A loss-of-function allele fixed during domestication reshapes nectar chemistry, microbial diversity, and pollinator visits.

Nectar is a hub for plant-pollinator interactions, yet gene-level causal links between plant genetic variation, pollinator foraging, and nectar microbial assembly remain poorly resolved. Using near-isogenic lines, innovative field time-lapse monitoring of pollinator visits, and long-read amplicon sequencing of nectar microbiota, we show that a natural single-nucleotide variant at a cell-wall invertase gene (HaCWINV2) controls sunflower nectar chemistry and influences both pollinators and microbes. Plants homozygous for a loss-of-function HaCWINV2 allele produce sucrose-rich nectar, resulting in fewer bee visits under field conditions. In pollinator-excluded flowers, invertase-deficient plants harbored greater fungal diversity and compositionally distinct communities, indicating that nectar sugar profiles act as ecological filters shaping the nectar microbiome. This loss-of-function allele is rare in wild sunflowers, but fixed in 35% of cultivated lines, indicating positive selection during domestication. Our findings establish a causal link between a single gene and nectar chemistry, with cascading ecological effects in a plant-pollinator system, thus illustrating how subtle genetic changes scale up to alter nectar traits, microbial assembly, and pollinator foraging behavior.