An Ephemeral Sexual Population of Phytophthora infestans in the Northeastern United States and Canada

Phytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013, 20 rare and diverse genotypes of P. infestans were detected in a region that centered around central New York State. The ratio of A1 to A2 mating types among these genotypes was close to the 50:50 ratio expected for sexual recombination. These genotypes were diverse at the glucose-6-phosphate isomerase locus, differed in their microsatellite profiles, showed different banding patterns in a restriction fragment length polymorphism assay using a moderately repetitive and highly polymorphic probe (RG57), were polymorphic for four different nuclear genes and differed in their sensitivity to the systemic fungicide mefenoxam. The null hypothesis of linkage equilibrium was not rejected, which suggests the population could be sexual. These new genotypes were monomorphic in their mitochondrial haplotype that was the same as US-22. Through parentage exclusion testing using microsatellite data and sequences of four nuclear genes, recent dominant lineages US-8, US-11, US-23, and US-24 were excluded as possible parents for these genotypes. Further analyses indicated that US-22 could not be eliminated as a possible parent for 14 of the 20 genotypes. We conclude that US-22 could be a parent of some, but not all, of the new genotypes found in 2010 and 2011. There were at least two other parents for this population and the genotypic characteristics of the other parents were identified

An Illustrated Manual on Soil Health Assessment Protocols and Management Options for Training and Outreach

The Cornell Soil Health Team has made considerable progress in promoting soil health literacy, developing cost-effective protocols for assessing the health status of soils in New York, demonstrating soil health management options, and conducting hands-on trainings and workshops. The Cornell Soil Health Team has prepared and will soon disseminate an illustrated, user-friendly, color manual on soil health constraints, assessment protocols and management practices for improving the health status of soils in New York State and the Northeast region. The primary purpose of the manual is to: 1) provide an overview of the concept of soil health;2) describe soil constraints and soil quality issues common to soils in New York and the Northeast region, especially in vegetable and field crop production systems; 3) provide guidelines on how-to conduct in-field soil health assessment;4) provide an overview of laboratory methods used to assess the health status of soil; 5) identify management options for improving soil health based on identified constraints ;6) increase awareness of and literacy on soil health issues; and 7) provide a list of additional resources on soil health and soil health related topics

Soil Sampling for Plant-Parasitic Nematode Assessment

NYS IPM Type: Vegetables IPM Fact SheetDiagnosis of nematode damage and management on an as-needed basis requires assessing nematode soil infestation levels in representative soil samples collected from the target field or a section of the field. Inclusion of roots in the collected soil samples is advantageous and might be necessary in the case of sedentary and migratory endoparasites including the root-knot, cyst and lesion nematodes that complete part or their entire lifecycle in host tissue. However, the accuracy of diagnosing the problem nematode(s) involved and especially determining the level of its infestation will depend largely on the thoroughness of the sampling method, time of sampling, handling and storage of the samples as well as on the biology of nematode species involved

Species of Dickeya and Pectobacterium Isolated during an Outbreak of Blackleg and Soft Rot of Potato in Northeastern and North Central United States

An outbreak of bacterial soft rot and blackleg of potato has occurred since 2014 with the epicenter being in the northeastern region of the United States. Multiple species of Pectobacterium and Dickeya are causal agents, resulting in losses to commercial and seed potato production over the past decade in the Northeastern and North Central United States. To clarify the pathogen present at the outset of the epidemic in 2015 and 2016, a phylogenetic study was made of 121 pectolytic soft rot bacteria isolated from symptomatic potato; also included were 27 type strains of Dickeya and Pectobacterium species, and 47 historic reference strains. Phylogenetic trees constructed based on multilocus sequence alignments of concatenated dnaJ, dnaX and gyrB fragments revealed the epidemic isolates to cluster with type strains of D. chrysanthemi, D. dianthicola, D. dadantii, P. atrosepticum, P. brasiliense, P. carotovorum, P. parmentieri, P. polaris, P. punjabense, and P. versatile. Genetic diversity within D. dianthicola strains was low, with one sequence type (ST1) identified in 17 of 19 strains. Pectobacterium parmentieri was more diverse, with ten sequence types detected among 37 of the 2015–2016 strains. This study can aid in monitoring future shifts in potato soft rot pathogens within the U.S. and inform strategies for disease management

