Genetic diversity and phylogeny of South African Meloidogyne populations using genotyping by sequencing

Genome scans for selection signatures identify candidate virulence genes for adaptation of the soybean cyst nematode to host resistance

Plant pathogens are constantly under selection pressure for host resistance adaptation. Soybean cyst nematode (SCN, Heterodera glycines) is a major pest of soybean primarily managed through resistant cultivars; however, SCN populations have evolved virulence in response to selection pressures driven by repeated monoculture of the same genetic resistance. Resistance to SCN is mediated by multiple epistatic interactions between Rhg (for resistance to H. glycines) genes. However, the identity of SCN virulence genes that confer the ability to overcome resistance remains unknown. To identify candidate genomic regions showing signatures of selection for increased virulence, we conducted whole genome resequencing of pooled individuals (Pool-Seq) from two pairs of SCN populations adapted on soybeans with Peking-type (rhg1-a, rhg2, and Rhg4) resistance. Population differentiation and principal component analysis-based approaches identified approximately 0.72-0.79 million SNPs, the frequency of which showed potential selection signatures across multiple genomic regions. Chromosomes 3 and 6 between population pairs showed the greatest density of outlier SNPs with high population differentiation. Conducting multiple outlier detection tests to identify overlapping SNPs resulted in a total of 966 significantly differentiated SNPs, of which 285 exon SNPs were mapped to 97 genes. Of these, six genes encoded members of known stylet-secreted effector protein families potentially involved in host defence modulation including venom-allergen-like, annexin, glutathione synthetase, SPRYSEC, chitinase, and CLE effector proteins. Further functional analysis of identified candidate genes will provide new insights into the genetic mechanisms by which SCN overcomes soybean resistance and inform the development of molecular markers for rapidly screening the virulence profile of an SCN-infested field.

Genetic diversity of the recovered populations of Mesocriconema xenoplax (Nematoda: Criconematidae) from orchards in Fars province, Southern Iran

In this survey, 14 populations of Mesocriconema xenoplax were collected from the rhizosphere of eight fruit and nut trees in Fars province, Southern Iran. The phylogenetic relationships of these populations with other representatives of the species were investigated using sequences of cytochrome c oxidase subunit 1 mitochondrial gene (COI) and D2-D3 expansion fragments of 28S rDNA. Phylogenetic studies indicated a close relationship of the currently sequenced populations with known haplotype groups (HG) in the COI tree and revealed two separate lineages in the 28S rDNA tree. Moreover, the genetic diversity of the populations was analyzed using seven ISSR primers as molecular markers. The estimated genetic diversity among populations regarding associated trees and geographic regions were low values of 3.3% and 5.9%, respectively, indicating high gene flow among the recovered nematode populations. On the other hand, the estimated fixation index (FST) was higher for associated plants than for geographic regions (0.611 vs 0.504) indicating that plant-based population segregation better explains genetic diversity in this species. This work expands our knowledge of the genetic structure of this cosmopolitan species of plant-parasitic nematodes.

Characterization of Meloidogyne enterolobii intercepted from baobab (Adansonia digitata L.) seedlings from Thailand during Japanese import plant quarantine inspection

In April 2019, baobab (Adansonia digitata L.) seedlings from Thailand, exhibiting galls on the roots, were intercepted during an import plant quarantine inspection at Chubu Centrair International Airport, Japan. Root-knot nematodes (RKNs) were extracted from the galled roots of baobab seedlings and identified by morphological, morphometrical and molecular methods as the guava root-knot nematode, Meloidogyne enterolobii Yang & Eisenback. The morphology and morphometrics of the intercepted population were similar to those of the original and subsequent descriptions of M. enterolobii. The sequences of D2-D3 of 28S rRNA, mtDNA intergenic COII-16S rRNA and COI genes obtained in this study matched well (99-100% similarity) with each of the gene sequences of M. enterolobii deposited in GenBank. Phylogenetic analysis of these genes revealed that the intercepted population clustered with M. enterolobii and clearly differed from other RKN species. To the best of our knowledge, this is the first report of M. enterolobii from baobab.

Population Genetic Structure of Meloidogyne javanica Recovered from Different Regions of Iran

In a survey of root-knot nematodes in Iran, twenty-nine populations were collected from eleven provinces. All populations were identified as Meloidogyne javanica based on morphological and morphometric characteristics of females, males, J2s, and perineal patterns. Sequence Characterized Amplified Region (SCAR) primers confirmed the morphological studies, and all these populations produced a specific band in 670 bp using Fjav and Rjav primers. Genetic structure analyses using the combination of RAPD and ISSR markers revealed four different groups, which was in agreement with UPGMA cluster analyses. These four groups were related to four different geographic regions with a high geographic distance. The total estimated genetic diversity was 8%, which was a low value. Values of FST and Nm were 0.628 and 0.148, indicating that populations of these four regions were separated from each other; however, some gene flow between them could be attributed to human activities. Mantel test also revealed a negative correlation between genetic diversity and geographic distance.

