QTL mapping of fruit-related traits in pepper (Capsicum annuum)

QTL analysis of pepper fruit characters was performed in an F, population derived from a cross between two Capsicum annum genotypes, the bell-type cultivar Maor and the Indian small-fruited line Perennial. RFLP, AFLP((R)1), RAPD and morphological markers (a total of 177) were used to construct a comparative pepper-tomato genetic map for this cross, and 14 quantitatively inherited traits were evaluated in 180 Fg families. A total of 55 QTL were identified by interval analysis using LOD 3.0 as the threshold for QTL detection. QTL for several traits including fruit diameter and weight, pericarp thickness and pedicel diameter were often located in similar chromosomal regions, thus reflecting high genetic correlations among these traits. A major QTL that accounts for more than 60% of the phenotypic variation for fruit shape (ratio of fruit length to fruit diameter) was detected in chromosome 3. This chromosome also contained QTL for most of the traits scored in the population. Markers in linkage groups 2, 3, 8 and 10 were associated with QTL for multiple traits, thereby suggesting their importance as loci that control developmental processes in pepper. Several QTL in pepper appeared to correspond to positions in tomato for loci controlling the same traits, suggesting the hypothesis that these QTL may be orthologous in the two species.