An Ephemeral Sexual Population of <i>Phytophthora infestans</i> in the Northeastern United States and Canada

<div><p><i>Phytophthora infestans</i>, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of <i>P. infestans</i>. In 2010 and 2011, but not in 2012 or 2013, 20 rare and diverse genotypes of <i>P. infestans</i> were detected in a region that centered around central New York State. The ratio of A1 to A2 mating types among these genotypes was close to the 50∶50 ratio expected for sexual recombination. These genotypes were diverse at the <i>glucose-6-phosphate isomerase</i> locus, differed in their microsatellite profiles, showed different banding patterns in a restriction fragment length polymorphism assay using a moderately repetitive and highly polymorphic probe (RG57), were polymorphic for four different nuclear genes and differed in their sensitivity to the systemic fungicide mefenoxam. The null hypothesis of linkage equilibrium was not rejected, which suggests the population could be sexual. These new genotypes were monomorphic in their mitochondrial haplotype that was the same as US-22. Through parentage exclusion testing using microsatellite data and sequences of four nuclear genes, recent dominant lineages US-8, US-11, US-23, and US-24 were excluded as possible parents for these genotypes. Further analyses indicated that US-22 could not be eliminated as a possible parent for 14 of the 20 genotypes. We conclude that US-22 could be a parent of some, but not all, of the new genotypes found in 2010 and 2011. There were at least two other parents for this population and the genotypic characteristics of the other parents were identified.</p></div

Discriminant Analysis of Principal Components (DAPC) using 12 microsatellite loci.

<p>This scatterplot shows the first two principal components of the DAPC of <i>Phytophthora infestans</i> genotypes found in the United States. Groups are shown by different colors and inertia ellipses, while dots represent individual strains. Cluster 1 includes lineages US-6, US-7, US-11, US-12, and US-16; Cluster 2 includes isolates in lineage US-23; Cluster 3 includes lineages GDT-02, GDT-07, GDT-13, GDT-18, and GDT-20; Cluster 4 includes lineages GDT-03, GDT-04, GDT-08, GDT-08.1, GDT-14 and GDT-15; Cluster 5 includes lineages US-8, US-14, US-20, and US-24; Cluster 6 includes lineages GDT-05, GDT-06, GDT-09, GDT-10, GDT-11, GDT-12, GDT-16, GDT-17, and GDT-19; Cluster 7 includes lineages US-1; and Cluster 8 included lineages US-17, US-19, US-21 and GDT-01.</p

Spatial occurrence of the NYS-2010/11 population of <i>Phytophthora infestans</i> detected in western New York State.

<p>Genotypes that are underlined are those detected in 2010 all other genotypes were detected in 2011. Genotypes shown in bold are those that were found in several counties (GDT-01, GDT-04, and GDT-08). In New York State we detected only A1 individuals in six counties, and only A2 individuals in another three counties. However, both A1 and A2 individuals were reported from yet two other counties. Because of our limited sample size, we cannot conclude with certainty that both mating types were not present in counties where only a single mating type was detected.</p

Replicated isolates included as controls in the GBS analysis, and average genetic distances among replicates and within their respective lineages.

<p>Replicated isolates included as controls in the GBS analysis, and average genetic distances among replicates and within their respective lineages.</p

Neighbor-joining tree of US-24 isolates.

<p>Bootstrap values below 50% are not shown. Taxa are labeled by isolate code: collection year: collection state: host (P = potato, T = tomato, NA = information not available).</p