Genomic analyses of globodera pallida, a quarantine agricultural pathogen in Idaho

Authors: WASALA, S - Oregon State University; HOWE, D - Oregon State University; DANDURAND, L - University Of Idaho; Zasada, Inga; DENVER, D - Oregon State University

Submitted to: Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/8/2021
Publication Date: 3/18/2021
Citation: Wasala, S.K., Howe, D.K., Dandurand, L.M., Zasada, I.A., Denver, D.R. 2021. Genomic analyses of globodera pallida, a quarantine agricultural pathogen in Idaho. Pathogens. 10(3):363. https://doi.org/10.3390/pathogens10030363.
DOI: https://doi.org/10.3390/pathogens10030363

Interpretive Summary: Globodera pallida is a quarantine nematode pest that was discovered in Idaho in 2006. This species is among the most significant plant-parasitic nematodes (microscopic roundworm) worldwide, causing major damage to potato production. It is important for farmers and regulators to understand how and when this nematode was introduced into Idaho in order to eradicate it from Idaho potato fields. We used a genetic analysis approach of nematode DNA to understand if G. pallida was introduced once or multiple times into Idaho. It was found that there was very little difference in the genetics of nematodes collected from different fields in Idaho. These results are significant because they provide further evidence that G. pallida was only introduced into Idaho once. A single introduction with low genetic diversity reduces the likelihood of nematode adaptation in Idaho. The findings from this study will be used by regulators and farms to develop strategies to contain this quarantine nematode.

Technical Abstract: Globodera pallida is a quarantine nematode pest that was discovered in Idaho in 2006. This species is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since 2007, Idaho 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 likely resulted from a single introduction, and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples 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 five pre-fumigation Idaho field samples analyzed, indicating that the infestation likely resulted from a single introduction. A comparison of pre-fumigation field samples collected in 2007 and 2014 revealed nucleotide variants with significantly differentiated allele frequencies, suggesting the genes in these regions might have undergone local adaptation. A comparison of pre-and post-fumigation field samples also revealed outlier alleles, possibly reflecting the earliest stages of incipient adaptation to fumigation or other unknown stressors. Our study demonstrates the power of whole-genome sequencing strategies in providing insights into the genetic origins and evolutionary potential of parasite populations invading new environments.