UC Davis

Leaf shape is a complex trait in tomato, controlled by many different genes across the genome, resulting in a wide array of shapes, sizes, and complexity within a single domesticated species Solanum lycopersicum L.. Exploring leaf shape requires an array of tools to both quantify shapes and their effects as well as genomic tools such as RNA-seq to explore potential regulators. Because of the complexity of its regulation, beyond being the primary site of photosynthesis, the role of leaf shape in crop output such as BRIX (fruit sugar) and yield has been largely ignored. This has led to a major focus on crop improvement centering around increasing photosynthesis. However, increasing photosynthesis for increased fruit BRIX and yield may not be feasible, and instead, causes increases in vegetative mass, an undesirable effect in crops such as tomato.Domesticated tomato (Solanum lycopersicum L.) is one of the most widely grown vegetable crops worldwide, and heirloom tomatoes retain genetic diversity and a considerable range of fruit quality and leaf morphological traits. I first investigated leaf morphology in a variety of heirloom tomatoes for its impact on fruit quality. Photosynthesis contributed strongly to vegetative bio-mass and sugar content of fruits but had a negative impact on yield. Conversely aspects of leaf shape, specifically rounder leaves, had a strong positive impact on both fruit sugar content and yield (BY). This study revealed the importance of leaf shape to fruit quality in tomato. I also looked at defined genetic loci that alter leaf shape for their influence on yield and BRIX in fruit. Tomato bipinnate (bip) is a classic leaf mutant, with highly increased leaf complexity resulting from the loss of function of a BEL-LIKE HOMEODAMAIN (BELL) gene. Several bip mutants and their isogenic wildtype backgrounds were analyzed for a suite of leaf morphology traits, ranging from leaf complexity, leaflet shape and size, to leaf vascular density to investigate how changes in leaf morphology could influence fruit traits. Our analyses showed an unexpected relationship between leaf vein density and fruit sugar levels, where leaf vein density was negatively correlated with fruit BRIX. A set of introgression lines (IL), backcross IL (BIL), and sub IL were used to study the link between leaf shape and BY in tomato. Two lines were identified which had increased yield (sub IL 4-3-4) and BY (BIL 260) and which had rounder leaves than M82. BIL 260 was further found to have reduced vascular density, a feature unique to this BIL among this set of IL’s. RNA-Seq analysis for young leaves identified a cluster of genes which had GO Enrichment for sugar related activities and included a transcription factor, bHLH032, which was also unique to the BIL 260 introgression region compared to sub IL 4-3-4. We generated CRISPR mutants of bHLH032 in the M82 background and characterized them, finding homozygous knockout mutants had decreased vascular density and increased BY. Because leaf shape vasculature are complex traits regulated by many genes, bHLH032 is only one target for altering this morphology which leads to improved crop output and remains an excellent target for future research.