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Research Project: Use performance of 300 hybrids in established trials to map Huanglongbing tolerance/resistance genes and release superior new rootstocks

Location: Subtropical Insects and Horticulture Research

Project Number: 6034-21000-020-011-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Jan 4, 2022
End Date: Sep 14, 2024

1. Identify the best of new hybrid rootstocks for commercial use in HLB-endemic and HLB-threatened areas from multi-year rootstock performance in the field trials. 2. Leverage quantitative field performance traits of 300 rootstocks to locate and map new genes for HLB-tolerance/resistance, along with other traits of horticultural importance.

Objective 1. Beginning in 2014 ARS researchers have collected yearly metrics on tree survival, tree and canopy characteristics, fruit yield and quality, and yield efficiency across 14 replicated trials spanning three locations. Each trial contains three to four common commercial rootstocks for comparison. Rootstock hybrids with performance superior to the current best HLB-tolerant commercial rootstocks will be identified to select a minimum of three new rootstock cultivars for release to growers before the end of 2023. Researchers will also evaluate the level of resistance of these selected rootstocks to other soilborne diseases relevant to citrus including Phytophthora root rot and gummosis and Fusarium dry root rot and wilt. Researchers will assess the root pathogens incidence and abundance levels in the field for HLB-tolerant rootstocks compared to commercial rootstock controls using an amplicon-based DNA metabarcoding approach. Molecular-based data analysis will be validated with plant bioassays that measure resistance levels to Phytophthora and Fusarium pathogens relative to commercial rootstocks with known susceptibility to these pathogens. Objective 2. The genetic composition of the 300 rootstock hybrids combined with measurements of tree performance and fruit quality enables genome-wide association mapping to dissect the genetic basis of traits associated with tolerance to HLB in the field. This approach has been successful in uncovering gene-trait associations in field trials in other crop species. To facilitate genetic mapping researchers will perform whole-genome Illumina sequencing of the rootstock hybrids and their 33 founding parents to capture genetic information and high-quality polymorphisms will be discovered using standard practices. Researchers will then develop convenient and affordable molecular markers tightly linked to genomic regions discovered to have significant effects on rootstock-mediated HLB-tolerance. These markers will enable marker-assisted selection for HLB-tolerance to accelerate future rootstock breeding efforts by reducing the number of hybrid progeny with poor field performance included in trials.