HR02 transformant to observe the fungal infection process on B. xylophilus and its colonization on Arabidopsis roots. Then, we compared the fungal parasitism on three species of nematodes with different lifestyles, and we found that the fungal parasitism is correlated with nematode species and stages. The parasitic effect of H. rhossiliensis on adults of B. xylophilus is similar to that on second-stage juveniles (J2) of the root-knot nematode Meloidogyne incognita after 24 h of inoculation, although the virulence of the fungus to second-stage juveniles of M. incognita is stronger than that to those of B. xylophilus and Caenorhabditis elegans. Moreover, the endophytism of H. rhossiliensis was confirmed. By applying an appropriate concentration of H. rhossiliensis conidial suspension (5 × 106 spores/mL) in rhizosphere soil, it was found that the endophytic fungus can promote A. thaliana growth and reproduction, as well as improve host resistance against M. incognita. Our results provide a deeper understanding of the fungus H. rhossiliensis as a promising biocontrol agent against plant-parasitic nematodes.

Molecular Techniques for Root-Knot Nematode Identification

Among plant-parasitic nematodes, root-knot nematodes (RKN), Meloidogyne spp., are the most important parasite infecting economically important crops globally and causing severe losses in crop production. The use of efficient nematode control methods against these parasites depends upon their correct detection in roots and soil samples. Currently, the use of integrated identification methods, including biochemical, molecular, and morphological-based characters, is preferred. But the techniques using morphology and phylogenetic analysis are time-consuming and not suitable for routine analysis. They have only been used for studies of cryptic species, which were identified using integrative taxonomy. Here we describe the enzymatic and molecular-based methods that have successfully been used in Brazil for more than 25 years in the Nematology Lab at Embrapa Genetic Resources and Biotechnology for routine analysis. This technique is a combination of isozyme esterase profiling and molecular markers, with the aim of having a rapid and correct diagnosis of Meloidogyne spp. populations from field and greenhouse.

Identification, Diversity, and Distribution of Meloidogyne spp. in Vegetable Fields of South Georgia, U.S.A

Root-knot nematode (RKN; Meloidogyne spp.) is the most prevalent plant-parasitic nematode in vegetable fields of Georgia, with an incidence of 67.3%. Because aggressive RKN species are reported in the southeastern United States, molecular-based identification of RKN species was conducted on soil samples taken from a nematode surveillance study in 2018 from 292 RKN-infested vegetable fields in southern Georgia. The RKN-infested soil was potted with tomato cultivar Rutgers, and individual nematode females were isolated from galled roots and subjected to species-specific PCR and mitochondrial haplotype-based RKN species identification. The incidence (%), mean, and maximum relative abundance (second-stage juveniles per 100 cm3 of soil) of the five RKN species identified consisted of M. incognita (91.9, 486, 14,144), M. arenaria (36.0, 707, 14,144), M. floridensis (2.2, 909, 5,264), M. javanica (5.5, 352, 1,488), and M. haplanaria (0.7, 8, 14). A large proportion of fields (29%) had mixed populations of M. incognita and M. arenaria, which may reflect the region's long history of cotton and peanut cultivation. For unknown reasons, mixed populations of M. incognita and M. arenaria were associated with higher population densities. M. incognita is the most important RKN species in vegetable fields, followed by M. arenaria; therefore, pure or mixed populations of these species should be addressed in nematode management programs. Although at a lower incidence, the newly detected species, M. floridensis and M. haplanaria, have the potential to become a major threat since they reproduce on vegetables with Mi-resistant genes.

First Report of Meloidogyne arenaria Infecting Maize in Guizhou Province of China

Maize (Zea mays L.) as the most important crops is globally cultivated for food, feedstuff and industrial raw materials. During August to September 2021, we carried out a survey on the soil-borne diseases of tobacco in Guizhou Province. Poorly developed maize plants were observed in the same field of root-knot nematode (RKN) infected tobacco (Nicotiana tabacum L.) in Dafang County, Bijie City (106º00'08"E, 22º24'81"N) (Figure 1A). Roots of maize plant were taken back to laboratory for nematode identification and infecting confirmation in greenhouse. Females, males, second-stage juveniles (J2s) and eggs were collected from the sampling roots and nematodes were identified based on morphological and molecular characteristics. The identification of the nematode was performed by observations of morphological characters of adults (n= 30) and molecular analysis. Perineal pattern of female showed distinct characteristics of a low dorsal arch and lateral field marked by forked and broken striae and without punctate markings between the anus and tail terminus (Fig. 1B). J2s hatched from eggs demonstrated the morphometric characters of body length = 433.25 µm, body width = 16.31 µm, stylet length = 10.43 µm. DGO = 3.62 μm, tail length = 52.78 μm, and hyaline tail terminus = 11.14 μm (Fig. 1C). For molecular analysis, females from infected roots of maize in fields and in Koch's postulate experiment were definitively identified via PCR using the M. arenaria species-specific markers (Far/Rar：TCGGCGATAGAGGTAAATGAC/TCGGCGATAGACACTACAACT). PCR products of females amplification were run in the agar gel, and a PCR product of 420 bp band was identified for M. arenaria for all tested female samples (Fig. 1E). The obtained specific fragment was sequenced and submitted to GenBank with accession number of OP503512. A 100% identity of the Fare/Rare sequence with M. arenaria (Accession: GQ395518.1, J. Phytopathol. 160(2): 59-66, 2012, MZ555757.1，MZ555753.1, U42342.1）were found through NCBI blast. Therefore, based on morphological and molecular analysis, the nematodes from maize were determined to be M. arenaria according to the related description of (Perry et al., 2009). Koch's postulate was conducted in greenhouse by inoculation of J2 from the original population to pots containing two-week old maize seedlings (n= 15, 1000 J2/seedling) and 5 seedlings were nonincubated as controls. Plants were maintained in greenhouse at 26 to 28°C. On day 50 after inoculation, all the inoculated plants showed typical RKN symptoms such as stunting and galled roots which were similar to those observed in the field (Fig. 2A). Females, J2 and eggs were found in the roots after staining(Fig. 2B, C, D) by the method of Bybd et al. (1983), while uninoculated control plants presented normal development, confirming that Maize was a host of M. arenaria. M. arenaria is one of the most damaging plant-parasitic nematodes, which can infect many crops worldwide, resulting in great losses on the crop quality and yield. The Southern Root-Knot Nematode (M. incognita) had been known to cause root-knot nematode disease on maize in Shandong Province of China(Shi et al.,2020). As a major rotation crop, maize was recommended for the management of RKNs and most soil-born pathogens in tobacco planting systems in China. However, the findings of M. arenaria on maize demonstrates that further investigation and management strategies should be conduct. To our knowledge, this is the first report of M. arenaria parasitizing maize in Guizhou province of China.

First Record of Meloidogyne incognita on Maize (Zea mays) in Shaanxi Province of China

Meloidogyne incognita can severely infect and harm some crops in temperate zones under open field in some cases, even though it's more widespread and economically important in tropical and subtropical regions (Eisenback, 2020). In early June 2022, patches with poor growth maize plants were observed in Dali County (109.93E, 34.80N) of Shaanxi province, China. The infected maize plants were stunted with galled and small roots. Females, males, second-stage juveniles (J2s) and egg masses were extracted and collected from galled roots and soil for morphological identification. The perineal pattern of females had a dorsally high square arch lacking obvious lateral lines. Stylet knobs of females were rounded and set off. The excretory pores were at level of or posterior to stylet knobs, 10-20 annules behind head. The head cap of males was flat to centrally concave, the stylet shaft constricted slightly at the junction with the knobs, and stylet knobs were broadly elongate to round, set off, flat and the width usually greater than the height. Measurements of females (n=20) were: body length (L)= 734.63 ± 79.24 µm (642.15 µm to 788.48 µm); maximum body width (W)= 487.14 ± 50.79 µm (426.09 µm to 556.42 µm); stylet length (ST)= 14.78 ± 1.57 µm (13.17 µm to 16.56 µm); and distance from dorsal esophageal gland opening to the stylet knobs (DGO)= 3.55 ± 0.13 µm (3.17 µm to 3.90 µm). Measurements of males (n=10) were: L=1483.76 ± 134.81 µm (1174.39 µm to 1635.62 µm); W=44.37 ± 3.28 µm (39.76 µm to 50.26 µm); ST= 19.76 ± 1.05 µm (17.84 µm to 22.36 µm); and DGO= 3.48 ± 0.28 µm (3.08 µm to 3.87 µm). The morphological characteristics of this nematode were consistent with Meloidogyne incognita (Kofoid and White, 1919) Chitwood, 1949 (Williams, 1973; Eisenback and Hirschmann, 1981). Moreover, the identification was further confirmed by PCR using two pairs of primers, D2A/D3B and NAD5F/R, with DNA extracted from 20 individual females, respectively (Subbotin et al., 2006; Janssen et al., 2016). Both the D2-D3 region sequence (MZ665547) amplified by D2A/D3B and the 597 bp sequence (MZ665548) amplified by NAD5F/R showed >99% identity with sequences of other M. incognita isolates. Both morphological and molecular data identified the root-knot nematodes on maize as M. incognita. Then ten maize seedlings maintained in pots containing autoclaved sandy soil at 25°C were each inoculated with 2000 freshly hatched J2s of the original population of M. incognita. At 45 days after inoculation, all inoculated plants developed gall symptoms on the roots similar to those in the field. And five non-inoculated maize seedlings showed no symptoms. Females dissected from inoculated plants were identified to be M. incognita with species-specific primers IncK-14F/IncK-14R (Randig et al., 2002). According to consultation, in the same field root-knot nematode infected carrots were harvested in November last year, the field was left unploughed until March when maize was sowed. As Dali County locates in north temperate zone with a warm temperate climate, where the average annual temperature is 14.4°C, and the highest and lowest temperature was 18°C and -9°C in last winter, the overwintering rate of M. incognita in open field in such area needs further study.

