QTL mapping of Phytophthora capsici resistance and horticultural traits in a pepper (Capsicum annuum) recombinant inbred line populatio

Root rot disease, caused by Phytophthora capsici, is a major disease of pepper (Capsicum annuum), an important vegetable crop. P. capsici is widespread in the US and increasingly in other pepper production areas of the world. Breeding of resistant pepper varieties with acceptable horticultural attributes has been difficult due to the quantitative nature of resistance, negative traits in resistant donor lines, and the genetic diversity of the pathogen. The main goals of this study were to locate P. capsici resistance QTL that are effective against diverse P. capsici isolates and determine linkage relationships among QTL for horticultural traits and resistance QTL. An F 6 recombinant inbred line (RIL) population (n = 257), derived from an intraspecific Capsicum annuum F1 cross between P. capsici resistant Criollo de Morellos-334 and an elite dihaploid ancho breeding line, was evaluated in multiple disease screens using five different P. capsici isolates and in the field for horticultural traits (fruit length, fruit width, fruit shape, 10-fruit weight, and maturity). Twenty-five significant QTL (P < 0.05) for P. capsici resistance traits and 46 horticultural trait QTL were detected. The 3 QTL explaining the largest proportion of phenotypic variation (% PV) for resistance were linked on chromosome 5 (24-46 % PV). None of the horticultural trait QTL were linked to the resistance QTL on chromosome 5. Seventeen significant and synergistic epistatic QTL x QTL interactions were detected between P. capsici resistance QTL, suggesting that pyramiding of multiple QTL would likely increase the level of resistance. Supplementary materials included: Supplementary Table 1: Markers used for QTL mapping; Supplementary Table 2: Genotypes (RILs and controls) and trait means separations for disease phenotype and horticultural trait data; Supplementary Table 3: Pearson's Correlations of necrosis and necrosis AUDPC; Supplementary Table 4: Pearson's Correlations of horticultural traits.