AbstractIdentifying genetic variation that increases crop yields is a primary objective in plant breeding. We have used association analyses of Brassica napus (oilseed rape/canola) accessions to identify variation in the expression of a HECT E3 ligase gene, BnaUPL3.C03, that influences seed size and final yield. We establish a mechanism in which UPL3 mediates the proteasomal degradation of LEC2, a master regulator of seed maturation. Reduced UPL3 expression increases LEC2 protein levels and prolongs expression of lipid biosynthetic genes and seed maturation. Natural variation in BnaUPL3.C03 expression has not yet been exploited in current Brassica napus breeding lines and can therefore be used as a new approach to maximize future yields in this important oil crop.