Molecular marker development, QTL pyramiding, and comparative analysis of phenotypic and marker-assisted selection in cucumber

Several theoretically-based simulation studies suggest that the effectiveness of marker-assisted selection (MAS) for polygenic traits can be greater than phenotypic selection (PHE), but empirical comparisons are scarce and often conflicting. Therefore, existing molecular tools [i.e., genetic linkage maps with defined quantitative trait loci (QTL)-marker associations] were leveraged to compare the effectiveness of MAS to PHE for several quantitative (conditioned by 2-6 QTL), yield-related traits [multiple lateral branching (MLB), gynoecious sex expression (GYN), earliness (EAR), and fruit length to diameter ratio (L:D)] in cucumber. Four complementary inbred lines were intermated to produce four populations which underwent MAS, PHE, and random mating (no selection) for three cycles of recurrent selection. Although both MAS and PHE improved all traits, except for EAR by MAS, their effectiveness depended upon the traits and populations under selection. PHE was most effective for GYN, EAR, and L:D, while MAS was most effective for MLB and yield (fruit per plant). To increase the efficiency of existing molecular markers, 43 random amplified polymorphic DNA (RAPD) markers were sequenced to produce 22 polymorphic sequence characterized amplified region (SCAR) markers. Sequences from bacterial artificial chromosome (BAC) clones and monomorphic SCARs were obtained to identify single nucleotide polymorphisms (SNPs), and four novel marker design approaches were utilized to create allele-specific markers based on SNPs with an 80% success rate (20 markers created from 25 loci containing SNPs). A total of 32 RAPDs were converted into SCAR or SNP markers that will increase the efficiency of MAS in cucumber. Although QTL-marker associations have provided for improvement of MLB by MAS, the epistatic effects of individual QTL have not been characterized. A set of nearly-isogenic lines (NIL) was created in two genetic backgrounds (standard and little leaf type) with varying numbers of QTL associated with MLB. Comparative analysis of specific QTL combinations among NIL characterized epistatic interactions, which were detected among QTL in the little leaf background, but not in standard leaf NIL. Genotype and QTL by environment interactions were also identified, indicating that lateral branch production is determined by environmental effects, interactions among other cucumber traits, and interactions among QTL conditioning MLB.