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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Research Project #441206

Research Project: Development of Marketable Root-knot Nematode Resistant Sweetpotato Varieties: Translation of Genomics & Phenomics into On-farm Management Solutions

Location: Vegetable Research

Project Number: 6080-22000-030-006-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Oct 1, 2021
End Date: Aug 31, 2025

This project proposes to use next generation genomic and phenomic breeding strategies and integrated crop management production methods to: 1. Identify the factors that mediate resistance to M. enterolobii (Me) and M. incognita (Mi) in sweetpotato. 2. Translate this knowledge into the development of market-acceptable, root-knot nematode resistant varieties. 3. Implement new nematode management strategies to support the commercial sweetpotato industry. Achievement of these goals will enable stakeholders along the American sweetpotato supply chain to maintain a competitive advantage in the U.S. and global marketplace for this superfood.

Objective 1: Accelerate breeding efforts for resistance to M. enterolobii and M. incognita by identifying genes/QTL and deploying marker-assisted/genomic selection. We have already identified two major QTL on separate linkage groups explaining >60% of the variation in gall formation and egg production for Mi and Me in two biparental mapping populations. We propose to: 1) develop KASP or similar markers and test them in our breeding germplasm; 2) conduct RNAseq studies in collaboration with PI’s at LSU and USVL to validate and improve our understanding of resistance; and 3) expand proof-of-concept genomic selection research that has already been initiated for Me resistance under the SweetGAINS project. Root shape and quality will be evaluated in marker-assisted/genomic selection experiments to ensure an integrated multi-trait breeding approach. Objective 2: Characterize sweetpotato germplasm for resistance to Me and Mi in controlled greenhouse studies. Root penetration, nematode development, and the histology of infection sites will be examined in selected susceptible and resistant sweetpotato genotypes to understand the underlying mechanisms of nematode resistance. Root system architecture will be examined in response to nematode parasitism in selected sweetpotato genotypes to determine specific root traits associated with nematode resistance. Time-scale transcriptome analysis will be used to develop a gene co-expression network to integrate with QTL results as well as microscopic observations of root histology and root architecture to validate genes and associated pathways involved in resistance mechanisms for subsequent marker development and utilization in breeding programs. Objective 3: Develop high-throughput 2D and 3D storage root phenotyping technologies for the examination of nematode infection and storage root yield and quality. The NCSU, LSU and USVL teams have exceptional experience developing technologies for root system research. High-throughput visualization and phenotyping technologies will be deployed to increase germplasm phenotyping speed and precision. Objective 4: Identify cultural and weed control practices impacting Me and Mi populations and crop damage, and evaluate how these may be integrated with chemical nematicides to provide sustainable management solutions for Me and Mi. Root-knot nematodes typically have a broad host range, and alternate plant species, including those grown as rotational or cover crops in sweetpotato systems may serve as key hosts for Me and Mi. Rotational crops in sweetpotato systems may vary in their relative host status for these nematodes and knowing their host suitability (excellent to poor or non-hosts) can provide a management tool to control nematodes. Non-host rotational crops and cover crops will be explored as a management tool to suppress Me and Mi populations. Objective 5: Present progress, economic findings, and recommendations to stakeholders through diverse platforms. Stakeholders are only likely to adopt novel varieties and control practices if they are a good fit with their current production system and are expected to have a positive net return.