Source-sink synergy is the key unlocking sweet potato starch yield potential.

Sweet potato starch is in high demand globally for food and industry. However, starch content is negatively correlated with fresh yield. It is urgent to uncover the genetic basis and molecular mechanisms underlying the starch yield of sweet potato. Here we systematically explore source-sink synergy-mediated sweet potato starch yield formation: the production, loading, and transport of photosynthates in leaves, as well as their unloading and allocation in storage roots, lead to starch content divergence between sweet potato varieties. Moreover, we find that six haplotypes of IbPMA1 encoding a plasma membrane H-ATPase are significantly linked with starch accumulation. Overexpression of IbPMA1 in sweet potato results in significantly increased starch and sucrose contents, while its knockdown exhibits an opposing effect. Furthermore, a basic helix-loop-helix (bHLH) transcription factor IbbHLH49 directly targets IbPMA1 and activates its transcription. Overexpression of IbbHLH49 notably improves source-sink synergy-mediated fresh yield and starch accumulation in sweet potato. Both IbbHLH49 and IbPMA1 substantially influence sugar transport and starch biosynthesis in source and sink tissues. These findings expand our understanding of starch yield formation and provide strategies and candidate genes for high starch breeding in root and tuber crops.