A mutant allele of the flowering promoting factor 1 gene at the tomato BRACHYTIC locus reduces plant height with high quality fruit

Reduced plant height due to shortened stems is beneficial for improving crop yield potential, better resilience to biotic/abiotic stresses, and rapid crop producer adoption of the agronomic and management practices. Breeding tomato plants with a reduced height, however, poses a particular challenge because this trait is often associated with a significant fruit size (weight) reduction. The tomato BRACHYTIC (BR) locus controls plant height. Genetic mapping and genome assembly revealed three flowering promoting factor 1 (FPF1) genes located within the BR mapping interval, and a complete coding sequence deletion of the telomere proximal FPF1 (Solyc01g066980) was found in the br allele but not in BR. The knock-out of Solyc01g066980 in BR large-fruited fresh-market tomato reduced the height and fruit yield, but the ability to produce large size fruits was retained. However, concurrent yield evaluation of a pair of sister lines with or without the br allele revealed that artificial selection contributes to commercially acceptable yield potential in br tomatoes. A network analysis of gene-expression patterns across genotypes, tissues, and the gibberellic acid (GA) treatment revealed that member(s) of the FPF1 family may play a role in the suppression of the GA biosynthesis in roots and provided a framework for identifying the responsible molecular signaling pathways in br-mediated phenotypic changes. Lastly, mutations of br homologs also resulted in reduced height. These results shed light on the genetic and physiological mechanisms by which the br allele alters tomato architecture.

Automated summary

Reducing plant height can improve crop yield potential, resilience to stresses, and adoption of management practices. Breeding tomato plants with reduced height is challenging due to the potential decrease in fruit size. This study identified the BR locus that controls plant height in tomatoes and discovered three FPF1 genes within this genomic region. A complete deletion of the FPF1 gene (Solyc01g066980) was found in the br allele but not in BR. Knocking out Solyc01g066980 in large-fruited tomatoes reduced height and yield but retained the ability to produce large fruits. The study also showed that artificial selection contributes to commercially acceptable yield potential in br tomatoes. Network analysis of gene expression patterns revealed the involvement of FPF1 genes in suppressing gibberellic acid biosynthesis in roots. Mutations in br homologs also resulted in reduced height. These findings provide insights into the genetic and physiological mechanisms underlying tomato architecture changes caused by the br allele.