Genomic Analyses of Globodera pallida, A Quarantine Agricultural Pathogen in Idaho.

Sulochana K Wasala,Dee R Denver,Inga A Zasada,Louise-Marie Dandurand,Dana K Howe

doi:10.3390/pathogens10030363

Abstract

Globodera pallida is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since it was discovered in Idaho in 2006, eradication efforts have aimed to contain and eradicate G. pallida through phytosanitary action and soil fumigation. In this study, we investigated genome-wide patterns of G. pallida genetic variation across Idaho fields to evaluate whether the infestation resulted from a single or multiple introduction(s) and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples (~1,042,000 individuals) were collected and analyzed, representing five different fields in Idaho, a greenhouse population, and a field in Scotland that was used for external comparison. According to genome-wide allele frequency and fixation index (Fst) analyses, most of the genetic variation was shared among the G. pallida populations in Idaho fields pre-fumigation, indicating that the infestation likely resulted from a single introduction. Temporal patterns of genome-wide polymorphisms involving (1) pre-fumigation field samples collected in 2007 and 2014 and (2) pre- and post-fumigation samples revealed nucleotide variants (SNPs, single-nucleotide polymorphisms) with significantly differentiated allele frequencies indicating genetic differentiation. This study provides insights into the genetic origins and adaptive potential of G. pallida invading new environments.

Highlights

As major agricultural pathogens, plant-parasitic nematodes cause numerous diseases in plants and are responsible for more than US$100 billion in annual agriculture loss worldwide [1,2]
To compare patterns of genome-wide genetic variation among G. pallida populations from Idaho fields, the whole genomes from 53 cyst samples were sequenced; a population maintained in the greenhouse and a population from Scotland were analyzed for comparative purposes
This study focused on a whole genome sequencing approach followed by population genetic analyses of a recent G. pallida infestation in Idaho

Summary

Introduction

Plant-parasitic nematodes cause numerous diseases in plants and are responsible for more than US$100 billion in annual agriculture loss worldwide [1,2]. Among the top three most significant plant-parasitic nematodes are the potato cyst nematodes Globodera pallida and Globodera rostochiensis [3]. These nematodes have a narrow host range that includes potato, tomato, and some solanaceous weeds, they can reduce potato yield by 80% [4,5]. Potato cyst nematodes are widely distributed in Europe; they are not widespread in North America [6]. Both species are considered quarantine pests in the U.S Globodera pallida was first discovered in Idaho in April 2006 [7].

Methods

Results

Conclusion