A novel soybean hairy root system for gene functional validation

Agrobacterium rhizogenes-mediated transformation has long been explored as a versatile and reliable method for gene function validation in many plant species, including soybean (Glycine max). Likewise, detached-leaf assays have been widely used for rapid and mass screening of soybean genotypes for disease resistance. The present study combines these two methods to establish an efficient and practical system to generate transgenic soybean hairy roots from detached leaves and their subsequent culture under ex vitro conditions. We demonstrated that hairy roots derived from leaves of two (tropical and temperate) soybean cultivars could be successfully infected by economically important species of root-knot nematodes (Meloidogyne incognita and M. javanica). The established detached-leaf method was further explored for functional validation of two candidate genes encoding for cell wall modifying proteins (CWMPs) to promote resistance against M. incognita through distinct biotechnological strategies: the overexpression of a wild Arachis α-expansin transgene (AdEXPA24) and the dsRNA-mediated silencing of an endogenous soybean polygalacturonase gene (GmPG). AdEXPA24 overexpression in hairy roots of RKN-susceptible soybean cultivar significantly reduced nematode infection by approximately 47%, whereas GmPG downregulation caused an average decrease of 37%. This novel system of hairy root induction from detached leaves showed to be an efficient, practical, fast, and low-cost method suitable for high throughput in root analysis of candidate genes in soybean.

First report of the root-knot nematode Meloidogyne incognita on Salvia miltiorrhiza Bunge in Henan Province, China

Salvia miltiorrhiza Bunge is an important Chinese herbal medicine, mainly used to treat cardiovascular disease. At present, the planting area of S. miltiorrhiza is near 20,000 hectares in China, mainly in Shandong, Henan, Shanxi, Shaanxi and Sichuan provinces. Root-knot nematode (Meloidogyne spp.) is one of the most devastating pathogens on S. miltiorrhiza. In November 2020, we observed that some S. miltiorrhiza plants grew poorly with smaller, fewer and chlorotic leaves and even necrosis on some middle and lower ones in a Chinese herbal medicine planting base (34° 4' 11.52'' N; 113° 25' 51.40'' E) in Yuzhou City, Henan Province, China. Furthermore, the galls and egg masses were visible on the roots of S. miltiorrhiza, which were the typical symptoms caused by root-knot nematodes. Ten samples of galled roots and rhizosphere soils were collected, bagged and taken to the lab for tests. Females and J2s were extracted from these samples. White, pear-shaped females were observed in the roots, and the average number of second-stage juveniles (J2s) was 121.5 ± 10.8 per 100 ml of soil. The perineal patterns of females showed a high dorsal arch, which was either square or trapezoid with either smooth or wavy striae and without obvious lateral lines. The main morphometrics of females (n=20, mean ± SE; range) were as follows: body length (L)  = 609.0  ±  62.5 μm (492.4 to 716.4 μm); maximum body width (W) = 377.0  ±  28.6 μm (329.7 to 436.1 μm); stylet length  =  17.0  ±  1.8 μm (14.2 to 20.5 μm); and distance from dorsal esophageal gland orifice to stylet knobs (DGO) =  3.3  ±  0.3 μm (2.8 to 3.9 μm). The J2s were in vermiform, and stylet knobs were prominent and rounded. The tail of J2s possessed a transparent area with an obtuse tip. J2s (n  =  20) were measured (mean ± SD; range) as follows: L  =  401.2  ±  29.3 μm (358.2 to 456.1 μm); W = 14.1 ± 1.1 µm (12.5 to 16.0 µm); L/W  = 28.6  ±  1.0 (26.7 to 30.4); stylet length =  10.3  ±  0.6 μm (9.1 to 11.2 μm); DGO  =  2.4  ±  0.1 μm (2.1 to 2.6 μm); and tail length  =  49.3  ± 2.8 μm (45.2 to 54.7 μm). All the key morphometrics were similar to those of the M. incognita population described by Song et al. (2019). The PCR amplifications of rDNA-internal transcribed spacer (ITS) fragments generated an amplicon of 544 bp from a single female or/and J2s (n = 22) using the universal primers M18S (5'-AACCTGCTGCTGGATCATTAC-3') and M28S (5'-GTATGCTTAAGTTCAGCG-3') (Feng et al. 2010). The PCR amplifications were repeated five times for each sample, and the products were purified and sequenced. The obtained sequnce was deposited in GenBank with Acc. No. OM304617.1. The amplified ITS region sequence was identical to those of M. incognita from India (KT869139.1) and China (MT490926.1 and MT071559.1). For confirmation, the primers species-specific for M. incognita (Inc-K14-F, 5'- GGGATGTGTAAATGCTCCTG -3' and Inc-K14-R, 5'- CCCGCTACACCCTCAACTTC -3') were further used for amplification. Expected PCR amplicon of 399 bp was acquired, which was consistent with previous report for M. incognita (Randig et al. 2002). Pathogenicity and reproduction of this M. incognita population on S. miltiorrhiza was confirmed and examined. Seeds of S. miltiorrhiza were sown in the pots filled with 200 ml of autoclaved soil mixture (loamy soil/sand, 1:1). Two weeks later, a total of 12 plants were inoculated each with 400 J2s, which were hatched from a field-derived M. incognita population. Four plants without nematode inoculation were used as the control. The plants grew in a chamber at 25/30 °C under 12-h dark/12-h light conditions. The parasitic J2s, J3s, J4s and females in roots were observed under a stereomicroscope at 5, 15 and 30 days post inoculation (dpi). At 35 dpi, an average of 98.3 ± 15.7 galls and 23.8 ± 6.9 egg masses per S. miltiorrhiza plant were counted, and the root gall index reached 6 according to the 0-10 RKN rating scale (Poudyal et al. 2005). Nematodes were re-isolated from the roots and their morphological and molecular characteristics were identical to the nematodes obtained from the original samples. Furthermore, all the inoculated S. miltiorrhiza roots showed typical RKN galls with the same symptoms as those initially observed in the field. No symptoms were developed on the non-inoculated control plants, and from which no nematodes were isolated. The nematode on S. miltiorrhiza was therefore certified as M. incognita. Han et al. (2019) isolated and morphologically identified M. incognita from the roots of S. miltiorrhiza and Trichosanthes kirilowii Maximin in Changqing area of Shandong Province, China, but did not perform the Koch's Rule. To our knowledge, this is the first formal report of M. incognita infecting S. miltiorrhiza in Henan Province, China. With the increase of Chinese herbal medicine planting area, plant parasitic nematodes are becoming more and more serious and have become an limiting factor on medicinal plant production, and the yield losses can be as high as 70%. This finding provides important and solid information for growers of Chinese medicinal plants, based on which suitable management action should be taken.

