Quantitative trait loci analysis of flowering time and vegetative traits in tomato plants grown using different seedling raising methods.

Several quantitative trait loci (QTL) analysis have been conducted on the flowering time of tomato plants, but only few studies have examined both epistatic interaction between QTLs and QTL x environment interaction effects. Using a mixed linear-model composite-interval mapping technique, we have identified additive and the epistatic QTLs that control days to flowering (DTF), number of leaves before the first inflorescence (LN), plant height (PH), length of largest leaf (LL), number of lateral shoots (LS) and shoot fresh weight (SFW) in tomato plants cultivated using two seedling raising methods (raising in 128-cell trays with subsequent transplantation or cultivation in 1 L pots). Two experiments were conducted in autumn 2007 and spring 2009. Cell-raised plants flowered later than pot-raised plants in both experiments, and environment effects were significant for flowering time. However, the genotype x environment interaction at the phenotypic level was significant only in autumn 2007. Eight additive QTLs and nine epistatic QTL pairs were detected for DTF and LN, and eight additive QTLs and six epistatic interactions were detected for the vegetative traits. Only one additive QTL (ll1a) and an epistatic QTL pair (sfw1-sfw5) exhibited QTL x environment interactions. Most of the epistatic QTLs identified in this study did not have additive effects. Flowering-time QTLs that did not have QTL x environment interaction effects may be nonspecific QTLs, i.e., QTLs not affected by internal or external factors, which are desirable for marker-assisted breeding.