Leaf form diversification in an ornamental heirloom tomato results from alterations in two different HOMEOBOX genes.

Domesticated plants display diverse phenotypic traits. However, the influence of breeding effort on this phenotypic diversity remains unknown. Here, we demonstrate that a single nucleotide deletion in the homeobox motif of BIPINNATA, a BEL-LIKE HOMEODOMAIN gene, led to a highly complex leaf phenotype in an heirloom tomato (Solanum lycopersicum), Silvery Fir Tree (SiFT), which is used as a landscaping and ornamental plant.

Leaf shape is a predictor of fruit quality and cultivar performance in tomato.

Commercial tomato (Solanum lycopersicum) is one of the most widely grown vegetable crops worldwide. Heirloom tomatoes retain extensive genetic diversity and a considerable range of fruit quality and leaf morphological traits. Here the role of leaf morphology was investigated for its impact on fruit quality.

Using gene networks in EvoDevo analyses.

An intricate web of regulatory relationships between DNA, RNA, proteins and metabolites regulates how organisms achieve form and function. Genome sequencing combined with computational methods has allowed us to look at diverse readouts and generate a comprehensive framework for how molecules generate morphological phenotypes. RNAseq has evolved and proved useful for identifying links between transcription factor activity and transcript abundance, and for the generation of transcriptomes in non-model species through de novo assembly.

eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato.

Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological, and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression quantitative trait loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desert-adapted Solanum pennellii and domesticated tomato (Solanum lycopersicum) to identify the genetic basis of transcript level variation.