Fruit size and shape are among the most important traits that were under selection during domestication of the fruit-bearing Solanaceae crops, tomato and pepper. To determine the level of conservation of the locations of quantitative trait locus (QTL) controlling these traits in the two species, we conducted whole genome comparative QTL analysis for fruit weight, pericarp thickness, and fruit shape. The pepper QTLs data were obtained from previous studies using two mapping populations from crosses of the same blocky-type parent, cv. Maor (Capsicum annuum), with small-fruited accessions of C. annuum and C. frutescens. The tomato QTLs data were derived from the analysis of two populations containing introgressions from Solanum pennellii and S. habrochaites in the background of the cultivated tomato S. lycopersicum. A total of 95 QTLs in 34 genomic regions were detected in the four populations. Most of the QTLs (52%, 64%, and 89% for fruit weight, pericarp thickness, and fruit shape, respectively) were population-specific. The degree of conservation of the QTL locations in pepper and tomato varied among the traits; eight QTLs for fruit weight, five QTLs for pericarp thickness, and only one QTL for fruit shape were identified in common genomic regions in the two genera. Only two QTLs for fruit weight were found to be common in all four populations. The difference in the degree of QTL conservation in pepper and tomato between fruit weight and fruit shape indicates that while the genetic control of fruit weight is in part similar in pepper and tomato and convergent domestication in these crops resulted from mutations and selection at common loci, selection for fruit shape occurred for the most part at independent loci in these two genera.
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