High-Density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Leaf-Scab Resistance in Pecan (Carya illinoinensis)

Authors: Bhattarai, Gaurab; CAO, SHANSHAN - University Of Georgia; BENTLEY, NOLAN - University Of Texas At Austin; KLEIN, PATRICIA - University Of Texas At Austin; BOCK, CLIVE - US Department Of Agriculture (USDA); Pisani, Cristina; CONNER, PATRICK - University Of Georgia

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2024
Publication Date: 3/7/2025
Citation: Bhattarai, G., Cao, S., Bentley, N., Klein, P., Bock, C., Pisani, C., Conner, P.J. 2025. High-Density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Leaf-Scab Resistance in Pecan (Carya illinoinensis). Journal of the American Society for Horticultural Science. 150/2. https://doi.org/10.21273/JASHS05460-24.
DOI: https://doi.org/10.21273/JASHS05460-24

Interpretive Summary: Pecan scab is the most significant fungal disease affecting pecans in the Southeastern United States, making the development of a scab-resistant cultivar a top priority of pecan breeding for this region. However, due to the extended juvenile period of pecan trees, it takes nearly a decade to select suitable parent trees, perform controlled crosses, and evaluate the resulting seedlings to identify those with desirable characteristics, including scab resistance. This process requires substantial resources to maintain the trees over a long period. To facilitate DNA marker-based selection of pecan seedlings for scab resistance, a genetic study was conducted to identify DNA markers associated with leaf scab resistance. A population of 119 seedlings was developed from a controlled cross between two widely planted pecan cultivars, ‘Pawnee’ and ‘Elliott’. This cross was designed so the seedlings would exhibit varying levels of scab resistance. DNA was extracted from both parent cultivars and their seedlings, sequenced to generate DNA markers, and used to develop genetic maps for ‘Pawnee’ and ‘Elliott’. Young leaflets of the grafted seedlings were inoculated with two scab isolates in a greenhouse setting, and fungal infection in the leaf tissues was measured under a microscope. DNA sequence information and scab resistance levels were analyzed to identify DNA markers linked to scab resistance. Several potential disease-resistance-related genes were also identified in the ‘Elliott’ cultivar. These DNA markers linked to scab resistance provide an essential genetic tool for marker-assisted breeding in pecan, enabling the selection of scab-resistant seedlings at the early stage and thus reducing the resources needed to maintain trees through a long growth period before evaluation.

Technical Abstract: Genetic maps are essential tools for gene positional cloning and marker-assisted breeding. A pecan mapping population of 119 F1 trees was derived from a cross of the widely planted cultivars Pawnee and Elliott. Whereas ‘Pawnee’ is susceptible, ‘Elliott’ has long-standing resistance to pecan scab caused by the fungal pathogen Venturia effusa. Molecular markers were developed using genotyping-by-sequencing, and linkage maps were constructed for each parent following the two-way pseudo-test-cross strategy used for cross-pollinated species. The ‘Pawnee’ and ‘Elliott’ maps contain 1,347 and 1,050 single nucleotide polymorphism markers spanning a genetic distance of 4,493.0 and 3,758.4 cM, respectively. While these map lengths are likely inflated due to genotyping errors, a high level of synteny between genetic and physical distances of the markers in both parental maps was achieved. Scab resistance was evaluated through controlled inoculations in the greenhouse using two scab isolates, and a significant quantitative trait locus (QTL) for scab resistance was identified on chromosome 5 in ‘Elliott’. Candidate gene searches within the 2-logarithm of the odds interval of the scab-resistant QTL identified a number of disease resistance related genes, including genes encoding wall-associated receptor kinases, cytochrome P450s, leucine-rich repeats receptor-like serine/threonine-protein kinases, a pectinesterase inhibitor, a cellulose synthase, a flavonol synthase, a 4-coumarate-CoA ligase, a caffeic acid 3-O-methyltransferase, and a MYB domain transcription factor.