Mycorrhizal fungi and Pseudomonas fluorescens application reduces root-knot nematode (Meloidogyne javanica) infestation in eggplant

Eggplant cultivation is subjected to attacks by numbers of pests and diseases from the nursery stage until harvest. Root-knot nematode (M. javanica) is one of the most significant restrictions in the successful cultivation of eggplant as it damages the crop year-round. One of the most essential classes of plant symbionts is arbuscular mycorrhizal fungi (AMF) and phosphate solubilizing bacteria (PSB), which significantly impact plant development, feeding, disease tolerance, and resistance to M. javanica. Eggplant seedlings were inoculated with two mycorrhizal fungi, Glomus mosseae (Gm) and Gigaspora gigantea (Gg), together with the phosphate-solubilizing bacteria (PSB) Pseudomonas fluorescens (Pf; ATCC-17400) under the presence of nematodes inoculation of Meloidogyne javanica as 1000 eggs of M. javanica in each pot. Observations were recorded for 9 morphological traits, 6 fruit morphometric traits using Tomato Analyzer (version 4) software program, and 4 fruit biochemical traits. Along with the data recorded for mycorrhization (%), number of galls and reaction to RKN. Plants inoculated with the consortium (Pf + Gm + Gg) performed substantially better for most traits. Furthermore, the eggplant plants treated with consortium developed the highest levels of fruit biochemical content along with the highest level of mycorrhization (68.20%). Except for certain fruit morphometric traits, the treatment containing Pf + Gg outperformed the treatment containing Pf + Gm. Overall, this research showed that AM fungi could be a sustainable solution to the eggplant RKN problem.

Recent Advances in Population Genomics of Plant-Parasitic Nematodes

Plant-parasitic nematodes are a costly burden of crop production. Ubiquitous in nature, phytoparasitic nematodes are associated with nearly every important agricultural crop and represent a significant constraint on global food security. Population genetics is a key discipline in plant nematology to understand aspects of the life strategies of these parasites, in particular their modes of reproduction, geographic origins, evolutionary histories, and dispersion abilities. Advances in high-throughput sequencing technologies have enabled a recent but active effort in genomic analyses of plant-parasitic nematodes. Such genomic approaches applied to multiple populations are providing new insights into the molecular and evolutionary processes that underpin the establishment of these nematodes and into a better understanding of the genetic and mechanistic basis of their pathogenicity and adaptation to their host plants. In this review, we attempt to update information about genome resources and genotyping techniques useful for nematologists who are thinking about initiating population genomics or genome sequencing projects. This review is intended also to foster the development of population genomics in plant-parasitic nematodes through highlighting recent publications that illustrate the potential for this approach to identify novel molecular markers or genes of interest and improve our knowledge of the genome variability, pathogenicity, and evolutionary potential of plant-parasitic nematodes.

Further observations on Meloidogyne enterolobii (Nematoda: Meloidogynidae) infecting guava (Psidium guajava) in India

Root-knot nematodes (Meloidogyne spp.) infect a large number of crops including guava. We investigated a population of Meloidogyne sp. infecting guava in the Coimbatore region of Tamil Nadu, India for identification and species confirmation. Detailed morphological and morphometric observations based on second-stage juveniles, males, females, and perineal patterns showed resemblance of the isolated population with the original and subsequent descriptions of M. enterolobii. Isozyme analysis of the young egg-laying females displayed the characteristic esterase phenotype pattern similar to that of M. enterolobii. Additionally, the identity of the nematode population was further validated by M. enterolobii specific SCAR marker and ITS rDNA. Recently published reports on the occurrence and morphological descriptions of M. enterolobii from India are largely incongruent with the original and subsequent redescriptions of the species. Here, we present the most comprehensive morphology and morphometrics of an Indian population of M. enterolobii for its authentic identification.

Meloidogyne enterolobii, a Major Threat to Tomato Production: Current Status and Future Prospects for Its Management

The guava root-knot nematode, Meloidogyne enterolobii (Syn. M. mayaguensis), is an emerging pathogen to many crops in the world. This nematode can cause chlorosis, stunting, and reduce yields associated with the induction of many root galls on host plants. Recently, this pathogen has been considered as a global threat for tomato (Solanum lycopersicum L.) production due to the lack of known resistance in commercially accepted varieties and the aggressiveness of M. enterolobii. Both conventional morphological and molecular approaches have been used to identify M. enterolobii, an important first step in an integrated management. To combat root-knot nematodes, integrated disease management strategies such as crop rotation, field sanitation, biocontrol agents, fumigants, and resistant cultivars have been developed and successfully used in the past. However, the resistance in tomato varieties mediated by known Mi-genes does not control M. enterolobii. Here, we review the current knowledge on geographic distribution, host range, population biology, control measures, and proposed future strategies to improve M. enterolobii control in tomato.

Genetic Diversity of the root-knot nematode Meloidogyne enterolobii in Mulberry Based on the Mitochondrial COI Gene

This study explores the genetic diversity and structure of Meloidogyne enterolobii in mulberry in China. The COI mitochondrial gene (mtCOI) in M.enterolobii populations in Guangdong, Guangxi, and Hunan Provinces was PCR-amplified, sequenced, and analyzed for genetic diversity. The total number of variations, haplotypes (Hap), the average number of nucleotide differences (k), haplotype diversity (H), and nucleotide diversity (π) of mtCOI were 25, 11, 4.248, 0.900, and 0.00596, respectively. Insignificant differences in Fst value (0.0169) and a high level of gene flow (7.02) were detected among the 19-mulberry root-knot nematode populations, and high genetic variation within each population and a small genetic distance among populations were observed. Both phylogenetic analyses and network mapping of the 11 haplotypes revealed a dispersed distribution pattern of 19 mulberry root-knot nematode populations and an absence of branches strictly corresponding to the 19 range sampling sites. The neutrality test and mismatch analysis indicated that mulberry root-knot nematode populations experienced a population expansion in the past. The analysis of molecular variance (AMOVA) revealed that the genetic differentiation of M. enterolobii was mainly contributed by the variation within each group. No significant correlation was found between the genetic distance and geographical distance of M. enterolobii populations. The findings of this study provide a profound understanding of the M. enterolobii population and will inform the development of strategies to combat and manage root-knot nematodes in mulberry.

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.