Development of a High-Density Genetic Map for QTL Analysis of Resistance to Phytophthora cinnamomi in an Interspecific American × Chinese Chestnut Population

Phytophthora root rot, caused by Phytophthora cinnamomi (Pc) and also called ink disease, is one of the major factors affecting restoration of American chestnut (Castanea dentata) in the southeastern U.S. Due to a lack of reproductive barriers, introducing resistance to Pc from Chinese chestnut (C. mollissima) into American chestnut is a feasible task for molecular breeding.  To identify genomic regions in Chinese chestnut controlling resistance to Pc in interspecific BC₁F₁ progenies, we used a traditional approach—quantitative trait locus (QTL) analysis in bi-parental populations based on fine-scale linkage maps. Using genotyping-by-sequencing (Pst1-Msp1 double digestion, Illumina paired-end sequencing), we generated linkage maps for the HB2 (KY115 × AD98) cross consisting of 238 individuals segregating for severity of root rot symptoms. Parental female and male maps were composed of 626 and 497 non-redundant and non-distorted (P<0.05) SNP markers, respectively.  The markers were organized into 12 linkage groups covering genetic distances of 581.2 cM on the KY115 map and 691.5 cM on the AD98 map. Using sequenced marker information, the HB2 linkage groups were anchored to the C. mollissima genome v1.1 scaffolds and oriented against the C. mollissima reference map. Three significant QTLs (LG_A, LG_E and LG_K) were detected for the KY115 parent, which was derived from the Chinese chestnut cultivar ‘Mahogany.’ Details on the bioinformatic pipeline used for genotypic data processing, anchoring HB2 maps to the Chinese chestnut reference map, and QTL analyses will be presented.