Location: Crops Pathology and Genetics Research
Project Number: 2032-22000-017-072-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 15, 2025
End Date: Sep 14, 2026
Objective:
This agreement aims to develop genomic and transcriptomic resources for Meloidogyne floridensis and Meloidogyne incognita, two root-knot nematodes impacting almond production. M. floridensis, a recently introduced species, can overcome resistance in commonly used rootstocks, posing a major threat to the industry. The Cooperator will generate high-quality, chromosome-level genome assemblies using long-read and Hi-C sequencing, and perform stage-specific transcriptome sequencing to identify genes linked to parasitism and resistance-breaking. An in vitro almond-nematode pathosystem will be established to validate findings and support resistance screening. The research is urgently needed to support almond growers, stakeholders, and rural communities, as this emerging disease could be devastating to California’s multibillion-dollar almond industry. The outcomes will aid in diagnostic development and resistant rootstock breeding for long-term nematode management.
Approach:
To achieve the objectives, the Cooperator will generate high-quality, chromosome-level genome assemblies for Meloidogyne floridensis and Meloidogyne incognita. High molecular weight DNA will be extracted from nematodes and sequenced using long-read technology, with additional short-read sequencing for error correction. Hi-C sequencing will be applied to enable chromosome-level scaffolding and improve structural resolution. These assemblies will support comparative genomic analysis to identify genetic determinants linked to host adaptation and resistance evasion.
To enhance functional annotation, the Cooperator will conduct stage-specific transcriptome sequencing across multiple nematode life stages, including eggs, infective juveniles, and mature females. Full-length isoform sequencing will be used to improve gene prediction and enable analysis of genes associated with parasitism, host interaction, and development.
An in vitro almond-nematode pathosystem will be developed to study plant-nematode interactions under controlled conditions. This system will enable reproducible screening of rootstocks and facilitate experimental validation of genomic findings. Data will be analyzed using bioinformatics pipelines for genome assembly, gene annotation, and expression profiling. Together, these approaches will provide critical resources for diagnostic tool development and resistance breeding to manage emerging nematode threats in almond production.