Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (Capsicum annuum)

Bell pepper (Capsicum annuum L.) is a group of fruit vegetables that has large variation in fruit shape, fruit size, and horticultural traits. Using unadapted sources of germplasm to bring in novel alleles while maintaining favorable quality and horticultural traits is challenging for breeding in pepper. A genetic map with 318 loci from genotype-by-sequencing (GBS) and single nucleotide polymorphism assays was generated from a recombinant inbred line population derived from a cultivated bell-type C. annuum 'Maor' and a landrace highly resistant to Phytophthora capsici, 'Criollo de Morelos-334'. Forty-nine quantitative trait loci (QTLs) were detected for fruit, leaf, and horticultural traits with the scantwo permutation and stepwiseqtl methods from R/qtl. With the availability of a pepper reference genome and GBS data, candidate genes for pepper organ size and other horticultural traits were predicted. Big Brother, Ovate, and KLUH/CYP78A5 genes were candidate genes for controlling organ sizes on chromosome 1, 2, and 3, respectively. Two candidate genes controlling trichome formation in pepper are located at chromosome 10: TRICHOME BIREFRINGENCE-LIKE 5 and GLABROUS INFLORESCENCE STEMS. The A locus on chromosome 10, which encodes a member of the R2R3 MYB-domain family of proteins, has a function in anthocyanin accumulation. These QTL results and the candidate genes for each trait emphasize the genetic basis of the important traits for breeding with unadapted parents in bell pepper.