Tomato SD1, encoding a kinase interacting protein, is a major locus controlling stem development.

Stems serve as key determinants of plant development by connecting and supporting parts of the plant body, transporting nutrients important for long-distance communication that affect crop yield and producing new organs. Nonetheless, studies on the regulation of stem development in crops are rather limited. Here, we found a significant correlation (P<0.001) between stem diameter (SD) and fruit size in tomato (Solanum lycopersicum). We performed a genome-wide association study (GWAS) and identified a novel quantitative trait locus SDR9 (stem diameter regulator on CHROMOSOME 9) that co-localized with a gene encoding a kinase interacting family protein (KIP), which is the most likely candidate gene related to SD (hereafter referred to as SD1). Overexpression of SD1 in thin-stem accessions resulted in increased SD. In contrast, suppressed expression of SD1 in thick-stem accession using RNA interference (RNAi) exhibited the opposite effect. Further microscopic analyses showed that SD1 affected the stem diameter by controlling the size and number of secondary phloem cells. An 11-bp indel in the promoter region of SD1 that disrupts a gibberellin responsive cis-element was linked to SD. Expression analysis revealed that SD1 was mainly expressed at the cambium of stem and positively regulates stem development. Evolutionary analysis revealed that the thick-stem allele of SD1 was selected during recent process of tomato improvement. Our results provide novel genetic and molecular insight into natural variation of SD in tomato and might accelerate the breeding of high yield tomato.