Plant-Parasitic Nematodes and their Effects on Ornamental Plants: A Review

Worldwide, the ornamental plant industry is estimated to be valued at $70 billion, with the United States' ornamental plant industry valued at $4.8 billion in 2020. Ornamental plants are cultivated for numerous reasons worldwide, such as decorative, medicinal, social, and utility purposes, making the ornamental field a high growth industry. One of the main pathogen groups affecting the yield and growth of the ornamental plant industry is plant-parasitic nematodes, which are microscopic roundworms that feed on plant parts causing significant yield loss. There are many kinds of plant-parasitic nematodes that affect ornamental plants, with the main genera being Meloidogyne spp., Aphelenchoides spp., Paratylenchus spp., Pratylenchus spp., Helicotylenchus spp., Radopholus spp., Xiphinema spp., Trichodorus spp., Paratrichodorus spp., Rotylenchulus spp., and Longidorus spp. The aim of this review is to focus on the effects, hosts, and symptoms of these major plant-parasitic nematodes on ornamental plants and synthesize current management strategies in the ornamental plant industry.

Exploring Machine Learning Algorithms to Unveil Genomic Regions Associated With Resistance to Southern Root-Knot Nematode in Soybeans

Southern root-knot nematode [SRKN, Meloidogyne incognita (Kofold & White) Chitwood] is a plant-parasitic nematode challenging to control due to its short life cycle, a wide range of hosts, and limited management options, of which genetic resistance is the main option to efficiently control the damage caused by SRKN. To date, a major quantitative trait locus (QTL) mapped on chromosome (Chr.) 10 plays an essential role in resistance to SRKN in soybean varieties. The confidence of discovered trait-loci associations by traditional methods is often limited by the assumptions of individual single nucleotide polymorphisms (SNPs) always acting independently as well as the phenotype following a Gaussian distribution. Therefore, the objective of this study was to conduct machine learning (ML)-based genome-wide association studies (GWAS) utilizing Random Forest (RF) and Support Vector Machine (SVM) algorithms to unveil novel regions of the soybean genome associated with resistance to SRKN. A total of 717 breeding lines derived from 330 unique bi-parental populations were genotyped with the Illumina Infinium BARCSoySNP6K BeadChip and phenotyped for SRKN resistance in a greenhouse. A GWAS pipeline involving a supervised feature dimension reduction based on Variable Importance in Projection (VIP) and SNP detection based on classification accuracy was proposed. Minor effect SNPs were detected by the proposed ML-GWAS methodology but not identified using Bayesian-information and linkage-disequilibrium Iteratively Nested Keyway (BLINK), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Enriched Compressed Mixed Linear Model (ECMLM) models. Besides the genomic region on Chr. 10 that can explain most of SRKN resistance variance, additional minor effects SNPs were also identified on Chrs. 10 and 11. The findings in this study demonstrated that overfitting in GWAS may lead to lower prediction accuracy, and the detection of significant SNPs based on classification accuracy limited false-positive associations. The expansion of the basis of the genetic resistance to SRKN can potentially reduce the selection pressure over the major QTL on Chr. 10 and achieve higher levels of resistance.

Esophageal Gland RNA-Seq Resource of a Virulent and Avirulent Population of the Soybean Cyst Nematode Heterodera glycines

The soybean cyst nematode Heterodera glycines is the most economically devastating pathogen of soybean in the United States and threatens to become even more damaging through the selection of virulent nematode populations in the field that can overcome natural resistance mechanisms in soybean cultivars. This pathogen, therefore, demands intense transcriptomic/genomic research inquiries into the biology of its parasitic mechanisms. H. glycines delivers effector proteins that are produced in specialized gland cells into the soybean root to enable infection. The study of effector proteins, thus, is particularly promising when exploring novel management options against this pathogen. Here, we announce the availability of a gland cell-specific RNA-seq resource. These data represent an expression snapshot of gland cell activity during early soybean infection of a virulent and an avirulent H. glycines population, providing a unique and highly valuable resource for scientists examining effector biology and nematode virulence.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Impact of Grapevine (Vitis vinifera) Varieties on Reproduction of the Northern Root-Knot Nematode (Meloidogyne hapla)

One of the most commonly encountered plant-parasitic nematodes in eastern Washington Vitis vinifera vineyards is Meloidogyne hapla; however, limited research exists on the impact of this nematode on V. vinifera. The objectives of this research were to determine the impact of M. hapla on Chardonnay and Cabernet Sauvignon vine establishment and to determine the host status of V. vinifera varieties/clones predominantly grown in Washington to M. hapla. In a microplot experiment, Chardonnay and Cabernet Sauvignon vines were planted into soil inoculated with different densities of M. hapla; population dynamics of M. hapla and vine performance were monitored over 3 yr. In greenhouse experiments, several clones representing five V. vinifera varieties, Chardonnay, Riesling, Cabernet Sauvignon, Merlot, and Syrah, were evaluated as hosts for M. hapla. In both microplot and greenhouse experiments, white varieties were significantly better hosts than red varieties. In the greenhouse experiments, Chardonnay and Riesling had 40% higher reproduction factor values than Syrah and Merlot, however, all varieties/clones screened were good hosts for M. hapla (reproduction factors > 3). In the microplot experiment, M. hapla eggs/g root were 4.5 times greater in Chardonnay compared to Cabernet Sauvignon 3 yr after planting but there was no evident impact of M. hapla on vine establishment.

Spatial Distribution of Plant-Parasitic Nematodes in Semi-Arid Vitis vinifera Vineyards in Washington

The most commonly encountered plant-parasitic nematodes in eastern Washington Vitis vinifera vineyards are Meloidogyne hapla, Mesocriconema xenoplax, Pratylenchus spp., Xiphinema americanum, and Paratylenchus sp.; however, little is known about their distribution in the soil profile. The vertical and horizontal spatial distribution of plant-parasitic nematodes was determined in two Washington V. vinifera vineyards. Others variables measured in these vineyards included soil moisture content, fine root biomass, and root colonization by arbuscular mycorhizal fungi (AMF). Meloidogyne hapla and M. xenoplax were aggregated under irrigation emitters within the vine row and decreased with soil depth. Conversely, Pratylenchus spp. populations were primarily concentrated in vineyard alleyways and decreased with depth. Paratylenchus sp. and X. americanum were randomly distributed within the vineyards. Soil water content played a dominant role in the distribution of fine roots and plant-parasitic nematodes. Colonization of fine roots by AMF decreased directly under irrigation emitters; in addition, galled roots had lower levels of AMF colonization compared with healthy roots. These findings will help facilitate sampling and management decisions for plant-parasitic nematodes in Washington semi-arid vineyards.