Location: Crop Germplasm Research
Project Number: 3091-21000-046-016-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Apr 17, 2026
End Date: Apr 16, 2027
Objective:
Pecan production in the southeastern United States is increasingly threatened by rising disease pressure, unpredictable weather patterns, and escalating production costs. Among these challenges, pecan scab remains the most limiting constraint to yield and nut quality. Growers currently rely heavily on fungicide programs that are costly, weather-dependent, and environmentally burdensome. Even with intensive spray schedules, disease escapes are common in wet years, resulting in significant economic losses across the industry. Developing cultivars with durable, broad-spectrum scab resistance is the most effective long-term strategy for reducing fungicide use and improving orchard sustainability. However, breeding progress has been slowed by the complex and poorly characterized genetic architecture of scab resistance. Multiple pathotypes of Venturia effusa interact with host genotypes in ways that obscure resistance mechanisms and complicate phenotypic selection. As a result, breeders lack robust markers and validated genomic targets needed to efficiently incorporate resistance into new cultivars. This project addresses these limitations directly by expanding the number of mapping progenies, increasing the resolution of QTL detection, and fine-mapping known resistance loci. The availability of haplotype-resolved genomes for all parents, combined with controlled inoculation assays and high-density SNP genotyping, provides an unprecedented opportunity to dissect resistance at a level of precision not previously possible in pecan. The resulting markers and candidate genes will substantially accelerate marker-assisted selection, improve breeding cycle efficiency, and increase the likelihood of developing cultivars with durable resistance that also meet commercial quality standards. The long-term impact of this work will be significant: fewer fungicide applications, lower production costs, improved environmental stewardship, and increased yield stability for growers. This research directly supports the development of a more sustainable and resilient pecan industry for the region.
Approach:
Quantitative Trait Loci (QTL) analysis will proceed through four major steps:
1. Constructing the mapping populations
2. Phenotyping
3. Genotyping the populations
4. Analyzing marker–trait associations
Mapping populations have been developed by the Cooperator from reciprocal crosses involving two resistant parents ('Lakota' and 'Elliott') and two susceptible parents ('Pawnee' and 'Schley') (Table 1). Seedlings from these populations were produced in 2024 and germinated in spring 2025. Importantly, haplotype-resolved genomes are available for all four parents.
Robust phenotyping is essential for generating reliable trait data for QTL mapping. The Cooperator has developed a greenhouse-based inoculation system in which seedling populations are exposed to genetically pure scab isolates under controlled environmental conditions. Multiple genetically pure scab isolates have been isolated from each susceptible parent and are available through the Cooperator for screening these populations. Leaf wetness, critical for infection, is provided using large ultrasonic humidifiers. Seedlings are monitored for 2–3 weeks and then rated for disease severity using validated Standard Area Diagrams developed by USDA ARS (Hilton et al., 2024). Disease ratings were completed by the Cooperator in 2025 and will continue next season.
Because resistance traits cannot be interpreted without a precise genomic framework, high-density genetic maps are required to convert marker–trait associations into meaningful genomic intervals. High-quality SNP markers will be generated using Data2Bio’s tGBS genotyping-by-sequencing technology (Ott et al., 2017) low-coverage whole genome sequencing of each individual, followed by haplotype mapping to the existing parental genomes. USDA will work with the Cooperator to perform the analyses to construct parental genetic maps in JoinMap following the double pseudo-testcross strategy. Marker grouping and ordering will produce 16 linkage groups corresponding to the pecan chromosomes.
Phenotypic data will be integrated with the genetic maps to identify QTL associated with scab resistance using R/qtl. Interval mapping and multiple-QTL modeling will be employed to detect significant associations. Genome-wide LOD thresholds will be determined via permutation testing. For each significant QTL, support intervals and the proportion of phenotypic variance explained will be calculated. Candidate genes will then be identified within the 2-LOD support interval of each QTL, focusing on the favorable haplotypes of resistant parents.