Mapping of CaUGT75C1 involved in the formation of pepper (Capsicum annuum L.) lateral branches via BSA

Branching architecture is a crucial agronomic trait in pepper cultivation. Conventional pepper varieties form lateral branches at each node, which restricts planting density, reduces photosynthetic efficiency, and increases both disease susceptibility and management costs. In this study, we identified an inbred pepper line, 20C1734, exhibiting a reduced-lateral-branch phenotype caused by defective axillary meristem (AM) formation. Genetic analysis of an F₂ population derived from a cross with the normal-branching line 20C1733 revealed indicated monogenic recessive inheritance. Bulked segregant analysis sequencing (BSA-seq) and map-based cloning localised the regulatory gene to a 1.44 Mb region on chromosome 9. Spatiotemporal expression profiling and promoter analysis identified Chr09g006470, encoding a UDP-glycosyltransferase designated CaUGT75C1, as the candidate gene. Virus-induced gene silencing (VIGS)-mediated suppression of CaUGT75C1 reproduced the 20C1734 phenotype, characterised by absent AMs and elevated levels of active hormones. Hormonal profiling of parental leaf axils showed that branchless sites accumulated abundant abscisic acid (ABA) and indole-2-acetic acid (IAA), along with markedly reduced concentrations of their glycosylated forms, ABA-glucose ester (ABA-GE) and a slight but significant increase in IAA-glutamate conjugate (IAA-Glu). Importantly, the deglycosylated/glycosylated ratios for both ABA and IAA were significantly higher in branchless axils. Transcriptome-based co-expression analysis further indicated that CaUGT75C1 regulates ABA and IAA homeostasis through glycosylation-mediated conversion to inactive forms. Loss of CaUGT75C1 function in 20C1734 results in excessive accumulation of active hormones, thereby suppressing AM initiation and reducing branching. Finally, a molecular marker tightly linked to the regulatory gene was developed.