Recombinase Polymerase Amplification assays for detection of the major tropical root-knot nematodes

Detection of root-knot nematodes (RKN) in soil and plant samples is crucial to prevent its spread and select effective control measures. In this study, Recombinase Polymerase Amplification (RPA) assays using lateral flow dipsticks (LF-RPA) and real-time fluorescence detection (real-time RPA) were developed to detect the RKN species from tropical complex using a group-specific primer-probe set and Meloidogyne javanica using a species-specific primer-probe set. The results of the real time RPA assays in series of crude nematode extracts showed reliable detection within 16 min with a sensitivity of 1/100 of a second-stage juvenile in a reaction tube. The results of the LF-RPA assays showed reliable detection within 30 min with a sensitivity of 1/20 to 1/100 of a second-stage juvenile and 1/10 of a female in a reaction tube. Real-time RPA and LF-RPA assays are highly specific and can identify their target DNA in mixtures with other nematodes and plant tissues. LF-RPA assay has great potential for diagnosing RKN in the lab, field or in areas with a minimal laboratory infrastructure.

Report of the Parana coffee root-knot nematode, Meloidogyne paranaensis (Tylenchida: Meloidogynidae) from Caladium sp. in the continental United States

In May 2021, the Parana coffee root-knot nematode, Meloidogyne paranaensis was identified using molecular markers from a potted elephant ear plant (Caladium sp.) originated from San Antonio, Texas, USA. This nematode was found in a mixture with the peanut root-knot nematode, Meloidogyne arenaria. The molecular analysis showed that the intergenic COII-16S gene region and the D2–D3 of 28S rRNA gene sequences allowed differentiating M. paranaensis from the related root-knot nematode species of the tropical group. To the best of our knowledge, it is the first report of M. paranaensis in the continental United States.

Genetic Diversity, Identification, and Utilization of Novel Genetic Resources for Resistance to Meloidogyne incognita in Mulberry (Morus spp.)

Mulberry (Morus spp.) is an important crop in the sericulture industry, as the leaves constitute the primary feed for the silkworm. The availability of diverse genetic sources of resistance to root-knot nematode (RKN; Meloidogyne spp.) are very scanty. To address this need, a set of 415 varied exotic and indigenous germplasm accessions were screened under glasshouse conditions. Twenty-one accessions were identified as highly resistant and 48 were resistant, with the highest numbers of highly resistant/resistant accessions being found in Morus alba. Further, 30 accessions based on rooting ability were evaluated for field resistance at four different locations with infested soil. Finally, eight germplasm accessions (BR-8, Karanjtoli-1, Hosur-C8, Nagalur Estate, Tippu, Calabresa, Thai Pecah, and SRDC-3) were identified as potential genetic sources in RKN-resistance breeding programs or as resistant rootstock for the establishment of mulberry gardens. Sixteen simple sequence repeat markers analyzed among the 77 resistant and susceptible accessions generated 55 alleles, ranging from two to five, with an average of 3.43 alleles per locus. Principal coordinates analysis grouped the accessions on the basis of susceptibility and resistance to RKN infestation. The RKN-susceptible accessions exhibited higher variability as compared with resistant accessions, and they were more dispersed. Analysis of molecular variance showed maximum molecular variance was 78% within the population, and 22% between populations. Results of this study indicate that simple sequence repeat markers are reliable for assessing genetic variability among the RKN-resistant and RKN-susceptible mulberry accessions.

Species-Specific Molecular Detection of the Root Knot Nematode Meloidogyne luci

Simple Summary

The root knot nematode Meloidogyne luci has been identified in various countries around the world parasitizing economically important crops. Due to its potential to cause serious damage to agriculture, the need for an accurate diagnosis at the species level has become mandatory. In the present study, a specific amplification product on M. luci was obtained from a random amplified polymorphic DNA (RAPD) analysis. The DNA was sequenced and converted into a sequence characterized amplified region (SCAR) marker used for the species-specific molecular detection of this root knot nematode. The developed methodology is essential to monitoring the distribution and spread of M. luci in order to implement future effective and integrated pest management programs.

Abstract

Meloidogyne luci has been identified in various countries around the world parasitizing economically important crops and, due to its potential to cause serious damage to agriculture, was included in the European and Mediterranean Plant Protection Organization Alert List in 2017. This species shares morphological and molecular similarities with M. ethiopica and M. inornata, and a M. ethiopica group was therefore established. Although specific primers for the DNA amplification of species belonging to the M. ethiopica group have been developed previously, the primers were not species-specific, so molecular markers for the specific detection of M. luci are still needed. The objective of this study was to develop a SCAR marker for the detection of M. luci and the discrimination from other Meloidogyne spp. based on the intraspecific variability found in RAPD markers. RAPD screening of M. luci and M. ethiopica genome was used for the identification of a specific amplification product on M. luci, which was cloned, sequenced and converted into a SCAR marker. The specificity of the designed primers (Mlf/r) was tested and produced a fragment (771 bp) for all nine M. luci isolates with no amplification for the other nine Meloidogyne spp., including M. ethiopica and M. inornata. Additionally, the proper amplification of the M. luci SCAR-marker was also successful with DNA from galls of M. luci infected tomato roots. The results obtained in this study reveal that the specific molecular detection of M. luci was achieved and that the developed methodology can be used for routine diagnosis purposes, which are essential to monitoring the distribution and spread of M. luci in order to implement future effective and integrated nematode pest management programs.

First report of Meloidogyne incognita infecting Cannabis sativa in Alabama

Hemp (Cannabis sativa L.) is a new crop in Alabama. In 2019, symptomatic plants with stunted growth, poor root development, and numerous galls were observed in hemp plants grown in Geneva County, AL. After harvest, soil samples were collected from areas with the symptomatic plants and root-knot nematode (Meloidogyne spp.) were found in the soil. Based on morphological features and the polymerase chain reactions using species-specific primers, it was identified as Meloidogyne incognita. Further, a host differential test in a greenhouse assay confirmed it to be M. incognita race 3. The pathogenicity of the nematode to the hemp was confirmed by a modified version of Koch’s postulates. To our knowledge, this is the first report of M. incognita infecting Cannabis sativa in Alabama.

First report of southern root-knot nematode, Meloidogyne incognita, infecting Brassica nigra in Peru

Brassica nigra plants showing symptoms caused by root-knot nematodes were detected in the municipality of La Joya, Arequipa Province, Peru. Based on morphology, esterase phenotypes, and species-specific characterized amplified region (SCAR) sequence, the causal agent was identified as Meloidogyne incognita. Pathogenicity was confirmed by a modified version of Koch’s postulates. To our knowledge, this is the first report of M. incognita infecting Brassica nigra in Peru.

Chenopodium album is a weed host of Meloidogyne incognita (Nematoda: Meloidogynidae) in Peru

Chenopodium album plants showing symptoms caused by root-knot nematodes were detected in the La Joya, Arequipa, Peru. Based on the morphological, esterase phenotypes, and molecular analyses of the mitochondrial DNA region between the cytochome oxidase subunit II and 16S rRNA genes (mtDNA) and species-specific characterized amplified region, the causal agent of the observed symptoms was identified as Meloidogyne incognita. Pathogenicity was confirmed by fulfilling a modified version of Koch’s postulates. To our knowledge, this is the first report of M. incognita parasitizing C. album in Peru.

First report of root-knot nematode, Meloidogyne incognita on calendula in Turkey

Calendula officinalis L. (Asteraceae) is a traditional medicinal plant called pot marigold or English marigold. In this study, galled roots of pot marigold were collected from Balıkesir province of Turkey and egg masses were picked up from the roots of each plant with fine forceps. DNA was then extracted from samples and analyzed by species-specific primers referring to the most common Meloidogyne spp. Our results showed that Meloidogyne incognita was found as the only species in all the samples taken. The determination of M. incognita on calendula was done for the first time in Turkey.

A new root-knot nematode, Meloidogyne vitis sp. nov. (Nematoda: Meloidogynidae), parasitizing grape in Yunnan

An unknown root-knot nematode was found at high density on grape roots collected from Yunnan Province. Morphometric traits and measurements, isozyme phenotypes, and molecular analysis clearly differentiated this nematode from previously described root-knot nematodes. This new species is described, illustrated and named Meloidogyne vitis sp. nov. The new species can be distinguished from other Meloidogyne spp. by a unique combination of characters. Females display a prominent neck, an excretory pore is located on the ventral region between 23rd and 25th annule behind lips, an EP/ST ratio of approximately 2.5 (1.98-2.96), a perineal pattern with two large and prominent phasmids, and a labial disc fused with the medial lips to form a dumbbell-shaped structure. Males display an obvious head region, a labial disc fused with the medial lips to form a dumbbell-shaped structure, no lateral lips, a prominent slit-like opening between the labial disc and medial lips, a distinct sunken appearance of the middle of the medial lips, and four incisures in the lateral field. Second-stage juveniles are characterized by a head region with slightly wrinkled mark, a labial disc fused with the medial lips to form a dumbbell-shaped structure, a slightly sunken appearance of the middle of the medial lips, a slit-like amphidial openings between the labial disc and lateral lips, and four incisures in the lateral field. The new species has rare Mdh (N3d) and Est phenotypes (VF1). Phylogenetic analysis based on ITS1-5.8S-ITS2, D2D3 fragments of rDNA, and coxI and coxII fragments of mtDNA sequences clearly separated the new species from other root-knot nematodes, and the closest relative was Meloidogyne mali. Meloidogyne mali was collected for amplifying these sequences as mentioned above, which were compared with the corresponding sequences of new species, the result showed that all of these sequences with highly base divergence (48-210 base divergence). Moreover, sequence characterized amplified region (SCAR) primers for rapid identification of this new species were designed.

