Tomato locule number and fruit size controlled by natural alleles of lc and fas

Improving yield by increasing the size of produce is an important selection criterion during the domestication of fruit and vegetable crops. Genes controlling meristem organization and organ formation work in concert to regulate the size of reproductive organs. In tomato, lc and fas control locule number, which often leads to enlarged fruits compared to the wild progenitors. LC is encoded by the tomato ortholog of WUSCHEL (WUS), whereas FAS is encoded by the tomato ortholog of CLAVATA3 (CLV3). The critical role of the WUS‐CLV3 feedback loop in meristem organization has been demonstrated in several plant species. We show that mutant alleles for both loci in tomato led to an expansion of the SlWUS expression domain in young floral buds 2–3 days after initiation. Single and double mutant alleles of lc and fas maintain higher SlWUS expression during the development of the carpel primordia in the floral bud. This augmentation and altered spatial expression of SlWUS provided a mechanistic basis for the formation of multilocular and large fruits. Our results indicated that lc and fas are gain‐of‐function and partially loss‐of‐function alleles, respectively, while both mutations positively affect the size of tomato floral meristems. In addition, expression profiling showed that lc and fas affected the expression of several genes in biological processes including those involved in meristem/flower development, patterning, microtubule binding activity, and sterol biosynthesis. Several differentially expressed genes co‐expressed with SlWUS have been identified, and they are enriched for functions in meristem regulation. Our results provide new insights into the transcriptional regulation of genes that modulate meristem maintenance and floral organ determinacy in tomato.