High-density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Scab Resistance in Pecan

Genetic maps are essential tools for gene positional cloning and marker-assisted breeding. A pecan ( Carya illinoinensis ) mapping population of 119 F 1 trees was developed 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 1347 and 1050 single-nucleotide polymorphism markers spanning a genetic distance of 4493 and 3758 centimorgans, 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–coenzyme A ligase, caffeic acid 3- O -methyltransferase, and a myeloblastosis (MYB) domain transcription factor.