Incidence, Population Density, and Spatial Heterogeneity of Plant-Parasitic Nematodes in Corn Fields in Ohio

Screening and Validation of Leaf Width-Related Genes in Inbred Maize Lines

Leaf width is a key determinant of planting density and photosynthetic efficiency. In an effort to determine which genes regulate maize plant leaf width, we performed a genome-wide association study (GWAS) of 1.49 × 106 single nucleotide polymorphisms (SNPs) in 80 sequenced backbone inbred maize lines in Jilin Province, China, based upon phenotypic leaf width data from two years. In total, 14 SNPs were identified as being significantly related to leaf width (p < 0.000001), with these SNPs being located on chromosomes 1, 2, 3, 5, 6, 7, 8, and 9. A total of five candidate genes were identified within a mean linkage disequilibrium (LD) distance of 9.7 kb, with a significant SNP being identified within the Zm00001d044327 candidate gene. RNA was then isolated from 12 different inbred maize lines from this GWAS study cohort and was used to conduct qPCR analyses which revealed significant differences in Zm00001d044327 expression among strains exhibiting significant differences in leaf width. Based on an assessment of EMS mutant lines harboring a conserved amino acid stop mutation and two non-synonymous mutations in Zm00001d044327 that exhibited a narrow leaf width, these data suggested that Zm00001d044327 is a key regulator of maize leaf width.

Identification of Meloidogyne Species on Traditional Chinese Medicine Plants in the Qinling Mountain Area of China and Their Aggressiveness to Different Medicinal Herbs

Root-knot nematodes (Meloidogyne spp.) are plant-parasitic nematodes that cause serious damage worldwide. There are many species of traditional Chinese medicine (TCM) plants, but only a few have been reported to be infected by Meloidogyne species. From 2020 to 2022, a survey was conducted in the Qinling mountain area, which is the main production region of TCM plants in China. Obvious galling symptoms were observed on the root systems of 15 species of TCM plants. Females were collected from diverse diseased TCM plants and subsequently identified at morphological and molecular levels. Among the 20 diseased root samples collected, Meloidogyne hapla populations were identified in 12 samples (60%), and M. incognita populations were identified in eight samples (40%). Among the 15 species of diseased TCM plants, eight species, namely, Scutellaria baicalensis, Leonurus japonicus, Dioscorea zingiberensis, Cornus officinalis, Viola philippica, Achyranthes bidentata, Senecio scandens, and Plantago depressa, were reported to be infected by Meloidogyne species for the first time. The host status of five species of TCM plants for two M. hapla isolates and one M. incognita isolate from TCM plants in this study was then evaluated. Differences in TCM plants' response to nematode infection were apparent when susceptibility was evaluated by the egg counts per gram of fresh root and the reproduction factor of the nematodes. Among the five species of TCM plants tested, Salvia miltiorrhiza and Gynostemma pentaphyllum were the most susceptible, while S. baicalensis and V. philippica were not considered suitable hosts for M. hapla or M. incognita.

Prevalence of pest nematodes associated with soybean (Glycine max) in Wisconsin from 1998 to 2021

The prevalence of Heterodera glycines and other cyst and vermiform genera was determined from 8,009 soil samples over two decades. Prevalence of cyst nematodes for farms increased from 16% in 1998 to 1999, reaching a peak of 40%, with marked differences among Wisconsin's nine agricultural districts in how much the odds of a positive test increased. Estimates at the sample scale also increased over time but peaked at 29%. Assay of all nematodes beginning in 2012 showed Pratylenchus, Helicotylenchus, and Xiphinema to be more prevalent in Wisconsin soybean fields than cyst nematodes. Prevalence estimates for Pratylenchus and Helicotylenchus for soybean and rotation crops ranged from 76 to 89% and 58 to 83%, respectively. Species identification of Pratylenchus from a subset of the samples revealed six species. The majority of cyst-positive samples were infested with Pratylenchus, and count data showed that the number of cyst eggs and juveniles per 100 cm3 soil was 60% lower in samples positive for Pratylenchus. The influence was reciprocal, as Pratylenchus population densities were 41% lower in samples positive for cyst nematodes, suggesting a competitive interaction. The Wisconsin soybean nematode testing program provides a useful model for estimating nematode prevalence using citizen-based surveys.