Rapid and Sensitive Detection of Meloidogyne graminicola in Soil Using Conventional PCR, Loop-Mediated Isothermal Amplification, and Real-Time PCR Methods

Meloidogyne graminicola is one of the major plant-parasitic nematodes (PPNs) that affect rice agriculture. Rapid identification and quantification of M. graminicola in soil is crucial for early diagnosis so that measures can be taken to reduce the impact of PPN diseases and ensure food security. In this study, M. graminicola species-specific primers for conventional PCR, loop-mediated isothermal amplification (LAMP), and real-time PCR were designed based on the sequence-characterized amplified region. The primers were highly specific and sensitive, and only samples containing M. graminicola DNA showed positive results. The sensitivity of LAMP and real-time PCR (two second-stage juvenile [J2] M. graminicola in 100 g of soil) was higher than that of conventional PCR (200 J2s in 100 g of soil). A standard curve (correlation coefficient R² = 0.970, P < 0.001) was generated by amplifying DNA extracted from 0.5 g of soil, and a significant correlation was observed between the number of M. graminicola determined by microscopic examination and that predicted from the standard curve (R² = 0.477, P = 0.0160). In quantification analyses of M. graminicola isolated from 31 naturally infested soils, the sensitivity of LAMP and real-time PCR (22 M. graminicola in 100 g of soil) was higher than that of conventional PCR (211 M. graminicola in 100 g of soil). The conventional PCR, LAMP, and real-time PCR methods have the potential to provide a useful platform for rapid species identification according to the experimental conditions. The real-time PCR assay and standard curve can be used for quantification of M. graminicola. These newly developed assays will help to facilitate the control of these economically important PPNs.

Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes

Plant-parasitic nematodes cause extensive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. Chemical methods that have been deployed to control nematodes have largely been banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasite-specific proteins, ca. 1000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of these, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasite-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis constitutes a unique resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.

First report of southern root-knot nematode, Meloidogyne incognita, infecting pomegranate, Punica granatum, in Peru

Punica granatum plants showing symptoms caused by root-knot nematodes were detected in the municipality of Majes, Arequipa, Peru. Based on the morphological, esterase phenotypes, and molecular analyses of the mitochondrial DNA region between the cytochome oxidase subunit II and 16 S rRNA genes (mtDNA) and species-specific sequence characterized amplified region, the causal agent of the observed symptoms was identified as Meloidogyne incognita. Pathogenicity was confirmed by fulfilling a modified version of Koch’s postulates. To our knowledge, this is the first report of M. incognita infecting P. granatum in Peru.

Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest

The root-knot nematodes are the most devastating worms to worldwide agriculture with Meloidogyne incognita being the most widely distributed and damaging species. This parasitic and ecological success seems surprising given its supposed obligatory clonal reproduction. Clonal reproduction has been suspected based on cytological observations but, so far, never confirmed by population genomics data. As a species, M. incognita is highly polyphagous with thousands of host plants. However, different M. incognita isolates present distinct and overlapping patterns of host compatibilities. Historically, four "host races" had been defined as a function of ranges of compatible and incompatible plants. In this study, we used population genomics to assess whether (a) reproduction is actually clonal in this species, (b) the host races follow an underlying phylogenetic signal or, rather represent multiple independent transitions, and (c) how genome variations associate with other important biological traits such as the affected crops and geographical distribution. We sequenced the genomes of 11 M. incognita isolates across Brazil that covered the four host races in replicates. By aligning the genomic reads of these isolates to the M. incognita reference genome assembly, we identified point variations. Analysis of linkage disequilibrium and 4-gametes test showed no evidence for recombination, corroborating the clonal reproduction of M. incognita. The few point variations between the isolates showed no significant association with the host races, the geographical origin of the samples, or the crop on which they have been collected. Addition of isolates from other locations around the world confirmed this lack of underlying phylogenetic signal. This suggests multiple gains and losses of parasitic abilities and adaptations to different environments account for the broad host spectrum and wide geographical distribution of M. incognita and thus to its high economic impact. This surprising adaptability without sex poses both evolutionary and agro-economic challenges.

The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato

The Meloidogyne-based disease complexes (MDCs) are caused by the interaction of different root-knot nematode species and phytopathogenic fungi. These complexes are devastating several important crops worldwide including tomato and coffee. Despite their relevance, little is known about the role of the bacterial communities in the MDCs. In this study 16s rDNA gene sequencing was used to analyze the bacterial microbiome associated with healthy and infested roots, as well with females and eggs of Meloidogyne enterolobii and M. paranaensis, the causal agents of MDC in tomato and coffee, respectively. Each MDC pathosystems displayed a specific taxonomic diversity and relative abundances constituting a very complex system. The main bacterial drivers of the MDC infection process were identified for both crops at order level. While corky-root coffee samples presented an enrichment of Bacillales and Burkholderiales, the corcky-root tomato samples presented an enrichment on Saprospirales, Chthoniobacterales, Alteromonadales, and Xanthomonadales. At genus level, Nocardia was common to both systems, and it could be related to the development of tumor symptoms by altering both nematode and plant systems. Furthermore, we predicted the healthy metabolic profile of the roots microbiome and a shift that may result in an increment of activity of central metabolism and the presence of pathogenic genes in both crops.

Genetic intraspecific diversity of Meloidogyne javanica parasitizing vegetables in southern Iran

In order to investigate different species of root-knot nematodes associated with vegetable production in southern regions of Iran, 37 populations of the most predominant species, Meloidogyne javanica, were recovered. Morphological and morphometric studies were carried on the characters of females, males, J2s and perineal patterns. Species-specific Sequence Characterized Amplified Region (SCAR) primers confirmed morphological studies, and all these populations produced specific band in 670 bp using Fjav and Rjav primers. Genetic diversity of different populations was studied by Inter Simple Sequence Repeats (ISSR) and Random Amplified Polymorphic DNA (RAPD) markers implementing 10 primers for each approach. Results revealed a relatively low genetic diversity (the percentage of polymorphic bands were 19.08 and 24.60 for ISSR and RAPD, respectively). The analyses of molecular variance indicated that the variation resulted from genotypic variations within region and variances among regions are 81% and 19% for RAPD, and 86% and 14% for ISSR, respectively. On the other hand, F_ST and Nm values are 0.140 and 1.535 for ISSR while these values are 0.188 and 1.079 for RAPD. So it can be concluded that there is a great deal of gene flow between populations due to the movement of plant material contaminated with nematodes, which results in high mixing between populations. ISSR and RAPD datasets failed to group populations according to their geographic region. There were no pathotypes or other intraspecific biological entities observed in the species.

First report of root-knot nematode, Meloidogyne arenaria, on lavender in Turkey

Lavender is a medicinal and aromatic plant that is widely grown in Turkey. Gall symptoms were observed on roots of lavender (Lavandula angustifolia Mill.) collected from Kırklareli and Edirne provinces. Egg masses were collected from galled roots. DNA isolated from all samples was screened by species-specific primers belonging to the most common species of root-knot nematodes and M. arenaria was the only species that was identified in all of the samples analyzed. This is the first report of M. arenaria infecting lavender in Turkey.

Lavender is a medicinal and aromatic plant that is widely grown in Turkey. Gall symptoms were observed on roots of lavender (Lavandula angustifolia Mill.) collected from Kırklareli and Edirne provinces. Egg masses were collected from galled roots. DNA isolated from all samples was screened by species-specific primers belonging to the most common species of root-knot nematodes and M. arenaria was the only species that was identified in all of the samples analyzed. This is the first report of M. arenaria infecting lavender in Turkey.

