Fruit Weight Regulation in Tomato: Identification and Validation of Novel QTLs

Domestication of fruit and vegetable crops was accompanied by selection for edible parts weight. This increase in fruit weight is controlled by multiple quantitative trait loci (QTL) of large and small effects. To date, only two fruit weight genes have been cloned and a third has been fine-mapped. To efficiently identify additional fruit weight loci, three populations were generated from crosses between cultivated tomato and wild relatives followed by bulked-segregant analysis coupled with whole genome sequencing (QTL-seq) approach. This method led to the identification of three fruit weight QTLs. fw11.2, was identified at the distal part of chromosome 11 and the location confirmed to a 1.62-Mb interval. fw1.1 was found in the peri-centromeric region of chromosome 1. Extremely low recombination frequencies preclude the cloning of this gene. Lastly, fw3.3 was mapped to a region ~1.6-Mb below the known fruit weight gene, SlKLUH/FW3.2. To confirm the location of the genes underlying fw11.2 and fw3.3, we used the genome sequence data to develop additional markers and conducted recombinant screens. The recombinant progeny tests allowed us to narrow down fw11.2 QTL to a region of ~750-kb corresponding to 66 candidate genes. Our research approach provides a cost and time-effective basis for the identification of additional genes involved in fruit weight that could be used for tomato improvement.