Sampling Depth and Crop Growth Stage Affect Estimates of the Population Density of Lesion Nematodes (Pratylenchus spp.) in Corn Fields in Ohio

The effects of sampling depth and crop growth stage on the population density of lesion nematodes were investigated in three commercial fields in Wayne and Fulton Counties, Ohio, during the 2016 and 2017 growing seasons. Soil samples were collected at five growth stages by removing 15 soil cores to a depth of 70 cm from each of 25 plots per field-year. Cores were divided into seven 10-cm sections, and nematodes were extracted from the soil and root fractions of each of them. Pratylenchus crenatus and P. thornei were detected in approximately 84 and 78% of the samples collected in Wayne and Fulton Counties, respectively. Depth significantly affected total population density of both species as well as densities in the soil and root factions in all field-years, but the effects of growth stage and its interaction with depth varied with field-year. In most cases, mean population densities were higher from 10 to 40 cm soil depth than at the reference 40 to 50 cm depth and lower from 50 to 70 cm. There were quadratic relationships between population density (on the log link scale) and depth, with the highest peaks in estimated predicted densities generally occurring between 20 and 40 cm, depending on crop growth stage and growing conditions. These findings suggest that the standard practice of sampling between growth stages V3 and V6 to a depth of 45 to 50 cm and using the entire core for extraction and enumeration could lead to underestimation of population densities of P. crenatus and P. thornei.

Whole-genome sequencing and analysis of Streptomyces strains producing multiple antinematode drugs

Background

Nematodes are parasitic animals that cause over 100 billion US dollars loss in agricultural business. The whole-genomes of two Streptomyces strains, Streptomyces spectabilis KCTC9218^T and Streptomyces sp. AN091965, were sequenced. Both strains produce spectinabilin, an antinematode drug. Its secondary metabolism was examined to aid the development of an efficient nematicidal drug-producing host strain.

Results

The whole-genome sequences of S. spectabilis KCTC9218^T and Streptomyces sp. AN091965 were analyzed using PacBio and Illumina sequencing platforms, and assembled using hybrid methodology. The total contig lengths for KCTC9218^T and AN091965 were 9.97 Mb and 9.84 Mb, respectively. A total of 8,374 and 8,054 protein-coding genes, as well as 39 and 45 secondary metabolite biosynthetic gene clusters were identified in KCTC9218^T and AN091965, respectively. 18.4 ± 6.45 mg/L and 213.89 ± 21.30 mg/L of spectinabilin were produced by S. spectabilis KCTC9218^T and Streptomyces sp. AN091965, respectively. Pine wilt disease caused by nematode was successfully prevented by lower concentration of spectinabilin injection than that of abamectin recommended by its manufacturer. Production of multiple antinematode drugs, including spectinabilin, streptorubin B, and undecylprodigiosin was observed in both strains using high-resolution liquid chromatography mass spectrometry (LC–MS) analysis.

Conclusions

Whole-genome sequencing of spectinabilin-producing strains, coupled with bioinformatics and mass spectrometry analyses, revealed the production of multiple nematicidal drugs in the KCTC9218^T and AN091965 strains. Especially, Streptomyces sp. AN091965 showed high production level of spectinabilin, and this study provides crucial information for the development of potential nematicidal drug producers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08847-4.

Cropping Practices and Soil Properties Associated with Plant-Parasitic Nematodes in Corn Fields in Ohio

Ten morphological groups of plant-parasitic nematodes (spiral, lesion, lance, dagger, stunt, pin, ring, stubby-root, cyst, and miscellaneous tylenchids) were detected in corn fields in Ohio, but the presence and population density of these groups varied among fields. Binary and ordinal logistic regression models were fitted to the data to estimate the odds of each group being present, and the lesion, lance, spiral, and pin nematode population densities being at moderate-high risk levels based on soil region, cropping sequence, tillage, and soil pH, silt content, and electrical conductivity. All covariates were associated with at least one nematode group, but soil region had the greatest and most consistent effect. Dagger and ring nematodes were more likely to be present in region 6 than in any of the other regions, whereas lance, stunt, pin, stubby-root, and spiral nematodes were more likely to be present in regions 1 to 5 than 6. Spiral, lance, and pin nematode population densities were more likely to be at moderate-high risk levels in regions 3 and 4 than in region 6. Fields under conservation tillage were two times more likely to have moderate-high risk lance nematode population densities than fields under conventional tillage. Similarly, pin nematode population densities were two times more likely to be at moderate-high risk levels in fields under rotation than in continuous corn. For every unit increase in soil pH, the odds of the spiral nematode population density being at moderate-high risk levels increased by 43%, but the odds of the lesion and pin nematode population densities being at the same risk level decreased by 63 and 29%, respectively. The predicted probability of lesion and lance population densities being at moderate-high risk levels decreased as the silt content of the soil increased. These finding will be useful for developing future nematode sampling protocols and for assessing the risk associated with nematodes in corn fields in Ohio.