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ARS Home » Pacific West Area » Wapato, Washington » Temperate Tree Fruit and Vegetable Research » Research » Research Project #442488

Research Project: Exploring Differences in P. allius Populations through Whole-genome Sequencing and the Effect of Different Potato Cultivars on Population Fecundity

Location: Temperate Tree Fruit and Vegetable Research

Project Number: 2092-21220-003-017-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2022
End Date: Oct 30, 2023

Project objectives are two-fold: 1) Use of whole-genome sequencing to compare P. allius populations originating from North Dakota and Washington states. 2) Use of controlled greenhouse trials to compare nematode fecundity between North Dakota and Washington state P. allius populations when maintained on different potato cultivars.

Objective 1 is to be completed by Cooperator (Whole-genome sequencing of P. allius populations from ND and WA): Soil samples will be collected from known P. allius infested potato fields from North Dakota and Washington. Stubby root nematodes will be extracted from soil and then identified and quantified using a microscope to determine the population density. The nematode populations will be increased in the infested soil using a susceptible potato cultivar in the greenhouse. The ultra-low DNA input protocol will be selected owing to the small genome size and low initial DNA requirements. For the preparation of genomic DNA, 500 mixed-stage nematodes of P. allius from each location will be crushed in liquid nitrogen and high-quality DNA will be extracted. Whole genome sequencing of P. allis will be performed at Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign. This method was reported to sequence the genome of root-knot nematode Meloidogyne chitwoodi, an important pest of potato in the Pacific Northwest.