Natural variation in Solanum pimpinellifolium reveals novel QTLs for stem architecture and secondary growth in tomato

• Our study advances in the understanding of genetic architecture of stem diameter in tomato and generates new materials for breeding. • Twelve major QTLs associated to stem diameter traits were identified. • QTLs sd3.1, sd4.1 and sd11.1 influence stem secondary xylem, pith and cortex areas. • Pyramiding positive-effect alleles enhances stem width trough extended lateral growth. This study aims at deciphering the complex genetic architecture of stem diameter variation in tomato ( Solanum lycopersicum L.) through a comprehensive phenotyping across multiple developmental stages and heights using an interespecific recombinant inbred line population and introgression lines between the cultivated tomato S. lycopersicum var. ‘Moneymaker’ and the acc. ‘TO-937’ of its wild ancestor S. pimpinellifolium , exhibiting a thinner stem. Our analysis identified twelve QTLs with different direction effects associated with stem diameter. Major loci were detected predominantly for the basal internode diameter and were validated in both single and double introgression lines. Pyramiding positive- and negative-effects wild alleles in the genetic background of cultivated tomato resulted in significant enhancement or reduction of stem diameter demonstrating the additive potential of combining same direction effects alleles. In addition, histological examinations of introgression line stems revealed that sd3.1, sd4.1 , and sd11.1 QTLs influence distinct anatomical stem structures including pith size, cortex area and secondary xylem development. Overall, the findings reveal a polygenic, multilocus regulation of stem architecture in tomato, with promising implications for breeding.