Molecular characterization of root-knot nematodes (Meloidogyne spp.) from Arkansas, USA

Root-knot nematodes (Meloidogyne spp.) are the most common major pathogens of many crops throughout the world, impacting both the quantity and quality of marketable yields. In this study, a total of 244 root-knot nematode populations from various hosts from 39 counties in Arkansas were tested to determine the species diversity. Molecular characterization was performed on these populations by DNA sequencing of the ribosomal DNA 18S-ITS-5.8S, 28S D2/D3 and a mitochondrial DNA fragment flanking cytochrome oxidase gene subunit II - the intergenic spacer. Five species were identified, including M. incognita (Kofoid & White, 1919) Chitwood, 1949 from soybean, cotton, corn and various vegetables (232 samples); M. hapla Chitwood, 1949 from rose (1 sample); M. haplanaria Eisenback, Bernard, Starr, Lee & Tomaszewski, 2003 from okra, tomato, peanut, Indian hawthorn, ash, willow and elm trees (7 samples); M. marylandi Jepson & Golden in Jepson, 1987 from grasses (3 samples); and M. partityla Kleynhans, 1986 from pecan (1 sample) through a combined analysis of DNA sequencing and PCR by species-specific primers. Meloidogyne incognita is the most abundant species that was identified in 95% samples and was the only species in field crops including soybean and cotton, except for one population of M. haplanaria from soybean in Logan County (TK201). Species-specific primers were used to verify M. incognita through PCR by species-specific primers. Unlike historical data, M. arenaria, M. javanica and M. graminis were not detected from any of the samples collected during this study. This result is essential for effective and sustainable management strategies against root-knot nematodes in Arkansas.

Rice susceptibility to root-knot nematodes is enhanced by the Meloidogyne incognita MSP18 effector gene

MAIN CONCLUSION

This study revealed novel insights into the function of MSP18 effector during root-knot nematode parasitism in rice roots. MSP18 may modulate host immunity and enhance plant susceptibility to Meloidogyne spp. Rice (Oryza sativa) production is seriously impacted by root-knot nematodes (RKN), including Meloidogyne graminicola, Meloidogyne incognita, and Meloidogyne javanica, in upland and irrigated culture systems. Successful plant infection by RKN is likely achieved by releasing into the host cells some effector proteins to suppress the activation of immune responses. Here, we conducted a series of functional analyses to assess the role of the Meloidogyne-secreted protein (MSP) 18 from M. incognita (Mi-MSP18) during rice infection by RKN. Developmental expression profiles of M. javanica and M. graminicola showed that the MSP18 gene is up-regulated throughout nematode parasitic stages in rice. Reproduction of M. javanica and M. graminicola is enhanced in rice plants overexpressing Mi-MSP18, indicating that the Mi-MSP18 protein facilitates RKN parasitism. Transient expression assays in onion cells suggested that Mi-MSP18 is localized to the cytoplasm of the host cells. In tobacco, Mi-MSP18 suppressed the cell death induced by the INF1 elicitin, suggesting that Mi-MSP18 can interfere with the plant defense pathways. The data obtained in this study highlight Mi-MSP18 as a novel RKN effector able to enhance plant susceptibility and modulate host immunity.

Additional information on Meloidogyne polycephannulata and its proposal as a junior synonym of M. incognita

The type population ofMeloidogyne polycephannulatais synonymised withM. incognitabased on morphological and morphometric characters, as well as biochemical, molecular and phylogenetic studies. Morphological variability and a wide host range were reported forM. incognitaduring its first description and later re-description.Meloidogyne polycephannulatawas described in Brazil from specimens collected in a carrot field (type population). The esterase phenotype (Est) characterised for this species was identical to the phenotype Est I2 ofM. incognita, the most ubiquitous phenotype used for diagnostics. Morphological and morphometric characters of the descriptions of the two nominal species showed major similarities, as well as variability within the range of variation detected inM. incognita. In PCR assays, three SCAR markers species-specific forM. incognita(incK14 F/R, Mi/FR and incB06 F/R) amplified the same fragments of 399 bp, 955 bp and 1200 bp, respectively, for populations in both species. In phylogenetic studies based either on concatenated sequences of ITS1-5.8S-ITS2, D2-D3 rRNA, mitochondrialCOII regions or on RAPD and AFLP data, the populations of both species grouped in the same clade with high bootstrap support. Altogether, these results provide congruent evidence that theM. polycephannulatatype isolate deposited at the Embrapa Cryopreserved National Collection of Root-knot Nematodes is not a valid species but rather a junior synonym ofM. incognita.

Development of Diagnostic SCAR Markers for Meloidogyne graminicola, M. oryzae, and M. salasi Associated with Irrigated Rice Fields in Americas

Root-knot nematodes (RKN) cause important production losses of rice (Oryza sativa L.) in the world. Together with Meloidogyne graminicola Golden and Birchfield 1965, M. oryzae Maas, Sanders and Dede, 1978 and M. salasi López, 1984 have been causing damages in irrigated rice fields in Central and South America. In addition, six other RKN species may occur in rice fields in other regions of the world. Correct identification of Meloidogyne spp. is difficult but essential for the management of rice RKNs. The objective of this study was to develop some species-specific molecular markers for the diagnosis of South American RKN rice-related species. Isozyme phenotypes indicated the occurrence of some RKN species in the Brazilian samples, namely M. graminicola, M. oryzae, M. javanica, and two cryptic species designated as Meloidogyne sp. 2 and Meloidogyne sp. 3. Random amplified polymorphic DNA (RAPD) analysis of 16 isolates revealed interspecific genetic polymorphism between Meloidogyne spp., but isolates belonging to the same species (i.e., sharing the same esterase phenotype) always clustered together, whatever the species considered. Specific SCAR markers of 230, 120, and 160 bp were developed for M. graminicola, M. oryzae, and M. salasi, respectively. These SCAR markers may be potential molecular tools for application in routine diagnostic procedures subject to their validation with other rice RKN field populations in the world.

Occurrence of the Root-Knot Nematode species in Vegetable Crops in Souss Region of Morocco

Root-knot nematodes 'Meloidogyne spp' are the most destructive group of plant parasitic nematodes causeing serious losses in vegetables crops and this damages worsened when crops grown under greenhouses conditions. In this sutdy, the distribution and characterization of root-knot nematode species collected from the Souss region of Morocco where vegetables crops intensively cultivated were determined by using both morphological and molecular tools. Out of the 110 samples collected from different greenhouses 91 (81.7%) were found to be infested with root-knot nematodes. Thirty-seven populations of root-knot nematodes were morphologically identified based on perineal patterns as well as molecularlly using species-specific primers. The obtained results indicated that Meloidogyne javanica and M. incognita were identified in 86.4% and 13.5% of the total populations, respectively. The lowest incidence of root-knot nematodes (64%) was found in Toussous, whereas the highest frequencies of 100% and 90% were detected in Taddart and Biogra, respectively. As the majority of the samples have been infested with Meloidogyne species; this indicates that there is an urgent need to provide farmers with a proper control strategy.

A High-Throughput Molecular Pipeline Reveals the Diversity in Prevalence and Abundance of Pratylenchus and Meloidogyne Species in Coffee Plantations

Coffee yields are adversely affected by plant-parasitic nematodes and the pathogens are largely underreported because a simple and reliable identification method is not available. We describe a polymerase chain reaction-based approach to rapidly detect and quantify the major Pratylenchus and Meloidogyne nematode species that are capable of parasitizing coffee. The procedure was applied to soil samples obtained from a number of coffee farms in Brazil, Vietnam, and Indonesia to assess the prevalence of these species associated both with coffee (Coffea arabica and C. canephora) and its intercropped species Musa acuminata (banana) and Piper nigrum (black pepper). Pratylenchus coffeae and P. brachyurus were associated with coffee in all three countries but there were distinct profiles of Meloidogyne spp. Meloidogyne incognita, M. exigua, and M. paranaensis were identified in samples from Brazil and M. incognita and M. hapla were detected around the roots of coffee in Vietnam. No Meloidogyne spp. were detected in samples from Indonesia. There was a high abundance of Meloidogyne spp. in soil samples in which Pratylenchus spp. were low or not detected, suggesting that the success of one genus may deter another. Meloidogyne spp. in Vietnam and Pratylenchus spp. in Indonesia were more numerous around intercropped plants than in association with coffee. The data suggest a widespread but differential nematode problem associated with coffee production across the regions studied. The issue is compounded by the current choice of intercrops that support large nematode populations. Wider application of the approach would elucidate the true global scale of the nematode problem and the cost to coffee production. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Integrative taxonomy of root-knot nematodes reveals multiple independent origins of mitotic parthenogenesis

