Identification of QTLs for Capsaicinoids, Fruit Quality, and Plant Architecture-Related Traits in an Interspecific Capsicum RIL Population

Quantitative trait loci (QTL) analyses in pepper are common for horticultural, disease resistance and fruit quality traits; although none of the studies to-date have used sequence-based markers associated with genes. In this study we measured plant-architectural, phenological, and fruit quality traits in a pepper mapping population consisting of 92 recombinant inbred lines derived from a cross between Capsicum frutescens acc. 2814-6 and C. annuum var. NuMexRNAKY.  Phenotypic measurements were correlated to loci in a high-density EST-based genetic map. In total, 96 QTL were identified for 38 traits, including twelve QTL associated with capsaicinoid levels. Twenty-one loci showed correlation among seemingly unrelated phenotypic categories, highlighting tight linkage or shared genetics between previously unassociated traits in pepper.