Discovery and introgression of beneficial loci from Lycopersicon hirsutum, LA407, a wild species of tomato

Wild species of plants assume an important role as sources of beneficial loci for the improvement of agronomic traits. Strategies to introgress, identify and evaluate beneficial loci from wild species include traditional breeding methods and quantitative trait loci (QTL) analysis with molecular markers. While QTL analysis can facilitate the breeding process, most QTL studies have been uncoupled from breeding activities and the direct creation of improved breeding lines. The method of inbred backcross (IBC) breeding allows integration of QTL studies and variety improvement.;This research identifies beneficial loci from Lycopersicon hirsutum , accession LA407, a wild species of tomato. In this study, we couple QTL analysis while advancing material in a breeding context by evaluating an IBC population derived from L. hirsutum LA407 with L. esculentum (LA407 IBC population). DNA-based molecular markers provided coverage of the LA407 IBC population with at least two markers per chromosome arm. Appropriate statistical models were developed and applied to accommodate a population structure characterized by unequal allele frequencies.;Two agronomic traits of importance were evaluated; resistance to bacterial canker of tomato and tomato fruit color. Single marker-QTL analysis identified two major loci originating from L. hirsutum LA407 contributing to bacterial canker resistance with linkage verified in multiple confirming generations. Single marker-QTL analysis identified eight putative QTLs originating from L. hirsutum LA407 associated with tomato fruit color. None of the lines with outstanding color within the LA407 IBC population possessed these loci. Two additional QTLs of L. esculentum origin were identified influencing tomato color within a superior line of the LA407 IBC population. Epistasis was observed between these QTLs and a L. hirsutum LA407 introgression previously not found associated with tomato color on single marker-QTL analysis. Interactions between the L. esculentum QTLs and the L. hirsutum LA407 introgression may explain the superior color in this line.;Evaluation of the LA407 IBC population with molecular markers allowed introgression and identification of beneficial loci from L. hirsutum LA407 while advancing material in a breeding context. The LA407 IBC population and its genetic marker data are available for future analyses of quantitative traits of economic importance in tomato.