During sampling of several Coffea arabica plantations in Tanzania severe root galling, caused by a root-knot nematode was observed. From pure cultures, morphology and morphometrics of juveniles and females matched perfectly with Meloidogyne africana, whereas morphology of the males matched identically with those of Meloidogyne decalineata. Based on their Cox1 sequence, however, the recovered juveniles, females and males were confirmed to belong to the same species, creating a taxonomic conundrum. Adding further to this puzzle, re-examination of M. oteifae type material showed insufficient morphological evidence to maintain its status as a separate species. Consequently, M. decalineata and M. oteifae are synonymized with M. africana, which is herewith redescribed based on results of light and scanning electron microscopy, ribosomal and mitochondrial DNA sequences, isozyme electrophoresis, along with bionomic and cytogenetic features. Multi-gene phylogenetic analysis placed M. africana outside of the three major clades, together with M. coffeicola, M. ichinohei and M. camelliae. This phylogenetic position was confirmed by several morphological features, including cellular structure of the spermatheca, egg mass position, perineal pattern and head shape. Moreover, M. africana was found to be a polyphagous species, demonstrating that "early-branching" Meloidogyne spp. are not as oligophagous as had previously been assumed. Cytogenetic information indicates M. africana (2n = 21) and M. ardenensis (2n = 51-54) to be a triploid mitotic parthenogenetic species, revealing at least four independent origins of mitotic parthenogenesis within the genus Meloidogyne. Furthermore, M. mali (n = 12) was found to reproduce by amphimixis, indicating that amphimictic species with a limited number of chromosomes are widespread in the genus, potentially reflecting the ancestral state of the genus. The wide variation in chromosome numbers and associated changes in reproduction modes indicate that cytogenetic evolution played a crucial role in the speciation of root-knot nematodes and plant-parasitic nematodes in general.

Characterisation of a Meloidogyne species complex parasitising rice in southern Brazil

Root-knot nematodes (RKN) are important plant pathogens affecting rice in South-East Asia and southern Brazil in irrigated rice fields. In order to investigate the specific diversity of RKN associated with irrigated rice in southern Brazil, Meloidogyne spp. from Rio Grande do Sul (RS) and Santa Catarina (SC) States were characterised biochemically by esterase (Est) and malate dehydrogenase (Mdh) phenotypes. Fifty-six Meloidogyne spp. populations were detected in 48% of rice samples, and a total of five esterase phenotypes were identified, four of which presented as drawn-out bands in different positions. In RS State, M. graminicola (Est VS1), Meloidogyne sp. 2 (Est R2) and Meloidogyne sp. 3 (Est R3) were identified, which corresponded to ca 80, 40 and 10% of samples, respectively. In SC State, M. graminicola, M. javanica (Est J3), Meloidogyne sp. 1 (Est R1), Meloidogyne sp. 2 and Meloidogyne sp. 3 accounted for ca 93.75, 12.50, 62.50, 12.25 and 6.25% of samples, respectively. The esterase phenotypes R1, R2 and R3 are new, never having been detected on rice before. Meloidogyne javanica showed a N1 Mdh phenotype (Rm: 1.0), while four other populations exhibited a N1a (Rm: 1.4) phenotype. All populations were tested with two SCAR markers specific to M. graminicola, which confirmed that, but no specificity was obtained with both markers in relation to the atypical populations analysed. Sequencing and phylogenetic analyses of internal transcribed spacer-rRNA (ITS) were performed to infer the phylogenetic relationship of these atypical Meloidogyne spp. populations. Meloidogyne sp. 1 grouped with the mitotic parthenogenetic species, while the two others (Meloidogyne sp. 2 and sp. 3) clustered with M. graminicola and other meiotic parthenogenetic species. Taken together, these data highlight the unprecedented specific diversity of RKN associated with irrigated rice in southern Brazil. Further morphological and phylogenetic studies involving these atypical isolates will be carried out to identify this complex of species.

Genetic diversity of Meloidogyne spp. parasitising potato in Brazil and aggressiveness of M. javanica populations on susceptible cultivars

Root-knot nematodes (Meloidogyne spp.) significantly impact potato production worldwide and in Brazil they are considered one of the most important group of nematodes affecting potatoes. The objectives of this study were to survey Meloidogyne spp. associated with potatoes in Brazil, determine their genetic diversity and assess the aggressiveness of M. javanica on two susceptible potato cultivars. Fifty-seven root-knot nematode populations were identified using esterase phenotyping, including Meloidogyne javanica, M. incognita, M. arenaria and M. ethiopica. Overall, root-knot nematodes were present in ca 43% of sampled sites, in which M. javanica was the most prevalent species, and the phenotypes Est J3, J2a and J2 occurred in 91.2, 6.7 and 2.1% of the positive samples, respectively. Other species, such as M. incognita, M. arenaria and M. ethiopica, were found less frequently and occurred at rates of 6.4, 4.3 and 2.1% of the samples, respectively. Sometimes, M. javanica was found in mixtures with other root-knot nematodes in ca 10.6% of sites containing Meloidogyne. After confirming the identification of 17 isolates of M. javanica and one isolate each of M. incognita, M. arenaria and M. ethiopica by SCAR markers, the populations were used to infer their genetic diversity using RAPD markers. Results revealed low intraspecifc genetic diversity among isolates (13.9%) for M. javanica. Similarly, M. javanica sub-populations (J2a) clustered together (81% of bootstrap), indicating subtle variation from typical J3 populations. The aggressiveness of four populations of M. javanica from different Brazilian states on two susceptible potato cultivars was tested under glasshouse conditions. Results indicated differences in aggressiveness among these populations and showed that potato disease was proportional to nematode reproduction factor.

Meloidogyne brasiliensis Charchar & Eisenback, 2002 is a junior synonym of M. ethiopica Whitehead, 1968

The type population ofMeloidogyne brasiliensisis synonymised underM. ethiopicabased on morphological and morphometric similarities, as well as through biochemical, molecular and phylogenetic studies.Meloidogyne ethiopicawas first described in 1968 in Tanzania using specimens from a single egg mass culture on tomato and re-described in 2004 using an isolate from Brazil.Meloidogyne brasiliensiswas described in 2002 in Brazil based on specimens collected from tomato (type population) and pea. Morphological and morphometric studies of their descriptions showed important similarities in major characters as well as some general variability in others. Characterisation of esterase isozyme phenotypes of three populations ofM. ethiopicafrom Brazil, Chile and Kenya, and twoM. brasiliensispopulations, resulted in only one esterase pattern (E3), a phenotype already known forM. ethiopica. In PCR assays, the species-specific 350 bp SCAR marker developed forM. ethiopicawas amplified from theM. brasiliensispopulations tested. In phylogenetic analyses based either on sequences of the ITS1-5.8S-ITS2 and D2-D3 (28S) rRNA regions or on RAPD and AFLP data, the populations of both species clustered together with a strong bootstrap support. Altogether, these results provide congruent evidence thatM. brasiliensisis not a valid species but rather a junior synonym ofM. ethiopica.

Resistance of Coffea arabica genotypes against Meloidogyne paranaensis and M. incognita under controlled and field conditions

Root-knot nematodes negatively impact on coffee yield worldwide. The use of resistant cultivars is the most effective way to manage these pests. The goal of this study was to identify Coffea arabica genotypes with resistance to Meloidogyne paranaensis and M. incognita race 1. Eighteen C. arabica genotypes (EPAMIG’s Germplasm Bank), previously selected for poor host suitability in a M. paranaensis-infested field, plus a resistant and a susceptible standard, were inoculated with these two Meloidogyne species to determine their resistance using nematode reproduction factor (). Accessions for which were considered resistant, while those for which were considered moderately resistant or susceptible, also according to statistical analysis. Five accessions from crossing ‘Catuaí Vermelho’ × ‘Amphillo MR 2-161’, one from ‘Catuaí Vermelho’ × ‘Amphillo MR 2-474’, two from ‘Timor Hybrid (UFV 408-01)’ and the standard ‘IPR-100’ were resistant to M. incognita race 1 with . Four accessions from ‘Catuaí Vermelho’ × ‘Amphillo MR 2-161’, one from ‘Timor Hybrid (UFV 408-01)’, one from ‘Catuaí Vermelho’ × ‘Amphillo MR 2-474’ and the resistant standard ‘IPR100’ were resistant to M. paranaensis (). Field evaluations with parental genotypes showed that plants that originated from progenies ‘Catuaí Vermelho’ × ‘Amphillo MR 2-161’ were resistant to M. paranaensis and also gave a good yield compared to commercial cultivars, showing promising agronomic traits that can be used in breeding programmes to develop new cultivars of C. arabica.

