EPSPS regulates cell elongation by disturbing the balance of lignin and flavonoid biosynthesis in cotton

EPSPS is a key gene in the shikimic acid synthesis pathway and has been widely used in breeding crops with herbicide resistance. However, its role in regulating cell elongation is poorly understood. Through the overexpression of EPSPS genes, we generated lines resistant to glyphosate that exhibited an unexpected dwarf phenotype. A representative line, DHR1, exhibits a stable dwarf phenotype throughout its entire growth period. Except for plant height, the other agronomic traits of DHR1 were similar to its transgenic explants ZM24. Paraffin section experiments showed that DHR1 internodes were shortened due to reduced elongation and division of internode cells. Exogenous hormones confirmed that DHR1 is not a classical BR- or GA-related dwarfing mutant. Hybridization analysis and fine mapping confirmed that the EPSPS gene is the causal gene for dwarfism, and the phenotype can be inherited in different genotypes. Transcriptome and metabolome analyses showed that genes associated with the phenylpropanoid synthesis pathway were enriched in DHR1 when compared with ZM24. Flavonoid metabolites were enriched in DHR1, whereas lignin metabolites were decreased. The enhancement of flavonoids likely resulted in differential expression of auxin signal pathway genes and altered the auxin response, subsequently affecting cell elongation. This study provides a new strategy for generating dwarfs and will accelerate advancements in light simplification of cultivation and mechanized harvesting for cotton.