Root-Knot Nematodes (Meloidogyne spp.) Parasitizing Resistant Tobacco Cultivars in Southern Brazil

Our study surveyed Meloidogyne spp. from tobacco cultivars in Brazil carrying the Rk gene, which confers resistance to Meloidogyne incognita races 1 and 3. Identification of Meloidogyne populations from 39 tobacco fields was based on the analysis of esterase phenotypes, perineal patterns, and 18S-internal transcribed spacer (ITS)1-5.8S ribosomal RNA sequences. Biometric characterization and differential host tests of isolates were determined as well. We detected M. incognita, M. javanica, M. enterolobii, M. arenaria, and M. inornata in 18 (46.2%), 16 (41%), 10 (25.6%), 2 (5.1%), and 1 (2.6%) samples, respectively. Mixtures of species were found in 25.6% of the samples. This is the first report of M. inornata parasitizing tobacco in Brazil's southern region. Two morphological and biochemically unusual populations had host ranges and ITS1 sequences nearly identical to M. enterolobii and M. incognita, respectively. Pathogenic and biometric intraspecific variations were observed. Based on our results and considering the limited efficiency of the Rk gene, it is indispensable not only to search for resistance sources to M. incognita virulent strains but also to consider resistance to M. enterolobii, M. inornata, M. arenaria, and M. javanica in tobacco breeding programs. Changes in integrated management procedures should be considered to avoid increased crop damage in the future.

Meloidogyne spp. populations from native Cerrado and soybean cultivated areas: genetic variability and aggressiveness

A significant portion of the Cerrado (Brazilian savanna) has been replaced by major crops such as soybean. This may reveal populations of nematodes with different genetic backgrounds compared to cultivated fields. The objectives of this study were to evaluate the genetic variability and aggressiveness of isolates ofMeloidogynespp., contrasting nematodes from preserved areas of the Cerrado with those originating from cultivated soybean fields. Cluster analysis separated isolates ofMeloidogynespp. and isolates from Cerrado and soybean but did not separate an aggressiveMeloidogyne morocciensisisolate. The aggressiveness of six selected populations ofMeloidogynespp. from Cerrado and soybean against soybean cultivars was evaluated. Results showed that populations ofM. javanicaandM. incognitafrom Cerrado and soybean showed similar aggressiveness. However, forM. morocciensis, the population from soybean was much more aggressive than the one from Cerrado. Aggressiveness is a very intriguing subject that needs special attention for future research in nematology.

First report of, and additional information on, Meloidogyne konaensis (Nematoda: Meloidogyninae) parasitising various crops in Brazil

In a survey for Meloidogyne spp. in different crops from 11 regions in Ceará State, Brazil, using esterase isozyme electrophoresis as a specific identification method, four atypical populations were characterised from cabbage, papaya, noni and canapum plants, all of which showed an esterase profile different from those previously detected in Brazil. Morphological studies showed typical characteristics of Meloidogyne konaensis. Perineal patterns of females were variable, similar to M. arenaria and M. incognita, stylet length 14-20 μm. In females, the knobs gradually merged with the shaft and the dorsal pharyngeal gland orifice (DGO) ranged from 4 to 7 μm. Although males are not frequently found, the stylet morphology provides the most useful source of diagnostic character for the species, having 6-12 large projections protruding from the shaft. The esterase pattern K3 is unique and species-specific with three major bands Rm 1.0, 1.17, 1.27 and a secondary band Rm 1.10. Some confusion about the true identity of this species was clarified in this study, including differentiation from M. paranaensis. A species-specific SCAR marker developed for M. paranaensis was tested and no amplification products were observed. In Neighbour-Joining analyses of ITS and D2-D3 rRNA sequences, M. konaensis from Brazil appeared clearly separated from M. paranaensis. Pathological tests indicated that coffee is not a host of M. konaensis as previously reported in the original description of this species.

Molecular Characterisation and Diagnosis of Root-Knot Nematodes (Meloidogyne spp.) from Turfgrasses in North Carolina, USA

Root-knot nematodes (Meloidogyne spp.) are the most common and destructive plant-parasitic nematode group worldwide and adversely influence both crop quality and yield. In this study, a total of 51 root-knot nematode populations from turfgrasses were tested, of which 44 were from North Carolina, 6 from South Carolina and 1 from Virginia. Molecular characterisation was performed on these samples by DNA sequencing on the ribosomal DNA 18S, ITS and 28S D2/D3. Species-specific primers were developed to identify turfgrass root-knot nematode through simplex or duplex PCR. Four species were identified, including M. marylandi Jepson & Golden in Jepson, 1987, M. graminis (Sledge & Golden, 1964) Whitehead, 1968, M. incognita (Kofoid & White, 1919) Chitwood, 1949 and M. naasi Franklin, 1965 through a combined analysis of DNA sequencing and PCR by species-specific primers. M. marylandi has been reported from North Carolina and South Carolina for the first time. Molecular diagnosis using PCR by species-specific primers provides a rapid and cheap species identification approach for turfgrass root-knot nematodes.

Tracking changes in life-history traits related to unnecessary virulence in a plant-parasitic nematode

Evaluating trade-offs in life-history traits of plant pathogens is essential to understand the evolution and epidemiology of diseases. In particular, virulence costs when the corresponding host resistance gene is lacking play a major role in the adaptive biology of pathogens and contribute to the maintenance of their genetic diversity. Here, we investigated whether life-history traits directly linked to the establishment of plant-nematode interactions, that is, ability to locate and move toward the roots of the host plant, and to invade roots and develop into mature females, are affected in Meloidogyne incognita lines virulent against the tomato Mi-1.2 resistance gene. Virulent and avirulent near-isogenic lines only differing in their capacity to reproduce or not on resistant tomatoes were compared in single inoculation or pairwise competition experiments. Data highlighted (1) a global lack of trade-off in traits associated with unnecessary virulence with respect to the nematode ability to successfully infest plant roots and (2) variability in these traits when the genetic background of the nematode is considered irrespective of its (a)virulence status. These data suggest that the variation detected here is independent from the adaptation of M. incognita to host resistance, but rather reflects some genetic polymorphism in this asexual organism.

The Multi-Resistant Reaction of Drought-Tolerant Coffee 'Conilon Clone 14' to Meloidogyne spp. and Late Hypersensitive-Like Response in Coffea canephora

Root-knot nematodes (RKN), Meloidogyne spp., have major economic impact on coffee production in Central and South America. Genetic control of RKN constitutes an essential part for integrated pest management strategy. The objective of this study was to evaluate the resistance of Coffea canephora genotypes (clones) to Meloidogyne spp. Sensitive and drought-tolerant coffee genotypes were used to infer their resistance using nematode reproduction factor and histopathology. Eight clonal genotypes were highly resistant to M. paranaensis. 'Clone 14' (drought-tolerant) and 'ESN2010-04' were the only genotypes highly resistant and moderately resistant, respectively, to both M. incognita races 3 and 1. Several clones were highly resistant to both avirulent and virulent M. exigua. Clone 14 and ESN2010-04 showed multiple resistance to major RKNs tested. Roots of 'clone 14' (resistant) and 'clone 22' (susceptible) were histologically studied against infection by M. incognita race 3 and M. paranaensis. Reduction of juvenile (J2) penetration in clone 14 was first seen at 2 to 6 days after inoculation (DAI). Apparent early hypersensitive reaction (HR) was seen in root cortex between 4 and 6 DAI, which led to cell death and prevention of some nematode development. At 12 to 20 DAI, giant cells formed in the vascular cylinder, besides normal development into J3/J4. From 32 to 45 DAI, giant cells were completely degenerated. Late, intense HR and cell death were frequently observed around young females and giant cells reported for the first time in coffee pathosystem. These results provide rational bases for future studies, including prospection, characterization, and expression profiling of genomic loci involved in both drought tolerance and resistance to multiple RKN species.

Intraspecific variability of the facultative meiotic parthenogenetic root-knot nematode (Meloidogyne graminicola) from rice fields in Vietnam

Twenty years ago, the facultative meiotic parthenogenetic root-knot nematode (RKN), Meloidogyne graminicola, was recognised as an important rice pathogen in South Vietnam. Although this country is one of the most important rice exporters worldwide, a comprehensive picture of the occurrence of M. graminicola in Vietnamese rice fields is still not available. Therefore a nematode survey was carried out with the aim of better understanding the geographical distribution, and the pathogenic and genetic variability of the RKN in Vietnam. From the fields surveyed in a range of ecosystems, 21 RKN populations were recovered from infected rice roots. A diagnostic SCAR marker was developed showing that all Vietnamese populations belong to M. graminicola. Furthermore, sequencing of the Internal Transcribed Spacer (ITS) of the rDNA genes confirmed this identification. These populations were then characterised using morphometrics and pathogenicity tests (host plant range diversity, reproduction and virulence diversity) revealing intraspecific variability. We showed that morphometric traits are mainly genetically heritable characters with significant differences among the studied populations. Finally, a distinctive trait signature was found for the populations isolated from the upland rice cultures. All together, our study reveals the prevalence of M. graminicola populations in Vietnamese rice. Further investigations need to be developed to explore the population dynamics and evolutionary history of this species in South East Asia.

Mitochondrial haplotype-based identification of ethanol-preserved root-knot nematodes from Africa

The asexual root-knot nematodes (RKNs) (Meloidogyne spp.) exemplified by Meloidogyne incognita are widespread and damaging pests in tropical and subtropical regions worldwide. Comparison of amplification products of two adjacent polymorphic regions of the mitochondrial genome using DNA extracts of characterized RKN strains, including 15 different species, indicate that several species are derived from the same or closely related female lineages. Nevertheless, M. javanica, M. enterolobii, M. incognita, and other key species could each be assigned unique mitochondrial haplotypes based on polymerase chain reaction fragment size and restriction cleavage patterns. M. arenaria isolates did not group as a single haplotype, consistent with other reports of diversity within this species. To test the utility of this assay, we characterized ethanol-preserved samples from 103 single-species isolates from four countries in sub-Saharan Africa (Benin, Nigeria, Kenya, and Tanzania). Mitochondrial haplotypes corresponding to M. javanica and M. incognita were the most prevalent. Samples from western Africa included several instances of M. enterolobii but this species was not detected in samples from East Africa. This protocol provides progress toward a standardized strategy for identification of RKN species from small, preserved samples and a rational starting point for classifying species present in regions where previous knowledge has been limited.

Mitochondrial genome plasticity among species of the nematode genus Meloidogyne (Nematoda: Tylenchina)

The mitochondrial (mt) genomes of the plant-parasitic root-knot nematodes Meloidogyne arenaria, Meloidogyne enterolobii and Meloidogyne javanica were sequenced and compared with those of three other root-knot nematode species in order to explore the mt genome plasticity within Meloidogyne. The mt genomes of M. arenaria, M. enterolobii and M. javanica are circular, with an estimated size of 18.8, 18.9 and 19.6 kb, respectively. Compared to other nematodes these mt genomes are larger, due to the presence of large non-coding regions. The mt genome architecture within the genus Meloidogyne varied in the position of trn genes and in the position, length and nucleotide composition of non-coding regions. These variations were observed independent of the species' natural environments or reproductive modes. M. enterolobii showed three main non-coding regions whereas Meloidogyne chitwoodi, Meloidogyne incognita, M. javanica and M. arenaria had two non-coding regions, and Meloidogyne graminicola had a unique large non-coding region interrupted by two trn genes. trn genes were positioned in different regions of the mt genomes in M. chitwoodi, M. enterolobii and M. graminicola, whereas the trn gene order was identical between M. arenaria, M. incognita and M. javanica. Importantly, M. graminicola had extra copies of trnV and trnS2. High divergence levels between the two copies of each trn might indicate duplication events followed by random loss and mutations in the anticodon. Tree-based methods based on amino acid sequences of 12 mt protein-coding genes support the monophyly for the tropical and mitotic parthenogenetic species, M. arenaria, M. enterolobii, M. incognita and M. javanica and for a clade that includes the meiotic parthenogenetic species, M. chitwoodi and M. graminicola. A comparison of the mt genome architecture in plant-parasitic nematodes and phylogenetic analyses support that Pratylenchus is the most recent ancestor of root-knot nematodes.

Meloidogyne lopezi n. sp. (Nematoda: Meloidogynidae), a new root-knot nematode associated with coffee (Coffea arabica L.) in Costa Rica, its diagnosis and phylogenetic relationship with other coffee-parasitising Meloidogyne species

Coffee (Coffea arabica L. cv. Catuai) seedlings with abundant small root galls caused by an unknown root-knot nematode were found in southern Costa Rica. Morphology, esterase and malate dehydrogenase isozyme phenotypes and DNA markers differentiated this nematode from known Meloidogyne spp. A new species, M. lopezi n. sp., with common name Costa Rican root-knot nematode, is suggested. Meloidogyne lopezi n. sp. is distinguished from other coffee-associated Meloidogyne spp. by size of female lips and stylet, male body length and stylet and second-stage juvenile body and tail morphology. The region of the mitochondrial genome between COII and 16S rRNA showed a unique amplicon size of 1370 bp, and digestions with restriction enzymes HinfI, AluI, DraI and DraIII revealed characteristic PCR-RFLP patterns that differed from the tropical root-knot nematode species M. arabicida, M. incognita, M. izalcoensis, M. javanica and M. paranaensis. Characterisation of the protein-coding map-1 gene and phylogenetic analyses suggested that M. lopezi n. sp. might reproduce by mitotic parthenogenesis. Phylogenies estimated using Bayesian analyses based on the region between the COII and 16S rRNA mitochondrial genes, as well as the 18S and 28S ribosomal nuclear genes, indicated that M. lopezi n. sp. is closely related to other tropical Meloidogyne spp. that infect coffee, especially M. arabicida, M. izalcoensis and M. paranaensis from Central and South America. Isozyme analyses and PCR-RFLP of the COII-16S rRNA mitochondrial gene region enable a clear diagnostic differentiation between these species.

Meloidogyne luci n. sp. (Nematoda: Meloidogynidae), a root-knot nematode parasitising different crops in Brazil, Chile and Iran

A new root-knot nematode parasitising vegetables, flowers and fruits in Brazil, Iran and Chile, is described as Meloidogyne luci n. sp. The female has an oval to squarish perineal pattern with a low to moderately high dorsal arc and without shoulders, similar to M. ethiopica. The female stylet is robust and 15-16 μm long; the distance from the dorsal pharyngeal gland orifice to the stylet base (DGO) is 3-4 μm. Males have a high, rounded head cap continuous with the body contour. The labial disc is fused with the medial lips to form an elongated lip structure. The head region is not marked by incomplete annulations. Male stylet robust, 20.8-23.0 μm long with rounded knobs; the DGO is 2.5-4.5 μm. The stylet of second-stage juveniles (J2) is 12.0-13.5 μm long and the DGO to the stylet base is 2.3-3.3 μm. The J2 tail is conoid with finely rounded terminus and is 40.0-48.5 μm long. Biochemically, the esterase phenotype L3 (: 1.05, 1.10, 1.25) is unique and is the most useful character to differentiate M. luci n. sp. from all other Meloidogyne species. Reproduction is by mitotic parthenogenesis (2n = 42-46 chromosomes). In a differential host test, the population from Lavandula spica, Caxias do Sul, RS State, Brazil, reproduced on tomato cv. Rutgers, tobacco cv. NC95 and pepper cv. California Wonder. No reproduction occurred on watermelon cv. Charleston Gray, cotton cv. Deltapine 61 or peanut cv. Florunner. In Neighbour-Joining analyses of ITS and D2-D3 rRNA sequences, populations of M. luci n. sp. from Brazil, Chile and Iran clustered together and were clearly separated from other Meloidogyne spp., thus confirming that all three populations are very similar and conspecific.

Major emerging problems with minor meloidogyne species

Root-knot nematodes (Meloidogyne spp.) represent one of the most polyphagous genera of plant-parasitic nematodes. To date, close to 100 valid species are recognized. In contrast to the size of the genus, the majority of past research focused on a small number of species, i.e., the so-called 'major' species M. arenaria, M. hapla, M. incognita, and M. javanica. This review highlights recent work aimed at 'minor' root-knot nematodes: M. chitwoodi, M. fallax, M. minor, M. enterolobii (=M. mayaguensis), M. exigua, and M. paranaensis. Some of these species have been described only recently. After a brief profile of each species, identification methods and their application in Meloidogyne spp. are summarized. Intraspecific variation and its impact on plant resistance breeding are discussed and interactions between M. enterolobii and Fusarium solani are highlighted as an example of synergistic interactions with other plant pathogens. Future research on Meloidogyne spp. is not only shaped by recent breakthroughs such as completing the genome sequences of M. hapla and M. incognita, but is also influenced by changes in agriculture. Taken together, the aim of this review is to draw attention to previously neglected and newly described Meloidogyne spp. that are developing into major problems for agriculture in tropical and temperate climates.